From a64c84f7f50f83dfc1607ef6a6e70fbe9454dd92 Mon Sep 17 00:00:00 2001 From: miykael Date: Sun, 1 Nov 2015 10:25:34 +0100 Subject: [PATCH 01/19] FIX: PEP8 - W191 indentation contains tabs --- nipype/algorithms/tests/test_errormap.py | 126 +++++++++++------------ 1 file changed, 63 insertions(+), 63 deletions(-) diff --git a/nipype/algorithms/tests/test_errormap.py b/nipype/algorithms/tests/test_errormap.py index 3dea795ee0..361646add0 100644 --- a/nipype/algorithms/tests/test_errormap.py +++ b/nipype/algorithms/tests/test_errormap.py @@ -11,66 +11,66 @@ def test_errormap(): - tempdir = mkdtemp() - # Single-Spectual - # Make two fake 2*2*2 voxel volumes - volume1 = np.array([[[2.0, 8.0], [1.0, 2.0]], [[1.0, 9.0], [0.0, 3.0]]]) # John von Neumann's birthday - volume2 = np.array([[[0.0, 7.0], [2.0, 3.0]], [[1.0, 9.0], [1.0, 2.0]]]) # Alan Turing's birthday - mask = np.array([[[1, 0], [0, 1]], [[1, 0], [0, 1]]]) - - img1 = nib.Nifti1Image(volume1, np.eye(4)) - img2 = nib.Nifti1Image(volume2, np.eye(4)) - maskimg = nib.Nifti1Image(mask, np.eye(4)) - - nib.save(img1, os.path.join(tempdir, 'von.nii.gz')) - nib.save(img2, os.path.join(tempdir, 'alan.nii.gz')) - nib.save(maskimg, os.path.join(tempdir, 'mask.nii.gz')) - - # Default metric - errmap = ErrorMap() - errmap.inputs.in_tst = os.path.join(tempdir, 'von.nii.gz') - errmap.inputs.in_ref = os.path.join(tempdir, 'alan.nii.gz') - errmap.out_map = os.path.join(tempdir, 'out_map.nii.gz') - result = errmap.run() - yield assert_equal, result.outputs.distance, 1.125 - - # Square metric - errmap.inputs.metric = 'sqeuclidean' - result = errmap.run() - yield assert_equal, result.outputs.distance, 1.125 - - # Linear metric - errmap.inputs.metric = 'euclidean' - result = errmap.run() - yield assert_equal, result.outputs.distance, 0.875 - - # Masked - errmap.inputs.mask = os.path.join(tempdir, 'mask.nii.gz') - result = errmap.run() - yield assert_equal, result.outputs.distance, 1.0 - - # Multi-Spectual - volume3 = np.array([[[1.0, 6.0], [0.0, 3.0]], [[1.0, 9.0], [3.0, 6.0]]]) # Raymond Vahan Damadian's birthday - - msvolume1 = np.zeros(shape=(2, 2, 2, 2)) - msvolume1[:, :, :, 0] = volume1 - msvolume1[:, :, :, 1] = volume3 - msimg1 = nib.Nifti1Image(msvolume1, np.eye(4)) - - msvolume2 = np.zeros(shape=(2, 2, 2, 2)) - msvolume2[:, :, :, 0] = volume3 - msvolume2[:, :, :, 1] = volume1 - msimg2 = nib.Nifti1Image(msvolume2, np.eye(4)) - - nib.save(msimg1, os.path.join(tempdir, 'von-ray.nii.gz')) - nib.save(msimg2, os.path.join(tempdir, 'alan-ray.nii.gz')) - - errmap.inputs.in_tst = os.path.join(tempdir, 'von-ray.nii.gz') - errmap.inputs.in_ref = os.path.join(tempdir, 'alan-ray.nii.gz') - errmap.inputs.metric = 'sqeuclidean' - result = errmap.run() - yield assert_equal, result.outputs.distance, 5.5 - - errmap.inputs.metric = 'euclidean' - result = errmap.run() - yield assert_equal, result.outputs.distance, np.float32(1.25 * (2**0.5)) + tempdir = mkdtemp() + # Single-Spectual + # Make two fake 2*2*2 voxel volumes + volume1 = np.array([[[2.0, 8.0], [1.0, 2.0]], [[1.0, 9.0], [0.0, 3.0]]]) # John von Neumann's birthday + volume2 = np.array([[[0.0, 7.0], [2.0, 3.0]], [[1.0, 9.0], [1.0, 2.0]]]) # Alan Turing's birthday + mask = np.array([[[1, 0], [0, 1]], [[1, 0], [0, 1]]]) + + img1 = nib.Nifti1Image(volume1, np.eye(4)) + img2 = nib.Nifti1Image(volume2, np.eye(4)) + maskimg = nib.Nifti1Image(mask, np.eye(4)) + + nib.save(img1, os.path.join(tempdir, 'von.nii.gz')) + nib.save(img2, os.path.join(tempdir, 'alan.nii.gz')) + nib.save(maskimg, os.path.join(tempdir, 'mask.nii.gz')) + + # Default metric + errmap = ErrorMap() + errmap.inputs.in_tst = os.path.join(tempdir, 'von.nii.gz') + errmap.inputs.in_ref = os.path.join(tempdir, 'alan.nii.gz') + errmap.out_map = os.path.join(tempdir, 'out_map.nii.gz') + result = errmap.run() + yield assert_equal, result.outputs.distance, 1.125 + + # Square metric + errmap.inputs.metric = 'sqeuclidean' + result = errmap.run() + yield assert_equal, result.outputs.distance, 1.125 + + # Linear metric + errmap.inputs.metric = 'euclidean' + result = errmap.run() + yield assert_equal, result.outputs.distance, 0.875 + + # Masked + errmap.inputs.mask = os.path.join(tempdir, 'mask.nii.gz') + result = errmap.run() + yield assert_equal, result.outputs.distance, 1.0 + + # Multi-Spectual + volume3 = np.array([[[1.0, 6.0], [0.0, 3.0]], [[1.0, 9.0], [3.0, 6.0]]]) # Raymond Vahan Damadian's birthday + + msvolume1 = np.zeros(shape=(2, 2, 2, 2)) + msvolume1[:, :, :, 0] = volume1 + msvolume1[:, :, :, 1] = volume3 + msimg1 = nib.Nifti1Image(msvolume1, np.eye(4)) + + msvolume2 = np.zeros(shape=(2, 2, 2, 2)) + msvolume2[:, :, :, 0] = volume3 + msvolume2[:, :, :, 1] = volume1 + msimg2 = nib.Nifti1Image(msvolume2, np.eye(4)) + + nib.save(msimg1, os.path.join(tempdir, 'von-ray.nii.gz')) + nib.save(msimg2, os.path.join(tempdir, 'alan-ray.nii.gz')) + + errmap.inputs.in_tst = os.path.join(tempdir, 'von-ray.nii.gz') + errmap.inputs.in_ref = os.path.join(tempdir, 'alan-ray.nii.gz') + errmap.inputs.metric = 'sqeuclidean' + result = errmap.run() + yield assert_equal, result.outputs.distance, 5.5 + + errmap.inputs.metric = 'euclidean' + result = errmap.run() + yield assert_equal, result.outputs.distance, np.float32(1.25 * (2**0.5)) From 347f089f2f308d416069d8388f21bfb7d0b3a7c1 Mon Sep 17 00:00:00 2001 From: miykael Date: Sun, 1 Nov 2015 10:26:56 +0100 Subject: [PATCH 02/19] FIX: PEP8 - W291 trailing whitespace --- examples/test_spm.py | 8 ++++---- nipype/utils/tests/test_docparse.py | 8 ++++---- 2 files changed, 8 insertions(+), 8 deletions(-) diff --git a/examples/test_spm.py b/examples/test_spm.py index 4162a39769..da35185329 100644 --- a/examples/test_spm.py +++ b/examples/test_spm.py @@ -15,8 +15,8 @@ stc.inputs.num_slices = 21 stc.inputs.time_repetition = 1.0 stc.inputs.time_acquisition = 2. - 2. / 32 -stc.inputs.slice_order = list(range(21, 0, -1)) -stc.inputs.ref_slice = 10 +stc.inputs.slice_order = list(range(21, 0, -1)) +stc.inputs.ref_slice = 10 realign_estimate = pe.Node(interface=spm.Realign(), name='realign_estimate') realign_estimate.inputs.jobtype = "estimate" @@ -50,8 +50,8 @@ stc.inputs.num_slices = 21 stc.inputs.time_repetition = 1.0 stc.inputs.time_acquisition = 2. - 2. / 32 -stc.inputs.slice_order = list(range(21, 0, -1)) -stc.inputs.ref_slice = 10 +stc.inputs.slice_order = list(range(21, 0, -1)) +stc.inputs.ref_slice = 10 realign_estimate = pe.Node(interface=spm.Realign(), name='realign_estimate') realign_estimate.inputs.jobtype = "estimate" diff --git a/nipype/utils/tests/test_docparse.py b/nipype/utils/tests/test_docparse.py index 9e3871d301..84f3d99097 100644 --- a/nipype/utils/tests/test_docparse.py +++ b/nipype/utils/tests/test_docparse.py @@ -23,9 +23,9 @@ class Foo(object): fmtd_doc = """Parameters ---------- -outline : +outline : something about an outline -fun : +fun : intensity of fun factor Others Parameters @@ -50,9 +50,9 @@ def test_build_doc(): The name of the input file outfile : str The name of the output file -outline : +outline : something about an outline -fun : +fun : intensity of fun factor Others Parameters From a1775914ca439a6513bd05c4f2fa6dc88b67ea4c Mon Sep 17 00:00:00 2001 From: miykael Date: Sun, 1 Nov 2015 10:27:58 +0100 Subject: [PATCH 03/19] FIX: PEP8 - W292 no newline at end of file --- examples/smri_cbs_skullstripping.py | 2 +- nipype/interfaces/mrtrix/__init__.py | 2 +- nipype/interfaces/vista/__init__.py | 2 +- nipype/workflows/fmri/spm/__init__.py | 2 +- nipype/workflows/smri/__init__.py | 2 +- nipype/workflows/smri/ants/__init__.py | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/examples/smri_cbs_skullstripping.py b/examples/smri_cbs_skullstripping.py index 0fd80926bb..16fe3de000 100644 --- a/examples/smri_cbs_skullstripping.py +++ b/examples/smri_cbs_skullstripping.py @@ -29,4 +29,4 @@ skullstrip.inputs.xDefaultMem = 6000 wf.connect(mask, 'outMasked', skullstrip, 'inInput') -wf.run() \ No newline at end of file +wf.run() diff --git a/nipype/interfaces/mrtrix/__init__.py b/nipype/interfaces/mrtrix/__init__.py index a71b85c6a1..4b5a4270d5 100644 --- a/nipype/interfaces/mrtrix/__init__.py +++ b/nipype/interfaces/mrtrix/__init__.py @@ -11,4 +11,4 @@ GenerateWhiteMatterMask, DWI2Tensor, Tensor2ApparentDiffusion, Tensor2FractionalAnisotropy, Tensor2Vector, MedianFilter3D, Erode, Threshold) -from .convert import MRTrix2TrackVis \ No newline at end of file +from .convert import MRTrix2TrackVis diff --git a/nipype/interfaces/vista/__init__.py b/nipype/interfaces/vista/__init__.py index 755a98ae4a..e1777c408d 100644 --- a/nipype/interfaces/vista/__init__.py +++ b/nipype/interfaces/vista/__init__.py @@ -1,3 +1,3 @@ # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*- # vi: set ft=python sts=4 ts=4 sw=4 et: -from .vista import (Vnifti2Image, VtoMat) \ No newline at end of file +from .vista import (Vnifti2Image, VtoMat) diff --git a/nipype/workflows/fmri/spm/__init__.py b/nipype/workflows/fmri/spm/__init__.py index e89a009cf0..8ddf878d12 100644 --- a/nipype/workflows/fmri/spm/__init__.py +++ b/nipype/workflows/fmri/spm/__init__.py @@ -1,2 +1,2 @@ from .preprocess import (create_spm_preproc, create_vbm_preproc, - create_DARTEL_template) \ No newline at end of file + create_DARTEL_template) diff --git a/nipype/workflows/smri/__init__.py b/nipype/workflows/smri/__init__.py index 98dd34812f..06a1e16e33 100644 --- a/nipype/workflows/smri/__init__.py +++ b/nipype/workflows/smri/__init__.py @@ -1,2 +1,2 @@ from . import freesurfer -from . import ants \ No newline at end of file +from . import ants diff --git a/nipype/workflows/smri/ants/__init__.py b/nipype/workflows/smri/ants/__init__.py index 5cfe6259a2..f22640eb1e 100644 --- a/nipype/workflows/smri/ants/__init__.py +++ b/nipype/workflows/smri/ants/__init__.py @@ -1,2 +1,2 @@ from .ANTSBuildTemplate import ANTSTemplateBuildSingleIterationWF -from .antsRegistrationBuildTemplate import antsRegistrationTemplateBuildSingleIterationWF \ No newline at end of file +from .antsRegistrationBuildTemplate import antsRegistrationTemplateBuildSingleIterationWF From 08b94e815694bba38df9f389b96453a5828d7650 Mon Sep 17 00:00:00 2001 From: miykael Date: Sun, 1 Nov 2015 10:28:39 +0100 Subject: [PATCH 04/19] FIX: PEP8 - W293 blank line contains whitespace --- nipype/utils/nipype_cmd.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/nipype/utils/nipype_cmd.py b/nipype/utils/nipype_cmd.py index d32b33da7d..93ddcd16be 100644 --- a/nipype/utils/nipype_cmd.py +++ b/nipype/utils/nipype_cmd.py @@ -27,7 +27,7 @@ def add_options(parser=None, module=None, function=None): for name, spec in sorted(interface.inputs.traits(transient=None).items()): desc = "\n".join(interface._get_trait_desc(inputs, name, spec))[len(name)+2:] args = {} - + if spec.is_trait_type(traits.Bool): args["action"] = 'store_true' From e9dc25618d1d85f8a46c7b6ab551f9f19f3cbaad Mon Sep 17 00:00:00 2001 From: miykael Date: Sun, 1 Nov 2015 10:30:43 +0100 Subject: [PATCH 05/19] FIX: PEP8 - W391 blank line at end of file --- build_docs.py | 2 -- doc/sphinxext/numpy_ext/numpydoc.py | 1 - examples/dmri_dtk_dti.py | 2 -- examples/dmri_dtk_odf.py | 2 -- examples/dmri_fsl_dti.py | 2 -- examples/fmri_freesurfer_smooth.py | 1 - examples/fmri_fsl.py | 2 -- examples/fmri_fsl_reuse.py | 2 -- examples/fmri_nipy_glm.py | 1 - examples/fmri_spm_auditory.py | 1 - examples/fmri_spm_dartel.py | 2 -- examples/fmri_spm_face.py | 1 - examples/fmri_spm_nested.py | 1 - examples/howto_caching_example.py | 3 --- nipype/algorithms/__init__.py | 2 -- nipype/caching/__init__.py | 1 - nipype/caching/memory.py | 1 - nipype/caching/tests/test_memory.py | 1 - nipype/fixes/numpy/testing/nosetester.py | 1 - nipype/interfaces/ants/resampling.py | 1 - nipype/interfaces/camino/connectivity.py | 1 - nipype/interfaces/camino/odf.py | 2 -- nipype/interfaces/dcmstack.py | 1 - nipype/interfaces/diffusion_toolkit/odf.py | 1 - nipype/interfaces/freesurfer/tests/test_preprocess.py | 1 - nipype/interfaces/fsl/model.py | 1 - nipype/interfaces/fsl/tests/test_XFibres.py | 1 - nipype/interfaces/fsl/tests/test_dti.py | 1 - nipype/interfaces/fsl/tests/test_epi.py | 3 --- nipype/interfaces/mrtrix/tensors.py | 1 - nipype/interfaces/nipy/model.py | 1 - nipype/interfaces/nitime/tests/test_nitime.py | 2 -- nipype/interfaces/tests/test_io.py | 1 - nipype/interfaces/traits_extension.py | 3 --- nipype/interfaces/vista/vista.py | 1 - nipype/pipeline/plugins/base.py | 1 - nipype/pipeline/plugins/debug.py | 1 - nipype/pipeline/plugins/linear.py | 1 - nipype/pipeline/plugins/tests/test_multiproc_nondaemon.py | 1 - nipype/utils/__init__.py | 1 - nipype/utils/config.py | 1 - nipype/utils/misc.py | 3 --- nipype/utils/tests/__init__.py | 1 - nipype/utils/tmpdirs.py | 2 -- nipype/workflows/dmri/camino/__init__.py | 1 - nipype/workflows/dmri/connectivity/group_connectivity.py | 1 - nipype/workflows/dmri/fsl/tests/test_dti.py | 1 - nipype/workflows/dmri/fsl/tests/test_epi.py | 1 - nipype/workflows/fmri/fsl/preprocess.py | 1 - nipype/workflows/graph/__init__.py | 1 - nipype/workflows/misc/__init__.py | 1 - nipype/workflows/warp/__init__.py | 1 - tools/make_examples.py | 1 - tools/nipype_nightly.py | 3 --- tools/setup.py | 1 - 55 files changed, 76 deletions(-) diff --git a/build_docs.py b/build_docs.py index f50281fce0..433584d444 100644 --- a/build_docs.py +++ b/build_docs.py @@ -193,5 +193,3 @@ def run(self): 'api_docs': APIDocs, 'clean': Clean, } - - diff --git a/doc/sphinxext/numpy_ext/numpydoc.py b/doc/sphinxext/numpy_ext/numpydoc.py index 981c1d0270..8e8f78f2d5 100644 --- a/doc/sphinxext/numpy_ext/numpydoc.py +++ b/doc/sphinxext/numpy_ext/numpydoc.py @@ -176,4 +176,3 @@ def run(self): return base_directive.run(self) return directive - diff --git a/examples/dmri_dtk_dti.py b/examples/dmri_dtk_dti.py index f3c5b3e0dc..7cd8c52a90 100755 --- a/examples/dmri_dtk_dti.py +++ b/examples/dmri_dtk_dti.py @@ -214,5 +214,3 @@ def getstripdir(subject_id): if __name__ == '__main__': dwiproc.run() dwiproc.write_graph() - - diff --git a/examples/dmri_dtk_odf.py b/examples/dmri_dtk_odf.py index 2cc4e6ea1d..7246f1a495 100755 --- a/examples/dmri_dtk_odf.py +++ b/examples/dmri_dtk_odf.py @@ -208,5 +208,3 @@ if __name__ == '__main__': dwiproc.run() dwiproc.write_graph() - - diff --git a/examples/dmri_fsl_dti.py b/examples/dmri_fsl_dti.py index 879c5b8ec5..3f92fdc6b8 100755 --- a/examples/dmri_fsl_dti.py +++ b/examples/dmri_fsl_dti.py @@ -274,5 +274,3 @@ def getstripdir(subject_id): if __name__ == '__main__': dwiproc.run() dwiproc.write_graph() - - diff --git a/examples/fmri_freesurfer_smooth.py b/examples/fmri_freesurfer_smooth.py index 315030d3e6..00e6fa8009 100755 --- a/examples/fmri_freesurfer_smooth.py +++ b/examples/fmri_freesurfer_smooth.py @@ -648,4 +648,3 @@ def list2tuple(listoflist): if __name__ == '__main__': l2flow.run() l2flow.write_graph(graph2use='flat') - diff --git a/examples/fmri_fsl.py b/examples/fmri_fsl.py index 285fc81d78..e3702350a8 100755 --- a/examples/fmri_fsl.py +++ b/examples/fmri_fsl.py @@ -648,5 +648,3 @@ def subjectinfo(subject_id): l1pipeline.write_graph() outgraph = l1pipeline.run() # l1pipeline.run(plugin='MultiProc', plugin_args={'n_procs':2}) - - diff --git a/examples/fmri_fsl_reuse.py b/examples/fmri_fsl_reuse.py index 8dd05b19ab..b3d49c8414 100755 --- a/examples/fmri_fsl_reuse.py +++ b/examples/fmri_fsl_reuse.py @@ -259,5 +259,3 @@ def subjectinfo(subject_id): # level1_workflow.write_graph() level1_workflow.run() # level1_workflow.run(plugin='MultiProc', plugin_args={'n_procs':2}) - - diff --git a/examples/fmri_nipy_glm.py b/examples/fmri_nipy_glm.py index f97d7e7189..86debf4124 100755 --- a/examples/fmri_nipy_glm.py +++ b/examples/fmri_nipy_glm.py @@ -268,4 +268,3 @@ def subjectinfo(subject_id): if __name__ == '__main__': l1pipeline.run() - diff --git a/examples/fmri_spm_auditory.py b/examples/fmri_spm_auditory.py index 1b34cb6b49..a1a413d751 100755 --- a/examples/fmri_spm_auditory.py +++ b/examples/fmri_spm_auditory.py @@ -396,4 +396,3 @@ def getstripdir(subject_id): if __name__ == '__main__': level1.run() level1.write_graph() - diff --git a/examples/fmri_spm_dartel.py b/examples/fmri_spm_dartel.py index 0c150999ca..dad8293cd9 100755 --- a/examples/fmri_spm_dartel.py +++ b/examples/fmri_spm_dartel.py @@ -531,5 +531,3 @@ def getstripdir(subject_id): if __name__ == '__main__': l2pipeline.run() - - diff --git a/examples/fmri_spm_face.py b/examples/fmri_spm_face.py index 948475e8f5..7fe6c64772 100755 --- a/examples/fmri_spm_face.py +++ b/examples/fmri_spm_face.py @@ -488,4 +488,3 @@ def getstripdir(subject_id): if __name__ == '__main__': level1.run() level1.write_graph() - diff --git a/examples/fmri_spm_nested.py b/examples/fmri_spm_nested.py index 28d3d0e755..dc098f18b1 100755 --- a/examples/fmri_spm_nested.py +++ b/examples/fmri_spm_nested.py @@ -484,4 +484,3 @@ def getstripdir(subject_id): if __name__ == '__main__': l2pipeline.run('MultiProc') - diff --git a/examples/howto_caching_example.py b/examples/howto_caching_example.py index 41f9bb5ccd..b5c548fc76 100644 --- a/examples/howto_caching_example.py +++ b/examples/howto_caching_example.py @@ -46,6 +46,3 @@ # or what wasn't used since the start of 2011 # mem.clear_runs_since(year=2011) - - - diff --git a/nipype/algorithms/__init__.py b/nipype/algorithms/__init__.py index c8f2549532..0aa096f1f9 100644 --- a/nipype/algorithms/__init__.py +++ b/nipype/algorithms/__init__.py @@ -7,5 +7,3 @@ """ __docformat__ = 'restructuredtext' - - diff --git a/nipype/caching/__init__.py b/nipype/caching/__init__.py index b6815e9724..db0261ebea 100644 --- a/nipype/caching/__init__.py +++ b/nipype/caching/__init__.py @@ -1,2 +1 @@ from .memory import Memory - diff --git a/nipype/caching/memory.py b/nipype/caching/memory.py index d3b842459d..6948bd51e6 100644 --- a/nipype/caching/memory.py +++ b/nipype/caching/memory.py @@ -300,4 +300,3 @@ def _clear_all_but(self, runs, warn=True): def __repr__(self): return '%s(base_dir=%s)' % (self.__class__.__name__, self.base_dir) - diff --git a/nipype/caching/tests/test_memory.py b/nipype/caching/tests/test_memory.py index c48d23fec9..784eca1b93 100644 --- a/nipype/caching/tests/test_memory.py +++ b/nipype/caching/tests/test_memory.py @@ -50,4 +50,3 @@ def test_caching(): if __name__ == '__main__': test_caching() - diff --git a/nipype/fixes/numpy/testing/nosetester.py b/nipype/fixes/numpy/testing/nosetester.py index 25f2538c99..5c3b3d9e73 100644 --- a/nipype/fixes/numpy/testing/nosetester.py +++ b/nipype/fixes/numpy/testing/nosetester.py @@ -409,4 +409,3 @@ def bench(self, label='fast', verbose=1, extra_argv=None): add_plugins = [Unplugger('doctest')] return nose.run(argv=argv, addplugins=add_plugins) - diff --git a/nipype/interfaces/ants/resampling.py b/nipype/interfaces/ants/resampling.py index 9473740a30..f1bcd4cda1 100644 --- a/nipype/interfaces/ants/resampling.py +++ b/nipype/interfaces/ants/resampling.py @@ -401,4 +401,3 @@ def _format_arg(self, opt, spec, val): if opt == "transforms": return self._getTransformFileNames() return super(ApplyTransformsToPoints, self)._format_arg(opt, spec, val) - diff --git a/nipype/interfaces/camino/connectivity.py b/nipype/interfaces/camino/connectivity.py index fde488d13f..3a41c801e2 100644 --- a/nipype/interfaces/camino/connectivity.py +++ b/nipype/interfaces/camino/connectivity.py @@ -153,4 +153,3 @@ def _gen_filename(self, name): _, filename, _ = split_filename(self.inputs.in_file) filename = filename + "_" return filename - diff --git a/nipype/interfaces/camino/odf.py b/nipype/interfaces/camino/odf.py index bd39f06760..e39bc81117 100644 --- a/nipype/interfaces/camino/odf.py +++ b/nipype/interfaces/camino/odf.py @@ -438,5 +438,3 @@ def _list_outputs(self): def _gen_outfilename(self): _, name, _ = split_filename(self.inputs.in_file) return name + '_peaks.Bdouble' - - diff --git a/nipype/interfaces/dcmstack.py b/nipype/interfaces/dcmstack.py index b3f7dc0c53..9d5b2fd744 100644 --- a/nipype/interfaces/dcmstack.py +++ b/nipype/interfaces/dcmstack.py @@ -424,4 +424,3 @@ def _list_outputs(self): outputs = self._outputs().get() outputs['out_list'] = self.out_list return outputs - diff --git a/nipype/interfaces/diffusion_toolkit/odf.py b/nipype/interfaces/diffusion_toolkit/odf.py index 87495410f5..77dbf1c81d 100644 --- a/nipype/interfaces/diffusion_toolkit/odf.py +++ b/nipype/interfaces/diffusion_toolkit/odf.py @@ -233,4 +233,3 @@ def _list_outputs(self): outputs = self.output_spec().get() outputs['track_file'] = os.path.abspath(self.inputs.out_file) return outputs - diff --git a/nipype/interfaces/freesurfer/tests/test_preprocess.py b/nipype/interfaces/freesurfer/tests/test_preprocess.py index 509964ddf5..28ed61113b 100644 --- a/nipype/interfaces/freesurfer/tests/test_preprocess.py +++ b/nipype/interfaces/freesurfer/tests/test_preprocess.py @@ -117,4 +117,3 @@ def test_synthesizeflash(): syn2 = freesurfer.SynthesizeFLASH(t1_image=filelist[0], pd_image=filelist[1], flip_angle=20, te=5, tr=25) yield assert_equal, syn2.cmdline, ('mri_synthesize 25.00 20.00 5.000 %s %s %s' % (filelist[0], filelist[1], os.path.join(outdir, 'synth-flash_20.mgz'))) - diff --git a/nipype/interfaces/fsl/model.py b/nipype/interfaces/fsl/model.py index ecbe766986..0a0d686e8a 100644 --- a/nipype/interfaces/fsl/model.py +++ b/nipype/interfaces/fsl/model.py @@ -1961,4 +1961,3 @@ def _list_outputs(self): self.inputs.out_vnscales_name) return outputs - diff --git a/nipype/interfaces/fsl/tests/test_XFibres.py b/nipype/interfaces/fsl/tests/test_XFibres.py index ba315c0354..c38f642f86 100644 --- a/nipype/interfaces/fsl/tests/test_XFibres.py +++ b/nipype/interfaces/fsl/tests/test_XFibres.py @@ -1,3 +1,2 @@ from nipype.testing import assert_equal from nipype.interfaces.fsl.dti import XFibres - diff --git a/nipype/interfaces/fsl/tests/test_dti.py b/nipype/interfaces/fsl/tests/test_dti.py index 0b7f27c165..e32a079a43 100644 --- a/nipype/interfaces/fsl/tests/test_dti.py +++ b/nipype/interfaces/fsl/tests/test_dti.py @@ -503,4 +503,3 @@ def test_distancemap(): # Not much else to do here clean_directory(newdir, olddir) - diff --git a/nipype/interfaces/fsl/tests/test_epi.py b/nipype/interfaces/fsl/tests/test_epi.py index ec209808c2..9e9036224c 100644 --- a/nipype/interfaces/fsl/tests/test_epi.py +++ b/nipype/interfaces/fsl/tests/test_epi.py @@ -61,6 +61,3 @@ def test_eddy_correct2(): # test arguments for opt_map # eddy_correct class doesn't have opt_map{} clean_directory(outdir, cwd) - - - diff --git a/nipype/interfaces/mrtrix/tensors.py b/nipype/interfaces/mrtrix/tensors.py index 5577f0d564..52ad0d33da 100644 --- a/nipype/interfaces/mrtrix/tensors.py +++ b/nipype/interfaces/mrtrix/tensors.py @@ -421,4 +421,3 @@ class Directions2Amplitude(CommandLine): _cmd = 'dir2amp' input_spec = Directions2AmplitudeInputSpec output_spec = Directions2AmplitudeOutputSpec - diff --git a/nipype/interfaces/nipy/model.py b/nipype/interfaces/nipy/model.py index 54fc6c26ca..5daaf1a41e 100644 --- a/nipype/interfaces/nipy/model.py +++ b/nipype/interfaces/nipy/model.py @@ -318,4 +318,3 @@ def _list_outputs(self): outputs["p_maps"] = self._p_maps outputs["z_maps"] = self._z_maps return outputs - diff --git a/nipype/interfaces/nitime/tests/test_nitime.py b/nipype/interfaces/nitime/tests/test_nitime.py index a270a5c0ab..c55c2b1aa9 100644 --- a/nipype/interfaces/nitime/tests/test_nitime.py +++ b/nipype/interfaces/nitime/tests/test_nitime.py @@ -73,5 +73,3 @@ def test_coherence_analysis(): coh = np.mean(C.coherence[:, :, freq_idx], -1) # Averaging on the last dimension yield assert_equal, o.outputs.coherence_array, coh - - diff --git a/nipype/interfaces/tests/test_io.py b/nipype/interfaces/tests/test_io.py index a46b6c14b4..495ebbf773 100644 --- a/nipype/interfaces/tests/test_io.py +++ b/nipype/interfaces/tests/test_io.py @@ -420,4 +420,3 @@ def test_jsonsink(): os.chdir(curdir) shutil.rmtree(outdir) - diff --git a/nipype/interfaces/traits_extension.py b/nipype/interfaces/traits_extension.py index 084eb5ea7f..14f1c82aaf 100644 --- a/nipype/interfaces/traits_extension.py +++ b/nipype/interfaces/traits_extension.py @@ -250,6 +250,3 @@ def has_metadata(trait, metadata, value=None, recursive=True): count += has_metadata(handler, metadata, recursive) return count > 0 - - - diff --git a/nipype/interfaces/vista/vista.py b/nipype/interfaces/vista/vista.py index 9f6286ade3..d7b23e120a 100644 --- a/nipype/interfaces/vista/vista.py +++ b/nipype/interfaces/vista/vista.py @@ -72,4 +72,3 @@ class VtoMat(CommandLine): _cmd = 'vtomat' input_spec = VtoMatInputSpec output_spec = VtoMatOutputSpec - diff --git a/nipype/pipeline/plugins/base.py b/nipype/pipeline/plugins/base.py index e4aea237c8..511548b81e 100644 --- a/nipype/pipeline/plugins/base.py +++ b/nipype/pipeline/plugins/base.py @@ -656,4 +656,3 @@ def _get_result(self, taskid): result_out['result'] = result_data return result_out - diff --git a/nipype/pipeline/plugins/debug.py b/nipype/pipeline/plugins/debug.py index 3afa3f80fa..9d0a52adaa 100644 --- a/nipype/pipeline/plugins/debug.py +++ b/nipype/pipeline/plugins/debug.py @@ -34,4 +34,3 @@ def run(self, graph, config, updatehash=False): logger.info("Executing debug plugin") for node in nx.topological_sort(graph): self._callable(node, graph) - diff --git a/nipype/pipeline/plugins/linear.py b/nipype/pipeline/plugins/linear.py index fd6648c4ac..216d037757 100644 --- a/nipype/pipeline/plugins/linear.py +++ b/nipype/pipeline/plugins/linear.py @@ -55,4 +55,3 @@ def run(self, graph, config, updatehash=False): if self._status_callback: self._status_callback(node, 'exception') report_nodes_not_run(notrun) - diff --git a/nipype/pipeline/plugins/tests/test_multiproc_nondaemon.py b/nipype/pipeline/plugins/tests/test_multiproc_nondaemon.py index 5682965de1..89336c2026 100644 --- a/nipype/pipeline/plugins/tests/test_multiproc_nondaemon.py +++ b/nipype/pipeline/plugins/tests/test_multiproc_nondaemon.py @@ -144,4 +144,3 @@ def test_run_multiproc_nondaemon_true(): # with nondaemon_flag = True, the execution should succeed result = run_multiproc_nondaemon_with_flag(True) yield assert_equal, result, 180 # n_procs (2) * numberOfThreads (2) * 45 == 180 - diff --git a/nipype/utils/__init__.py b/nipype/utils/__init__.py index 93b967edb8..926f228876 100644 --- a/nipype/utils/__init__.py +++ b/nipype/utils/__init__.py @@ -2,4 +2,3 @@ from .onetime import OneTimeProperty, setattr_on_read from .tmpdirs import TemporaryDirectory, InTemporaryDirectory - diff --git a/nipype/utils/config.py b/nipype/utils/config.py index 4cae18d2a7..12e7e4cae0 100644 --- a/nipype/utils/config.py +++ b/nipype/utils/config.py @@ -175,4 +175,3 @@ def update_matplotlib(self): def enable_provenance(self): self._config.set('execution', 'write_provenance', 'true') self._config.set('execution', 'hash_method', 'content') - diff --git a/nipype/utils/misc.py b/nipype/utils/misc.py index de19f5843c..dc9ed23b2d 100644 --- a/nipype/utils/misc.py +++ b/nipype/utils/misc.py @@ -242,6 +242,3 @@ def unflatten(in_list, prev_structure): for item in prev_structure: out.append(unflatten(in_list, item)) return out - - - diff --git a/nipype/utils/tests/__init__.py b/nipype/utils/tests/__init__.py index d43673c6ac..00d7c65d5a 100644 --- a/nipype/utils/tests/__init__.py +++ b/nipype/utils/tests/__init__.py @@ -18,4 +18,3 @@ you contribute. Often, writing tests for your code before the code is written helps to frame your thoughts about what the code should look like. """ - diff --git a/nipype/utils/tmpdirs.py b/nipype/utils/tmpdirs.py index 274c08caed..aa7c5da67c 100644 --- a/nipype/utils/tmpdirs.py +++ b/nipype/utils/tmpdirs.py @@ -44,5 +44,3 @@ def __enter__(self): def __exit__(self, exc, value, tb): os.chdir(self._pwd) return super(InTemporaryDirectory, self).__exit__(exc, value, tb) - - diff --git a/nipype/workflows/dmri/camino/__init__.py b/nipype/workflows/dmri/camino/__init__.py index ef72229cde..fef8c6aae1 100644 --- a/nipype/workflows/dmri/camino/__init__.py +++ b/nipype/workflows/dmri/camino/__init__.py @@ -2,4 +2,3 @@ from .diffusion import create_camino_dti_pipeline from .connectivity_mapping import create_connectivity_pipeline from .group_connectivity import create_group_connectivity_pipeline - diff --git a/nipype/workflows/dmri/connectivity/group_connectivity.py b/nipype/workflows/dmri/connectivity/group_connectivity.py index 2f8438bfe8..f0c3e7c67b 100644 --- a/nipype/workflows/dmri/connectivity/group_connectivity.py +++ b/nipype/workflows/dmri/connectivity/group_connectivity.py @@ -524,4 +524,3 @@ def create_average_networks_by_group_workflow(group_list, data_dir, subjects_dir l4pipeline.connect([(merge_gexf_averages, l4datasink, [('out', '@l4output.gexf')])]) return l4pipeline - diff --git a/nipype/workflows/dmri/fsl/tests/test_dti.py b/nipype/workflows/dmri/fsl/tests/test_dti.py index c012c1b3b6..346ac5c23a 100644 --- a/nipype/workflows/dmri/fsl/tests/test_dti.py +++ b/nipype/workflows/dmri/fsl/tests/test_dti.py @@ -84,4 +84,3 @@ def test_create_bedpostx_pipeline(): pipeline.run(plugin='Linear') shutil.rmtree(pipeline.base_dir) - diff --git a/nipype/workflows/dmri/fsl/tests/test_epi.py b/nipype/workflows/dmri/fsl/tests/test_epi.py index c814b85d71..dbac8f2db8 100644 --- a/nipype/workflows/dmri/fsl/tests/test_epi.py +++ b/nipype/workflows/dmri/fsl/tests/test_epi.py @@ -45,4 +45,3 @@ def test_create_eddy_correct_pipeline(): pipeline.run(plugin='Linear') shutil.rmtree(pipeline.base_dir) - diff --git a/nipype/workflows/fmri/fsl/preprocess.py b/nipype/workflows/fmri/fsl/preprocess.py index 2d8cbea2f3..15e9091a1b 100644 --- a/nipype/workflows/fmri/fsl/preprocess.py +++ b/nipype/workflows/fmri/fsl/preprocess.py @@ -1241,4 +1241,3 @@ def create_reg_workflow(name='registration'): outputnode, 'anat2target_transform') return register - diff --git a/nipype/workflows/graph/__init__.py b/nipype/workflows/graph/__init__.py index 8b13789179..e69de29bb2 100644 --- a/nipype/workflows/graph/__init__.py +++ b/nipype/workflows/graph/__init__.py @@ -1 +0,0 @@ - diff --git a/nipype/workflows/misc/__init__.py b/nipype/workflows/misc/__init__.py index 8b13789179..e69de29bb2 100644 --- a/nipype/workflows/misc/__init__.py +++ b/nipype/workflows/misc/__init__.py @@ -1 +0,0 @@ - diff --git a/nipype/workflows/warp/__init__.py b/nipype/workflows/warp/__init__.py index 8b13789179..e69de29bb2 100644 --- a/nipype/workflows/warp/__init__.py +++ b/nipype/workflows/warp/__init__.py @@ -1 +0,0 @@ - diff --git a/tools/make_examples.py b/tools/make_examples.py index 20481427a4..a0520e822d 100755 --- a/tools/make_examples.py +++ b/tools/make_examples.py @@ -97,4 +97,3 @@ def show(): figure_basename = pjoin('fig', os.path.splitext(script)[0]) execfile(script) plt.close('all') - diff --git a/tools/nipype_nightly.py b/tools/nipype_nightly.py index 363fcc1988..5206c8afe9 100644 --- a/tools/nipype_nightly.py +++ b/tools/nipype_nightly.py @@ -88,6 +88,3 @@ def setup_paths(): build_docs() # push_to_sf() os.chdir(prev_dir) - - - diff --git a/tools/setup.py b/tools/setup.py index 1b427eaba5..fba34de078 100644 --- a/tools/setup.py +++ b/tools/setup.py @@ -10,4 +10,3 @@ url='http://nipy.sourceforge.net', scripts=['./nipype_nightly.py', './report_coverage.py'] ) - From e6695bc6466c669925709ba2a7b5b0d9260194b8 Mon Sep 17 00:00:00 2001 From: miykael Date: Sun, 1 Nov 2015 10:31:22 +0100 Subject: [PATCH 06/19] FIX: PEP8 - W503 line break before binary operator --- doc/sphinxext/numpy_ext/docscrape.py | 6 +-- doc/sphinxext/numpy_ext/docscrape_sphinx.py | 4 +- nipype/algorithms/metrics.py | 4 +- nipype/algorithms/rapidart.py | 4 +- nipype/caching/memory.py | 4 +- nipype/fixes/numpy/testing/noseclasses.py | 4 +- nipype/interfaces/base.py | 28 +++++------ nipype/interfaces/fsl/dti.py | 50 +++++++++---------- nipype/interfaces/fsl/model.py | 55 ++++++++++----------- nipype/interfaces/fsl/utils.py | 4 +- nipype/pipeline/engine.py | 33 ++++++------- nipype/pipeline/utils.py | 10 ++-- setup.py | 4 +- tools/apigen.py | 4 +- tools/interfacedocgen.py | 4 +- 15 files changed, 108 insertions(+), 110 deletions(-) diff --git a/doc/sphinxext/numpy_ext/docscrape.py b/doc/sphinxext/numpy_ext/docscrape.py index 71beb6bbc9..5cc9492247 100644 --- a/doc/sphinxext/numpy_ext/docscrape.py +++ b/doc/sphinxext/numpy_ext/docscrape.py @@ -504,9 +504,9 @@ def methods(self): if self._cls is None: return [] return [name for name, func in inspect.getmembers(self._cls) - if ((not name.startswith('_') - or name in self.extra_public_methods) - and callable(func))] + if ((not name.startswith('_') or + name in self.extra_public_methods) and + callable(func))] @property def properties(self): diff --git a/doc/sphinxext/numpy_ext/docscrape_sphinx.py b/doc/sphinxext/numpy_ext/docscrape_sphinx.py index 70f7ecd695..fa89899bb9 100644 --- a/doc/sphinxext/numpy_ext/docscrape_sphinx.py +++ b/doc/sphinxext/numpy_ext/docscrape_sphinx.py @@ -164,8 +164,8 @@ def _str_references(self): def _str_examples(self): examples_str = "\n".join(self['Examples']) - if (self.use_plots and 'import matplotlib' in examples_str - and 'plot::' not in examples_str): + if (self.use_plots and 'import matplotlib' in examples_str and + 'plot::' not in examples_str): out = [] out += self._str_header('Examples') out += ['.. plot::', ''] diff --git a/nipype/algorithms/metrics.py b/nipype/algorithms/metrics.py index 5284b1f201..48a686a420 100644 --- a/nipype/algorithms/metrics.py +++ b/nipype/algorithms/metrics.py @@ -335,8 +335,8 @@ def _run_interface(self, runtime): self._labels = labels self._ove_rois = results - self._vol_rois = (np.array(volumes1) - - np.array(volumes2)) / np.array(volumes1) + self._vol_rois = (np.array(volumes1) - + np.array(volumes2)) / np.array(volumes1) self._dice = round(np.sum(weights*results['dice']), 5) self._jaccard = round(np.sum(weights*results['jaccard']), 5) diff --git a/nipype/algorithms/rapidart.py b/nipype/algorithms/rapidart.py index 6f90c70e75..69ea3b90d8 100644 --- a/nipype/algorithms/rapidart.py +++ b/nipype/algorithms/rapidart.py @@ -461,8 +461,8 @@ def _detect_outliers_core(self, imgfile, motionfile, runidx, cwd=None): traval = mc[:, 0:3] # translation parameters (mm) rotval = mc[:, 3:6] # rotation parameters (rad) tidx = find_indices(np.sum(abs(traval) > - self.inputs.translation_threshold, 1) - > 0) + self.inputs.translation_threshold, 1) > + 0) ridx = find_indices(np.sum(abs(rotval) > self.inputs.rotation_threshold, 1) > 0) diff --git a/nipype/caching/memory.py b/nipype/caching/memory.py index 6948bd51e6..67ef605e32 100644 --- a/nipype/caching/memory.py +++ b/nipype/caching/memory.py @@ -51,8 +51,8 @@ def __init__(self, interface, base_dir, callback=None): An optional callable called each time after the function is called. """ - if not (isinstance(interface, type) - and issubclass(interface, BaseInterface)): + if not (isinstance(interface, type) and + issubclass(interface, BaseInterface)): raise ValueError('the interface argument should be a nipype ' 'interface class, but %s (type %s) was passed.' % (interface, type(interface))) diff --git a/nipype/fixes/numpy/testing/noseclasses.py b/nipype/fixes/numpy/testing/noseclasses.py index 2a1c6900c9..daab4247d7 100644 --- a/nipype/fixes/numpy/testing/noseclasses.py +++ b/nipype/fixes/numpy/testing/noseclasses.py @@ -87,8 +87,8 @@ def _find(self, tests, obj, name, module, source_lines, globs, seen): if ismodule(obj) and self._recurse: for valname, val in list(obj.__dict__.items()): valname1 = '%s.%s' % (name, valname) - if ((isroutine(val) or isclass(val)) - and self._from_module(module, val)): + if ((isroutine(val) or isclass(val)) and + self._from_module(module, val)): self._find(tests, val, valname1, module, source_lines, globs, seen) diff --git a/nipype/interfaces/base.py b/nipype/interfaces/base.py index fd1f3e1dd5..c905881a08 100644 --- a/nipype/interfaces/base.py +++ b/nipype/interfaces/base.py @@ -514,8 +514,8 @@ def _clean_container(self, object, undefinedval=None, skipundefined=False): else: if not skipundefined: out[key] = undefinedval - elif (isinstance(object, TraitListObject) or isinstance(object, list) - or isinstance(object, tuple)): + elif (isinstance(object, TraitListObject) or + isinstance(object, list) or isinstance(object, tuple)): out = [] for val in object: if isdefined(val): @@ -564,9 +564,8 @@ def get_hashval(self, hash_method=None): if has_metadata(trait.trait_type, "nohash", True): continue hash_files = (not has_metadata(trait.trait_type, "hash_files", - False) - and not has_metadata(trait.trait_type, - "name_source")) + False) and not + has_metadata(trait.trait_type, "name_source")) dict_nofilename.append((name, self._get_sorteddict(val, hash_method=hash_method, hash_files=hash_files))) @@ -1522,8 +1521,8 @@ def _format_arg(self, name, trait_spec, value): # traits.Either turns into traits.TraitCompound and does not have any # inner_traits elif trait_spec.is_trait_type(traits.List) \ - or (trait_spec.is_trait_type(traits.TraitCompound) - and isinstance(value, list)): + or (trait_spec.is_trait_type(traits.TraitCompound) and + isinstance(value, list)): # This is a bit simple-minded at present, and should be # construed as the default. If more sophisticated behavior # is needed, it can be accomplished with metadata (e.g. @@ -1771,13 +1770,14 @@ def validate(self, object, name, value): newvalue = value if not isinstance(value, list) \ - or (self.inner_traits() - and isinstance(self.inner_traits()[0].trait_type, traits.List) - and not isinstance(self.inner_traits()[0].trait_type, - InputMultiPath) - and isinstance(value, list) - and value - and not isinstance(value[0], list)): + or (self.inner_traits() and + isinstance(self.inner_traits()[0].trait_type, + traits.List) and not + isinstance(self.inner_traits()[0].trait_type, + InputMultiPath) and + isinstance(value, list) and + value and not + isinstance(value[0], list)): newvalue = [value] value = super(MultiPath, self).validate(object, name, newvalue) diff --git a/nipype/interfaces/fsl/dti.py b/nipype/interfaces/fsl/dti.py index 3e13ddccbe..a0b7a5bad6 100644 --- a/nipype/interfaces/fsl/dti.py +++ b/nipype/interfaces/fsl/dti.py @@ -96,8 +96,8 @@ def _list_outputs(self): outputs = self.output_spec().get() for k in list(outputs.keys()): if k not in ('outputtype', 'environ', 'args'): - if k != 'tensor' or (isdefined(self.inputs.save_tensor) - and self.inputs.save_tensor): + if k != 'tensor' or (isdefined(self.inputs.save_tensor) and + self.inputs.save_tensor): outputs[k] = self._gen_fname(self.inputs.base_name, suffix='_' + k) return outputs @@ -623,27 +623,27 @@ def _list_outputs(self): outputs[k] = [] for n in range(self.inputs.fibres): - outputs['merged_thsamples'].append(self._gen_fname('merged_th' + repr(n + 1) - + 'samples', suffix='', - cwd=outputs['bpx_out_directory'])) - outputs['merged_phsamples'].append(self._gen_fname('merged_ph' + repr(n + 1) - + 'samples', suffix='', - cwd=outputs['bpx_out_directory'])) - outputs['merged_fsamples'].append(self._gen_fname('merged_f' + repr(n + 1) - + 'samples', suffix='', - cwd=outputs['bpx_out_directory'])) - outputs['mean_thsamples'].append(self._gen_fname('mean_th' + repr(n + 1) - + 'samples', suffix='', - cwd=outputs['bpx_out_directory'])) - outputs['mean_phsamples'].append(self._gen_fname('mean_ph' + repr(n + 1) - + 'samples', suffix='', - cwd=outputs['bpx_out_directory'])) - outputs['mean_fsamples'].append(self._gen_fname('mean_f' + repr(n + 1) - + 'samples', suffix='', - cwd=outputs['bpx_out_directory'])) - outputs['dyads'].append(self._gen_fname('dyads' + repr(n + 1), - suffix='', - cwd=outputs['bpx_out_directory'])) + outputs['merged_thsamples'].append(self._gen_fname( + 'merged_th' + repr(n + 1) + 'samples', + suffix='', cwd=outputs['bpx_out_directory'])) + outputs['merged_phsamples'].append(self._gen_fname( + 'merged_ph' + repr(n + 1) + 'samples', + suffix='', cwd=outputs['bpx_out_directory'])) + outputs['merged_fsamples'].append(self._gen_fname( + 'merged_f' + repr(n + 1) + 'samples', + suffix='', cwd=outputs['bpx_out_directory'])) + outputs['mean_thsamples'].append(self._gen_fname( + 'mean_th' + repr(n + 1) + 'samples', + suffix='', cwd=outputs['bpx_out_directory'])) + outputs['mean_phsamples'].append(self._gen_fname( + 'mean_ph' + repr(n + 1) + 'samples', + suffix='', cwd=outputs['bpx_out_directory'])) + outputs['mean_fsamples'].append(self._gen_fname( + 'mean_f' + repr(n + 1) + 'samples', + suffix='', cwd=outputs['bpx_out_directory'])) + outputs['dyads'].append(self._gen_fname( + 'dyads' + repr(n + 1), + suffix='', cwd=outputs['bpx_out_directory'])) return outputs @@ -735,8 +735,8 @@ class ProbTrackXBaseInputSpec(FSLCommandInputSpec): class ProbTrackXInputSpec(ProbTrackXBaseInputSpec): mode = traits.Enum("simple", "two_mask_symm", "seedmask", - desc='options: simple (single seed voxel), seedmask (mask of seed voxels), ' - + 'twomask_symm (two bet binary masks) ', + desc='options: simple (single seed voxel), seedmask (mask of seed voxels), ' + + 'twomask_symm (two bet binary masks) ', argstr='--mode=%s', genfile=True) mask2 = File(exists=True, desc='second bet binary mask (in diffusion space) in twomask_symm mode', argstr='--mask2=%s') diff --git a/nipype/interfaces/fsl/model.py b/nipype/interfaces/fsl/model.py index 0a0d686e8a..62e16e9319 100644 --- a/nipype/interfaces/fsl/model.py +++ b/nipype/interfaces/fsl/model.py @@ -1818,31 +1818,30 @@ class GLMInputSpec(FSLCommandInputSpec): in_file = File(exists=True, argstr='-i %s', mandatory=True, position=1, desc='input file name (text matrix or 3D/4D image file)') out_file = File(name_template="%s_glm", argstr='-o %s', position=3, - desc=('filename for GLM parameter estimates' - + ' (GLM betas)'), + desc=('filename for GLM parameter estimates' + + ' (GLM betas)'), name_source="in_file", keep_extension=True) design = File(exists=True, argstr='-d %s', mandatory=True, position=2, - desc=('file name of the GLM design matrix (text time' - + ' courses for temporal regression or an image' - + ' file for spatial regression)')) - contrasts = File(exists=True, argstr='-c %s', desc=('matrix of t-statics' - + ' contrasts')) - mask = File(exists=True, argstr='-m %s', desc=('mask image file name if' - + ' input is image')) - dof = traits.Int(argstr='--dof=%d', desc=('set degrees of freedom' - + ' explicitly')) - des_norm = traits.Bool(argstr='--des_norm', desc=('switch on normalization' - + ' of the design matrix' - + ' columns to unit std' - + ' deviation')) + desc=('file name of the GLM design matrix (text time' + + ' courses for temporal regression or an image' + + ' file for spatial regression)')) + contrasts = File(exists=True, argstr='-c %s', desc=('matrix of t-statics' + + ' contrasts')) + mask = File(exists=True, argstr='-m %s', desc=('mask image file name if' + + ' input is image')) + dof = traits.Int(argstr='--dof=%d', desc=('set degrees of freedom' + + ' explicitly')) + des_norm = traits.Bool(argstr='--des_norm', + desc=('switch on normalization of the design' + + ' matrix columns to unit std deviation')) dat_norm = traits.Bool(argstr='--dat_norm', desc=('switch on normalization' - + ' of the data time' - + ' series to unit std' - + ' deviation')) - var_norm = traits.Bool(argstr='--vn', desc=('perform MELODIC variance-' - + 'normalisation on data')) - demean = traits.Bool(argstr='--demean', desc=('switch on demeaining of ' - + ' design and data')) + ' of the data time' + + ' series to unit std' + + ' deviation')) + var_norm = traits.Bool(argstr='--vn', desc=('perform MELODIC variance-' + + 'normalisation on data')) + demean = traits.Bool(argstr='--demean', desc=('switch on demeaining of ' + + ' design and data')) out_cope = File(argstr='--out_cope=%s', desc='output file name for COPE (either as txt or image') out_z_name = File(argstr='--out_z=%s', @@ -1851,8 +1850,8 @@ class GLMInputSpec(FSLCommandInputSpec): desc='output file name for t-stats (either as txt or image') out_p_name = File(argstr='--out_p=%s', - desc=('output file name for p-values of Z-stats (either as' - + ' text file or image)')) + desc=('output file name for p-values of Z-stats (either as' + + ' text file or image)')) out_f_name = File(argstr='--out_f=%s', desc='output file name for F-value of full model fit') out_pf_name = File(argstr='--out_pf=%s', @@ -1863,13 +1862,13 @@ class GLMInputSpec(FSLCommandInputSpec): desc='output file name for variance of COPEs') out_sigsq_name = File(argstr='--out_sigsq=%s', - desc=('output file name for residual noise variance' - + ' sigma-square')) + desc=('output file name for residual noise variance' + + ' sigma-square')) out_data_name = File(argstr='--out_data=%s', desc='output file name for pre-processed data') out_vnscales_name = File(argstr='--out_vnscales=%s', - desc=('output file name for scaling factors for variance' - + ' normalisation')) + desc=('output file name for scaling factors for variance' + + ' normalisation')) class GLMOutputSpec(TraitedSpec): diff --git a/nipype/interfaces/fsl/utils.py b/nipype/interfaces/fsl/utils.py index 214f308e03..4f5d2c4aed 100644 --- a/nipype/interfaces/fsl/utils.py +++ b/nipype/interfaces/fsl/utils.py @@ -739,8 +739,8 @@ def _list_outputs(self): out_file = self.inputs.out_file if not isdefined(out_file): if isdefined(self.inputs.stat_image2) and ( - not isdefined(self.inputs.show_negative_stats) - or not self.inputs.show_negative_stats): + not isdefined(self.inputs.show_negative_stats) or not + self.inputs.show_negative_stats): stem = "%s_and_%s" % (split_filename(self.inputs.stat_image)[1], split_filename(self.inputs.stat_image2)[1]) else: diff --git a/nipype/pipeline/engine.py b/nipype/pipeline/engine.py index 151441c7b2..6ed2f53c66 100644 --- a/nipype/pipeline/engine.py +++ b/nipype/pipeline/engine.py @@ -1337,19 +1337,19 @@ def run(self, updatehash=False): logger.debug(('updatehash, overwrite, always_run, hash_exists', updatehash, self.overwrite, self._interface.always_run, hash_exists)) - if (not updatehash and (((self.overwrite is None - and self._interface.always_run) - or self.overwrite) or - not hash_exists)): + if (not updatehash and (((self.overwrite is None and + self._interface.always_run) or + self.overwrite) or not + hash_exists)): logger.debug("Node hash: %s" % hashvalue) # by rerunning we mean only nodes that did finish to run previously json_pat = op.join(outdir, '_0x*.json') json_unfinished_pat = op.join(outdir, '_0x*_unfinished.json') - need_rerun = (op.exists(outdir) - and not isinstance(self, MapNode) - and len(glob(json_pat)) != 0 - and len(glob(json_unfinished_pat)) == 0) + need_rerun = (op.exists(outdir) and not + isinstance(self, MapNode) and + len(glob(json_pat)) != 0 and + len(glob(json_unfinished_pat)) == 0) if need_rerun: logger.debug("Rerunning node") logger.debug(("updatehash = %s, " @@ -1379,9 +1379,8 @@ def run(self, updatehash=False): logging.logdebug_dict_differences(prev_inputs, hashed_inputs) cannot_rerun = (str2bool( - self.config['execution']['stop_on_first_rerun']) - and not (self.overwrite is None - and self._interface.always_run)) + self.config['execution']['stop_on_first_rerun']) and not + (self.overwrite is None and self._interface.always_run)) if cannot_rerun: raise Exception(("Cannot rerun when 'stop_on_first_rerun' " "is set to True")) @@ -1390,10 +1389,10 @@ def run(self, updatehash=False): hashvalue) if op.exists(hashfile): os.remove(hashfile) - rm_outdir = (op.exists(outdir) - and not (op.exists(hashfile_unfinished) - and self._interface.can_resume) - and not isinstance(self, MapNode)) + rm_outdir = (op.exists(outdir) and not + (op.exists(hashfile_unfinished) and + self._interface.can_resume) and not + isinstance(self, MapNode)) if rm_outdir: logger.debug("Removing old %s and its contents" % outdir) try: @@ -1762,8 +1761,8 @@ def write_report(self, report_type=None, cwd=None): fp = open(report_file, 'at') fp.writelines(write_rst_header('Execution Inputs', level=1)) fp.writelines(write_rst_dict(self.inputs.get())) - exit_now = (not hasattr(self.result, 'outputs') - or self.result.outputs is None) + exit_now = (not hasattr(self.result, 'outputs') or + self.result.outputs is None) if exit_now: return fp.writelines(write_rst_header('Execution Outputs', level=1)) diff --git a/nipype/pipeline/utils.py b/nipype/pipeline/utils.py index 25931f1310..b3a0b65a21 100644 --- a/nipype/pipeline/utils.py +++ b/nipype/pipeline/utils.py @@ -620,9 +620,9 @@ def generate_expanded_graph(graph_in): # the join successor nodes of the current iterable node jnodes = [node for node in graph_in.nodes_iter() - if hasattr(node, 'joinsource') - and inode.name == node.joinsource - and nx.has_path(graph_in, inode, node)] + if hasattr(node, 'joinsource') and + inode.name == node.joinsource and + nx.has_path(graph_in, inode, node)] # excise the join in-edges. save the excised edges in a # {jnode: {source name: (destination name, edge data)}} @@ -649,8 +649,8 @@ def generate_expanded_graph(graph_in): # find the unique iterable source node in the graph try: iter_src = next((node for node in graph_in.nodes_iter() - if node.name == src_name - and nx.has_path(graph_in, node, inode))) + if node.name == src_name and + nx.has_path(graph_in, node, inode))) except StopIteration: raise ValueError("The node %s itersource %s was not found" " among the iterable predecessor nodes" diff --git a/setup.py b/setup.py index 7f282eb7e2..e6f20ae4f4 100755 --- a/setup.py +++ b/setup.py @@ -208,8 +208,8 @@ def version_getter(pkg_name): version)) log.warn(msgs['version too old'] % (have_version, pkg_name, - version) - + msgs['opt suffix']) + version) + + msgs['opt suffix']) return # setuptools mode if optional_tf and not isinstance(optional, string_types): diff --git a/tools/apigen.py b/tools/apigen.py index 348e0e0677..dba2ce0a37 100644 --- a/tools/apigen.py +++ b/tools/apigen.py @@ -221,8 +221,8 @@ def generate_api_doc(self, uri): ad = '.. AUTO-GENERATED FILE -- DO NOT EDIT!\n\n' chap_title = uri_short - ad += (chap_title + '\n' + self.rst_section_levels[1] * len(chap_title) - + '\n\n') + ad += (chap_title + '\n' + + self.rst_section_levels[1] * len(chap_title) + '\n\n') # Set the chapter title to read 'module' for all modules except for the # main packages diff --git a/tools/interfacedocgen.py b/tools/interfacedocgen.py index bc49e6f78b..c60bde743f 100644 --- a/tools/interfacedocgen.py +++ b/tools/interfacedocgen.py @@ -275,8 +275,8 @@ def generate_api_doc(self, uri): ad = '.. AUTO-GENERATED FILE -- DO NOT EDIT!\n\n' chap_title = uri_short - ad += (chap_title+'\n' + self.rst_section_levels[1] * len(chap_title) - + '\n\n') + ad += (chap_title + '\n' + + self.rst_section_levels[1] * len(chap_title) + '\n\n') # Set the chapter title to read 'module' for all modules except for the # main packages From ba7f1bbc988a29bcf3a0a6682617e934c4b0934d Mon Sep 17 00:00:00 2001 From: miykael Date: Sun, 1 Nov 2015 10:34:06 +0100 Subject: [PATCH 07/19] FIX: PEP8 - E401 multiple imports on one line --- doc/conf.py | 3 ++- doc/sphinxext/autosummary_generate.py | 7 ++++++- doc/sphinxext/numpy_ext/docscrape_sphinx.py | 5 ++++- doc/sphinxext/numpy_ext/numpydoc.py | 4 +++- examples/dmri_connectivity_advanced.py | 3 ++- examples/dmri_mrtrix_dti.py | 3 ++- examples/smri_ants_build_template.py | 4 +++- examples/smri_ants_registration.py | 4 +++- examples/smri_antsregistration_build_template.py | 4 +++- examples/tessellation_tutorial.py | 3 ++- nipype/interfaces/base.py | 4 +++- nipype/interfaces/cmtk/convert.py | 3 ++- nipype/interfaces/mrtrix/convert.py | 3 ++- nipype/interfaces/mrtrix/tracking.py | 3 ++- nipype/interfaces/vista/vista.py | 3 ++- nipype/utils/tests/test_cmd.py | 3 ++- 16 files changed, 43 insertions(+), 16 deletions(-) diff --git a/doc/conf.py b/doc/conf.py index 5bfb1f402f..d2953e8ef2 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -12,7 +12,8 @@ # All configuration values have a default; values that are commented out # serve to show the default. -import sys, os +import sys +import os nipypepath = os.path.abspath('..') sys.path.insert(1, nipypepath) diff --git a/doc/sphinxext/autosummary_generate.py b/doc/sphinxext/autosummary_generate.py index 0b562f9975..0e48b744b7 100755 --- a/doc/sphinxext/autosummary_generate.py +++ b/doc/sphinxext/autosummary_generate.py @@ -18,7 +18,12 @@ """ from __future__ import print_function -import glob, re, inspect, os, optparse, pydoc +import glob +import re +import inspect +import os +import optparse +import pydoc from autosummary import import_by_name try: diff --git a/doc/sphinxext/numpy_ext/docscrape_sphinx.py b/doc/sphinxext/numpy_ext/docscrape_sphinx.py index fa89899bb9..21d43cceae 100644 --- a/doc/sphinxext/numpy_ext/docscrape_sphinx.py +++ b/doc/sphinxext/numpy_ext/docscrape_sphinx.py @@ -1,5 +1,8 @@ from __future__ import absolute_import -import re, inspect, textwrap, pydoc +import re +import inspect +import textwrap +import pydoc import sphinx from .docscrape import NumpyDocString, FunctionDoc, ClassDoc from nipype.external.six import string_types diff --git a/doc/sphinxext/numpy_ext/numpydoc.py b/doc/sphinxext/numpy_ext/numpydoc.py index 8e8f78f2d5..cb4dc3ba90 100644 --- a/doc/sphinxext/numpy_ext/numpydoc.py +++ b/doc/sphinxext/numpy_ext/numpydoc.py @@ -24,7 +24,9 @@ if sphinx.__version__ < '1.0.1': raise RuntimeError("Sphinx 1.0.1 or newer is required") -import os, re, pydoc +import os +import re +import pydoc from .docscrape_sphinx import get_doc_object, SphinxDocString from sphinx.util.compat import Directive import inspect diff --git a/examples/dmri_connectivity_advanced.py b/examples/dmri_connectivity_advanced.py index bbf648aeb7..2515d393a2 100755 --- a/examples/dmri_connectivity_advanced.py +++ b/examples/dmri_connectivity_advanced.py @@ -56,7 +56,8 @@ import nipype.interfaces.cmtk as cmtk import nipype.interfaces.dipy as dipy import inspect -import os, os.path as op # system functions +import os +import os.path as op # system functions from nipype.workflows.dmri.fsl.dti import create_eddy_correct_pipeline from nipype.workflows.dmri.camino.connectivity_mapping import select_aparc_annot from nipype.utils.misc import package_check diff --git a/examples/dmri_mrtrix_dti.py b/examples/dmri_mrtrix_dti.py index d010518874..5d7c7336c4 100755 --- a/examples/dmri_mrtrix_dti.py +++ b/examples/dmri_mrtrix_dti.py @@ -25,7 +25,8 @@ import nipype.interfaces.mrtrix as mrtrix # <---- The important new part! import nipype.interfaces.fsl as fsl import nipype.algorithms.misc as misc -import os, os.path as op # system functions +import os +import os.path as op # system functions fsl.FSLCommand.set_default_output_type('NIFTI') diff --git a/examples/smri_ants_build_template.py b/examples/smri_ants_build_template.py index 49100be967..6b14550f0f 100644 --- a/examples/smri_ants_build_template.py +++ b/examples/smri_ants_build_template.py @@ -28,7 +28,9 @@ 2. Download T1 volumes into home directory """ -import urllib.request, urllib.error, urllib.parse +import urllib.request +import urllib.error +import urllib.parse homeDir = os.getenv("HOME") requestedPath = os.path.join(homeDir, 'nipypeTestPath') mydatadir = os.path.realpath(requestedPath) diff --git a/examples/smri_ants_registration.py b/examples/smri_ants_registration.py index d77fd1b250..6a91c358f3 100644 --- a/examples/smri_ants_registration.py +++ b/examples/smri_ants_registration.py @@ -17,7 +17,9 @@ standard_library.install_aliases() import os -import urllib.request, urllib.error, urllib.parse +import urllib.request +import urllib.error +import urllib.parse from nipype.interfaces.ants import Registration """ diff --git a/examples/smri_antsregistration_build_template.py b/examples/smri_antsregistration_build_template.py index 1e49a2c0bb..46cd680599 100644 --- a/examples/smri_antsregistration_build_template.py +++ b/examples/smri_antsregistration_build_template.py @@ -28,7 +28,9 @@ 2. Download T1 volumes into home directory """ -import urllib.request, urllib.error, urllib.parse +import urllib.request +import urllib.error +import urllib.parse homeDir = os.getenv("HOME") requestedPath = os.path.join(homeDir, 'nipypeTestPath') mydatadir = os.path.realpath(requestedPath) diff --git a/examples/tessellation_tutorial.py b/examples/tessellation_tutorial.py index 6ca738e0d3..dcd0328120 100644 --- a/examples/tessellation_tutorial.py +++ b/examples/tessellation_tutorial.py @@ -37,7 +37,8 @@ import nipype.pipeline.engine as pe # pypeline engine import nipype.interfaces.cmtk as cmtk import nipype.interfaces.io as nio # Data i/o -import os, os.path as op +import os +import os.path as op from nipype.workflows.smri.freesurfer import create_tessellation_flow """ diff --git a/nipype/interfaces/base.py b/nipype/interfaces/base.py index c905881a08..96351fcd40 100644 --- a/nipype/interfaces/base.py +++ b/nipype/interfaces/base.py @@ -27,7 +27,9 @@ import select import subprocess import sys -import random, time, fnmatch +import random +import time +import fnmatch from textwrap import wrap from datetime import datetime as dt from dateutil.parser import parse as parseutc diff --git a/nipype/interfaces/cmtk/convert.py b/nipype/interfaces/cmtk/convert.py index f874aa186f..33ee7616b9 100644 --- a/nipype/interfaces/cmtk/convert.py +++ b/nipype/interfaces/cmtk/convert.py @@ -7,7 +7,8 @@ """ -import os, os.path as op +import os +import os.path as op import datetime import string import warnings diff --git a/nipype/interfaces/mrtrix/convert.py b/nipype/interfaces/mrtrix/convert.py index b7369524ae..e916b720c8 100644 --- a/nipype/interfaces/mrtrix/convert.py +++ b/nipype/interfaces/mrtrix/convert.py @@ -13,7 +13,8 @@ # -*- coding: utf-8 -*- import os.path as op -import nibabel as nb, nibabel.trackvis as trk +import nibabel as nb +import nibabel.trackvis as trk import numpy as np from nibabel.trackvis import HeaderError from nibabel.volumeutils import native_code diff --git a/nipype/interfaces/mrtrix/tracking.py b/nipype/interfaces/mrtrix/tracking.py index cce2b38c6e..126bd930e3 100644 --- a/nipype/interfaces/mrtrix/tracking.py +++ b/nipype/interfaces/mrtrix/tracking.py @@ -8,7 +8,8 @@ >>> os.chdir(datadir) """ -import os, os.path as op +import os +import os.path as op from ..base import CommandLineInputSpec, CommandLine, traits, TraitedSpec, File from ..traits_extension import isdefined diff --git a/nipype/interfaces/vista/vista.py b/nipype/interfaces/vista/vista.py index d7b23e120a..fdb054a5ad 100644 --- a/nipype/interfaces/vista/vista.py +++ b/nipype/interfaces/vista/vista.py @@ -11,7 +11,8 @@ from nipype.interfaces.base import CommandLineInputSpec, CommandLine, traits, TraitedSpec, File from nipype.utils.filemanip import split_filename -import os, os.path as op +import os +import os.path as op from nipype.interfaces.traits_extension import isdefined diff --git a/nipype/utils/tests/test_cmd.py b/nipype/utils/tests/test_cmd.py index 91e565e6c3..a4bb0ae060 100644 --- a/nipype/utils/tests/test_cmd.py +++ b/nipype/utils/tests/test_cmd.py @@ -3,7 +3,8 @@ from future import standard_library standard_library.install_aliases() -import unittest, sys +import unittest +import sys from contextlib import contextmanager from nipype.external.six import PY2, PY3, StringIO From faa13a5174501fe4e0c4d27847074a6340e0bcd2 Mon Sep 17 00:00:00 2001 From: miykael Date: Sun, 1 Nov 2015 10:34:42 +0100 Subject: [PATCH 08/19] FIX: PEP8 - E502 the backslash is redundant between brackets --- nipype/interfaces/camino/dti.py | 70 ++++++++++++------------- nipype/interfaces/cmtk/nbs.py | 2 +- nipype/interfaces/cmtk/nx.py | 2 +- nipype/interfaces/freesurfer/utils.py | 2 +- nipype/interfaces/fsl/tests/test_dti.py | 8 +-- nipype/interfaces/meshfix.py | 14 ++--- nipype/interfaces/mrtrix/tensors.py | 8 +-- nipype/interfaces/mrtrix/tracking.py | 14 ++--- nipype/interfaces/spm/model.py | 4 +- nipype/interfaces/spm/utils.py | 2 +- nipype/interfaces/utility.py | 4 +- nipype/pipeline/plugins/ipython.py | 2 +- nipype/pipeline/plugins/ipythonx.py | 2 +- nipype/pipeline/tests/test_engine.py | 4 +- nipype/utils/docparse.py | 4 +- 15 files changed, 71 insertions(+), 71 deletions(-) diff --git a/nipype/interfaces/camino/dti.py b/nipype/interfaces/camino/dti.py index 5043b83ff8..8402fcf45f 100644 --- a/nipype/interfaces/camino/dti.py +++ b/nipype/interfaces/camino/dti.py @@ -262,29 +262,29 @@ def _gen_outfilename(self): class DTLUTGenInputSpec(StdOutCommandLineInputSpec): - lrange = traits.List(traits.Float, desc='Index to one-tensor LUTs. This is the ratio L1/L3 and L2 / L3.' \ - 'The LUT is square, with half the values calculated (because L2 / L3 cannot be less than L1 / L3 by definition).' \ - 'The minimum must be >= 1. For comparison, a ratio L1 / L3 = 10 with L2 / L3 = 1 corresponds to an FA of 0.891, '\ - 'and L1 / L3 = 15 with L2 / L3 = 1 corresponds to an FA of 0.929. The default range is 1 to 10.', \ + lrange = traits.List(traits.Float, desc='Index to one-tensor LUTs. This is the ratio L1/L3 and L2 / L3.' + 'The LUT is square, with half the values calculated (because L2 / L3 cannot be less than L1 / L3 by definition).' + 'The minimum must be >= 1. For comparison, a ratio L1 / L3 = 10 with L2 / L3 = 1 corresponds to an FA of 0.891, ' + 'and L1 / L3 = 15 with L2 / L3 = 1 corresponds to an FA of 0.929. The default range is 1 to 10.', argstr='-lrange %s', minlen=2, maxlen=2, position=1, units='NA') - frange = traits.List(traits.Float, desc='Index to two-tensor LUTs. This is the fractional anisotropy \ - of the two tensors. The default is 0.3 to 0.94', \ + frange = traits.List(traits.Float, desc='Index to two-tensor LUTs. This is the fractional anisotropy' + ' of the two tensors. The default is 0.3 to 0.94', argstr='-frange %s', minlen=2, maxlen=2, position=1, units='NA') step = traits.Float(argstr='-step %f', units='NA', - desc='Distance between points in the LUT.' \ - 'For example, if lrange is 1 to 10 and the step is 0.1, LUT entries will be computed ' \ - 'at L1 / L3 = 1, 1.1, 1.2 ... 10.0 and at L2 / L3 = 1.0, 1.1 ... L1 / L3.' \ + desc='Distance between points in the LUT.' + 'For example, if lrange is 1 to 10 and the step is 0.1, LUT entries will be computed ' + 'at L1 / L3 = 1, 1.1, 1.2 ... 10.0 and at L2 / L3 = 1.0, 1.1 ... L1 / L3.' 'For single tensor LUTs, the default step is 0.2, for two-tensor LUTs it is 0.02.') samples = traits.Int(argstr='-samples %d', units='NA', desc='The number of synthetic measurements to generate at each point in the LUT. The default is 2000.') snr = traits.Float(argstr='-snr %f', units='NA', - desc='The signal to noise ratio of the unweighted (q = 0) measurements.'\ + desc='The signal to noise ratio of the unweighted (q = 0) measurements.' 'This should match the SNR (in white matter) of the images that the LUTs are used with.') bingham = traits.Bool(argstr='-bingham', desc="Compute a LUT for the Bingham PDF. This is the default.") @@ -351,27 +351,27 @@ class PicoPDFsInputSpec(StdOutCommandLineInputSpec): argstr='-inputmodel %s', position=2, desc='input model type', usedefault=True) luts = InputMultiPath(File(exists=True), argstr='-luts %s', mandatory=True, - desc='Files containing the lookup tables.'\ - 'For tensor data, one lut must be specified for each type of inversion used in the image (one-tensor, two-tensor, three-tensor).'\ - 'For pds, the number of LUTs must match -numpds (it is acceptable to use the same LUT several times - see example, above).'\ + desc='Files containing the lookup tables.' + 'For tensor data, one lut must be specified for each type of inversion used in the image (one-tensor, two-tensor, three-tensor).' + 'For pds, the number of LUTs must match -numpds (it is acceptable to use the same LUT several times - see example, above).' 'These LUTs may be generated with dtlutgen.') pdf = traits.Enum('bingham', 'watson', 'acg', - argstr='-pdf %s', position=4, desc=' Specifies the PDF to use. There are three choices:'\ - 'watson - The Watson distribution. This distribution is rotationally symmetric.'\ - 'bingham - The Bingham distributionn, which allows elliptical probability density contours.'\ + argstr='-pdf %s', position=4, desc=' Specifies the PDF to use. There are three choices:' + 'watson - The Watson distribution. This distribution is rotationally symmetric.' + 'bingham - The Bingham distributionn, which allows elliptical probability density contours.' 'acg - The Angular Central Gaussian distribution, which also allows elliptical probability density contours', usedefault=True) directmap = traits.Bool(argstr='-directmap', desc="Only applicable when using pds as the inputmodel. Use direct mapping between the eigenvalues and the distribution parameters instead of the log of the eigenvalues.") maxcomponents = traits.Int(argstr='-maxcomponents %d', units='NA', - desc='The maximum number of tensor components in a voxel (default 2) for multitensor data.'\ + desc='The maximum number of tensor components in a voxel (default 2) for multitensor data.' 'Currently, only the default is supported, but future releases may allow the input of three-tensor data using this option.') numpds = traits.Int(argstr='-numpds %d', units='NA', - desc='The maximum number of PDs in a voxel (default 3) for PD data.' \ - 'This option determines the size of the input and output voxels.' \ - 'This means that the data file may be large enough to accomodate three or more PDs,'\ + desc='The maximum number of PDs in a voxel (default 3) for PD data.' + 'This option determines the size of the input and output voxels.' + 'This means that the data file may be large enough to accomodate three or more PDs,' 'but does not mean that any of the voxels are classified as containing three or more PDs.') @@ -835,19 +835,19 @@ class ComputeMeanDiffusivityInputSpec(CommandLineInputSpec): inputmodel = traits.Enum('dt', 'twotensor', 'threetensor', argstr='-inputmodel %s', - desc='Specifies the model that the input tensor data contains parameters for.' \ - 'Possible model types are: "dt" (diffusion-tensor data), "twotensor" (two-tensor data), '\ - '"threetensor" (three-tensor data). By default, the program assumes that the input data '\ + desc='Specifies the model that the input tensor data contains parameters for.' + 'Possible model types are: "dt" (diffusion-tensor data), "twotensor" (two-tensor data), ' + '"threetensor" (three-tensor data). By default, the program assumes that the input data ' 'contains a single diffusion tensor in each voxel.') inputdatatype = traits.Enum('char', 'short', 'int', 'long', 'float', 'double', argstr='-inputdatatype %s', - desc='Specifies the data type of the input file. The data type can be any of the' \ + desc='Specifies the data type of the input file. The data type can be any of the' 'following strings: "char", "short", "int", "long", "float" or "double".') outputdatatype = traits.Enum('char', 'short', 'int', 'long', 'float', 'double', argstr='-outputdatatype %s', - desc='Specifies the data type of the output data. The data type can be any of the' \ + desc='Specifies the data type of the output data. The data type can be any of the' 'following strings: "char", "short", "int", "long", "float" or "double".') @@ -891,19 +891,19 @@ class ComputeFractionalAnisotropyInputSpec(StdOutCommandLineInputSpec): inputmodel = traits.Enum('dt', 'twotensor', 'threetensor', 'multitensor', argstr='-inputmodel %s', - desc='Specifies the model that the input tensor data contains parameters for.' \ - 'Possible model types are: "dt" (diffusion-tensor data), "twotensor" (two-tensor data), '\ - '"threetensor" (three-tensor data). By default, the program assumes that the input data '\ + desc='Specifies the model that the input tensor data contains parameters for.' + 'Possible model types are: "dt" (diffusion-tensor data), "twotensor" (two-tensor data), ' + '"threetensor" (three-tensor data). By default, the program assumes that the input data ' 'contains a single diffusion tensor in each voxel.') inputdatatype = traits.Enum('char', 'short', 'int', 'long', 'float', 'double', argstr='-inputdatatype %s', - desc='Specifies the data type of the input file. The data type can be any of the' \ + desc='Specifies the data type of the input file. The data type can be any of the' 'following strings: "char", "short", "int", "long", "float" or "double".') outputdatatype = traits.Enum('char', 'short', 'int', 'long', 'float', 'double', argstr='-outputdatatype %s', - desc='Specifies the data type of the output data. The data type can be any of the' \ + desc='Specifies the data type of the output data. The data type can be any of the' 'following strings: "char", "short", "int", "long", "float" or "double".') @@ -953,19 +953,19 @@ class ComputeTensorTraceInputSpec(StdOutCommandLineInputSpec): inputmodel = traits.Enum('dt', 'twotensor', 'threetensor', 'multitensor', argstr='-inputmodel %s', - desc='Specifies the model that the input tensor data contains parameters for.' \ - 'Possible model types are: "dt" (diffusion-tensor data), "twotensor" (two-tensor data), '\ - '"threetensor" (three-tensor data). By default, the program assumes that the input data '\ + desc='Specifies the model that the input tensor data contains parameters for.' + 'Possible model types are: "dt" (diffusion-tensor data), "twotensor" (two-tensor data), ' + '"threetensor" (three-tensor data). By default, the program assumes that the input data ' 'contains a single diffusion tensor in each voxel.') inputdatatype = traits.Enum('char', 'short', 'int', 'long', 'float', 'double', argstr='-inputdatatype %s', - desc='Specifies the data type of the input file. The data type can be any of the' \ + desc='Specifies the data type of the input file. The data type can be any of the' 'following strings: "char", "short", "int", "long", "float" or "double".') outputdatatype = traits.Enum('char', 'short', 'int', 'long', 'float', 'double', argstr='-outputdatatype %s', - desc='Specifies the data type of the output data. The data type can be any of the' \ + desc='Specifies the data type of the output data. The data type can be any of the' 'following strings: "char", "short", "int", "long", "float" or "double".') diff --git a/nipype/interfaces/cmtk/nbs.py b/nipype/interfaces/cmtk/nbs.py index 8a64ad95f6..8fd539691f 100644 --- a/nipype/interfaces/cmtk/nbs.py +++ b/nipype/interfaces/cmtk/nbs.py @@ -43,7 +43,7 @@ class NetworkBasedStatisticInputSpec(BaseInterfaceInputSpec): number_of_permutations = traits.Int(1000, usedefault=True, desc='Number of permutations to perform') threshold = traits.Float(3, usedefault=True, desc='T-statistic threshold') t_tail = traits.Enum('left', 'right', 'both', usedefault=True, desc='Can be one of "left", "right", or "both"') - edge_key = traits.Str('number_of_fibers', usedefault=True, desc='Usually "number_of_fibers, "fiber_length_mean", "fiber_length_std" for matrices made with CMTK' \ + edge_key = traits.Str('number_of_fibers', usedefault=True, desc='Usually "number_of_fibers, "fiber_length_mean", "fiber_length_std" for matrices made with CMTK' 'Sometimes "weight" or "value" for functional networks.') out_nbs_network = File(desc='Output network with edges identified by the NBS') out_nbs_pval_network = File(desc='Output network with p-values to weight the edges identified by the NBS') diff --git a/nipype/interfaces/cmtk/nx.py b/nipype/interfaces/cmtk/nx.py index 1716ad0c8d..33bdb7e278 100644 --- a/nipype/interfaces/cmtk/nx.py +++ b/nipype/interfaces/cmtk/nx.py @@ -505,7 +505,7 @@ def _gen_outfilename(self, name, ext): class AverageNetworksInputSpec(BaseInterfaceInputSpec): in_files = InputMultiPath(File(exists=True), mandatory=True, desc='Networks for a group of subjects') - resolution_network_file = File(exists=True, desc='Parcellation files from Connectome Mapping Toolkit. This is not necessary' \ + resolution_network_file = File(exists=True, desc='Parcellation files from Connectome Mapping Toolkit. This is not necessary' ', but if included, the interface will output the statistical maps as networkx graphs.') group_id = traits.Str('group1', usedefault=True, desc='ID for group') out_gpickled_groupavg = File(desc='Average network saved as a NetworkX .pck') diff --git a/nipype/interfaces/freesurfer/utils.py b/nipype/interfaces/freesurfer/utils.py index 7a79386c7e..2f8d59c20e 100644 --- a/nipype/interfaces/freesurfer/utils.py +++ b/nipype/interfaces/freesurfer/utils.py @@ -814,7 +814,7 @@ class MRIsConvertInputSpec(FSTraitedSpec): # Not really sure why the ./ is necessary but the module fails without it out_datatype = traits.Enum("ico", "tri", "stl", "vtk", "gii", "mgh", "mgz", mandatory=True, - desc="These file formats are supported: ASCII: .asc" \ + desc="These file formats are supported: ASCII: .asc" "ICO: .ico, .tri GEO: .geo STL: .stl VTK: .vtk GIFTI: .gii MGH surface-encoded 'volume': .mgh, .mgz") diff --git a/nipype/interfaces/fsl/tests/test_dti.py b/nipype/interfaces/fsl/tests/test_dti.py index e32a079a43..f62aed96a5 100644 --- a/nipype/interfaces/fsl/tests/test_dti.py +++ b/nipype/interfaces/fsl/tests/test_dti.py @@ -285,11 +285,11 @@ def test_Randomise_parallel(): 'TFCE_height_param': ('--tfce_H=0.11', 0.11), 'TFCE_extent_param': ('--tfce_E=0.50', 0.50), 'TFCE_connectivity': ('--tfce_C=0.30', 0.30), - 'list_num_voxel_EVs_pos': ('--vxl=' \ - + repr([1, 2, 3, 4]), + 'list_num_voxel_EVs_pos': ('--vxl=' + + repr([1, 2, 3, 4]), repr([1, 2, 3, 4])), - 'list_img_voxel_EVs': ('--vxf=' \ - + repr([6, 7, 8, 9, 3]), + 'list_img_voxel_EVs': ('--vxf=' + + repr([6, 7, 8, 9, 3]), repr([6, 7, 8, 9, 3]))} for name, settings in list(opt_map.items()): diff --git a/nipype/interfaces/meshfix.py b/nipype/interfaces/meshfix.py index 36a25a2606..f5a891465e 100644 --- a/nipype/interfaces/meshfix.py +++ b/nipype/interfaces/meshfix.py @@ -38,7 +38,7 @@ class MeshFixInputSpec(CommandLineInputSpec): uniform_remeshing_steps = traits.Int(argstr='-u %d', requires=['uniform_remeshing_vertices'], desc="Number of steps for uniform remeshing of the whole mesh") - uniform_remeshing_vertices = traits.Int(argstr='--vertices %d', requires=['uniform_remeshing_steps'], desc="Constrains the number of vertices." \ + uniform_remeshing_vertices = traits.Int(argstr='--vertices %d', requires=['uniform_remeshing_steps'], desc="Constrains the number of vertices." "Must be used with uniform_remeshing_steps") laplacian_smoothing_steps = traits.Int(argstr='--smooth %d', desc="The number of laplacian smoothing steps to apply") @@ -48,23 +48,23 @@ class MeshFixInputSpec(CommandLineInputSpec): # Cutting, decoupling, dilation cut_outer = traits.Int(argstr='--cut-outer %d', desc="Remove triangles of 1st that are outside of the 2nd shell.") cut_inner = traits.Int(argstr='--cut-inner %d', desc="Remove triangles of 1st that are inside of the 2nd shell. Dilate 2nd by N; Fill holes and keep only 1st afterwards.") - decouple_inin = traits.Int(argstr='--decouple-inin %d', desc="Treat 1st file as inner, 2nd file as outer component." \ + decouple_inin = traits.Int(argstr='--decouple-inin %d', desc="Treat 1st file as inner, 2nd file as outer component." "Resolve overlaps by moving inners triangles inwards. Constrain the min distance between the components > d.") - decouple_outin = traits.Int(argstr='--decouple-outin %d', desc="Treat 1st file as outer, 2nd file as inner component." \ + decouple_outin = traits.Int(argstr='--decouple-outin %d', desc="Treat 1st file as outer, 2nd file as inner component." "Resolve overlaps by moving outers triangles inwards. Constrain the min distance between the components > d.") - decouple_outout = traits.Int(argstr='--decouple-outout %d', desc="Treat 1st file as outer, 2nd file as inner component." \ + decouple_outout = traits.Int(argstr='--decouple-outout %d', desc="Treat 1st file as outer, 2nd file as inner component." "Resolve overlaps by moving outers triangles outwards. Constrain the min distance between the components > d.") finetuning_inwards = traits.Bool(argstr='--fineTuneIn ', requires=['finetuning_distance', 'finetuning_substeps']) finetuning_outwards = traits.Bool(argstr='--fineTuneIn ', requires=['finetuning_distance', 'finetuning_substeps'], xor=['finetuning_inwards'], desc='Similar to finetuning_inwards, but ensures minimal distance in the other direction') - finetuning_distance = traits.Float(argstr='%f', requires=['finetuning_substeps'], desc="Used to fine-tune the minimal distance between surfaces." \ + finetuning_distance = traits.Float(argstr='%f', requires=['finetuning_substeps'], desc="Used to fine-tune the minimal distance between surfaces." "A minimal distance d is ensured, and reached in n substeps. When using the surfaces for subsequent volume meshing by gmsh, this step prevent too flat tetrahedra2)") - finetuning_substeps = traits.Int(argstr='%d', requires=['finetuning_distance'], desc="Used to fine-tune the minimal distance between surfaces." \ + finetuning_substeps = traits.Int(argstr='%d', requires=['finetuning_distance'], desc="Used to fine-tune the minimal distance between surfaces." "A minimal distance d is ensured, and reached in n substeps. When using the surfaces for subsequent volume meshing by gmsh, this step prevent too flat tetrahedra2)") dilation = traits.Int(argstr='--dilate %d', desc="Dilate the surface by d. d < 0 means shrinking.") - set_intersections_to_one = traits.Bool(argstr='--intersect', desc="If the mesh contains intersections, return value = 1." \ + set_intersections_to_one = traits.Bool(argstr='--intersect', desc="If the mesh contains intersections, return value = 1." "If saved in gmsh format, intersections will be highlighted.") in_file1 = File(exists=True, argstr="%s", position=1, mandatory=True) diff --git a/nipype/interfaces/mrtrix/tensors.py b/nipype/interfaces/mrtrix/tensors.py index 52ad0d33da..3ef2ecc901 100644 --- a/nipype/interfaces/mrtrix/tensors.py +++ b/nipype/interfaces/mrtrix/tensors.py @@ -104,7 +104,7 @@ class ConstrainedSphericalDeconvolutionInputSpec(CommandLineInputSpec): encoding_file = File(exists=True, argstr='-grad %s', position=1, desc='Gradient encoding, supplied as a 4xN text file with each line is in the format [ X Y Z b ], where [ X Y Z ] describe the direction of the applied gradient, and b gives the b-value in units (1000 s/mm^2). See FSL2MRTrix') filter_file = File(exists=True, argstr='-filter %s', position=-2, - desc='a text file containing the filtering coefficients for each even harmonic order.' \ + desc='a text file containing the filtering coefficients for each even harmonic order.' 'the linear frequency filtering parameters used for the initial linear spherical deconvolution step (default = [ 1 1 1 0 0 ]).') lambda_value = traits.Float(argstr='-lambda %s', desc='the regularisation parameter lambda that controls the strength of the constraint (default = 1.0).') @@ -268,7 +268,7 @@ class FSL2MRTrixInputSpec(TraitedSpec): class FSL2MRTrixOutputSpec(TraitedSpec): - encoding_file = File(desc='The gradient encoding, supplied as a 4xN text file with each line is in the format [ X Y Z b ], where [ X Y Z ] describe the direction of the applied gradient' \ + encoding_file = File(desc='The gradient encoding, supplied as a 4xN text file with each line is in the format [ X Y Z b ], where [ X Y Z ] describe the direction of the applied gradient' 'and b gives the b-value in units (1000 s/mm^2).') @@ -353,7 +353,7 @@ class FindShPeaksInputSpec(CommandLineInputSpec): peaks_image = File(exists=True, argstr='-peaks %s', desc='the program will try to find the peaks that most closely match those in the image provided') num_peaks = traits.Int(argstr='-num %s', desc='the number of peaks to extract (default is 3)') peak_directions = traits.List(traits.Float, argstr='-direction %s', sep=' ', minlen=2, maxlen=2, - desc='phi theta. the direction of a peak to estimate. The algorithm will attempt to find the same number of peaks as have been specified using this option ' \ + desc='phi theta. the direction of a peak to estimate. The algorithm will attempt to find the same number of peaks as have been specified using this option ' ' phi: the azimuthal angle of the direction (in degrees). theta: the elevation angle of the direction (in degrees, from the vertical z-axis)') peak_threshold = traits.Float(argstr='-threshold %s', desc='only peak amplitudes greater than the threshold will be considered') display_info = traits.Bool(argstr='-info', desc='Display information messages.') @@ -392,7 +392,7 @@ class Directions2AmplitudeInputSpec(CommandLineInputSpec): peaks_image = File(exists=True, argstr='-peaks %s', desc='the program will try to find the peaks that most closely match those in the image provided') num_peaks = traits.Int(argstr='-num %s', desc='the number of peaks to extract (default is 3)') peak_directions = traits.List(traits.Float, argstr='-direction %s', sep=' ', minlen=2, maxlen=2, - desc='phi theta. the direction of a peak to estimate. The algorithm will attempt to find the same number of peaks as have been specified using this option ' \ + desc='phi theta. the direction of a peak to estimate. The algorithm will attempt to find the same number of peaks as have been specified using this option ' ' phi: the azimuthal angle of the direction (in degrees). theta: the elevation angle of the direction (in degrees, from the vertical z-axis)') display_info = traits.Bool(argstr='-info', desc='Display information messages.') quiet_display = traits.Bool(argstr='-quiet', desc='do not display information messages or progress status.') diff --git a/nipype/interfaces/mrtrix/tracking.py b/nipype/interfaces/mrtrix/tracking.py index 126bd930e3..c4d49118a8 100644 --- a/nipype/interfaces/mrtrix/tracking.py +++ b/nipype/interfaces/mrtrix/tracking.py @@ -36,7 +36,7 @@ class FilterTracksInputSpec(CommandLineInputSpec): name_source=['in_file'], hash_files=False, name_template='%s_filt') no_mask_interpolation = traits.Bool(argstr='-nomaskinterp', desc="Turns off trilinear interpolation of mask images.") - invert = traits.Bool(argstr='-invert', desc="invert the matching process, so that tracks that would" \ + invert = traits.Bool(argstr='-invert', desc="invert the matching process, so that tracks that would" "otherwise have been included are now excluded and vice-versa.") quiet = traits.Bool(argstr='-quiet', position=1, desc="Do not display information messages or progress status.") @@ -128,8 +128,8 @@ def _gen_outfilename(self): class StreamlineTrackInputSpec(CommandLineInputSpec): - in_file = File(exists=True, argstr='%s', mandatory=True, position=-2, desc='the image containing the source data.' \ - 'The type of data required depends on the type of tracking as set in the preceeding argument. For DT methods, ' \ + in_file = File(exists=True, argstr='%s', mandatory=True, position=-2, desc='the image containing the source data.' + 'The type of data required depends on the type of tracking as set in the preceeding argument. For DT methods, ' 'the base DWI are needed. For SD methods, the SH harmonic coefficients of the FOD are needed.') seed_xor = ['seed_file', 'seed_spec'] @@ -164,11 +164,11 @@ class StreamlineTrackInputSpec(CommandLineInputSpec): desc="Set the step size of the algorithm in mm (default is 0.2).") minimum_radius_of_curvature = traits.Float(argstr='-curvature %s', units='mm', desc="Set the minimum radius of curvature (default is 2 mm for DT_STREAM, 0 for SD_STREAM, 1 mm for SD_PROB and DT_PROB)") - desired_number_of_tracks = traits.Int(argstr='-number %d', desc='Sets the desired number of tracks.' \ - 'The program will continue to generate tracks until this number of tracks have been selected and written to the output file' \ + desired_number_of_tracks = traits.Int(argstr='-number %d', desc='Sets the desired number of tracks.' + 'The program will continue to generate tracks until this number of tracks have been selected and written to the output file' '(default is 100 for *_STREAM methods, 1000 for *_PROB methods).') - maximum_number_of_tracks = traits.Int(argstr='-maxnum %d', desc='Sets the maximum number of tracks to generate.' \ - "The program will not generate more tracks than this number, even if the desired number of tracks hasn't yet been reached" \ + maximum_number_of_tracks = traits.Int(argstr='-maxnum %d', desc='Sets the maximum number of tracks to generate.' + "The program will not generate more tracks than this number, even if the desired number of tracks hasn't yet been reached" '(default is 100 x number).') minimum_tract_length = traits.Float(argstr='-minlength %s', units='mm', diff --git a/nipype/interfaces/spm/model.py b/nipype/interfaces/spm/model.py index c942161c8e..2a3472a648 100644 --- a/nipype/interfaces/spm/model.py +++ b/nipype/interfaces/spm/model.py @@ -375,8 +375,8 @@ def _make_matlab_command(self, _): try: tidx = cname.index(fcont[0]) except: - Exception("Contrast Estimate: could not get index of" \ - " T contrast. probably not defined prior " \ + Exception("Contrast Estimate: could not get index of" + " T contrast. probably not defined prior " "to the F contrasts") script += "consess{%d}.fcon.convec{%d} = consess{%d}.tcon.convec;\n" % (i + 1, cl0 + 1, tidx + 1) script += "jobs{1}.stats{1}.con.consess = consess;\n" diff --git a/nipype/interfaces/spm/utils.py b/nipype/interfaces/spm/utils.py index 9b7aa84dd3..17ddf6e94f 100644 --- a/nipype/interfaces/spm/utils.py +++ b/nipype/interfaces/spm/utils.py @@ -193,7 +193,7 @@ class ResliceInputSpec(SPMCommandInputSpec): desc='Volume defining space to slice in_file into') interp = traits.Range(low=0, high=7, usedefault=True, - desc='degree of b-spline used for interpolation'\ + desc='degree of b-spline used for interpolation' '0 is nearest neighbor (default)') out_file = File(desc='Optional file to save resliced volume') diff --git a/nipype/interfaces/utility.py b/nipype/interfaces/utility.py index 0cf6aa6e64..37883d4e5c 100644 --- a/nipype/interfaces/utility.py +++ b/nipype/interfaces/utility.py @@ -405,8 +405,8 @@ def __init__(self, input_names, output_names, function=None, imports=None, try: self.inputs.function_str = getsource(function) except IOError: - raise Exception('Interface Function does not accept ' \ - 'function objects defined interactively ' \ + raise Exception('Interface Function does not accept ' + 'function objects defined interactively ' 'in a python session') elif isinstance(function, string_types): self.inputs.function_str = function diff --git a/nipype/pipeline/plugins/ipython.py b/nipype/pipeline/plugins/ipython.py index 2599f3f76c..c12907f264 100644 --- a/nipype/pipeline/plugins/ipython.py +++ b/nipype/pipeline/plugins/ipython.py @@ -64,7 +64,7 @@ def run(self, graph, config, updatehash=False): __import__(name) self.iparallel = sys.modules[name] except ImportError: - raise ImportError("Ipython kernel not found. Parallel execution " \ + raise ImportError("Ipython kernel not found. Parallel execution " "will be unavailable") try: self.taskclient = self.iparallel.Client() diff --git a/nipype/pipeline/plugins/ipythonx.py b/nipype/pipeline/plugins/ipythonx.py index 47887e3a93..47f4bf525a 100644 --- a/nipype/pipeline/plugins/ipythonx.py +++ b/nipype/pipeline/plugins/ipythonx.py @@ -37,7 +37,7 @@ def run(self, graph, config, updatehash=False): __import__(name) self.ipyclient = sys.modules[name] except ImportError: - raise ImportError("Ipython kernel not found. Parallel execution " \ + raise ImportError("Ipython kernel not found. Parallel execution " "will be unavailable") try: self.taskclient = self.ipyclient.TaskClient() diff --git a/nipype/pipeline/tests/test_engine.py b/nipype/pipeline/tests/test_engine.py index 08c25aced6..5853319800 100644 --- a/nipype/pipeline/tests/test_engine.py +++ b/nipype/pipeline/tests/test_engine.py @@ -178,8 +178,8 @@ def test8(): pipe._execgraph = pe.generate_expanded_graph(deepcopy(pipe._flatgraph)) yield assert_equal, len(pipe._execgraph.nodes()), 8 yield assert_equal, len(pipe._execgraph.edges()), 8 - edgenum = sorted([(len(pipe._execgraph.in_edges(node)) + \ - len(pipe._execgraph.out_edges(node))) \ + edgenum = sorted([(len(pipe._execgraph.in_edges(node)) + + len(pipe._execgraph.out_edges(node))) for node in pipe._execgraph.nodes()]) yield assert_true, edgenum[0] > 0 diff --git a/nipype/utils/docparse.py b/nipype/utils/docparse.py index 4875ee6b95..f77035c3ce 100644 --- a/nipype/utils/docparse.py +++ b/nipype/utils/docparse.py @@ -287,8 +287,8 @@ def _parse_doc(doc, style=['--']): style = [style] for line in doclist: linelist = line.split() - flag = [item for i, item in enumerate(linelist) if i < 2 and \ - any([item.startswith(s) for s in style]) and \ + flag = [item for i, item in enumerate(linelist) if i < 2 and + any([item.startswith(s) for s in style]) and len(item) > 1] if flag: if len(flag) == 1: From 1034f304794a795f81374501aa231327f48b488a Mon Sep 17 00:00:00 2001 From: miykael Date: Sun, 1 Nov 2015 10:35:41 +0100 Subject: [PATCH 09/19] FIX: PEP8 - E701 multiple statements on one line (colon) --- doc/sphinxext/numpy_ext/docscrape.py | 12 ++++++++---- doc/sphinxext/numpy_ext/numpydoc.py | 6 ++++-- nipype/algorithms/modelgen.py | 3 ++- nipype/pipeline/engine.py | 3 ++- setup.py | 3 ++- 5 files changed, 18 insertions(+), 9 deletions(-) diff --git a/doc/sphinxext/numpy_ext/docscrape.py b/doc/sphinxext/numpy_ext/docscrape.py index 5cc9492247..03dbd37679 100644 --- a/doc/sphinxext/numpy_ext/docscrape.py +++ b/doc/sphinxext/numpy_ext/docscrape.py @@ -145,10 +145,12 @@ def _strip(self, doc): i = 0 j = 0 for i, line in enumerate(doc): - if line.strip(): break + if line.strip(): + break for j, line in enumerate(doc[::-1]): - if line.strip(): break + if line.strip(): + break return doc[i:len(doc)-j] @@ -227,7 +229,8 @@ def push_item(name, rest): rest = [] for line in content: - if not line.strip(): continue + if not line.strip(): + continue m = self._name_rgx.match(line) if m and line[m.end():].strip().startswith(':'): @@ -351,7 +354,8 @@ def _str_section(self, name): return out def _str_see_also(self, func_role): - if not self['See Also']: return [] + if not self['See Also']: + return [] out = [] out += self._str_header("See Also") last_had_desc = True diff --git a/doc/sphinxext/numpy_ext/numpydoc.py b/doc/sphinxext/numpy_ext/numpydoc.py index cb4dc3ba90..fd517a00f6 100644 --- a/doc/sphinxext/numpy_ext/numpydoc.py +++ b/doc/sphinxext/numpy_ext/numpydoc.py @@ -89,8 +89,10 @@ def mangle_signature(app, what, name, obj, options, sig, retann): 'initializes x; see ' in pydoc.getdoc(obj.__init__))): return '', '' - if not (callable(obj) or hasattr(obj, '__argspec_is_invalid_')): return - if not hasattr(obj, '__doc__'): return + if not (callable(obj) or hasattr(obj, '__argspec_is_invalid_')): + return + if not hasattr(obj, '__doc__'): + return doc = SphinxDocString(pydoc.getdoc(obj)) if doc['Signature']: diff --git a/nipype/algorithms/modelgen.py b/nipype/algorithms/modelgen.py index cb7e2ae4e8..2cf0bbbeed 100644 --- a/nipype/algorithms/modelgen.py +++ b/nipype/algorithms/modelgen.py @@ -50,7 +50,8 @@ def gcd(a, b): 11 """ - while b > 0: a, b = b, a % b + while b > 0: + a, b = b, a % b return a diff --git a/nipype/pipeline/engine.py b/nipype/pipeline/engine.py index 6ed2f53c66..0b8f77da32 100644 --- a/nipype/pipeline/engine.py +++ b/nipype/pipeline/engine.py @@ -1065,7 +1065,8 @@ def _get_dot(self, prefix=None, hierarchy=None, colored=False, colored=colored, simple_form=simple_form, level=level+3)) dotlist.append('}') - if level == 6: level = 2 + if level == 6: + level = 2 else: for subnode in self._graph.successors_iter(node): if node._hierarchy != subnode._hierarchy: diff --git a/setup.py b/setup.py index e6f20ae4f4..dc56beada3 100755 --- a/setup.py +++ b/setup.py @@ -20,7 +20,8 @@ # BEFORE importing distutils, remove MANIFEST. distutils doesn't properly # update it when the contents of directories change. -if os.path.exists('MANIFEST'): os.remove('MANIFEST') +if os.path.exists('MANIFEST'): + os.remove('MANIFEST') # For some commands, use setuptools. if len(set(('develop', 'bdist_egg', 'bdist_rpm', 'bdist', 'bdist_dumb', From 67f10e5776f4d5922dbe9b29687303eb025632f7 Mon Sep 17 00:00:00 2001 From: miykael Date: Sun, 1 Nov 2015 10:36:13 +0100 Subject: [PATCH 10/19] FIX: PEP8 - E703 statement ends with a semicolon --- nipype/algorithms/metrics.py | 4 ++-- nipype/interfaces/spm/tests/test_base.py | 2 +- nipype/workflows/dmri/fsl/epi.py | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/nipype/algorithms/metrics.py b/nipype/algorithms/metrics.py index 48a686a420..76abdd1c50 100644 --- a/nipype/algorithms/metrics.py +++ b/nipype/algorithms/metrics.py @@ -463,8 +463,8 @@ def _list_outputs(self): outputs[method] = getattr(self, '_' + method) # outputs['volume_difference'] = self._volume outputs['diff_file'] = os.path.abspath(self.inputs.out_file) - outputs['class_fji'] = np.array(self._jaccards).astype(float).tolist(); - outputs['class_fdi'] = self._dices.astype(float).tolist(); + outputs['class_fji'] = np.array(self._jaccards).astype(float).tolist() + outputs['class_fdi'] = self._dices.astype(float).tolist() return outputs diff --git a/nipype/interfaces/spm/tests/test_base.py b/nipype/interfaces/spm/tests/test_base.py index 4a7ce2c852..73e8ad9c12 100644 --- a/nipype/interfaces/spm/tests/test_base.py +++ b/nipype/interfaces/spm/tests/test_base.py @@ -93,7 +93,7 @@ class TestClass(spm.SPMCommand): yield assert_equal, dc._use_mcr, True yield assert_equal, dc._matlab_cmd, 'spmcmd' # restore environment - os.environ.clear(); + os.environ.clear() os.environ.update(saved_env) diff --git a/nipype/workflows/dmri/fsl/epi.py b/nipype/workflows/dmri/fsl/epi.py index 2fa7b012a0..76d7297f76 100644 --- a/nipype/workflows/dmri/fsl/epi.py +++ b/nipype/workflows/dmri/fsl/epi.py @@ -788,7 +788,7 @@ def _vsm_remove_mean(in_file, mask_file, in_unwarped): def _ms2sec(val): - return val*1e-3; + return val*1e-3 def _split_dwi(in_file): From 46635e585411b96157d81d6b90638605a9386239 Mon Sep 17 00:00:00 2001 From: miykael Date: Sun, 1 Nov 2015 10:36:57 +0100 Subject: [PATCH 11/19] FIX: PEP8 - E711 comparison to None should be 'if cond is (not) None:' --- nipype/external/provcopy.py | 2 +- nipype/interfaces/fsl/utils.py | 2 +- nipype/interfaces/traits_extension.py | 4 ++-- nipype/pipeline/utils.py | 4 ++-- 4 files changed, 6 insertions(+), 6 deletions(-) diff --git a/nipype/external/provcopy.py b/nipype/external/provcopy.py index 2a55f3b4ce..daf234571e 100644 --- a/nipype/external/provcopy.py +++ b/nipype/external/provcopy.py @@ -1820,7 +1820,7 @@ def add_bundle(self, bundle, identifier=None): '''Add a bundle to the current document ''' - if identifier == None: + if identifier is None: identifier = bundle.get_identifier() if not identifier: diff --git a/nipype/interfaces/fsl/utils.py b/nipype/interfaces/fsl/utils.py index 4f5d2c4aed..0db24df2a9 100644 --- a/nipype/interfaces/fsl/utils.py +++ b/nipype/interfaces/fsl/utils.py @@ -1502,7 +1502,7 @@ class Complex(FSLCommand): output_spec = ComplexOuputSpec def _parse_inputs(self, skip=None): - if skip == None: + if skip is None: skip = [] if self.inputs.real_cartesian: skip += self.inputs._ofs[:3] diff --git a/nipype/interfaces/traits_extension.py b/nipype/interfaces/traits_extension.py index 14f1c82aaf..1a6e804f05 100644 --- a/nipype/interfaces/traits_extension.py +++ b/nipype/interfaces/traits_extension.py @@ -239,13 +239,13 @@ def has_metadata(trait, metadata, value=None, recursive=True): Checks if a given trait has a metadata (and optionally if it is set to particular value) ''' count = 0 - if hasattr(trait, "_metadata") and metadata in list(trait._metadata.keys()) and (trait._metadata[metadata] == value or value == None): + if hasattr(trait, "_metadata") and metadata in list(trait._metadata.keys()) and (trait._metadata[metadata] == value or value is None): count += 1 if recursive: if hasattr(trait, 'inner_traits'): for inner_trait in trait.inner_traits(): count += has_metadata(inner_trait.trait_type, metadata, recursive) - if hasattr(trait, 'handlers') and trait.handlers != None: + if hasattr(trait, 'handlers') and trait.handlers is not None: for handler in trait.handlers: count += has_metadata(handler, metadata, recursive) diff --git a/nipype/pipeline/utils.py b/nipype/pipeline/utils.py index b3a0b65a21..5ae7ec3140 100644 --- a/nipype/pipeline/utils.py +++ b/nipype/pipeline/utils.py @@ -894,11 +894,11 @@ def _transpose_iterables(fields, values): for key, tuples in list(values.items()): for kvals in tuples: for idx, val in enumerate(kvals): - if val != None: + if val is not None: transposed[fields[idx]][key].append(val) return list(transposed.items()) else: - return list(zip(fields, [[v for v in list(transpose) if v != None] + return list(zip(fields, [[v for v in list(transpose) if v is not None] for transpose in zip(*values)])) From f28d822cb7c216e0b17fed34c5415fd4d2e360d0 Mon Sep 17 00:00:00 2001 From: miykael Date: Sun, 1 Nov 2015 10:37:48 +0100 Subject: [PATCH 12/19] FIX: PEP8 - E712 comparison to True/False should be 'if cond is True/False:' or 'if (not) cond:' --- nipype/fixes/numpy/testing/nosetester.py | 2 +- nipype/interfaces/cmtk/parcellation.py | 8 ++++---- nipype/interfaces/freesurfer/preprocess.py | 4 ++-- nipype/interfaces/fsl/dti.py | 2 +- nipype/interfaces/slicer/generate_classes.py | 2 +- nipype/pipeline/plugins/sgegraph.py | 6 +++--- nipype/pipeline/plugins/slurmgraph.py | 6 +++--- 7 files changed, 15 insertions(+), 15 deletions(-) diff --git a/nipype/fixes/numpy/testing/nosetester.py b/nipype/fixes/numpy/testing/nosetester.py index 5c3b3d9e73..5c392b63bd 100644 --- a/nipype/fixes/numpy/testing/nosetester.py +++ b/nipype/fixes/numpy/testing/nosetester.py @@ -245,7 +245,7 @@ def prepare_test_args(self, label='fast', verbose=1, extra_argv=None, plugins += [p() for p in nose.plugins.builtin.plugins] # add doctesting if required doctest_argv = '--with-doctest' in argv - if doctests == False and doctest_argv: + if doctests is False and doctest_argv: doctests = True plug = self._get_custom_doctester() if plug is None: diff --git a/nipype/interfaces/cmtk/parcellation.py b/nipype/interfaces/cmtk/parcellation.py index 140b7273ca..2297177e01 100644 --- a/nipype/interfaces/cmtk/parcellation.py +++ b/nipype/interfaces/cmtk/parcellation.py @@ -273,7 +273,7 @@ def create_roi(subject_id, subjects_dir, fs_dir, parcellation_name, dilation): iflogger.info("[ DONE ]") # dilate cortical regions - if (dilation == True): + if dilation is True: iflogger.info("Dilating cortical regions...") # loop throughout all the voxels belonging to the aseg GM volume for j in range(xx.size): @@ -463,7 +463,7 @@ def crop_and_move_datasets(subject_id, subjects_dir, fs_dir, parcellation_name, ds.append((op.abspath('ROI_%s.nii.gz' % parcellation_name), op.abspath('ROI_HR_th.nii.gz'))) - if(dilation == True): + if dilation is True: ds.append((op.abspath('ROIv_%s.nii.gz' % parcellation_name), op.abspath('ROIv_HR_th.nii.gz'))) orig = op.join(fs_dir, 'mri', 'orig', '001.mgz') @@ -588,7 +588,7 @@ def _list_outputs(self): else: outputs['roi_file'] = op.abspath( self._gen_outfilename('nii.gz', 'ROI')) - if(self.inputs.dilation == True): + if self.inputs.dilation is True: outputs['roiv_file'] = op.abspath(self._gen_outfilename( 'nii.gz', 'ROIv')) outputs['white_matter_mask_file'] = op.abspath('fsmask_1mm.nii.gz') @@ -597,7 +597,7 @@ def _list_outputs(self): outputs['aseg_file'] = op.abspath('aseg.nii.gz') outputs['roi_file_in_structural_space'] = op.abspath( 'ROI_HR_th.nii.gz') - if(self.inputs.dilation == True): + if self.inputs.dilation is True: outputs['dilated_roi_file_in_structural_space'] = op.abspath( 'ROIv_HR_th.nii.gz') return outputs diff --git a/nipype/interfaces/freesurfer/preprocess.py b/nipype/interfaces/freesurfer/preprocess.py index c2d634291b..a16938b655 100644 --- a/nipype/interfaces/freesurfer/preprocess.py +++ b/nipype/interfaces/freesurfer/preprocess.py @@ -1003,8 +1003,8 @@ class ApplyVolTransform(FSCommand): def _get_outfile(self): outfile = self.inputs.transformed_file if not isdefined(outfile): - if self.inputs.inverse == True: - if self.inputs.fs_target == True: + if self.inputs.inverse is True: + if self.inputs.fs_target is True: src = 'orig.mgz' else: src = self.inputs.target_file diff --git a/nipype/interfaces/fsl/dti.py b/nipype/interfaces/fsl/dti.py index a0b7a5bad6..b8db4a63b2 100644 --- a/nipype/interfaces/fsl/dti.py +++ b/nipype/interfaces/fsl/dti.py @@ -836,7 +836,7 @@ def _list_outputs(self): outputs['log'] = os.path.abspath(os.path.join(out_dir, 'probtrackx.log')) # utputs['way_total'] = os.path.abspath(os.path.join(out_dir, 'waytotal')) - if isdefined(self.inputs.opd == True): + if isdefined(self.inputs.opd is True): if isinstance(self.inputs.seed, list) and isinstance(self.inputs.seed[0], list): outputs['fdt_paths'] = [] for seed in self.inputs.seed: diff --git a/nipype/interfaces/slicer/generate_classes.py b/nipype/interfaces/slicer/generate_classes.py index 73ce553ce8..46b85af86a 100644 --- a/nipype/interfaces/slicer/generate_classes.py +++ b/nipype/interfaces/slicer/generate_classes.py @@ -227,7 +227,7 @@ def generate_class(module, launcher, strip_module_name_prefix=True, redirect_x=F param.nodeName.replace('-vector', '')]] else: values = [typesDict[param.nodeName.replace('-vector', '')]] - if mipav_hacks == True: + if mipav_hacks is True: traitsParams["sep"] = ";" else: traitsParams["sep"] = ',' diff --git a/nipype/pipeline/plugins/sgegraph.py b/nipype/pipeline/plugins/sgegraph.py index 60c8c4600b..10fde4d0e2 100644 --- a/nipype/pipeline/plugins/sgegraph.py +++ b/nipype/pipeline/plugins/sgegraph.py @@ -16,9 +16,9 @@ def node_completed_status(checknode): :return: boolean value True indicates that the node does not need to be run. """ """ TODO: place this in the base.py file and refactor """ - node_state_does_not_require_overwrite = (checknode.overwrite == False or - (checknode.overwrite == None and - not checknode._interface.always_run) + node_state_does_not_require_overwrite = (checknode.overwrite is False or + (checknode.overwrite is None and not + checknode._interface.always_run) ) hash_exists = False try: diff --git a/nipype/pipeline/plugins/slurmgraph.py b/nipype/pipeline/plugins/slurmgraph.py index 08abe4b394..0733412d38 100644 --- a/nipype/pipeline/plugins/slurmgraph.py +++ b/nipype/pipeline/plugins/slurmgraph.py @@ -16,9 +16,9 @@ def node_completed_status(checknode): :return: boolean value True indicates that the node does not need to be run. """ """ TODO: place this in the base.py file and refactor """ - node_state_does_not_require_overwrite = (checknode.overwrite == False or - (checknode.overwrite == None and - not checknode._interface.always_run) + node_state_does_not_require_overwrite = (checknode.overwrite is False or + (checknode.overwrite is None and not + checknode._interface.always_run) ) hash_exists = False try: From 89d13fa22d2da4a9ce66726ec4c85c0bba7647a5 Mon Sep 17 00:00:00 2001 From: miykael Date: Sun, 1 Nov 2015 10:38:23 +0100 Subject: [PATCH 13/19] FIX: PEP8 - E713 test for membership should be 'not in' --- nipype/interfaces/dcmstack.py | 4 ++-- nipype/interfaces/freesurfer/utils.py | 2 +- nipype/interfaces/io.py | 4 ++-- setup.py | 2 +- 4 files changed, 6 insertions(+), 6 deletions(-) diff --git a/nipype/interfaces/dcmstack.py b/nipype/interfaces/dcmstack.py index 9d5b2fd744..94dc14095d 100644 --- a/nipype/interfaces/dcmstack.py +++ b/nipype/interfaces/dcmstack.py @@ -37,7 +37,7 @@ def sanitize_path_comp(path_comp): result = [] for char in path_comp: - if not char in string.letters + string.digits + '-_.': + if char not in string.letters + string.digits + '-_.': result.append('_') else: result.append(char) @@ -303,7 +303,7 @@ def _run_interface(self, runtime): if self.inputs.exclude_classes: classes = [cls for cls in classes - if not cls in self.inputs.exclude_classes + if cls not in self.inputs.exclude_classes ] for cls in classes: diff --git a/nipype/interfaces/freesurfer/utils.py b/nipype/interfaces/freesurfer/utils.py index 2f8d59c20e..f816a38a99 100644 --- a/nipype/interfaces/freesurfer/utils.py +++ b/nipype/interfaces/freesurfer/utils.py @@ -641,7 +641,7 @@ def _run_interface(self, runtime): args = tuple([getattr(self.inputs, arg) for arg in stem_args]) stem = stem % args # Check if the DISPLAY variable is set -- should avoid crashes (might not?) - if not "DISPLAY" in os.environ: + if "DISPLAY" not in os.environ: raise RuntimeError("Graphics are not enabled -- cannot run tksurfer") runtime.environ["_SNAPSHOT_STEM"] = stem self._write_tcl_script() diff --git a/nipype/interfaces/io.py b/nipype/interfaces/io.py index 03123c39ae..ed2ec0a216 100644 --- a/nipype/interfaces/io.py +++ b/nipype/interfaces/io.py @@ -546,7 +546,7 @@ def __init__(self, infields=None, outfields=None, **kwargs): if not isdefined(self.inputs.template_args): self.inputs.template_args = {} for key in outfields: - if not key in self.inputs.template_args: + if key not in self.inputs.template_args: if infields: self.inputs.template_args[key] = [infields] else: @@ -789,7 +789,7 @@ def __init__(self, infields=None, outfields=None, **kwargs): if not isdefined(self.inputs.template_args): self.inputs.template_args = {} for key in outfields: - if not key in self.inputs.template_args: + if key not in self.inputs.template_args: if infields: self.inputs.template_args[key] = [infields] else: diff --git a/setup.py b/setup.py index dc56beada3..f20c7948c8 100755 --- a/setup.py +++ b/setup.py @@ -219,7 +219,7 @@ def version_getter(pkg_name): if version: dependency += '>=' + version if optional_tf: - if not 'extras_require' in setuptools_args: + if 'extras_require' not in setuptools_args: setuptools_args['extras_require'] = {} _add_append_key(setuptools_args['extras_require'], optional, From b60de4cd08b30e910f2baff3d1f458ece23f5489 Mon Sep 17 00:00:00 2001 From: miykael Date: Sun, 1 Nov 2015 10:38:59 +0100 Subject: [PATCH 14/19] FIX: PEP8 - E714 test for object identity should be 'is not' --- nipype/algorithms/misc.py | 2 +- nipype/interfaces/ants/registration.py | 2 +- nipype/interfaces/dcmstack.py | 2 +- nipype/interfaces/elastix/utils.py | 2 +- nipype/interfaces/fsl/utils.py | 2 +- nipype/interfaces/io.py | 2 +- nipype/pipeline/plugins/dagman.py | 2 +- setup.py | 2 +- tools/gitwash_dumper.py | 8 ++++---- 9 files changed, 12 insertions(+), 12 deletions(-) diff --git a/nipype/algorithms/misc.py b/nipype/algorithms/misc.py index 6d5aaf1dc0..7aee89a49f 100644 --- a/nipype/algorithms/misc.py +++ b/nipype/algorithms/misc.py @@ -1271,7 +1271,7 @@ def normalize_tpms(in_files, in_mask=None, out_files=[]): msk = np.ones_like(imgs[0].get_data()) msk[weights <= 0] = 0 - if not in_mask is None: + if in_mask is not None: msk = nib.load(in_mask).get_data() msk[msk <= 0] = 0 msk[msk > 0] = 1 diff --git a/nipype/interfaces/ants/registration.py b/nipype/interfaces/ants/registration.py index c4d6d6636b..aa2e1494e3 100644 --- a/nipype/interfaces/ants/registration.py +++ b/nipype/interfaces/ants/registration.py @@ -157,7 +157,7 @@ def _transformation_constructor(self): retval = ['--transformation-model %s' % model] parameters = [] for elem in (stepLength, timeStep, deltaTime, symmetryType): - if not elem is traits.Undefined: + if elem is not traits.Undefined: parameters.append('%#.2g' % elem) if len(parameters) > 0: if len(parameters) > 1: diff --git a/nipype/interfaces/dcmstack.py b/nipype/interfaces/dcmstack.py index 94dc14095d..a06065fa41 100644 --- a/nipype/interfaces/dcmstack.py +++ b/nipype/interfaces/dcmstack.py @@ -63,7 +63,7 @@ def _get_out_path(self, meta, idx=None): # If no out_format is specified, use a sane default that will work # with the provided meta data. out_fmt = [] - if not idx is None: + if idx is not None: out_fmt.append('%03d' % idx) if 'SeriesNumber' in meta: out_fmt.append('%(SeriesNumber)03d') diff --git a/nipype/interfaces/elastix/utils.py b/nipype/interfaces/elastix/utils.py index 2c857136e5..541cfa1ec4 100644 --- a/nipype/interfaces/elastix/utils.py +++ b/nipype/interfaces/elastix/utils.py @@ -137,7 +137,7 @@ def _list_outputs(self): def _get_outfile(self): val = getattr(self, '_out_file') - if not val is None and not val == '': + if val is not None and val != '': return val if isdefined(self.inputs.output_file): diff --git a/nipype/interfaces/fsl/utils.py b/nipype/interfaces/fsl/utils.py index 0db24df2a9..bf71a13bf5 100644 --- a/nipype/interfaces/fsl/utils.py +++ b/nipype/interfaces/fsl/utils.py @@ -1933,7 +1933,7 @@ def _run_interface(self, runtime): runtime = super(WarpPoints, self)._run_interface(runtime) newpoints = np.fromstring('\n'.join(runtime.stdout.split('\n')[1:]), sep=' ') - if not tmpfile is None: + if tmpfile is not None: try: os.remove(tmpfile.name) except: diff --git a/nipype/interfaces/io.py b/nipype/interfaces/io.py index ed2ec0a216..a12457ed48 100644 --- a/nipype/interfaces/io.py +++ b/nipype/interfaces/io.py @@ -1100,7 +1100,7 @@ def _match_path(self, target_path): return # Check if we can match the path match = self.match_regex.search(target_path) - if not match is None: + if match is not None: match_dict = match.groupdict() if self.result is None: self.result = {'out_paths': []} diff --git a/nipype/pipeline/plugins/dagman.py b/nipype/pipeline/plugins/dagman.py index a41fff6988..7b9ca27282 100644 --- a/nipype/pipeline/plugins/dagman.py +++ b/nipype/pipeline/plugins/dagman.py @@ -127,7 +127,7 @@ def _submit_graph(self, pyfiles, dependencies, nodes): basename=os.path.join(batch_dir, name), override_specs=override_specs ) - if not wrapper_cmd is None: + if wrapper_cmd is not None: specs['executable'] = wrapper_cmd specs['nodescript'] = \ '%s %s %s' % (wrapper_args % specs, # give access to variables diff --git a/setup.py b/setup.py index f20c7948c8..6341094694 100755 --- a/setup.py +++ b/setup.py @@ -172,7 +172,7 @@ def package_check(pkg_name, version=None, dependencies. If dict fill key values ``install_requires`` and ``extras_require`` for non-optional and optional dependencies. ''' - setuptools_mode = not setuptools_args is None + setuptools_mode = setuptools_args is not None optional_tf = bool(optional) if version_getter is None: def version_getter(pkg_name): diff --git a/tools/gitwash_dumper.py b/tools/gitwash_dumper.py index 3cd930066b..8803786c8c 100755 --- a/tools/gitwash_dumper.py +++ b/tools/gitwash_dumper.py @@ -116,8 +116,8 @@ def make_link_targets(proj_name, .. _`proj_name` mailing list: url """ link_contents = open(known_link_fname, 'rt').readlines() - have_url = not url is None - have_ml_url = not ml_url is None + have_url = url is not None + have_ml_url = ml_url is not None have_gh_url = None for line in link_contents: if not have_url: @@ -136,12 +136,12 @@ def make_link_targets(proj_name, raise RuntimeError('Need command line or known project ' 'and / or mailing list URLs') lines = [] - if not url is None: + if url is not None: lines.append('.. _%s: %s\n' % (proj_name, url)) if not have_gh_url: gh_url = 'http://github.com/%s/%s\n' % (user_name, repo_name) lines.append('.. _`%s github`: %s\n' % (proj_name, gh_url)) - if not ml_url is None: + if ml_url is not None: lines.append('.. _`%s mailing list`: %s\n' % (proj_name, ml_url)) if len(lines) == 0: # Nothing to do From f4d89d6725577999ca5b2f63185e367888ab0f0d Mon Sep 17 00:00:00 2001 From: miykael Date: Sun, 1 Nov 2015 10:50:07 +0100 Subject: [PATCH 15/19] FIX: PEP8 - missing whitespace around operator (E225) or arithmetic operator (E226) - 2nd clean up --- doc/sphinxext/autosummary_generate.py | 4 +- doc/sphinxext/numpy_ext/docscrape.py | 14 ++-- doc/sphinxext/numpy_ext/docscrape_sphinx.py | 4 +- doc/sphinxext/numpy_ext/numpydoc.py | 2 +- examples/fmri_ants_openfmri.py | 4 +- examples/fmri_freesurfer_smooth.py | 8 +-- examples/fmri_fsl.py | 6 +- examples/fmri_fsl_feeds.py | 2 +- examples/fmri_fsl_reuse.py | 2 +- examples/fmri_nipy_glm.py | 2 +- examples/fmri_spm.py | 4 +- examples/fmri_spm_dartel.py | 6 +- examples/fmri_spm_face.py | 2 +- examples/fmri_spm_nested.py | 4 +- .../frontiers_paper/smoothing_comparison.py | 2 +- .../frontiers_paper/workflow_from_scratch.py | 2 +- examples/rsfmri_vol_surface_preprocessing.py | 2 +- .../rsfmri_vol_surface_preprocessing_nipy.py | 2 +- examples/smri_ants_registration.py | 4 +- nipype/algorithms/mesh.py | 6 +- nipype/algorithms/metrics.py | 12 ++-- nipype/algorithms/misc.py | 24 +++---- nipype/algorithms/modelgen.py | 16 ++--- nipype/fixes/numpy/testing/noseclasses.py | 4 +- nipype/interfaces/afni/preprocess.py | 2 +- nipype/interfaces/base.py | 2 +- nipype/interfaces/camino/convert.py | 2 +- nipype/interfaces/cmtk/cmtk.py | 4 +- nipype/interfaces/cmtk/nx.py | 4 +- nipype/interfaces/diffusion_toolkit/dti.py | 2 +- nipype/interfaces/diffusion_toolkit/odf.py | 2 +- nipype/interfaces/dynamic_slicer.py | 6 +- nipype/interfaces/freesurfer/preprocess.py | 4 +- .../freesurfer/tests/test_preprocess.py | 4 +- .../interfaces/freesurfer/tests/test_utils.py | 6 +- nipype/interfaces/fsl/tests/test_dti.py | 14 ++-- nipype/interfaces/fsl/tests/test_epi.py | 4 +- nipype/interfaces/fsl/tests/test_maths.py | 68 +++++++++---------- nipype/interfaces/fsl/utils.py | 14 ++-- nipype/interfaces/io.py | 2 +- nipype/interfaces/matlab.py | 2 +- nipype/interfaces/mrtrix/convert.py | 12 ++-- nipype/interfaces/nipy/model.py | 8 +-- nipype/interfaces/spm/preprocess.py | 32 ++++----- nipype/interfaces/spm/tests/test_utils.py | 2 +- nipype/interfaces/spm/utils.py | 20 +++--- nipype/pipeline/engine.py | 6 +- nipype/pipeline/plugins/ipython.py | 2 +- nipype/pipeline/plugins/ipythonx.py | 2 +- nipype/pipeline/plugins/multiproc.py | 2 +- nipype/pipeline/tests/test_engine.py | 20 +++--- nipype/pipeline/utils.py | 4 +- nipype/utils/docparse.py | 8 +-- nipype/utils/filemanip.py | 6 +- nipype/utils/misc.py | 2 +- nipype/utils/nipype2boutiques.py | 20 +++--- nipype/utils/nipype_cmd.py | 10 +-- .../dmri/camino/group_connectivity.py | 2 +- nipype/workflows/dmri/fsl/epi.py | 4 +- .../dmri/mrtrix/group_connectivity.py | 2 +- nipype/workflows/fmri/fsl/preprocess.py | 8 +-- nipype/workflows/fmri/spm/preprocess.py | 2 +- nipype/workflows/rsfmri/fsl/resting.py | 2 +- .../workflows/smri/ants/ANTSBuildTemplate.py | 18 ++--- .../ants/antsRegistrationBuildTemplate.py | 20 +++--- tools/interfacedocgen.py | 2 +- tools/make_examples.py | 2 +- tools/report_coverage.py | 4 +- tools/run_examples.py | 2 +- 69 files changed, 252 insertions(+), 252 deletions(-) diff --git a/doc/sphinxext/autosummary_generate.py b/doc/sphinxext/autosummary_generate.py index 0e48b744b7..aefd8552d8 100755 --- a/doc/sphinxext/autosummary_generate.py +++ b/doc/sphinxext/autosummary_generate.py @@ -81,7 +81,7 @@ def main(): f = open(fn, 'w') try: - f.write('%s\n%s\n\n' % (name, '='*len(name))) + f.write('%s\n%s\n\n' % (name, '=' * len(name))) if inspect.isclass(obj): if issubclass(obj, Exception): @@ -210,7 +210,7 @@ def get_documented_in_lines(lines, module=None, filename=None): current_module = name documented.update(get_documented_in_docstring( name, filename=filename)) - elif current_module and not name.startswith(current_module+'.'): + elif current_module and not name.startswith(current_module + '.'): name = "%s.%s" % (current_module, name) documented.setdefault(name, []).append( (filename, current_title, "auto" + m.group(1), None)) diff --git a/doc/sphinxext/numpy_ext/docscrape.py b/doc/sphinxext/numpy_ext/docscrape.py index 03dbd37679..f7b155ff59 100644 --- a/doc/sphinxext/numpy_ext/docscrape.py +++ b/doc/sphinxext/numpy_ext/docscrape.py @@ -67,7 +67,7 @@ def read_to_condition(self, condition_func): return self[start:self._l] self._l += 1 if self.eof(): - return self[start:self._l+1] + return self[start:self._l + 1] return [] def read_to_next_empty_line(self): @@ -139,7 +139,7 @@ def _is_at_section(self): return True l2 = self._doc.peek(1).strip() # ---------- or ========== - return l2.startswith('-'*len(l1)) or l2.startswith('='*len(l1)) + return l2.startswith('-' * len(l1)) or l2.startswith('=' * len(l1)) def _strip(self, doc): i = 0 @@ -152,7 +152,7 @@ def _strip(self, doc): if line.strip(): break - return doc[i:len(doc)-j] + return doc[i:len(doc) - j] def _read_to_next_section(self): section = self._doc.read_to_next_empty_line() @@ -309,12 +309,12 @@ def _parse(self): # string conversion routines def _str_header(self, name, symbol='-'): - return [name, len(name)*symbol] + return [name, len(name) * symbol] def _str_indent(self, doc, indent=4): out = [] for line in doc: - out += [' '*indent + line] + out += [' ' * indent + line] return out def _str_signature(self): @@ -408,7 +408,7 @@ def __str__(self, func_role=''): def indent(str, indent=4): - indent_str = ' '*indent + indent_str = ' ' * indent if str is None: return indent_str lines = str.split('\n') @@ -421,7 +421,7 @@ def dedent_lines(lines): def header(text, style='-'): - return text + '\n' + style*len(text) + '\n' + return text + '\n' + style * len(text) + '\n' class FunctionDoc(NumpyDocString): diff --git a/doc/sphinxext/numpy_ext/docscrape_sphinx.py b/doc/sphinxext/numpy_ext/docscrape_sphinx.py index 21d43cceae..783f3be85a 100644 --- a/doc/sphinxext/numpy_ext/docscrape_sphinx.py +++ b/doc/sphinxext/numpy_ext/docscrape_sphinx.py @@ -23,7 +23,7 @@ def _str_field_list(self, name): def _str_indent(self, doc, indent=4): out = [] for line in doc: - out += [' '*indent + line] + out += [' ' * indent + line] return out def _str_signature(self): @@ -90,7 +90,7 @@ def _str_member_list(self, name): if others: maxlen_0 = max([len(x[0]) for x in others]) maxlen_1 = max([len(x[1]) for x in others]) - hdr = "="*maxlen_0 + " " + "="*maxlen_1 + " " + "="*10 + hdr = "=" * maxlen_0 + " " + "=" * maxlen_1 + " " + "=" * 10 fmt = '%%%ds %%%ds ' % (maxlen_0, maxlen_1) n_indent = maxlen_0 + maxlen_1 + 4 out += [hdr] diff --git a/doc/sphinxext/numpy_ext/numpydoc.py b/doc/sphinxext/numpy_ext/numpydoc.py index fd517a00f6..e9a225ef66 100644 --- a/doc/sphinxext/numpy_ext/numpydoc.py +++ b/doc/sphinxext/numpy_ext/numpydoc.py @@ -41,7 +41,7 @@ def mangle_docstrings(app, what, name, obj, options, lines, if what == 'module': # Strip top title title_re = re.compile(ur'^\s*[#*=]{4,}\n[a-z0-9 -]+\n[#*=]{4,}\s*', - re.I |re.S) + re.I | re.S) lines[:] = title_re.sub(u'', u"\n".join(lines)).split(u"\n") else: doc = get_doc_object(obj, what, u"\n".join(lines), config=cfg) diff --git a/examples/fmri_ants_openfmri.py b/examples/fmri_ants_openfmri.py index 7a42ee8432..875934faac 100755 --- a/examples/fmri_ants_openfmri.py +++ b/examples/fmri_ants_openfmri.py @@ -217,7 +217,7 @@ def create_reg_workflow(name='registration'): reg.inputs.convergence_window_size = [20] * 2 + [5] reg.inputs.smoothing_sigmas = [[4, 2, 1]] * 2 + [[1, 0.5, 0]] reg.inputs.sigma_units = ['vox'] * 3 - reg.inputs.shrink_factors = [[3, 2, 1]]*2 + [[4, 2, 1]] + reg.inputs.shrink_factors = [[3, 2, 1]] * 2 + [[4, 2, 1]] reg.inputs.use_estimate_learning_rate_once = [True] * 3 reg.inputs.use_histogram_matching = [False] * 2 + [True] reg.inputs.winsorize_lower_quantile = 0.005 @@ -428,7 +428,7 @@ def create_fs_reg_workflow(name='registration'): reg.inputs.convergence_window_size = [20] * 2 + [5] reg.inputs.smoothing_sigmas = [[4, 2, 1]] * 2 + [[1, 0.5, 0]] reg.inputs.sigma_units = ['vox'] * 3 - reg.inputs.shrink_factors = [[3, 2, 1]]*2 + [[4, 2, 1]] + reg.inputs.shrink_factors = [[3, 2, 1]] * 2 + [[4, 2, 1]] reg.inputs.use_estimate_learning_rate_once = [True] * 3 reg.inputs.use_histogram_matching = [False] * 2 + [True] reg.inputs.winsorize_lower_quantile = 0.005 diff --git a/examples/fmri_freesurfer_smooth.py b/examples/fmri_freesurfer_smooth.py index 00e6fa8009..ce8be2ff98 100755 --- a/examples/fmri_freesurfer_smooth.py +++ b/examples/fmri_freesurfer_smooth.py @@ -450,7 +450,7 @@ def subjectinfo(subject_id): from nipype.interfaces.base import Bunch from copy import deepcopy - print("Subject ID: %s\n" %str(subject_id)) + print("Subject ID: %s\n" % str(subject_id)) output = [] names = ['Task-Odd', 'Task-Even'] for r in range(4): @@ -539,7 +539,7 @@ def subjectinfo(subject_id): def getsubs(subject_id): - subs = [('_subject_id_%s/' %subject_id, '')] + subs = [('_subject_id_%s/' % subject_id, '')] return subs # store relevant outputs from various stages of the 1st level analysis @@ -579,7 +579,7 @@ def getsubs(subject_id): l2inputnode = pe.Node(interface=util.IdentityInterface(fields=['contrasts', 'hemi']), name='inputnode') -l2inputnode.iterables = [('contrasts', list(range(1, len(contrasts)+1))), +l2inputnode.iterables = [('contrasts', list(range(1, len(contrasts) + 1))), ('hemi', ['lh', 'rh'])] """ @@ -610,7 +610,7 @@ def ordersubjects(files, subj_list): outlist = [] for s in subj_list: for f in files: - if '/%s/' %s in f: + if '/%s/' % s in f: outlist.append(f) continue print(outlist) diff --git a/examples/fmri_fsl.py b/examples/fmri_fsl.py index e3702350a8..df1bb4bf03 100755 --- a/examples/fmri_fsl.py +++ b/examples/fmri_fsl.py @@ -191,7 +191,7 @@ def getmiddlevolume(func): def getthreshop(thresh): - return '-thr %.10f -Tmin -bin' %(0.1*thresh[0][1]) + return '-thr %.10f -Tmin -bin' % (0.1 * thresh[0][1]) preproc.connect(getthresh, ('out_stat', getthreshop), threshold, 'op_string') """ @@ -259,11 +259,11 @@ def getthreshop(thresh): def getbtthresh(medianvals): - return [0.75*val for val in medianvals] + return [0.75 * val for val in medianvals] def getusans(x): - return [[tuple([val[0], 0.75*val[1]])] for val in x] + return [[tuple([val[0], 0.75 * val[1]])] for val in x] preproc.connect(maskfunc2, 'out_file', smooth, 'in_file') preproc.connect(medianval, ('out_stat', getbtthresh), smooth, 'brightness_threshold') diff --git a/examples/fmri_fsl_feeds.py b/examples/fmri_fsl_feeds.py index f564074d20..88fb6a312c 100755 --- a/examples/fmri_fsl_feeds.py +++ b/examples/fmri_fsl_feeds.py @@ -79,7 +79,7 @@ modelspec.inputs.time_repetition = TR modelspec.inputs.high_pass_filter_cutoff = 100 modelspec.inputs.subject_info = [Bunch(conditions=['Visual', 'Auditory'], - onsets=[list(range(0, int(180*TR), 60)), list(range(0, int(180*TR), 90))], + onsets=[list(range(0, int(180 * TR), 60)), list(range(0, int(180 * TR), 90))], durations=[[30], [45]], amplitudes=None, tmod=None, diff --git a/examples/fmri_fsl_reuse.py b/examples/fmri_fsl_reuse.py index b3d49c8414..d5038218b7 100755 --- a/examples/fmri_fsl_reuse.py +++ b/examples/fmri_fsl_reuse.py @@ -202,7 +202,7 @@ def num_copes(files): def subjectinfo(subject_id): from nipype.interfaces.base import Bunch from copy import deepcopy - print("Subject ID: %s\n" %str(subject_id)) + print("Subject ID: %s\n" % str(subject_id)) output = [] names = ['Task-Odd', 'Task-Even'] for r in range(4): diff --git a/examples/fmri_nipy_glm.py b/examples/fmri_nipy_glm.py index 86debf4124..5dfbce03d4 100755 --- a/examples/fmri_nipy_glm.py +++ b/examples/fmri_nipy_glm.py @@ -159,7 +159,7 @@ def subjectinfo(subject_id): from nipype.interfaces.base import Bunch from copy import deepcopy - print("Subject ID: %s\n" %str(subject_id)) + print("Subject ID: %s\n" % str(subject_id)) output = [] names = ['Task-Odd', 'Task-Even'] for r in range(4): diff --git a/examples/fmri_spm.py b/examples/fmri_spm.py index b3fe92beb3..a4db27ff09 100755 --- a/examples/fmri_spm.py +++ b/examples/fmri_spm.py @@ -183,7 +183,7 @@ def subjectinfo(subject_id): from nipype.interfaces.base import Bunch from copy import deepcopy - print("Subject ID: %s\n" %str(subject_id)) + print("Subject ID: %s\n" % str(subject_id)) output = [] names = ['Task-Odd', 'Task-Even'] for r in range(4): @@ -351,7 +351,7 @@ def getstripdir(subject_id): """ # collect all the con images for each contrast. -contrast_ids = list(range(1, len(contrasts)+1)) +contrast_ids = list(range(1, len(contrasts) + 1)) l2source = pe.Node(nio.DataGrabber(infields=['fwhm', 'con']), name="l2source") # we use .*i* to capture both .img (SPM8) and .nii (SPM12) l2source.inputs.template = os.path.abspath('spm_tutorial/l1output/*/con*/*/_fwhm_%d/con_%04d.*i*') diff --git a/examples/fmri_spm_dartel.py b/examples/fmri_spm_dartel.py index dad8293cd9..529c541732 100755 --- a/examples/fmri_spm_dartel.py +++ b/examples/fmri_spm_dartel.py @@ -302,7 +302,7 @@ def pickFieldFlow(dartel_flow_fields, subject_id): from nipype.utils.filemanip import split_filename for f in dartel_flow_fields: _, name, _ = split_filename(f) - if name.find("subject_id_%s" %subject_id): + if name.find("subject_id_%s" % subject_id): return f raise Exception @@ -328,7 +328,7 @@ def pickFieldFlow(dartel_flow_fields, subject_id): def subjectinfo(subject_id): from nipype.interfaces.base import Bunch from copy import deepcopy - print("Subject ID: %s\n" %str(subject_id)) + print("Subject ID: %s\n" % str(subject_id)) output = [] names = ['Task-Odd', 'Task-Even'] for r in range(4): @@ -485,7 +485,7 @@ def getstripdir(subject_id): """ # collect all the con images for each contrast. -contrast_ids = list(range(1, len(contrasts)+1)) +contrast_ids = list(range(1, len(contrasts) + 1)) l2source = pe.Node(nio.DataGrabber(infields=['fwhm', 'con']), name="l2source") # we use .*i* to capture both .img (SPM8) and .nii (SPM12) l2source.inputs.template = os.path.abspath('spm_dartel_tutorial/l1output/*/con*/*/_fwhm_%d/con_%04d.*i*') diff --git a/examples/fmri_spm_face.py b/examples/fmri_spm_face.py index 7fe6c64772..532ddf0a33 100755 --- a/examples/fmri_spm_face.py +++ b/examples/fmri_spm_face.py @@ -228,7 +228,7 @@ def makelist(item): # Specify the subject directories subject_list = ['M03953'] # Map field names to individual subject runs. -info = dict(func=[['RawEPI', 'subject_id', 5, ["_%04d" %i for i in range(6, 357)]]], +info = dict(func=[['RawEPI', 'subject_id', 5, ["_%04d" % i for i in range(6, 357)]]], struct=[['Structural', 'subject_id', 7, '']]) infosource = pe.Node(interface=util.IdentityInterface(fields=['subject_id']), diff --git a/examples/fmri_spm_nested.py b/examples/fmri_spm_nested.py index dc098f18b1..2dc49c0399 100755 --- a/examples/fmri_spm_nested.py +++ b/examples/fmri_spm_nested.py @@ -290,7 +290,7 @@ def subjectinfo(subject_id): from nipype.interfaces.base import Bunch from copy import deepcopy - print("Subject ID: %s\n" %str(subject_id)) + print("Subject ID: %s\n" % str(subject_id)) output = [] names = ['Task-Odd', 'Task-Even'] for r in range(4): @@ -438,7 +438,7 @@ def getstripdir(subject_id): """ # collect all the con images for each contrast. -contrast_ids = list(range(1, len(contrasts)+1)) +contrast_ids = list(range(1, len(contrasts) + 1)) l2source = pe.Node(nio.DataGrabber(infields=['fwhm', 'con']), name="l2source") # we use .*i* to capture both .img (SPM8) and .nii (SPM12) l2source.inputs.template = os.path.abspath('spm_tutorial2/l1output/*/con*/*/_fwhm_%d/con_%04d.*i*') diff --git a/examples/frontiers_paper/smoothing_comparison.py b/examples/frontiers_paper/smoothing_comparison.py index 79bf3e2aeb..d4921142a8 100644 --- a/examples/frontiers_paper/smoothing_comparison.py +++ b/examples/frontiers_paper/smoothing_comparison.py @@ -111,7 +111,7 @@ def chooseindex(roi): specify_model.inputs.subject_info = [Bunch(conditions=['Task-Odd', 'Task-Even'], onsets=[list(range(15, 240, 60)), list(range(45, 240, 60))], - durations=[[15], [15]])]*4 + durations=[[15], [15]])] * 4 level1design = pe.Node(interface=spm.Level1Design(), name="level1design") level1design.inputs.bases = {'hrf': {'derivs': [0, 0]}} diff --git a/examples/frontiers_paper/workflow_from_scratch.py b/examples/frontiers_paper/workflow_from_scratch.py index 533da455fc..fa9bbd4cca 100644 --- a/examples/frontiers_paper/workflow_from_scratch.py +++ b/examples/frontiers_paper/workflow_from_scratch.py @@ -69,7 +69,7 @@ specify_model.inputs.subject_info = [Bunch(conditions=['Task-Odd', 'Task-Even'], onsets=[list(range(15, 240, 60)), list(range(45, 240, 60))], - durations=[[15], [15]])]*4 + durations=[[15], [15]])] * 4 level1design = pe.Node(interface=spm.Level1Design(), name="level1design") level1design.inputs.bases = {'hrf': {'derivs': [0, 0]}} diff --git a/examples/rsfmri_vol_surface_preprocessing.py b/examples/rsfmri_vol_surface_preprocessing.py index 35de677abe..953d07595f 100644 --- a/examples/rsfmri_vol_surface_preprocessing.py +++ b/examples/rsfmri_vol_surface_preprocessing.py @@ -514,7 +514,7 @@ def create_reg_workflow(name='registration'): reg.inputs.convergence_window_size = [20] * 2 + [5] reg.inputs.smoothing_sigmas = [[4, 2, 1]] * 2 + [[1, 0.5, 0]] reg.inputs.sigma_units = ['vox'] * 3 - reg.inputs.shrink_factors = [[3, 2, 1]]*2 + [[4, 2, 1]] + reg.inputs.shrink_factors = [[3, 2, 1]] * 2 + [[4, 2, 1]] reg.inputs.use_estimate_learning_rate_once = [True] * 3 reg.inputs.use_histogram_matching = [False] * 2 + [True] reg.inputs.winsorize_lower_quantile = 0.005 diff --git a/examples/rsfmri_vol_surface_preprocessing_nipy.py b/examples/rsfmri_vol_surface_preprocessing_nipy.py index 12abda6987..d3ace02535 100644 --- a/examples/rsfmri_vol_surface_preprocessing_nipy.py +++ b/examples/rsfmri_vol_surface_preprocessing_nipy.py @@ -496,7 +496,7 @@ def create_reg_workflow(name='registration'): reg.inputs.convergence_window_size = [20] * 2 + [5] reg.inputs.smoothing_sigmas = [[4, 2, 1]] * 2 + [[1, 0.5, 0]] reg.inputs.sigma_units = ['vox'] * 3 - reg.inputs.shrink_factors = [[3, 2, 1]]*2 + [[4, 2, 1]] + reg.inputs.shrink_factors = [[3, 2, 1]] * 2 + [[4, 2, 1]] reg.inputs.use_estimate_learning_rate_once = [True] * 3 reg.inputs.use_histogram_matching = [False] * 2 + [True] reg.inputs.winsorize_lower_quantile = 0.005 diff --git a/examples/smri_ants_registration.py b/examples/smri_ants_registration.py index 6a91c358f3..ca49b56aa0 100644 --- a/examples/smri_ants_registration.py +++ b/examples/smri_ants_registration.py @@ -68,7 +68,7 @@ reg.inputs.output_transform_prefix = "output_" reg.inputs.transforms = ['Translation', 'Rigid', 'Affine', 'SyN'] reg.inputs.transform_parameters = [(0.1,), (0.1,), (0.1,), (0.2, 3.0, 0.0)] -reg.inputs.number_of_iterations = ([[10000, 111110, 11110]]*3 + +reg.inputs.number_of_iterations = ([[10000, 111110, 11110]] * 3 + [[100, 50, 30]]) reg.inputs.dimension = 3 reg.inputs.write_composite_transform = True @@ -82,7 +82,7 @@ reg.inputs.convergence_window_size = [20] * 3 + [5] reg.inputs.smoothing_sigmas = [[4, 2, 1]] * 3 + [[1, 0.5, 0]] reg.inputs.sigma_units = ['vox'] * 4 -reg.inputs.shrink_factors = [[6, 4, 2]] + [[3, 2, 1]]*2 + [[4, 2, 1]] +reg.inputs.shrink_factors = [[6, 4, 2]] + [[3, 2, 1]] * 2 + [[4, 2, 1]] reg.inputs.use_estimate_learning_rate_once = [True] * 4 reg.inputs.use_histogram_matching = [False] * 3 + [True] reg.inputs.initial_moving_transform_com = True diff --git a/nipype/algorithms/mesh.py b/nipype/algorithms/mesh.py index e8bd62585d..ed51d7bf13 100644 --- a/nipype/algorithms/mesh.py +++ b/nipype/algorithms/mesh.py @@ -71,7 +71,7 @@ def _gen_fname(self, in_file, suffix='generated', ext=None): if fext == '.gz': fname, fext2 = op.splitext(fname) - fext = fext2+fext + fext = fext2 + fext if ext is None: ext = fext @@ -117,7 +117,7 @@ def _run_interface(self, runtime): ras2vox = np.linalg.inv(vox2ras) origin = affine[0:3, 3] voxpoints = np.array([np.dot(ras2vox, - (p-origin)) for p in points]) + (p - origin)) for p in points]) warps = [] for axis in warp_dims: @@ -132,7 +132,7 @@ def _run_interface(self, runtime): warps.append(warp) disps = np.squeeze(np.dstack(warps)) - newpoints = [p+d for p, d in zip(points, disps)] + newpoints = [p + d for p, d in zip(points, disps)] mesh.points = newpoints w = tvtk.PolyDataWriter() if vtk_major <= 5: diff --git a/nipype/algorithms/metrics.py b/nipype/algorithms/metrics.py index 76abdd1c50..91e4695058 100644 --- a/nipype/algorithms/metrics.py +++ b/nipype/algorithms/metrics.py @@ -284,7 +284,7 @@ def _run_interface(self, runtime): if self.inputs.vol_units == 'mm': voxvol = nii1.get_header().get_zooms() - for i in range(nii1.get_data().ndim-1): + for i in range(nii1.get_data().ndim - 1): scale = scale * voxvol[i] data1 = nii1.get_data() @@ -318,7 +318,7 @@ def _run_interface(self, runtime): results = dict(jaccard=[], dice=[]) results['jaccard'] = np.array(res) - results['dice'] = 2.0*results['jaccard'] / (results['jaccard'] + 1.0) + results['dice'] = 2.0 * results['jaccard'] / (results['jaccard'] + 1.0) weights = np.ones((len(volumes1),), dtype=np.float32) if self.inputs.weighting != 'none': @@ -338,9 +338,9 @@ def _run_interface(self, runtime): self._vol_rois = (np.array(volumes1) - np.array(volumes2)) / np.array(volumes1) - self._dice = round(np.sum(weights*results['dice']), 5) - self._jaccard = round(np.sum(weights*results['jaccard']), 5) - self._volume = np.sum(weights*self._vol_rois) + self._dice = round(np.sum(weights * results['dice']), 5) + self._jaccard = round(np.sum(weights * results['jaccard']), 5) + self._volume = np.sum(weights * self._vol_rois) return runtime @@ -529,7 +529,7 @@ def _run_interface(self, runtime): msk_idxs = np.where(mskvector == 1) refvector = ref_data.reshape(-1, comps)[msk_idxs].astype(np.float32) tstvector = tst_data.reshape(-1, comps)[msk_idxs].astype(np.float32) - diffvector = (refvector-tstvector) + diffvector = (refvector - tstvector) # Scale the difference if self.inputs.metric == 'sqeuclidean': diff --git a/nipype/algorithms/misc.py b/nipype/algorithms/misc.py index 7aee89a49f..e4e41326ce 100644 --- a/nipype/algorithms/misc.py +++ b/nipype/algorithms/misc.py @@ -391,7 +391,7 @@ def matlab2csv(in_array, name, reshape): if reshape: if len(np.shape(output_array)) > 1: output_array = np.reshape(output_array, ( - np.shape(output_array)[0]*np.shape(output_array)[1], 1)) + np.shape(output_array)[0] * np.shape(output_array)[1], 1)) iflogger.info(np.shape(output_array)) output_name = op.abspath(name + '.csv') np.savetxt(output_name, output_array, delimiter=',') @@ -512,7 +512,7 @@ def merge_csvs(in_list): ) except ValueError as ex: in_array = np.loadtxt( - in_file, delimiter=',', skiprows=1, usecols=list(range(1, n_cols-1))) + in_file, delimiter=',', skiprows=1, usecols=list(range(1, n_cols - 1))) if idx == 0: out_array = in_array else: @@ -530,7 +530,7 @@ def remove_identical_paths(in_files): out_names = list() commonprefix = op.commonprefix(in_files) lastslash = commonprefix.rfind('/') - commonpath = commonprefix[0:(lastslash+1)] + commonpath = commonprefix[0:(lastslash + 1)] for fileidx, in_file in enumerate(in_files): path, name, ext = split_filename(in_file) in_file = op.join(path, name) @@ -548,10 +548,10 @@ def maketypelist(rowheadings, shape, extraheadingBool, extraheading): if rowheadings: typelist.append(('heading', 'a40')) if len(shape) > 1: - for idx in range(1, (min(shape)+1)): + for idx in range(1, (min(shape) + 1)): typelist.append((str(idx), float)) else: - for idx in range(1, (shape[0]+1)): + for idx in range(1, (shape[0] + 1)): typelist.append((str(idx), float)) if extraheadingBool: typelist.append((extraheading, 'a40')) @@ -566,13 +566,13 @@ def makefmtlist(output_array, typelist, rowheadingsBool, fmtlist.append('%s') if len(shape) > 1: output = np.zeros(max(shape), typelist) - for idx in range(1, min(shape)+1): - output[str(idx)] = output_array[:, idx-1] + for idx in range(1, min(shape) + 1): + output[str(idx)] = output_array[:, idx - 1] fmtlist.append('%f') else: output = np.zeros(1, typelist) - for idx in range(1, len(output_array)+1): - output[str(idx)] = output_array[idx-1] + for idx in range(1, len(output_array) + 1): + output[str(idx)] = output_array[idx - 1] fmtlist.append('%f') if extraheadingBool: fmtlist.append('%s') @@ -1056,7 +1056,7 @@ def gen_noise(self, image, mask=None, snr_db=10.0, dist='normal', bg_dist='norma mask[mask < 1] = 0 if mask.ndim < image.ndim: - mask = np.rollaxis(np.array([mask]*image.shape[3]), 0, 4) + mask = np.rollaxis(np.array([mask] * image.shape[3]), 0, 4) signal = image[mask > 0].reshape(-1) @@ -1334,7 +1334,7 @@ def split_rois(in_file, mask=None, roishape=None): for i in range(nrois): first = i * roisize - last = (i+1) * roisize + last = (i + 1) * roisize fill = 0 if last > els: @@ -1343,7 +1343,7 @@ def split_rois(in_file, mask=None, roishape=None): droi = data[first:last, ...] iname = op.abspath('roi%010d_idx' % i) - out_idxs.append(iname+'.npz') + out_idxs.append(iname + '.npz') np.savez(iname, (nzels[0][first:last],)) if fill > 0: diff --git a/nipype/algorithms/modelgen.py b/nipype/algorithms/modelgen.py index 2cf0bbbeed..346000c39e 100644 --- a/nipype/algorithms/modelgen.py +++ b/nipype/algorithms/modelgen.py @@ -156,7 +156,7 @@ def gen_info(run_event_files): for event_file in event_files: _, name = os.path.split(event_file) if '.run' in name: - name, _ = name.split('.run%03d' % (i+1)) + name, _ = name.split('.run%03d' % (i + 1)) elif '.txt' in name: name, _ = name.split('.txt') runinfo.conditions.append(name) @@ -339,7 +339,7 @@ def _generate_standard_design(self, infolist, sessinfo[i]['regress'][j]['name'] = \ info.regressor_names[j] else: - sessinfo[i]['regress'][j]['name'] = 'UR%d' % (j+1) + sessinfo[i]['regress'][j]['name'] = 'UR%d' % (j + 1) sessinfo[i]['regress'][j]['val'] = info.regressors[j] sessinfo[i]['scans'] = functional_runs[i] if realignment_parameters is not None: @@ -365,7 +365,7 @@ def _generate_standard_design(self, infolist, for j, scanno in enumerate(out): colidx = len(sessinfo[i]['regress']) sessinfo[i]['regress'].insert(colidx, dict(name='', val=[])) - sessinfo[i]['regress'][colidx]['name'] = 'Outlier%d' %(j+1) + sessinfo[i]['regress'][colidx]['name'] = 'Outlier%d' % (j + 1) sessinfo[i]['regress'][colidx]['val'] = \ np.zeros((1, numscans))[0].tolist() sessinfo[i]['regress'][colidx]['val'][int(scanno)] = 1 @@ -492,7 +492,7 @@ def _concatenate_info(self, infolist): else: raise ValueError('Mismatch in number of onsets and \ durations for run {0}, condition \ - {1}'.format(i+2, j+1)) + {1}'.format(i + 2, j + 1)) if hasattr(info, 'amplitudes') and info.amplitudes: for j, val in enumerate(info.amplitudes): infoout.amplitudes[j].extend(info.amplitudes[j]) @@ -634,7 +634,7 @@ def _gen_regress(self, i_onsets, i_durations, i_amplitudes, nscans): dt = TA / 10.0 durations = np.round(np.array(i_durations) * 1000) if len(durations) == 1: - durations = durations*np.ones((len(i_onsets))) + durations = durations * np.ones((len(i_onsets))) onsets = np.round(np.array(i_onsets) * 1000) dttemp = gcd(TA, gcd(SILENCE, TR)) if dt < dttemp: @@ -703,7 +703,7 @@ def _gen_regress(self, i_onsets, i_durations, i_amplitudes, nscans): regderiv = [] for i, trial in enumerate(np.arange(nscans) / nvol): scanstart = int((SCANONSET + trial * TR + (i % nvol) * TA) / dt) - scanidx = scanstart+np.arange(int(TA / dt)) + scanidx = scanstart + np.arange(int(TA / dt)) timeline2[scanidx] = np.max(timeline) reg.insert(i, np.mean(timeline[scanidx]) * reg_scale) if isdefined(self.inputs.use_temporal_deriv) and \ @@ -759,7 +759,7 @@ def _cond_to_regress(self, info, nscans): # for sparse-clustered acquisitions enter T1-effect regressors nvol = self.inputs.volumes_in_cluster if nvol > 1: - for i in range(nvol-1): + for i in range(nvol - 1): treg = np.zeros((nscans / nvol, nvol)) treg[:, i] = 1 reg.insert(len(reg), treg.ravel().tolist()) @@ -783,7 +783,7 @@ def _generate_clustered_design(self, infolist): if hasattr(infoout[i], 'regressors') and infoout[i].regressors: if not infoout[i].regressor_names: infoout[i].regressor_names = \ - ['R%d' %j for j in range(len(infoout[i].regressors))] + ['R%d' % j for j in range(len(infoout[i].regressors))] else: infoout[i].regressors = [] infoout[i].regressor_names = [] diff --git a/nipype/fixes/numpy/testing/noseclasses.py b/nipype/fixes/numpy/testing/noseclasses.py index daab4247d7..9f69dc33db 100644 --- a/nipype/fixes/numpy/testing/noseclasses.py +++ b/nipype/fixes/numpy/testing/noseclasses.py @@ -134,8 +134,8 @@ def check_output(self, want, got, optionflags): # try to normalize out 32 and 64 bit default int sizes for sz in [4, 8]: - got = got.replace("' 4: directive = 'autorecon2' elif idx > 23: directive = 'autorecon3' else: - flags.append('-%s' %step) + flags.append('-%s' % step) cmd = cmd.replace(' -%s ' % self.inputs.directive, ' -%s ' % directive) cmd += ' ' + ' '.join(flags) iflogger.info('resume recon-all : %s' % cmd) diff --git a/nipype/interfaces/freesurfer/tests/test_preprocess.py b/nipype/interfaces/freesurfer/tests/test_preprocess.py index 28ed61113b..3086c85bf7 100644 --- a/nipype/interfaces/freesurfer/tests/test_preprocess.py +++ b/nipype/interfaces/freesurfer/tests/test_preprocess.py @@ -55,7 +55,7 @@ def test_robustregister(): reg.inputs.target_file = filelist[1] reg.inputs.auto_sens = True yield assert_equal, reg.cmdline, ('mri_robust_register ' - '--satit --lta %s_robustreg.lta --mov %s --dst %s' %(filelist[0][:-4], filelist[0], filelist[1])) + '--satit --lta %s_robustreg.lta --mov %s --dst %s' % (filelist[0][:-4], filelist[0], filelist[1])) # constructor based parameter setting reg2 = freesurfer.RobustRegister(source_file=filelist[0], target_file=filelist[1], outlier_sens=3.0, @@ -81,7 +81,7 @@ def test_fitmsparams(): # .inputs based parameters setting fit.inputs.in_files = filelist fit.inputs.out_dir = outdir - yield assert_equal, fit.cmdline, 'mri_ms_fitparms %s %s %s' %(filelist[0], filelist[1], outdir) + yield assert_equal, fit.cmdline, 'mri_ms_fitparms %s %s %s' % (filelist[0], filelist[1], outdir) # constructor based parameter setting fit2 = freesurfer.FitMSParams(in_files=filelist, te_list=[1.5, 3.5], flip_list=[20, 30], out_dir=outdir) diff --git a/nipype/interfaces/freesurfer/tests/test_utils.py b/nipype/interfaces/freesurfer/tests/test_utils.py index a1ce930dc2..876d7c8c0a 100644 --- a/nipype/interfaces/freesurfer/tests/test_utils.py +++ b/nipype/interfaces/freesurfer/tests/test_utils.py @@ -193,12 +193,12 @@ def test_applymask(): masker.inputs.in_file = filelist[0] masker.inputs.mask_file = filelist[1] outfile = os.path.join(testdir, "a_masked.nii") - yield assert_equal, masker.cmdline, "mri_mask a.nii b.nii %s" %outfile + yield assert_equal, masker.cmdline, "mri_mask a.nii b.nii %s" % outfile # Now test that optional inputs get formatted properly masker.inputs.mask_thresh = 2 - yield assert_equal, masker.cmdline, "mri_mask -T 2.0000 a.nii b.nii %s" %outfile + yield assert_equal, masker.cmdline, "mri_mask -T 2.0000 a.nii b.nii %s" % outfile masker.inputs.use_abs = True - yield assert_equal, masker.cmdline, "mri_mask -T 2.0000 -abs a.nii b.nii %s" %outfile + yield assert_equal, masker.cmdline, "mri_mask -T 2.0000 -abs a.nii b.nii %s" % outfile # Now clean up clean_directory(testdir, origdir) diff --git a/nipype/interfaces/fsl/tests/test_dti.py b/nipype/interfaces/fsl/tests/test_dti.py index f62aed96a5..077bc8c444 100644 --- a/nipype/interfaces/fsl/tests/test_dti.py +++ b/nipype/interfaces/fsl/tests/test_dti.py @@ -98,7 +98,7 @@ def test_dtifit2(): dti.inputs.max_z = 50 yield assert_equal, dti.cmdline, \ - 'dtifit -k %s -o foo.dti.nii -m %s -r %s -b %s -Z 50 -z 10' %(filelist[0], + 'dtifit -k %s -o foo.dti.nii -m %s -r %s -b %s -Z 50 -z 10' % (filelist[0], filelist[1], filelist[0], filelist[1]) @@ -440,7 +440,7 @@ def test_tbss_skeleton(): # First by implicit argument skeletor.inputs.skeleton_file = True yield assert_equal, skeletor.cmdline, \ - "tbss_skeleton -i a.nii -o %s" %os.path.join(newdir, "a_skeleton.nii") + "tbss_skeleton -i a.nii -o %s" % os.path.join(newdir, "a_skeleton.nii") # Now with a specific name skeletor.inputs.skeleton_file = "old_boney.nii" @@ -459,14 +459,14 @@ def test_tbss_skeleton(): # Now we get a command line yield assert_equal, bones.cmdline, \ - "tbss_skeleton -i a.nii -p 0.200 b.nii %s b.nii %s" %(Info.standard_image("LowerCingulum_1mm.nii.gz"), + "tbss_skeleton -i a.nii -p 0.200 b.nii %s b.nii %s" % (Info.standard_image("LowerCingulum_1mm.nii.gz"), os.path.join(newdir, "b_skeletonised.nii")) # Can we specify a mask? bones.inputs.use_cingulum_mask = Undefined bones.inputs.search_mask_file = "a.nii" yield assert_equal, bones.cmdline, \ - "tbss_skeleton -i a.nii -p 0.200 b.nii a.nii b.nii %s" %os.path.join(newdir, "b_skeletonised.nii") + "tbss_skeleton -i a.nii -p 0.200 b.nii a.nii b.nii %s" % os.path.join(newdir, "b_skeletonised.nii") # Looks good; clean up clean_directory(newdir, olddir) @@ -488,18 +488,18 @@ def test_distancemap(): mapper.inputs.in_file = "a.nii" # It should - yield assert_equal, mapper.cmdline, "distancemap --out=%s --in=a.nii" %os.path.join(newdir, "a_dstmap.nii") + yield assert_equal, mapper.cmdline, "distancemap --out=%s --in=a.nii" % os.path.join(newdir, "a_dstmap.nii") # And we should be able to write out a maxima map mapper.inputs.local_max_file = True yield assert_equal, mapper.cmdline, \ - "distancemap --out=%s --in=a.nii --localmax=%s" %(os.path.join(newdir, "a_dstmap.nii"), + "distancemap --out=%s --in=a.nii --localmax=%s" % (os.path.join(newdir, "a_dstmap.nii"), os.path.join(newdir, "a_lclmax.nii")) # And call it whatever we want mapper.inputs.local_max_file = "max.nii" yield assert_equal, mapper.cmdline, \ - "distancemap --out=%s --in=a.nii --localmax=max.nii" %os.path.join(newdir, "a_dstmap.nii") + "distancemap --out=%s --in=a.nii --localmax=max.nii" % os.path.join(newdir, "a_dstmap.nii") # Not much else to do here clean_directory(newdir, olddir) diff --git a/nipype/interfaces/fsl/tests/test_epi.py b/nipype/interfaces/fsl/tests/test_epi.py index 9e9036224c..297e2e0429 100644 --- a/nipype/interfaces/fsl/tests/test_epi.py +++ b/nipype/interfaces/fsl/tests/test_epi.py @@ -52,11 +52,11 @@ def test_eddy_correct2(): eddy.inputs.in_file = filelist[0] eddy.inputs.out_file = 'foo_eddc.nii' eddy.inputs.ref_num = 100 - yield assert_equal, eddy.cmdline, 'eddy_correct %s foo_eddc.nii 100' %filelist[0] + yield assert_equal, eddy.cmdline, 'eddy_correct %s foo_eddc.nii 100' % filelist[0] # .run based parameter setting eddy2 = fsl.EddyCorrect(in_file=filelist[0], out_file='foo_ec.nii', ref_num=20) - yield assert_equal, eddy2.cmdline, 'eddy_correct %s foo_ec.nii 20' %filelist[0] + yield assert_equal, eddy2.cmdline, 'eddy_correct %s foo_ec.nii 20' % filelist[0] # test arguments for opt_map # eddy_correct class doesn't have opt_map{} diff --git a/nipype/interfaces/fsl/tests/test_maths.py b/nipype/interfaces/fsl/tests/test_maths.py index 592b1f90f4..d4003e8d74 100644 --- a/nipype/interfaces/fsl/tests/test_maths.py +++ b/nipype/interfaces/fsl/tests/test_maths.py @@ -72,7 +72,7 @@ def test_maths_base(fsl_output_type=None): out_file = "a_maths%s" % out_ext # Now test the most basic command line - yield assert_equal, maths.cmdline, "fslmaths a.nii %s" %os.path.join(testdir, out_file) + yield assert_equal, maths.cmdline, "fslmaths a.nii %s" % os.path.join(testdir, out_file) # Now test that we can set the various data types dtypes = ["float", "char", "int", "short", "double", "input"] @@ -81,11 +81,11 @@ def test_maths_base(fsl_output_type=None): duo_cmdline = "fslmaths -dt %s a.nii " + os.path.join(testdir, out_file) + " -odt %s" for dtype in dtypes: foo = fsl.MathsCommand(in_file="a.nii", internal_datatype=dtype) - yield assert_equal, foo.cmdline, int_cmdline %dtype + yield assert_equal, foo.cmdline, int_cmdline % dtype bar = fsl.MathsCommand(in_file="a.nii", output_datatype=dtype) yield assert_equal, bar.cmdline, out_cmdline % dtype foobar = fsl.MathsCommand(in_file="a.nii", internal_datatype=dtype, output_datatype=dtype) - yield assert_equal, foobar.cmdline, duo_cmdline %(dtype, dtype) + yield assert_equal, foobar.cmdline, duo_cmdline % (dtype, dtype) # Test that we can ask for an outfile name maths.inputs.out_file = "b.nii" @@ -122,7 +122,7 @@ def test_changedt(fsl_output_type=None): cmdline = "fslmaths a.nii b.nii -odt %s" for dtype in dtypes: foo = fsl.MathsCommand(in_file="a.nii", out_file="b.nii", output_datatype=dtype) - yield assert_equal, foo.cmdline, cmdline %dtype + yield assert_equal, foo.cmdline, cmdline % dtype # Clean up our mess clean_directory(testdir, origdir) @@ -147,19 +147,19 @@ def test_threshold(fsl_output_type=None): cmdline = "fslmaths a.nii %s b.nii" for val in [0, 0., -1, -1.5, -0.5, 0.5, 3, 400, 400.5]: thresh.inputs.thresh = val - yield assert_equal, thresh.cmdline, cmdline %"-thr %.10f" %val + yield assert_equal, thresh.cmdline, cmdline % "-thr %.10f" % val - val = "%.10f" %42 + val = "%.10f" % 42 thresh = fsl.Threshold(in_file="a.nii", out_file="b.nii", thresh=42, use_robust_range=True) - yield assert_equal, thresh.cmdline, cmdline %("-thrp "+val) + yield assert_equal, thresh.cmdline, cmdline % ("-thrp " + val) thresh.inputs.use_nonzero_voxels = True - yield assert_equal, thresh.cmdline, cmdline %("-thrP "+val) + yield assert_equal, thresh.cmdline, cmdline % ("-thrP " + val) thresh = fsl.Threshold(in_file="a.nii", out_file="b.nii", thresh=42, direction="above") - yield assert_equal, thresh.cmdline, cmdline %("-uthr "+val) + yield assert_equal, thresh.cmdline, cmdline % ("-uthr " + val) thresh.inputs.use_robust_range = True - yield assert_equal, thresh.cmdline, cmdline %("-uthrp "+val) + yield assert_equal, thresh.cmdline, cmdline % ("-uthrp " + val) thresh.inputs.use_nonzero_voxels = True - yield assert_equal, thresh.cmdline, cmdline %("-uthrP "+val) + yield assert_equal, thresh.cmdline, cmdline % ("-uthrP " + val) # Clean up our mess clean_directory(testdir, origdir) @@ -184,11 +184,11 @@ def test_meanimage(fsl_output_type=None): cmdline = "fslmaths a.nii -%smean b.nii" for dim in ["X", "Y", "Z", "T"]: meaner.inputs.dimension = dim - yield assert_equal, meaner.cmdline, cmdline %dim + yield assert_equal, meaner.cmdline, cmdline % dim # Test the auto naming meaner = fsl.MeanImage(in_file="a.nii") - yield assert_equal, meaner.cmdline, "fslmaths a.nii -Tmean %s" %os.path.join(testdir, "a_mean%s" % out_ext) + yield assert_equal, meaner.cmdline, "fslmaths a.nii -Tmean %s" % os.path.join(testdir, "a_mean%s" % out_ext) # Clean up our mess clean_directory(testdir, origdir) @@ -213,11 +213,11 @@ def test_maximage(fsl_output_type=None): cmdline = "fslmaths a.nii -%smax b.nii" for dim in ["X", "Y", "Z", "T"]: maxer.inputs.dimension = dim - yield assert_equal, maxer.cmdline, cmdline %dim + yield assert_equal, maxer.cmdline, cmdline % dim # Test the auto naming maxer = fsl.MaxImage(in_file="a.nii") - yield assert_equal, maxer.cmdline, "fslmaths a.nii -Tmax %s" %os.path.join(testdir, "a_max%s" % out_ext) + yield assert_equal, maxer.cmdline, "fslmaths a.nii -Tmax %s" % os.path.join(testdir, "a_max%s" % out_ext) # Clean up our mess clean_directory(testdir, origdir) @@ -242,14 +242,14 @@ def test_smooth(fsl_output_type=None): cmdline = "fslmaths a.nii -s %.5f b.nii" for val in [0, 1., 1, 25, 0.5, 8 / 3.]: smoother = fsl.IsotropicSmooth(in_file="a.nii", out_file="b.nii", sigma=val) - yield assert_equal, smoother.cmdline, cmdline %val + yield assert_equal, smoother.cmdline, cmdline % val smoother = fsl.IsotropicSmooth(in_file="a.nii", out_file="b.nii", fwhm=val) val = float(val) / np.sqrt(8 * np.log(2)) - yield assert_equal, smoother.cmdline, cmdline %val + yield assert_equal, smoother.cmdline, cmdline % val # Test automatic naming smoother = fsl.IsotropicSmooth(in_file="a.nii", sigma=5) - yield assert_equal, smoother.cmdline, "fslmaths a.nii -s %.5f %s" %(5, os.path.join(testdir, "a_smooth%s" % out_ext)) + yield assert_equal, smoother.cmdline, "fslmaths a.nii -s %.5f %s" % (5, os.path.join(testdir, "a_smooth%s" % out_ext)) # Clean up our mess clean_directory(testdir, origdir) @@ -276,7 +276,7 @@ def test_mask(fsl_output_type=None): # Test auto name generation masker = fsl.ApplyMask(in_file="a.nii", mask_file="b.nii") - yield assert_equal, masker.cmdline, "fslmaths a.nii -mas b.nii "+os.path.join(testdir, "a_masked%s" % out_ext) + yield assert_equal, masker.cmdline, "fslmaths a.nii -mas b.nii " + os.path.join(testdir, "a_masked%s" % out_ext) # Clean up our mess clean_directory(testdir, origdir) @@ -301,14 +301,14 @@ def test_dilation(fsl_output_type=None): for op in ["mean", "modal", "max"]: cv = dict(mean="M", modal="D", max="F") diller.inputs.operation = op - yield assert_equal, diller.cmdline, "fslmaths a.nii -dil%s b.nii" %cv[op] + yield assert_equal, diller.cmdline, "fslmaths a.nii -dil%s b.nii" % cv[op] # Now test the different kernel options for k in ["3D", "2D", "box", "boxv", "gauss", "sphere"]: for size in [1, 1.5, 5]: diller.inputs.kernel_shape = k diller.inputs.kernel_size = size - yield assert_equal, diller.cmdline, "fslmaths a.nii -kernel %s %.4f -dilF b.nii" %(k, size) + yield assert_equal, diller.cmdline, "fslmaths a.nii -kernel %s %.4f -dilF b.nii" % (k, size) # Test that we can use a file kernel f = open("kernel.txt", "w").close() @@ -320,7 +320,7 @@ def test_dilation(fsl_output_type=None): # Test that we don't need to request an out name dil = fsl.DilateImage(in_file="a.nii", operation="max") - yield assert_equal, dil.cmdline, "fslmaths a.nii -dilF %s" %os.path.join(testdir, "a_dil%s" % out_ext) + yield assert_equal, dil.cmdline, "fslmaths a.nii -dilF %s" % os.path.join(testdir, "a_dil%s" % out_ext) # Clean up our mess clean_directory(testdir, origdir) @@ -347,7 +347,7 @@ def test_erosion(fsl_output_type=None): # Test that we don't need to request an out name erode = fsl.ErodeImage(in_file="a.nii") - yield assert_equal, erode.cmdline, "fslmaths a.nii -ero %s" %os.path.join(testdir, "a_ero%s" % out_ext) + yield assert_equal, erode.cmdline, "fslmaths a.nii -ero %s" % os.path.join(testdir, "a_ero%s" % out_ext) # Clean up our mess clean_directory(testdir, origdir) @@ -371,11 +371,11 @@ def test_spatial_filter(fsl_output_type=None): # Test the different operations for op in ["mean", "meanu", "median"]: filter.inputs.operation = op - yield assert_equal, filter.cmdline, "fslmaths a.nii -f%s b.nii" %op + yield assert_equal, filter.cmdline, "fslmaths a.nii -f%s b.nii" % op # Test that we don't need to ask for an out name filter = fsl.SpatialFilter(in_file="a.nii", operation="mean") - yield assert_equal, filter.cmdline, "fslmaths a.nii -fmean %s" %os.path.join(testdir, "a_filt%s" % out_ext) + yield assert_equal, filter.cmdline, "fslmaths a.nii -fmean %s" % os.path.join(testdir, "a_filt%s" % out_ext) # Clean up our mess clean_directory(testdir, origdir) @@ -400,12 +400,12 @@ def test_unarymaths(fsl_output_type=None): ops = ["exp", "log", "sin", "cos", "sqr", "sqrt", "recip", "abs", "bin", "index"] for op in ops: maths.inputs.operation = op - yield assert_equal, maths.cmdline, "fslmaths a.nii -%s b.nii" %op + yield assert_equal, maths.cmdline, "fslmaths a.nii -%s b.nii" % op # Test that we don't need to ask for an out file for op in ops: maths = fsl.UnaryMaths(in_file="a.nii", operation=op) - yield assert_equal, maths.cmdline, "fslmaths a.nii -%s %s" %(op, os.path.join(testdir, "a_%s%s" %(op, out_ext))) + yield assert_equal, maths.cmdline, "fslmaths a.nii -%s %s" % (op, os.path.join(testdir, "a_%s%s" % (op, out_ext))) # Clean up our mess clean_directory(testdir, origdir) @@ -434,15 +434,15 @@ def test_binarymaths(fsl_output_type=None): maths = fsl.BinaryMaths(in_file="a.nii", out_file="c.nii", operation=op) if ent == "b.nii": maths.inputs.operand_file = ent - yield assert_equal, maths.cmdline, "fslmaths a.nii -%s b.nii c.nii" %op + yield assert_equal, maths.cmdline, "fslmaths a.nii -%s b.nii c.nii" % op else: maths.inputs.operand_value = ent - yield assert_equal, maths.cmdline, "fslmaths a.nii -%s %.8f c.nii" %(op, ent) + yield assert_equal, maths.cmdline, "fslmaths a.nii -%s %.8f c.nii" % (op, ent) # Test that we don't need to ask for an out file for op in ops: maths = fsl.BinaryMaths(in_file="a.nii", operation=op, operand_file="b.nii") - yield assert_equal, maths.cmdline, "fslmaths a.nii -%s b.nii %s" %(op, os.path.join(testdir, "a_maths%s" % out_ext)) + yield assert_equal, maths.cmdline, "fslmaths a.nii -%s b.nii %s" % (op, os.path.join(testdir, "a_maths%s" % out_ext)) # Clean up our mess clean_directory(testdir, origdir) @@ -470,12 +470,12 @@ def test_multimaths(fsl_output_type=None): "-mas %s -add %s"] for ostr in opstrings: maths.inputs.op_string = ostr - yield assert_equal, maths.cmdline, "fslmaths a.nii %s c.nii" %ostr %("a.nii", "b.nii") + yield assert_equal, maths.cmdline, "fslmaths a.nii %s c.nii" % ostr % ("a.nii", "b.nii") # Test that we don't need to ask for an out file maths = fsl.MultiImageMaths(in_file="a.nii", op_string="-add %s -mul 5", operand_files=["b.nii"]) yield assert_equal, maths.cmdline, \ - "fslmaths a.nii -add b.nii -mul 5 %s" %os.path.join(testdir, "a_maths%s" % out_ext) + "fslmaths a.nii -add b.nii -mul 5 %s" % os.path.join(testdir, "a_maths%s" % out_ext) # Clean up our mess clean_directory(testdir, origdir) @@ -501,12 +501,12 @@ def test_tempfilt(fsl_output_type=None): for win in windows: filt.inputs.highpass_sigma = win[0] filt.inputs.lowpass_sigma = win[1] - yield assert_equal, filt.cmdline, "fslmaths a.nii -bptf %.6f %.6f b.nii" %win + yield assert_equal, filt.cmdline, "fslmaths a.nii -bptf %.6f %.6f b.nii" % win # Test that we don't need to ask for an out file filt = fsl.TemporalFilter(in_file="a.nii", highpass_sigma=64) yield assert_equal, filt.cmdline, \ - "fslmaths a.nii -bptf 64.000000 -1.000000 %s" %os.path.join(testdir, "a_filt%s" % out_ext) + "fslmaths a.nii -bptf 64.000000 -1.000000 %s" % os.path.join(testdir, "a_filt%s" % out_ext) # Clean up our mess clean_directory(testdir, origdir) diff --git a/nipype/interfaces/fsl/utils.py b/nipype/interfaces/fsl/utils.py index bf71a13bf5..7d173a4754 100644 --- a/nipype/interfaces/fsl/utils.py +++ b/nipype/interfaces/fsl/utils.py @@ -1441,15 +1441,15 @@ class ComplexInputSpec(FSLCommandInputSpec): 'complex_split', 'complex_merge', ] complex_out_file = File(genfile=True, argstr="%s", position=-3, - xor=_ofs+_conversion[:2]) + xor=_ofs + _conversion[:2]) magnitude_out_file = File(genfile=True, argstr="%s", position=-4, - xor=_ofs[:1]+_ofs[3:]+_conversion[1:]) + xor=_ofs[:1] + _ofs[3:] + _conversion[1:]) phase_out_file = File(genfile=True, argstr="%s", position=-3, - xor=_ofs[:1]+_ofs[3:]+_conversion[1:]) + xor=_ofs[:1] + _ofs[3:] + _conversion[1:]) real_out_file = File(genfile=True, argstr="%s", position=-4, - xor=_ofs[:3]+_conversion[:1]+_conversion[2:]) + xor=_ofs[:3] + _conversion[:1] + _conversion[2:]) imaginary_out_file = File(genfile=True, argstr="%s", position=-3, - xor=_ofs[:3]+_conversion[:1]+_conversion[2:]) + xor=_ofs[:3] + _conversion[:1] + _conversion[2:]) start_vol = traits.Int(position=-2, argstr='%d') end_vol = traits.Int(position=-1, argstr='%d') @@ -1507,7 +1507,7 @@ def _parse_inputs(self, skip=None): if self.inputs.real_cartesian: skip += self.inputs._ofs[:3] elif self.inputs.real_polar: - skip += self.inputs._ofs[:1]+self.inputs._ofs[3:] + skip += self.inputs._ofs[:1] + self.inputs._ofs[3:] else: skip += self.inputs._ofs[1:] return super(Complex, self)._parse_inputs(skip) @@ -1870,7 +1870,7 @@ def _vtk_to_coords(self, in_file, out_file=None): except ImportError: raise ImportError('This interface requires tvtk to run.') - reader = tvtk.PolyDataReader(file_name=in_file+'.vtk') + reader = tvtk.PolyDataReader(file_name=in_file + '.vtk') reader.update() points = reader.output.points diff --git a/nipype/interfaces/io.py b/nipype/interfaces/io.py index a12457ed48..616dced6d9 100644 --- a/nipype/interfaces/io.py +++ b/nipype/interfaces/io.py @@ -456,7 +456,7 @@ def localtos3(self, paths): # convert local path to s3 path bd_index = path.find(self.inputs.base_directory) if bd_index != -1: # base_directory is in path, maintain directory structure - s3path = path[bd_index+len(self.inputs.base_directory):] # cut out base directory + s3path = path[bd_index + len(self.inputs.base_directory):] # cut out base directory if s3path[0] == os.path.sep: s3path = s3path[1:] else: # base_directory isn't in path, simply place all files in bucket_path folder diff --git a/nipype/interfaces/matlab.py b/nipype/interfaces/matlab.py index e3e9081433..09f6002d55 100644 --- a/nipype/interfaces/matlab.py +++ b/nipype/interfaces/matlab.py @@ -180,7 +180,7 @@ def _gen_matlab_command(self, argstr, script_lines): # clean up the code of comments and replace newlines with commas script_lines = ','.join([line for line in script_lines.split("\n") if not line.strip().startswith("%")]) - script_lines = '\n'.join(prescript)+script_lines+'\n'.join(postscript) + script_lines = '\n'.join(prescript) + script_lines + '\n'.join(postscript) if mfile: with open(os.path.join(cwd, self.inputs.script_file), 'wt') as mfile: mfile.write(script_lines) diff --git a/nipype/interfaces/mrtrix/convert.py b/nipype/interfaces/mrtrix/convert.py index e916b720c8..4a12112538 100644 --- a/nipype/interfaces/mrtrix/convert.py +++ b/nipype/interfaces/mrtrix/convert.py @@ -84,7 +84,7 @@ def read_mrtrix_streamlines(in_file, header, as_generator=True): endianness = native_code f4dt = np.dtype(endianness + 'f4') pt_cols = 3 - bytesize = pt_cols*4 + bytesize = pt_cols * 4 def points_per_track(offset): n_streams = 0 @@ -96,12 +96,12 @@ def points_per_track(offset): pts = np.ndarray(shape=(num_triplets, pt_cols), dtype='f4', buffer=all_str) nonfinite_list = np.where(np.isfinite(pts[:, 2]) == False) nonfinite_list = list(nonfinite_list[0])[0:-1] # Converts numpy array to list, removes the last value - nonfinite_list_bytes = [offset+x*bytesize for x in nonfinite_list] + nonfinite_list_bytes = [offset + x * bytesize for x in nonfinite_list] for idx, value in enumerate(nonfinite_list): if idx == 0: track_points.append(nonfinite_list[idx]) else: - track_points.append(nonfinite_list[idx]-nonfinite_list[idx-1]-1) + track_points.append(nonfinite_list[idx] - nonfinite_list[idx - 1] - 1) return track_points, nonfinite_list def track_gen(track_points): @@ -140,7 +140,7 @@ def track_gen(track_points): iflogger.info('100% : {n} tracks read'.format(n=n_streams)) raise StopIteration if n_streams % int(stream_count / 100) == 0: - percent = int(float(n_streams)/float(stream_count)*100) + percent = int(float(n_streams) / float(stream_count) * 100) iflogger.info('{p}% : {n} tracks read'.format(p=percent, n=n_streams)) track_points, nonfinite_list = points_per_track(offset) fileobj.seek(offset) @@ -218,7 +218,7 @@ def _run_interface(self, runtime): iflogger.info(aff) axcode = aff2axcodes(reg_affine) - trk_header['voxel_order'] = axcode[0]+axcode[1]+axcode[2] + trk_header['voxel_order'] = axcode[0] + axcode[1] + axcode[2] final_streamlines = move_streamlines(transformed_streamlines, aff) trk_tracks = ((ii, None, None) for ii in final_streamlines) @@ -229,7 +229,7 @@ def _run_interface(self, runtime): else: iflogger.info('Applying transformation from scanner coordinates to {img}'.format(img=self.inputs.image_file)) axcode = aff2axcodes(affine) - trk_header['voxel_order'] = axcode[0]+axcode[1]+axcode[2] + trk_header['voxel_order'] = axcode[0] + axcode[1] + axcode[2] trk_header['vox_to_ras'] = affine transformed_streamlines = transform_to_affine(streamlines, trk_header, affine) trk_tracks = ((ii, None, None) for ii in transformed_streamlines) diff --git a/nipype/interfaces/nipy/model.py b/nipype/interfaces/nipy/model.py index 5daaf1a41e..637ec3e6c7 100644 --- a/nipype/interfaces/nipy/model.py +++ b/nipype/interfaces/nipy/model.py @@ -122,7 +122,7 @@ def _run_interface(self, runtime): for i in range(len(reg_names)): reg_vals[:, i] = np.array(session_info[0]['regress'][i]['val']).reshape(1, -1) - frametimes = np.linspace(0, (nscans-1)*self.inputs.TR, nscans) + frametimes = np.linspace(0, (nscans - 1) * self.inputs.TR, nscans) conditions = [] onsets = [] @@ -130,9 +130,9 @@ def _run_interface(self, runtime): for i, cond in enumerate(session_info[0]['cond']): onsets += cond['onset'] - conditions += [cond['name']]*len(cond['onset']) + conditions += [cond['name']] * len(cond['onset']) if len(cond['duration']) == 1: - duration += cond['duration']*len(cond['onset']) + duration += cond['duration'] * len(cond['onset']) else: duration += cond['duration'] @@ -146,7 +146,7 @@ def _run_interface(self, runtime): add_reg_names=reg_names ) if self.inputs.normalize_design_matrix: - for i in range(len(self._reg_names)-1): + for i in range(len(self._reg_names) - 1): design_matrix[:, i] = ((design_matrix[:, i] - design_matrix[:, i].mean()) / design_matrix[:, i].std()) diff --git a/nipype/interfaces/spm/preprocess.py b/nipype/interfaces/spm/preprocess.py index caec4af720..10810fdc91 100644 --- a/nipype/interfaces/spm/preprocess.py +++ b/nipype/interfaces/spm/preprocess.py @@ -329,7 +329,7 @@ def _format_arg(self, opt, spec, val): return np.array(filename_to_list(val), dtype=object) if opt == 'source' and self.inputs.jobtype == "write": if isdefined(self.inputs.apply_to_files): - return scans_for_fnames(val+self.inputs.apply_to_files) + return scans_for_fnames(val + self.inputs.apply_to_files) else: return scans_for_fnames(val) return super(Coregister, self)._format_arg(opt, spec, val) @@ -811,7 +811,7 @@ def _list_outputs(self): outfield = '%s_%s_image' % (image, tissue) outputs[outfield] = fname_presuffix(f, prefix='%sc%d' % (prefix, - tidx+1)) + tidx + 1)) if isdefined(self.inputs.save_bias_corrected) and \ self.inputs.save_bias_corrected: outputs['bias_corrected_image'] = fname_presuffix(f, prefix='m') @@ -963,16 +963,16 @@ def _list_outputs(self): if isdefined(self.inputs.tissues): for i, tissue in enumerate(self.inputs.tissues): if tissue[2][0]: - outputs['native_class_images'][i].append(os.path.join(pth, "c%d%s.nii" % (i+1, base))) + outputs['native_class_images'][i].append(os.path.join(pth, "c%d%s.nii" % (i + 1, base))) if tissue[2][1]: - outputs['dartel_input_images'][i].append(os.path.join(pth, "rc%d%s.nii" % (i+1, base))) + outputs['dartel_input_images'][i].append(os.path.join(pth, "rc%d%s.nii" % (i + 1, base))) if tissue[3][0]: - outputs['normalized_class_images'][i].append(os.path.join(pth, "wc%d%s.nii" % (i+1, base))) + outputs['normalized_class_images'][i].append(os.path.join(pth, "wc%d%s.nii" % (i + 1, base))) if tissue[3][1]: - outputs['modulated_class_images'][i].append(os.path.join(pth, "mwc%d%s.nii" % (i+1, base))) + outputs['modulated_class_images'][i].append(os.path.join(pth, "mwc%d%s.nii" % (i + 1, base))) else: for i in range(n_classes): - outputs['native_class_images'][i].append(os.path.join(pth, "c%d%s.nii" % (i+1, base))) + outputs['native_class_images'][i].append(os.path.join(pth, "c%d%s.nii" % (i + 1, base))) outputs['transformation_mat'].append(os.path.join(pth, "%s_seg8.mat" % base)) if isdefined(self.inputs.write_deformation_fields): @@ -1146,7 +1146,7 @@ def _list_outputs(self): outputs = self._outputs().get() outputs['template_files'] = [] for i in range(6): - outputs['template_files'].append(os.path.realpath('%s_%d.nii' % (self.inputs.template_prefix, i+1))) + outputs['template_files'].append(os.path.realpath('%s_%d.nii' % (self.inputs.template_prefix, i + 1))) outputs['final_template_file'] = os.path.realpath('%s_6.nii' % self.inputs.template_prefix) outputs['dartel_flow_fields'] = [] for filename in self.inputs.image_files[0]: @@ -1234,7 +1234,7 @@ def _format_arg(self, opt, spec, val): def _list_outputs(self): outputs = self._outputs().get() pth, base, ext = split_filename(self.inputs.template_file) - outputs['normalization_parameter_file'] = os.path.realpath(base+'_2mni.mat') + outputs['normalization_parameter_file'] = os.path.realpath(base + '_2mni.mat') outputs['normalized_files'] = [] prefix = "w" if isdefined(self.inputs.modulate) and self.inputs.modulate: @@ -1374,7 +1374,7 @@ class VBMSegmentInputSpec(SPMCommandInputSpec): exists=True, field='estwrite.tpm', desc='tissue probability map') gaussians_per_class = traits.Tuple( - (2, 2, 2, 3, 4, 2), *([traits.Int()]*6), + (2, 2, 2, 3, 4, 2), *([traits.Int()] * 6), usedefault=True, desc='number of gaussians for each tissue class') bias_regularization = traits.Enum( @@ -1562,25 +1562,25 @@ def _list_outputs(self): if getattr(self.inputs, '%s_native' % tis): outputs['native_class_images'][i].append( - os.path.join(pth, "p%d%s.nii" % (i+1, base))) + os.path.join(pth, "p%d%s.nii" % (i + 1, base))) if getattr(self.inputs, '%s_dartel' % tis) == 1: outputs['dartel_input_images'][i].append( - os.path.join(pth, "rp%d%s.nii" % (i+1, base))) + os.path.join(pth, "rp%d%s.nii" % (i + 1, base))) elif getattr(self.inputs, '%s_dartel' % tis) == 2: outputs['dartel_input_images'][i].append( - os.path.join(pth, "rp%d%s_affine.nii" % (i+1, base))) + os.path.join(pth, "rp%d%s_affine.nii" % (i + 1, base))) # normalized space if getattr(self.inputs, '%s_normalized' % tis): outputs['normalized_class_images'][i].append( - os.path.join(pth, "w%sp%d%s.nii" % (dartel_px, i+1, base))) + os.path.join(pth, "w%sp%d%s.nii" % (dartel_px, i + 1, base))) if getattr(self.inputs, '%s_modulated_normalized' % tis) == 1: outputs['modulated_class_images'][i].append(os.path.join( - pth, "mw%sp%d%s.nii" % (dartel_px, i+1, base))) + pth, "mw%sp%d%s.nii" % (dartel_px, i + 1, base))) elif getattr(self.inputs, '%s_modulated_normalized' % tis) == 2: outputs['normalized_class_images'][i].append(os.path.join( - pth, "m0w%sp%d%s.nii" % (dartel_px, i+1, base))) + pth, "m0w%sp%d%s.nii" % (dartel_px, i + 1, base))) if self.inputs.pve_label_native: outputs['pve_label_native_images'].append( diff --git a/nipype/interfaces/spm/tests/test_utils.py b/nipype/interfaces/spm/tests/test_utils.py index cd800949fb..38581b927f 100644 --- a/nipype/interfaces/spm/tests/test_utils.py +++ b/nipype/interfaces/spm/tests/test_utils.py @@ -21,7 +21,7 @@ def test_coreg(): assert_equal(isdefined(coreg.inputs.mat), False) pth, mov, _ = split_filename(moving) _, tgt, _ = split_filename(target) - mat = os.path.join(pth, '%s_to_%s.mat' %(mov, tgt)) + mat = os.path.join(pth, '%s_to_%s.mat' % (mov, tgt)) invmat = fname_presuffix(mat, prefix='inverse_') scrpt = coreg._make_matlab_command(None) assert_equal(coreg.inputs.mat, mat) diff --git a/nipype/interfaces/spm/utils.py b/nipype/interfaces/spm/utils.py index 17ddf6e94f..5c6da67080 100644 --- a/nipype/interfaces/spm/utils.py +++ b/nipype/interfaces/spm/utils.py @@ -25,11 +25,11 @@ class Analyze2nii(SPMCommand): output_spec = Analyze2niiOutputSpec def _make_matlab_command(self, _): - script = "V = spm_vol('%s');\n" %self.inputs.analyze_file + script = "V = spm_vol('%s');\n" % self.inputs.analyze_file _, name, _ = split_filename(self.inputs.analyze_file) self.output_name = os.path.join(os.getcwd(), name + ".nii") script += "[Y, XYZ] = spm_read_vols(V);\n" - script += "V.fname = '%s';\n" %self.output_name + script += "V.fname = '%s';\n" % self.output_name script += "spm_write_vol(V, Y);\n" return script @@ -89,7 +89,7 @@ def _make_mat_file(self): """ makes name for matfile if doesn exist""" pth, mv, _ = split_filename(self.inputs.moving) _, tgt, _ = split_filename(self.inputs.target) - mat = os.path.join(pth, '%s_to_%s.mat' %(mv, tgt)) + mat = os.path.join(pth, '%s_to_%s.mat' % (mv, tgt)) return mat def _make_matlab_command(self, _): @@ -108,7 +108,7 @@ def _make_matlab_command(self, _): save('%s' , 'M' ); M = inv(M); save('%s','M') - """ %(self.inputs.target, + """ % (self.inputs.target, self.inputs.moving, self.inputs.mat, self.inputs.invmat) @@ -166,7 +166,7 @@ def _make_matlab_command(self, _): V.fname = fullfile(outfile); spm_write_vol(V,X); - """ %(self.inputs.in_file, + """ % (self.inputs.in_file, self.inputs.out_file, self.inputs.mat) # img_space = spm_get_space(infile); @@ -222,7 +222,7 @@ def _make_matlab_command(self, _): infiles = strvcat(\'%s\', \'%s\'); invols = spm_vol(infiles); spm_reslice(invols, flags); - """ %(self.inputs.interp, + """ % (self.inputs.interp, self.inputs.space_defining, self.inputs.in_file) return script @@ -465,11 +465,11 @@ def _list_outputs(self): ext = self.inputs.format if self.inputs.output_dir_struct == "flat": - outputs['out_files'] = glob(os.path.join(od, '*.%s' %ext)) + outputs['out_files'] = glob(os.path.join(od, '*.%s' % ext)) elif self.inputs.output_dir_struct == 'series': - outputs['out_files'] = glob(os.path.join(od, os.path.join('*', '*.%s' %ext))) + outputs['out_files'] = glob(os.path.join(od, os.path.join('*', '*.%s' % ext))) elif self.inputs.output_dir_struct in ['patid', 'date_time', 'patname']: - outputs['out_files'] = glob(os.path.join(od, os.path.join('*', '*', '*.%s' %ext))) + outputs['out_files'] = glob(os.path.join(od, os.path.join('*', '*', '*.%s' % ext))) elif self.inputs.output_dir_struct == 'patid_date': - outputs['out_files'] = glob(os.path.join(od, os.path.join('*', '*', '*', '*.%s' %ext))) + outputs['out_files'] = glob(os.path.join(od, os.path.join('*', '*', '*', '*.%s' % ext))) return outputs diff --git a/nipype/pipeline/engine.py b/nipype/pipeline/engine.py index 0b8f77da32..1c73918bf8 100644 --- a/nipype/pipeline/engine.py +++ b/nipype/pipeline/engine.py @@ -1057,13 +1057,13 @@ def _get_dot(self, prefix=None, hierarchy=None, colored=False, nodename = fullname.replace('.', '_') dotlist.append('subgraph cluster_%s {' % nodename) if colored: - dotlist.append(prefix + prefix + 'edge [color="%s"];' % (colorset[level+1])) + dotlist.append(prefix + prefix + 'edge [color="%s"];' % (colorset[level + 1])) dotlist.append(prefix + prefix + 'style=filled;') - dotlist.append(prefix + prefix + 'fillcolor="%s";' % (colorset[level+2])) + dotlist.append(prefix + prefix + 'fillcolor="%s";' % (colorset[level + 2])) dotlist.append(node._get_dot(prefix=prefix + prefix, hierarchy=hierarchy + [self.name], colored=colored, - simple_form=simple_form, level=level+3)) + simple_form=simple_form, level=level + 3)) dotlist.append('}') if level == 6: level = 2 diff --git a/nipype/pipeline/plugins/ipython.py b/nipype/pipeline/plugins/ipython.py index c12907f264..96f47fd6ef 100644 --- a/nipype/pipeline/plugins/ipython.py +++ b/nipype/pipeline/plugins/ipython.py @@ -112,6 +112,6 @@ def _report_crash(self, node, result=None): def _clear_task(self, taskid): if IPyversion >= '0.11': - logger.debug("Clearing id: %d" %taskid) + logger.debug("Clearing id: %d" % taskid) self.taskclient.purge_results(self.taskmap[taskid]) del self.taskmap[taskid] diff --git a/nipype/pipeline/plugins/ipythonx.py b/nipype/pipeline/plugins/ipythonx.py index 47f4bf525a..db7c467d60 100644 --- a/nipype/pipeline/plugins/ipythonx.py +++ b/nipype/pipeline/plugins/ipythonx.py @@ -80,5 +80,5 @@ def _report_crash(self, node, result=None): def _clear_task(self, taskid): if IPyversion >= '0.10.1': - logger.debug("Clearing id: %d" %taskid) + logger.debug("Clearing id: %d" % taskid) self.taskclient.clear(taskid) diff --git a/nipype/pipeline/plugins/multiproc.py b/nipype/pipeline/plugins/multiproc.py index 062c8e5d04..861e2cc507 100644 --- a/nipype/pipeline/plugins/multiproc.py +++ b/nipype/pipeline/plugins/multiproc.py @@ -72,7 +72,7 @@ def __init__(self, plugin_args=None): def _get_result(self, taskid): if taskid not in self._taskresult: - raise RuntimeError('Multiproc task %d not found' %taskid) + raise RuntimeError('Multiproc task %d not found' % taskid) if not self._taskresult[taskid].ready(): return None return self._taskresult[taskid].get() diff --git a/nipype/pipeline/tests/test_engine.py b/nipype/pipeline/tests/test_engine.py index 5853319800..30b2981b4c 100644 --- a/nipype/pipeline/tests/test_engine.py +++ b/nipype/pipeline/tests/test_engine.py @@ -219,7 +219,7 @@ def test_iterable_expansion(): wf1.connect(node1, 'output1', node2, 'input2') wf3 = pe.Workflow(name='group') for i in [0, 1, 2]: - wf3.add_nodes([wf1.clone(name='test%d' %i)]) + wf3.add_nodes([wf1.clone(name='test%d' % i)]) wf3._flatgraph = wf3._create_flat_graph() yield assert_equal, len(pe.generate_expanded_graph(wf3._flatgraph).nodes()), 12 @@ -234,7 +234,7 @@ def test_synchronize_expansion(): wf1.connect(node1, 'output1', node2, 'input2') wf3 = pe.Workflow(name='group') for i in [0, 1, 2]: - wf3.add_nodes([wf1.clone(name='test%d' %i)]) + wf3.add_nodes([wf1.clone(name='test%d' % i)]) wf3._flatgraph = wf3._create_flat_graph() # Each expanded graph clone has: # 3 node1 expansion nodes and @@ -258,7 +258,7 @@ def test_synchronize_tuples_expansion(): wf3 = pe.Workflow(name='group') for i in [0, 1, 2]: - wf3.add_nodes([wf1.clone(name='test%d' %i)]) + wf3.add_nodes([wf1.clone(name='test%d' % i)]) wf3._flatgraph = wf3._create_flat_graph() # Identical to test_synchronize_expansion @@ -286,7 +286,7 @@ def test_itersource_expansion(): wf3 = pe.Workflow(name='group') for i in [0, 1, 2]: - wf3.add_nodes([wf1.clone(name='test%d' %i)]) + wf3.add_nodes([wf1.clone(name='test%d' % i)]) wf3._flatgraph = wf3._create_flat_graph() @@ -318,7 +318,7 @@ def test_itersource_synchronize1_expansion(): wf1.connect(node3, 'output1', node4, 'input1') wf3 = pe.Workflow(name='group') for i in [0, 1, 2]: - wf3.add_nodes([wf1.clone(name='test%d' %i)]) + wf3.add_nodes([wf1.clone(name='test%d' % i)]) wf3._flatgraph = wf3._create_flat_graph() # each expanded graph clone has: @@ -351,7 +351,7 @@ def test_itersource_synchronize2_expansion(): wf1.connect(node3, 'output1', node4, 'input1') wf3 = pe.Workflow(name='group') for i in [0, 1, 2]: - wf3.add_nodes([wf1.clone(name='test%d' %i)]) + wf3.add_nodes([wf1.clone(name='test%d' % i)]) wf3._flatgraph = wf3._create_flat_graph() # each expanded graph clone has: @@ -555,7 +555,7 @@ def func1(): return 1 def func2(a): - return a+1 + return a + 1 n1 = pe.Node(Function(input_names=[], output_names=['a'], function=func1), @@ -565,7 +565,7 @@ def func2(a): function=func2), name='n2') w1 = pe.Workflow(name='test') - modify = lambda x: x+1 + modify = lambda x: x + 1 n1.inputs.a = 1 w1.connect(n1, ('a', modify), n2, 'a') w1.base_dir = wd @@ -616,7 +616,7 @@ def func1(): return 1 def func2(a): - return a+1 + return a + 1 n1 = pe.Node(Function(input_names=[], output_names=['a'], function=func1), @@ -626,7 +626,7 @@ def func2(a): function=func2), name='n2') w1 = pe.Workflow(name='test') - modify = lambda x: x+1 + modify = lambda x: x + 1 n1.inputs.a = 1 w1.connect(n1, ('a', modify), n2, 'a') w1.base_dir = wd diff --git a/nipype/pipeline/utils.py b/nipype/pipeline/utils.py index 5ae7ec3140..19569d3332 100644 --- a/nipype/pipeline/utils.py +++ b/nipype/pipeline/utils.py @@ -150,7 +150,7 @@ def get_print_name(node, simple_form=True): if simple_form: parts = name.split('.') if len(parts) > 2: - return ' ('.join(parts[1:])+')' + return ' ('.join(parts[1:]) + ')' elif len(parts) == 2: return parts[1] return name @@ -281,7 +281,7 @@ def count_iterables(iterables, synchronize=False): if synchronize: op = max else: - op = lambda x, y: x*y + op = lambda x, y: x * y return reduce(op, [len(func()) for _, func in iterables.items()]) diff --git a/nipype/utils/docparse.py b/nipype/utils/docparse.py index f77035c3ce..c08cbdcad0 100644 --- a/nipype/utils/docparse.py +++ b/nipype/utils/docparse.py @@ -42,7 +42,7 @@ def grab_doc(cmd, trap_error=True): stdout, stderr = proc.communicate() if trap_error and proc.returncode: - msg = 'Attempting to run %s. Returned Error: %s' %(cmd, stderr) + msg = 'Attempting to run %s. Returned Error: %s' % (cmd, stderr) raise IOError(msg) if stderr: @@ -256,7 +256,7 @@ def get_doc(cmd, opt_map, help_flag=None, trap_error=True): terminal_output='allatonce').run() cmd_path = res.runtime.stdout.strip() if cmd_path == '': - raise Exception('Command %s not found' %cmd.split(' ')[0]) + raise Exception('Command %s not found' % cmd.split(' ')[0]) if help_flag: cmd = ' '.join((cmd, help_flag)) doc = grab_doc(cmd, trap_error) @@ -303,7 +303,7 @@ def _parse_doc(doc, style=['--']): break flag = flag[style_idx.index(min(style_idx))] style_idx = min(style_idx) - optmap[flag.split(style[style_idx])[1]] = '%s %%s' %flag + optmap[flag.split(style[style_idx])[1]] = '%s %%s' % flag return optmap @@ -332,7 +332,7 @@ def get_params_from_doc(cmd, style='--', help_flag=None, trap_error=True): terminal_output='allatonce').run() cmd_path = res.runtime.stdout.strip() if cmd_path == '': - raise Exception('Command %s not found' %cmd.split(' ')[0]) + raise Exception('Command %s not found' % cmd.split(' ')[0]) if help_flag: cmd = ' '.join((cmd, help_flag)) doc = grab_doc(cmd, trap_error) diff --git a/nipype/utils/filemanip.py b/nipype/utils/filemanip.py index ba364b153b..de6f6760f5 100644 --- a/nipype/utils/filemanip.py +++ b/nipype/utils/filemanip.py @@ -226,7 +226,7 @@ def copyfile(originalfile, newfile, copy=False, create_new=False, s = re.search('_c[0-9]{4,4}$', fname) i = 0 if s: - i = int(s.group()[2:])+1 + i = int(s.group()[2:]) + 1 fname = fname[:-6] + "_c%04d" % i else: fname += "_c%04d" % i @@ -452,11 +452,11 @@ def write_rst_list(items, prefix=''): out = [] for item in items: out.append(prefix + ' ' + str(item)) - return '\n'.join(out)+'\n\n' + return '\n'.join(out) + '\n\n' def write_rst_dict(info, prefix=''): out = [] for key, value in sorted(info.items()): out.append(prefix + '* ' + key + ' : ' + str(value)) - return '\n'.join(out)+'\n\n' + return '\n'.join(out) + '\n\n' diff --git a/nipype/utils/misc.py b/nipype/utils/misc.py index dc9ed23b2d..0c98900695 100644 --- a/nipype/utils/misc.py +++ b/nipype/utils/misc.py @@ -91,7 +91,7 @@ def create_function_from_source(function_source, imports=None): exec(function_source, ns) except Exception as msg: - msg = str(msg) + '\nError executing function:\n %s\n' %function_source + msg = str(msg) + '\nError executing function:\n %s\n' % function_source msg += '\n'.join(["Functions in connection strings have to be standalone.", "They cannot be declared either interactively or inside", "another function or inline in the connect string. Any", diff --git a/nipype/utils/nipype2boutiques.py b/nipype/utils/nipype2boutiques.py index bb7c515b34..e0931db165 100644 --- a/nipype/utils/nipype2boutiques.py +++ b/nipype/utils/nipype2boutiques.py @@ -72,8 +72,8 @@ def generate_boutiques_descriptor(module, interface_name, ignored_template_input # Tool description tool_desc = {} tool_desc['name'] = interface_name - tool_desc['command-line'] = "nipype_cmd "+str(module)+" "+interface_name+" " - tool_desc['description'] = interface_name+", as implemented in Nipype (module: "+str(module)+", interface: "+interface_name+")." + tool_desc['command-line'] = "nipype_cmd " + str(module) + " " + interface_name + " " + tool_desc['description'] = interface_name + ", as implemented in Nipype (module: " + str(module) + ", interface: " + interface_name + ")." tool_desc['inputs'] = [] tool_desc['outputs'] = [] tool_desc['tool-version'] = interface.version @@ -87,9 +87,9 @@ def generate_boutiques_descriptor(module, interface_name, ignored_template_input for name, spec in sorted(interface.inputs.traits(transient=None).items()): input = get_boutiques_input(inputs, interface, name, spec, ignored_template_inputs, verbose, ignore_template_numbers) tool_desc['inputs'].append(input) - tool_desc['command-line'] += input['command-line-key']+" " + tool_desc['command-line'] += input['command-line-key'] + " " if verbose: - print("-> Adding input "+input['name']) + print("-> Adding input " + input['name']) # Generates tool outputs for name, spec in sorted(outputs.traits(transient=None).items()): @@ -97,9 +97,9 @@ def generate_boutiques_descriptor(module, interface_name, ignored_template_input if output['path-template'] != "": tool_desc['outputs'].append(output) if verbose: - print("-> Adding output "+output['name']) + print("-> Adding output " + output['name']) elif verbose: - print("xx Skipping output "+output['name']+" with no path template.") + print("xx Skipping output " + output['name'] + " with no path template.") if tool_desc['outputs'] == []: raise Exception("Tool has no output.") @@ -135,10 +135,10 @@ def get_boutiques_input(inputs, interface, input_name, spec, ignored_template_in input['name'] = input_name.replace('_', ' ').capitalize() input['type'] = get_type_from_spec_info(spec_info) input['list'] = is_list(spec_info) - input['command-line-key'] = "["+input_name.upper()+"]" # assumes that input names are unique - input['command-line-flag'] = ("--%s" %input_name+" ").strip() + input['command-line-key'] = "[" + input_name.upper() + "]" # assumes that input names are unique + input['command-line-flag'] = ("--%s" % input_name + " ").strip() input['tempvalue'] = None - input['description'] = spec_info.capitalize()+". "+spec.desc.capitalize() + input['description'] = spec_info.capitalize() + ". " + spec.desc.capitalize() if not input['description'].endswith('.'): input['description'] += '.' if not (hasattr(spec, "mandatory") and spec.mandatory): @@ -155,7 +155,7 @@ def get_boutiques_input(inputs, interface, input_name, spec, ignored_template_in setattr(interface.inputs, input_name, tempvalue) input['tempvalue'] = tempvalue if verbose: - print("oo Path-template creation using "+input['id']+"="+str(tempvalue)) + print("oo Path-template creation using " + input['id'] + "=" + str(tempvalue)) # Now that temp values have been generated, set Boolean types to # Number (there is no Boolean type in Boutiques) diff --git a/nipype/utils/nipype_cmd.py b/nipype/utils/nipype_cmd.py index 93ddcd16be..9bdfd7df91 100644 --- a/nipype/utils/nipype_cmd.py +++ b/nipype/utils/nipype_cmd.py @@ -14,7 +14,7 @@ def listClasses(module=None): print("Available Interfaces:") for k, v in sorted(list(pkg.__dict__.items())): if inspect.isclass(v) and issubclass(v, Interface): - print("\t%s" %k) + print("\t%s" % k) def add_options(parser=None, module=None, function=None): @@ -25,7 +25,7 @@ def add_options(parser=None, module=None, function=None): inputs = interface.input_spec() for name, spec in sorted(interface.inputs.traits(transient=None).items()): - desc = "\n".join(interface._get_trait_desc(inputs, name, spec))[len(name)+2:] + desc = "\n".join(interface._get_trait_desc(inputs, name, spec))[len(name) + 2:] args = {} if spec.is_trait_type(traits.Bool): @@ -38,7 +38,7 @@ def add_options(parser=None, module=None, function=None): else: if spec.is_trait_type(InputMultiPath): args["nargs"] = "*" - parser.add_argument("--%s" %name, dest=name, + parser.add_argument("--%s" % name, dest=name, help=desc, **args) return parser, interface @@ -65,7 +65,7 @@ def run_instance(interface, options): setattr(interface.inputs, input_name, value) except ValueError as e: - print("Error when setting the value of %s: '%s'" %(input_name, str(e))) + print("Error when setting the value of %s: '%s'" % (input_name, str(e))) print(interface.inputs) res = interface.run() @@ -84,7 +84,7 @@ def main(argv): parsed = parser.parse_args(args=argv[1:3]) _, prog = os.path.split(argv[0]) - interface_parser = argparse.ArgumentParser(description="Run %s" %parsed.interface, prog=" ".join([prog] + argv[1:3])) + interface_parser = argparse.ArgumentParser(description="Run %s" % parsed.interface, prog=" ".join([prog] + argv[1:3])) interface_parser, interface = add_options(interface_parser, parsed.module, parsed.interface) args = interface_parser.parse_args(args=argv[3:]) run_instance(interface, args) diff --git a/nipype/workflows/dmri/camino/group_connectivity.py b/nipype/workflows/dmri/camino/group_connectivity.py index f2a03c1140..e61d1273ca 100644 --- a/nipype/workflows/dmri/camino/group_connectivity.py +++ b/nipype/workflows/dmri/camino/group_connectivity.py @@ -75,7 +75,7 @@ def create_group_connectivity_pipeline(group_list, group_id, data_dir, subjects_ datasink.inputs.base_directory = output_dir datasink.inputs.container = group_id - l1pipeline = pe.Workflow(name="l1pipeline_"+group_id) + l1pipeline = pe.Workflow(name="l1pipeline_" + group_id) l1pipeline.base_dir = output_dir l1pipeline.base_output_dir = group_id l1pipeline.connect([(subj_infosource, datasource, [('subject_id', 'subject_id')])]) diff --git a/nipype/workflows/dmri/fsl/epi.py b/nipype/workflows/dmri/fsl/epi.py index 76d7297f76..01a454f82d 100644 --- a/nipype/workflows/dmri/fsl/epi.py +++ b/nipype/workflows/dmri/fsl/epi.py @@ -723,7 +723,7 @@ def _prepare_phasediff(in_file): img = nib.load(in_file) max_diff = np.max(img.get_data().reshape(-1)) min_diff = np.min(img.get_data().reshape(-1)) - A = (2.0 * np.pi) / (max_diff-min_diff) + A = (2.0 * np.pi) / (max_diff - min_diff) B = np.pi - (A * max_diff) diff_norm = img.get_data() * A + B @@ -788,7 +788,7 @@ def _vsm_remove_mean(in_file, mask_file, in_unwarped): def _ms2sec(val): - return val*1e-3 + return val * 1e-3 def _split_dwi(in_file): diff --git a/nipype/workflows/dmri/mrtrix/group_connectivity.py b/nipype/workflows/dmri/mrtrix/group_connectivity.py index c4048c969a..37ff71409d 100644 --- a/nipype/workflows/dmri/mrtrix/group_connectivity.py +++ b/nipype/workflows/dmri/mrtrix/group_connectivity.py @@ -94,7 +94,7 @@ def create_group_connectivity_pipeline(group_list, group_id, data_dir, subjects_ datasink.inputs.base_directory = output_dir datasink.inputs.container = group_id - l1pipeline = pe.Workflow(name="l1pipeline_"+group_id) + l1pipeline = pe.Workflow(name="l1pipeline_" + group_id) l1pipeline.base_dir = output_dir l1pipeline.base_output_dir = group_id l1pipeline.connect([(subj_infosource, conmapper, [('subject_id', 'inputnode.subject_id')])]) diff --git a/nipype/workflows/fmri/fsl/preprocess.py b/nipype/workflows/fmri/fsl/preprocess.py index 15e9091a1b..6ac1d7b86d 100644 --- a/nipype/workflows/fmri/fsl/preprocess.py +++ b/nipype/workflows/fmri/fsl/preprocess.py @@ -14,7 +14,7 @@ def getthreshop(thresh): - return ['-thr %.10f -Tmin -bin' %(0.1*val[1]) for val in thresh] + return ['-thr %.10f -Tmin -bin' % (0.1 * val[1]) for val in thresh] def pickfirst(files): @@ -41,14 +41,14 @@ def pickvol(filenames, fileidx, which): elif which.lower() == 'middle': idx = int(np.ceil(load(filenames[fileidx]).get_shape()[3] / 2)) elif which.lower() == 'last': - idx = load(filenames[fileidx]).get_shape()[3]-1 + idx = load(filenames[fileidx]).get_shape()[3] - 1 else: raise Exception('unknown value for volume selection : %s' % which) return idx def getbtthresh(medianvals): - return [0.75*val for val in medianvals] + return [0.75 * val for val in medianvals] def chooseindex(fwhm): @@ -66,7 +66,7 @@ def getusans(x): return [[tuple([val[0], 0.75 * val[1]])] for val in x] tolist = lambda x: [x] -highpass_operand = lambda x: '-bptf %.10f -1' %x +highpass_operand = lambda x: '-bptf %.10f -1' % x def create_parallelfeat_preproc(name='featpreproc', highpass=True): diff --git a/nipype/workflows/fmri/spm/preprocess.py b/nipype/workflows/fmri/spm/preprocess.py index 1bcfcc39c8..dc190abf39 100644 --- a/nipype/workflows/fmri/spm/preprocess.py +++ b/nipype/workflows/fmri/spm/preprocess.py @@ -195,7 +195,7 @@ def compute_icv(class_images): img = load(session[0][0]).get_data() + \ load(session[1][0]).get_data() + \ load(session[2][0]).get_data() - img_icv = (img > 0.5).astype(int).sum()*voxel_volume*1e-3 + img_icv = (img > 0.5).astype(int).sum() * voxel_volume * 1e-3 icv.append(img_icv) return icv diff --git a/nipype/workflows/rsfmri/fsl/resting.py b/nipype/workflows/rsfmri/fsl/resting.py index a8e3f70cb5..5939c8707d 100644 --- a/nipype/workflows/rsfmri/fsl/resting.py +++ b/nipype/workflows/rsfmri/fsl/resting.py @@ -48,7 +48,7 @@ def select_volume(filename, which): elif which.lower() == 'middle': idx = int(np.ceil(load(filename).get_shape()[3] / 2)) else: - raise Exception('unknown value for volume selection : %s' %which) + raise Exception('unknown value for volume selection : %s' % which) return idx diff --git a/nipype/workflows/smri/ants/ANTSBuildTemplate.py b/nipype/workflows/smri/ants/ANTSBuildTemplate.py index 79b9918867..e59cf670ff 100644 --- a/nipype/workflows/smri/ants/ANTSBuildTemplate.py +++ b/nipype/workflows/smri/ants/ANTSBuildTemplate.py @@ -53,9 +53,9 @@ def RenestDeformedPassiveImages(deformedPassiveImages, flattened_image_nametypes image_dictionary_of_lists[curr_name].append(curr_file) for image_type, image_list in list(image_dictionary_of_lists.items()): nested_imagetype_list.append(image_list) - outputAverageImageName_list.append('AVG_'+image_type+'.nii.gz') - image_type_list.append('WARP_AVG_'+image_type) - print("\n"*10) + outputAverageImageName_list.append('AVG_' + image_type + '.nii.gz') + image_type_list.append('WARP_AVG_' + image_type) + print("\n" * 10) print("HACK: ", nested_imagetype_list) print("HACK: ", outputAverageImageName_list) print("HACK: ", image_type_list) @@ -120,7 +120,7 @@ def ANTSTemplateBuildSingleIterationWF(iterationPhasePrefix=''): outputspec.passive_deformed_templates : """ - TemplateBuildSingleIterationWF = pe.Workflow(name='ANTSTemplateBuildSingleIterationWF_'+str(str(iterationPhasePrefix))) + TemplateBuildSingleIterationWF = pe.Workflow(name='ANTSTemplateBuildSingleIterationWF_' + str(str(iterationPhasePrefix))) inputSpec = pe.Node(interface=util.IdentityInterface(fields=['images', 'fixed_image', 'ListOfPassiveImagesDictionaries']), @@ -139,7 +139,7 @@ def ANTSTemplateBuildSingleIterationWF(iterationPhasePrefix=''): # NOTE MAP NODE! warp each of the original images to the provided fixed_image as the template BeginANTS = pe.MapNode(interface=ANTS(), name='BeginANTS', iterfield=['moving_image']) BeginANTS.inputs.dimension = 3 - BeginANTS.inputs.output_transform_prefix = str(iterationPhasePrefix)+'_tfm' + BeginANTS.inputs.output_transform_prefix = str(iterationPhasePrefix) + '_tfm' BeginANTS.inputs.metric = ['CC'] BeginANTS.inputs.metric_weight = [1.0] BeginANTS.inputs.radius = [5] @@ -175,20 +175,20 @@ def ANTSTemplateBuildSingleIterationWF(iterationPhasePrefix=''): # Now Average All input_images deformed images together to create an updated template average AvgDeformedImages = pe.Node(interface=AverageImages(), name='AvgDeformedImages') AvgDeformedImages.inputs.dimension = 3 - AvgDeformedImages.inputs.output_average_image = str(iterationPhasePrefix)+'.nii.gz' + AvgDeformedImages.inputs.output_average_image = str(iterationPhasePrefix) + '.nii.gz' AvgDeformedImages.inputs.normalize = True TemplateBuildSingleIterationWF.connect(wimtdeformed, "output_image", AvgDeformedImages, 'images') # Now average all affine transforms together AvgAffineTransform = pe.Node(interface=AverageAffineTransform(), name='AvgAffineTransform') AvgAffineTransform.inputs.dimension = 3 - AvgAffineTransform.inputs.output_affine_transform = 'Avererage_'+str(iterationPhasePrefix)+'_Affine.mat' + AvgAffineTransform.inputs.output_affine_transform = 'Avererage_' + str(iterationPhasePrefix) + '_Affine.mat' TemplateBuildSingleIterationWF.connect(BeginANTS, 'affine_transform', AvgAffineTransform, 'transforms') # Now average the warp fields togther AvgWarpImages = pe.Node(interface=AverageImages(), name='AvgWarpImages') AvgWarpImages.inputs.dimension = 3 - AvgWarpImages.inputs.output_average_image = str(iterationPhasePrefix)+'warp.nii.gz' + AvgWarpImages.inputs.output_average_image = str(iterationPhasePrefix) + 'warp.nii.gz' AvgWarpImages.inputs.normalize = True TemplateBuildSingleIterationWF.connect(BeginANTS, 'warp_transform', AvgWarpImages, 'images') @@ -198,7 +198,7 @@ def ANTSTemplateBuildSingleIterationWF(iterationPhasePrefix=''): GradientStepWarpImage = pe.Node(interface=MultiplyImages(), name='GradientStepWarpImage') GradientStepWarpImage.inputs.dimension = 3 GradientStepWarpImage.inputs.second_input = -1.0 * GradientStep - GradientStepWarpImage.inputs.output_product_image = 'GradientStep0.25_'+str(iterationPhasePrefix)+'_warp.nii.gz' + GradientStepWarpImage.inputs.output_product_image = 'GradientStep0.25_' + str(iterationPhasePrefix) + '_warp.nii.gz' TemplateBuildSingleIterationWF.connect(AvgWarpImages, 'output_average_image', GradientStepWarpImage, 'first_input') # Now create the new template shape based on the average of all deformed images diff --git a/nipype/workflows/smri/ants/antsRegistrationBuildTemplate.py b/nipype/workflows/smri/ants/antsRegistrationBuildTemplate.py index 9a5c9c7e8e..e1be2d8372 100644 --- a/nipype/workflows/smri/ants/antsRegistrationBuildTemplate.py +++ b/nipype/workflows/smri/ants/antsRegistrationBuildTemplate.py @@ -58,13 +58,13 @@ def RenestDeformedPassiveImages(deformedPassiveImages, flattened_image_nametypes image_dictionary_of_lists[curr_name].append(curr_file) for image_type, image_list in list(image_dictionary_of_lists.items()): nested_imagetype_list.append(image_list) - outputAverageImageName_list.append('AVG_'+image_type+'.nii.gz') - image_type_list.append('WARP_AVG_'+image_type) + outputAverageImageName_list.append('AVG_' + image_type + '.nii.gz') + image_type_list.append('WARP_AVG_' + image_type) if image_type in interpolationMapping: nested_interpolation_type.append(interpolationMapping[image_type]) else: nested_interpolation_type.append('Linear') # Linear is the default. - print("\n"*10) + print("\n" * 10) print("HACK: ", nested_imagetype_list) print("HACK: ", outputAverageImageName_list) print("HACK: ", image_type_list) @@ -176,7 +176,7 @@ def antsRegistrationTemplateBuildSingleIterationWF(iterationPhasePrefix=''): outputspec.transforms_list : outputspec.passive_deformed_templates : """ - TemplateBuildSingleIterationWF = pe.Workflow(name='antsRegistrationTemplateBuildSingleIterationWF_'+str(iterationPhasePrefix)) + TemplateBuildSingleIterationWF = pe.Workflow(name='antsRegistrationTemplateBuildSingleIterationWF_' + str(iterationPhasePrefix)) inputSpec = pe.Node(interface=util.IdentityInterface(fields=[ 'ListOfImagesDictionaries', 'registrationImageTypes', @@ -196,7 +196,7 @@ def antsRegistrationTemplateBuildSingleIterationWF(iterationPhasePrefix=''): # NOTE MAP NODE! warp each of the original images to the provided fixed_image as the template BeginANTS = pe.MapNode(interface=Registration(), name='BeginANTS', iterfield=['moving_image']) BeginANTS.inputs.dimension = 3 - BeginANTS.inputs.output_transform_prefix = str(iterationPhasePrefix)+'_tfm' + BeginANTS.inputs.output_transform_prefix = str(iterationPhasePrefix) + '_tfm' BeginANTS.inputs.transforms = ["Affine", "SyN"] BeginANTS.inputs.transform_parameters = [[0.9], [0.25, 3.0, 0.0]] BeginANTS.inputs.metric = ['Mattes', 'CC'] @@ -207,7 +207,7 @@ def antsRegistrationTemplateBuildSingleIterationWF(iterationPhasePrefix=''): BeginANTS.inputs.use_estimate_learning_rate_once = [False, False] BeginANTS.inputs.shrink_factors = [[3, 2, 1], [3, 2, 1]] BeginANTS.inputs.smoothing_sigmas = [[3, 2, 0], [3, 2, 0]] - BeginANTS.inputs.sigma_units = ["vox"]*2 + BeginANTS.inputs.sigma_units = ["vox"] * 2 GetMovingImagesNode = pe.Node(interface=util.Function(function=GetMovingImages, input_names=['ListOfImagesDictionaries', 'registrationImageTypes', 'interpolationMapping'], @@ -237,14 +237,14 @@ def antsRegistrationTemplateBuildSingleIterationWF(iterationPhasePrefix=''): # Now Average All input_images deformed images together to create an updated template average AvgDeformedImages = pe.Node(interface=AverageImages(), name='AvgDeformedImages') AvgDeformedImages.inputs.dimension = 3 - AvgDeformedImages.inputs.output_average_image = str(iterationPhasePrefix)+'.nii.gz' + AvgDeformedImages.inputs.output_average_image = str(iterationPhasePrefix) + '.nii.gz' AvgDeformedImages.inputs.normalize = True TemplateBuildSingleIterationWF.connect(wimtdeformed, "output_image", AvgDeformedImages, 'images') # Now average all affine transforms together AvgAffineTransform = pe.Node(interface=AverageAffineTransform(), name='AvgAffineTransform') AvgAffineTransform.inputs.dimension = 3 - AvgAffineTransform.inputs.output_affine_transform = 'Avererage_'+str(iterationPhasePrefix)+'_Affine.mat' + AvgAffineTransform.inputs.output_affine_transform = 'Avererage_' + str(iterationPhasePrefix) + '_Affine.mat' SplitAffineAndWarpsNode = pe.Node(interface=util.Function(function=SplitAffineAndWarpComponents, input_names=['list_of_transforms_lists'], @@ -257,7 +257,7 @@ def antsRegistrationTemplateBuildSingleIterationWF(iterationPhasePrefix=''): # Now average the warp fields togther AvgWarpImages = pe.Node(interface=AverageImages(), name='AvgWarpImages') AvgWarpImages.inputs.dimension = 3 - AvgWarpImages.inputs.output_average_image = str(iterationPhasePrefix)+'warp.nii.gz' + AvgWarpImages.inputs.output_average_image = str(iterationPhasePrefix) + 'warp.nii.gz' AvgWarpImages.inputs.normalize = True TemplateBuildSingleIterationWF.connect(SplitAffineAndWarpsNode, 'warp_component_list', AvgWarpImages, 'images') @@ -267,7 +267,7 @@ def antsRegistrationTemplateBuildSingleIterationWF(iterationPhasePrefix=''): GradientStepWarpImage = pe.Node(interface=MultiplyImages(), name='GradientStepWarpImage') GradientStepWarpImage.inputs.dimension = 3 GradientStepWarpImage.inputs.second_input = -1.0 * GradientStep - GradientStepWarpImage.inputs.output_product_image = 'GradientStep0.25_'+str(iterationPhasePrefix)+'_warp.nii.gz' + GradientStepWarpImage.inputs.output_product_image = 'GradientStep0.25_' + str(iterationPhasePrefix) + '_warp.nii.gz' TemplateBuildSingleIterationWF.connect(AvgWarpImages, 'output_average_image', GradientStepWarpImage, 'first_input') # Now create the new template shape based on the average of all deformed images diff --git a/tools/interfacedocgen.py b/tools/interfacedocgen.py index c60bde743f..eda0c6a8b5 100644 --- a/tools/interfacedocgen.py +++ b/tools/interfacedocgen.py @@ -491,7 +491,7 @@ def write_index(self, outdir, froot='gen', relative_to=None): if self.written_modules is None: raise ValueError('No modules written') # Get full filename path - path = os.path.join(outdir, froot+self.rst_extension) + path = os.path.join(outdir, froot + self.rst_extension) # Path written into index is relative to rootpath if relative_to is not None: relpath = outdir.replace(relative_to + os.path.sep, '') diff --git a/tools/make_examples.py b/tools/make_examples.py index a0520e822d..605746cc7a 100755 --- a/tools/make_examples.py +++ b/tools/make_examples.py @@ -56,7 +56,7 @@ def show(): allfm = Gcf.get_all_fig_managers() for fcount, fm in enumerate(allfm): fm.canvas.figure.savefig('%s_%02i.png' % - (figure_basename, fcount+1)) + (figure_basename, fcount + 1)) _mpl_show = plt.show plt.show = show diff --git a/tools/report_coverage.py b/tools/report_coverage.py index 61b8ced640..0009ccc20d 100644 --- a/tools/report_coverage.py +++ b/tools/report_coverage.py @@ -36,8 +36,8 @@ def grab_coverage(output): if line.startswith('Ran '): tcount = line covout.insert(0, header) - covout.insert(1, '-'*70) - covout.append('-'*70) + covout.insert(1, '-' * 70) + covout.append('-' * 70) covout.append(tcount) return '\n'.join(covout) diff --git a/tools/run_examples.py b/tools/run_examples.py index cd75067ed1..a7903c9276 100644 --- a/tools/run_examples.py +++ b/tools/run_examples.py @@ -5,7 +5,7 @@ def run_examples(example, pipelines, plugin): - print('running example: %s with plugin: %s' %(example, plugin)) + print('running example: %s with plugin: %s' % (example, plugin)) from nipype import config config.enable_debug_mode() from nipype.interfaces.base import CommandLine From 1df2021f52b32423878fe8b5ec10ecb0a2c197e8 Mon Sep 17 00:00:00 2001 From: miykael Date: Sun, 1 Nov 2015 11:00:44 +0100 Subject: [PATCH 16/19] FIX: PEP8 - indentation correction for E121, E123, E124, E125, E126, E127, E128 - 2nd clean up --- build_docs.py | 2 +- doc/conf.py | 4 +- doc/sphinxext/numpy_ext/docscrape.py | 2 +- doc/sphinxext/numpy_ext/numpydoc.py | 2 +- examples/dmri_camino_dti.py | 14 +- examples/dmri_connectivity.py | 16 +- examples/dmri_connectivity_advanced.py | 10 +- examples/dmri_dtk_dti.py | 28 +- examples/dmri_dtk_odf.py | 34 +-- examples/dmri_fsl_dti.py | 64 ++--- examples/dmri_mrtrix_dti.py | 12 +- examples/dmri_preprocessing.py | 20 +- examples/fmri_ants_openfmri.py | 4 +- examples/fmri_freesurfer_smooth.py | 30 +- examples/fmri_fsl.py | 38 +-- examples/fmri_nipy_glm.py | 4 +- examples/fmri_openfmri.py | 2 +- examples/fmri_spm.py | 30 +- examples/fmri_spm_auditory.py | 12 +- examples/fmri_spm_dartel.py | 24 +- examples/fmri_spm_face.py | 20 +- examples/fmri_spm_nested.py | 24 +- .../frontiers_paper/smoothing_comparison.py | 4 +- examples/smri_ants_build_template.py | 14 +- examples/smri_ants_registration.py | 6 +- .../smri_antsregistration_build_template.py | 16 +- examples/workshop_dartmouth_2010.py | 14 +- nipype/__init__.py | 2 +- nipype/algorithms/metrics.py | 4 +- nipype/algorithms/modelgen.py | 14 +- nipype/algorithms/rapidart.py | 22 +- nipype/fixes/numpy/testing/nosetester.py | 2 +- nipype/interfaces/ants/legacy.py | 2 +- nipype/interfaces/ants/registration.py | 8 +- nipype/interfaces/ants/visualization.py | 44 +-- nipype/interfaces/base.py | 2 +- nipype/interfaces/camino/convert.py | 8 +- nipype/interfaces/freesurfer/utils.py | 2 +- nipype/interfaces/fsl/dti.py | 26 +- nipype/interfaces/fsl/tests/test_FILMGLS.py | 2 +- nipype/interfaces/fsl/tests/test_dti.py | 22 +- nipype/interfaces/fsl/tests/test_epi.py | 2 +- nipype/interfaces/fsl/utils.py | 4 +- nipype/interfaces/io.py | 5 +- nipype/interfaces/matlab.py | 4 +- nipype/interfaces/mrtrix/convert.py | 4 +- nipype/interfaces/nipy/model.py | 8 +- nipype/interfaces/nitime/tests/test_nitime.py | 4 +- nipype/interfaces/spm/utils.py | 26 +- nipype/interfaces/tests/test_io.py | 4 +- nipype/interfaces/traits_extension.py | 12 +- nipype/pipeline/plugins/base.py | 11 +- nipype/pipeline/plugins/dagman.py | 12 +- nipype/pipeline/plugins/ipythonx.py | 2 +- nipype/pipeline/plugins/sgegraph.py | 6 +- nipype/pipeline/plugins/slurmgraph.py | 6 +- nipype/utils/config.py | 10 +- nipype/utils/docparse.py | 4 +- nipype/utils/nipype2boutiques.py | 8 +- .../dmri/camino/connectivity_mapping.py | 28 +- nipype/workflows/dmri/camino/diffusion.py | 22 +- .../dmri/camino/group_connectivity.py | 2 +- .../dmri/connectivity/group_connectivity.py | 62 ++--- nipype/workflows/dmri/connectivity/nx.py | 2 +- nipype/workflows/dmri/dipy/denoise.py | 14 +- nipype/workflows/dmri/fsl/epi.py | 138 +++++----- nipype/workflows/dmri/fsl/tbss.py | 206 +++++++------- .../dmri/mrtrix/connectivity_mapping.py | 40 +-- nipype/workflows/dmri/mrtrix/diffusion.py | 4 +- .../dmri/mrtrix/group_connectivity.py | 2 +- nipype/workflows/fmri/fsl/estimate.py | 6 +- nipype/workflows/fmri/spm/preprocess.py | 28 +- nipype/workflows/rsfmri/fsl/resting.py | 14 +- .../workflows/smri/ants/ANTSBuildTemplate.py | 16 +- .../ants/antsRegistrationBuildTemplate.py | 38 +-- nipype/workflows/smri/freesurfer/bem.py | 12 +- nipype/workflows/smri/freesurfer/utils.py | 40 +-- setup.py | 256 +++++++++--------- tools/github.py | 2 +- 79 files changed, 835 insertions(+), 839 deletions(-) diff --git a/build_docs.py b/build_docs.py index 433584d444..77b55eba53 100644 --- a/build_docs.py +++ b/build_docs.py @@ -70,7 +70,7 @@ class APIDocs(TempInstall): user_options = [ ('None', None, 'this command has no options'), - ] + ] def run(self): # First build the project and install it to a temporary location. diff --git a/doc/conf.py b/doc/conf.py index d2953e8ef2..6066689c44 100644 --- a/doc/conf.py +++ b/doc/conf.py @@ -212,8 +212,8 @@ # Grouping the document tree into LaTeX files. List of tuples # (source start file, target name, title, author, documentclass [howto/manual]). latex_documents = [ - ('documentation', 'nipype.tex', u'nipype Documentation', - u'Neuroimaging in Python team', 'manual'), + ('documentation', 'nipype.tex', u'nipype Documentation', + u'Neuroimaging in Python team', 'manual'), ] # The name of an image file (relative to this directory) to place at the top of diff --git a/doc/sphinxext/numpy_ext/docscrape.py b/doc/sphinxext/numpy_ext/docscrape.py index f7b155ff59..affb1ba6b5 100644 --- a/doc/sphinxext/numpy_ext/docscrape.py +++ b/doc/sphinxext/numpy_ext/docscrape.py @@ -114,7 +114,7 @@ def __init__(self, docstring, config={}): 'References': '', 'Examples': '', 'index': {} - } + } self._parse() diff --git a/doc/sphinxext/numpy_ext/numpydoc.py b/doc/sphinxext/numpy_ext/numpydoc.py index e9a225ef66..ab375c112f 100644 --- a/doc/sphinxext/numpy_ext/numpydoc.py +++ b/doc/sphinxext/numpy_ext/numpydoc.py @@ -48,7 +48,7 @@ def mangle_docstrings(app, what, name, obj, options, lines, lines[:] = str(doc).split(u"\n") if app.config.numpydoc_edit_link and hasattr(obj, '__name__') and \ - obj.__name__: + obj.__name__: if hasattr(obj, '__module__'): v = dict(full_name=u"%s.%s" % (obj.__module__, obj.__name__)) else: diff --git a/examples/dmri_camino_dti.py b/examples/dmri_camino_dti.py index 4c81eebf09..bf94ebdae9 100755 --- a/examples/dmri_camino_dti.py +++ b/examples/dmri_camino_dti.py @@ -268,7 +268,7 @@ def get_affine(volume): tractography.connect([(dtifit, fa, [("tensor_fitted", "in_file")])]) tractography.connect([(fa, analyzeheader_fa, [("fa", "in_file")])]) tractography.connect([(inputnode, analyzeheader_fa, [(('dwi', get_vox_dims), 'voxel_dims'), - (('dwi', get_data_dims), 'data_dims')])]) + (('dwi', get_data_dims), 'data_dims')])]) tractography.connect([(fa, fa2nii, [('fa', 'data_file')])]) tractography.connect([(inputnode, fa2nii, [(('dwi', get_affine), 'affine')])]) tractography.connect([(analyzeheader_fa, fa2nii, [('header', 'header_file')])]) @@ -277,7 +277,7 @@ def get_affine(volume): tractography.connect([(dtifit, trace, [("tensor_fitted", "in_file")])]) tractography.connect([(trace, analyzeheader_trace, [("trace", "in_file")])]) tractography.connect([(inputnode, analyzeheader_trace, [(('dwi', get_vox_dims), 'voxel_dims'), - (('dwi', get_data_dims), 'data_dims')])]) + (('dwi', get_data_dims), 'data_dims')])]) tractography.connect([(trace, trace2nii, [('trace', 'data_file')])]) tractography.connect([(inputnode, trace2nii, [(('dwi', get_affine), 'affine')])]) tractography.connect([(analyzeheader_trace, trace2nii, [('header', 'header_file')])]) @@ -287,10 +287,10 @@ def get_affine(volume): tractography.connect([(trackpico, cam2trk_pico, [('tracked', 'in_file')])]) tractography.connect([(trackdt, cam2trk_dt, [('tracked', 'in_file')])]) tractography.connect([(inputnode, cam2trk_pico, [(('dwi', get_vox_dims), 'voxel_dims'), - (('dwi', get_data_dims), 'data_dims')])]) + (('dwi', get_data_dims), 'data_dims')])]) tractography.connect([(inputnode, cam2trk_dt, [(('dwi', get_vox_dims), 'voxel_dims'), - (('dwi', get_data_dims), 'data_dims')])]) + (('dwi', get_data_dims), 'data_dims')])]) """ @@ -303,9 +303,9 @@ def get_affine(volume): workflow.base_dir = os.path.abspath('camino_dti_tutorial') workflow.connect([(infosource, datasource, [('subject_id', 'subject_id')]), (datasource, tractography, [('dwi', 'inputnode.dwi'), - ('bvals', 'inputnode.bvals'), - ('bvecs', 'inputnode.bvecs') - ]) + ('bvals', 'inputnode.bvals'), + ('bvecs', 'inputnode.bvecs') + ]) ]) """ The following functions run the whole workflow and produce a .dot and .png graph of the processing pipeline. diff --git a/examples/dmri_connectivity.py b/examples/dmri_connectivity.py index 1206e1821e..35c7ee3c39 100755 --- a/examples/dmri_connectivity.py +++ b/examples/dmri_connectivity.py @@ -464,7 +464,7 @@ def select_aparc_annot(list_of_files): mapping.connect([(dtifit, fa, [("tensor_fitted", "in_file")])]) mapping.connect([(fa, analyzeheader_fa, [("fa", "in_file")])]) mapping.connect([(inputnode, analyzeheader_fa, [(('dwi', get_vox_dims), 'voxel_dims'), - (('dwi', get_data_dims), 'data_dims')])]) + (('dwi', get_data_dims), 'data_dims')])]) mapping.connect([(fa, fa2nii, [('fa', 'data_file')])]) mapping.connect([(inputnode, fa2nii, [(('dwi', get_affine), 'affine')])]) mapping.connect([(analyzeheader_fa, fa2nii, [('header', 'header_file')])]) @@ -473,7 +473,7 @@ def select_aparc_annot(list_of_files): mapping.connect([(dtifit, trace, [("tensor_fitted", "in_file")])]) mapping.connect([(trace, analyzeheader_trace, [("trace", "in_file")])]) mapping.connect([(inputnode, analyzeheader_trace, [(('dwi', get_vox_dims), 'voxel_dims'), - (('dwi', get_data_dims), 'data_dims')])]) + (('dwi', get_data_dims), 'data_dims')])]) mapping.connect([(trace, trace2nii, [('trace', 'data_file')])]) mapping.connect([(inputnode, trace2nii, [(('dwi', get_affine), 'affine')])]) mapping.connect([(analyzeheader_trace, trace2nii, [('header', 'header_file')])]) @@ -490,7 +490,7 @@ def select_aparc_annot(list_of_files): (camino2trackvis, trk2camino, [['trackvis', 'in_file']]) ]) mapping.connect([(inputnode, camino2trackvis, [(('dwi', get_vox_dims), 'voxel_dims'), - (('dwi', get_data_dims), 'data_dims')])]) + (('dwi', get_data_dims), 'data_dims')])]) """ Here the CMTK connectivity mapping nodes are connected. @@ -571,11 +571,11 @@ def select_aparc_annot(list_of_files): connectivity.connect([ (infosource, datasource, [('subject_id', 'subject_id')]), (datasource, mapping, [('dwi', 'inputnode.dwi'), - ('bvals', 'inputnode.bvals'), - ('bvecs', 'inputnode.bvecs') - ]), - (infosource, mapping, [('subject_id', 'inputnode.subject_id')]) - ]) + ('bvals', 'inputnode.bvals'), + ('bvecs', 'inputnode.bvecs') + ]), + (infosource, mapping, [('subject_id', 'inputnode.subject_id')]) +]) """ The following functions run the whole workflow and produce graphs describing the processing pipeline. diff --git a/examples/dmri_connectivity_advanced.py b/examples/dmri_connectivity_advanced.py index 2515d393a2..b1d3ae692f 100755 --- a/examples/dmri_connectivity_advanced.py +++ b/examples/dmri_connectivity_advanced.py @@ -581,11 +581,11 @@ connectivity.connect([ (infosource, datasource, [('subject_id', 'subject_id')]), (datasource, mapping, [('dwi', 'inputnode.dwi'), - ('bvals', 'inputnode.bvals'), - ('bvecs', 'inputnode.bvecs') - ]), - (infosource, mapping, [('subject_id', 'inputnode.subject_id')]) - ]) + ('bvals', 'inputnode.bvals'), + ('bvecs', 'inputnode.bvecs') + ]), + (infosource, mapping, [('subject_id', 'inputnode.subject_id')]) +]) """ The following functions run the whole workflow and produce a .dot and .png graph of the processing pipeline. diff --git a/examples/dmri_dtk_dti.py b/examples/dmri_dtk_dti.py index 7cd8c52a90..e71d519912 100755 --- a/examples/dmri_dtk_dti.py +++ b/examples/dmri_dtk_dti.py @@ -154,9 +154,9 @@ """ computeTensor.connect([ - (fslroi, bet, [('roi_file', 'in_file')]), - (eddycorrect, dtifit, [('outputnode.eddy_corrected', 'DWI')]) - ]) + (fslroi, bet, [('roi_file', 'in_file')]), + (eddycorrect, dtifit, [('outputnode.eddy_corrected', 'DWI')]) +]) """ @@ -177,8 +177,8 @@ """ tractography.connect([ - (dtk_tracker, smooth_trk, [('track_file', 'track_file')]) - ]) + (dtk_tracker, smooth_trk, [('track_file', 'track_file')]) +]) """ @@ -201,15 +201,15 @@ def getstripdir(subject_id): dwiproc = pe.Workflow(name="dwiproc") dwiproc.base_dir = os.path.abspath('dtk_dti_tutorial') dwiproc.connect([ - (infosource, datasource, [('subject_id', 'subject_id')]), - (datasource, computeTensor, [('dwi', 'fslroi.in_file'), - ('bvals', 'dtifit.bvals'), - ('bvecs', 'dtifit.bvecs'), - ('dwi', 'eddycorrect.inputnode.in_file')]), - (computeTensor, tractography, [('bet.mask_file', 'dtk_tracker.mask1_file'), - ('dtifit.tensor', 'dtk_tracker.tensor_file') - ]) - ]) + (infosource, datasource, [('subject_id', 'subject_id')]), + (datasource, computeTensor, [('dwi', 'fslroi.in_file'), + ('bvals', 'dtifit.bvals'), + ('bvecs', 'dtifit.bvecs'), + ('dwi', 'eddycorrect.inputnode.in_file')]), + (computeTensor, tractography, [('bet.mask_file', 'dtk_tracker.mask1_file'), + ('dtifit.tensor', 'dtk_tracker.tensor_file') + ]) +]) if __name__ == '__main__': dwiproc.run() diff --git a/examples/dmri_dtk_odf.py b/examples/dmri_dtk_odf.py index 7246f1a495..ff295b1d9f 100755 --- a/examples/dmri_dtk_odf.py +++ b/examples/dmri_dtk_odf.py @@ -153,11 +153,11 @@ """ compute_ODF.connect([ - (fslroi, bet, [('roi_file', 'in_file')]), - (eddycorrect, odf_recon, [('outputnode.eddy_corrected', 'DWI')]), - (eddycorrect, hardi_mat, [('outputnode.eddy_corrected', 'reference_file')]), - (hardi_mat, odf_recon, [('out_file', 'matrix')]) - ]) + (fslroi, bet, [('roi_file', 'in_file')]), + (eddycorrect, odf_recon, [('outputnode.eddy_corrected', 'DWI')]), + (eddycorrect, hardi_mat, [('outputnode.eddy_corrected', 'reference_file')]), + (hardi_mat, odf_recon, [('out_file', 'matrix')]) +]) """ @@ -177,8 +177,8 @@ """ tractography.connect([ - (odf_tracker, smooth_trk, [('track_file', 'track_file')]) - ]) + (odf_tracker, smooth_trk, [('track_file', 'track_file')]) +]) """ @@ -189,16 +189,16 @@ dwiproc = pe.Workflow(name="dwiproc") dwiproc.base_dir = os.path.abspath('dtk_odf_tutorial') dwiproc.connect([ - (infosource, datasource, [('subject_id', 'subject_id')]), - (datasource, compute_ODF, [('dwi', 'fslroi.in_file'), - ('bvals', 'hardi_mat.bvals'), - ('bvecs', 'hardi_mat.bvecs'), - ('dwi', 'eddycorrect.inputnode.in_file')]), - (compute_ODF, tractography, [('bet.mask_file', 'odf_tracker.mask1_file'), - ('odf_recon.ODF', 'odf_tracker.ODF'), - ('odf_recon.max', 'odf_tracker.max') - ]) - ]) + (infosource, datasource, [('subject_id', 'subject_id')]), + (datasource, compute_ODF, [('dwi', 'fslroi.in_file'), + ('bvals', 'hardi_mat.bvals'), + ('bvecs', 'hardi_mat.bvecs'), + ('dwi', 'eddycorrect.inputnode.in_file')]), + (compute_ODF, tractography, [('bet.mask_file', 'odf_tracker.mask1_file'), + ('odf_recon.ODF', 'odf_tracker.ODF'), + ('odf_recon.max', 'odf_tracker.max') + ]) +]) dwiproc.inputs.compute_ODF.hardi_mat.oblique_correction = True dwiproc.inputs.compute_ODF.odf_recon.n_directions = 31 diff --git a/examples/dmri_fsl_dti.py b/examples/dmri_fsl_dti.py index 3f92fdc6b8..1eb3c99bdd 100755 --- a/examples/dmri_fsl_dti.py +++ b/examples/dmri_fsl_dti.py @@ -76,12 +76,12 @@ bvals=[['subject_id', 'bvals']], seed_file=[['subject_id', 'MASK_average_thal_right']], target_masks=[['subject_id', ['MASK_average_M1_right', - 'MASK_average_S1_right', - 'MASK_average_occipital_right', - 'MASK_average_pfc_right', - 'MASK_average_pmc_right', - 'MASK_average_ppc_right', - 'MASK_average_temporal_right']]]) + 'MASK_average_S1_right', + 'MASK_average_occipital_right', + 'MASK_average_pfc_right', + 'MASK_average_pmc_right', + 'MASK_average_ppc_right', + 'MASK_average_temporal_right']]]) infosource = pe.Node(interface=util.IdentityInterface(fields=['subject_id']), name="infosource") @@ -165,11 +165,11 @@ """ computeTensor.connect([ - (fslroi, bet, [('roi_file', 'in_file')]), - (eddycorrect, dtifit, [('outputnode.eddy_corrected', 'dwi')]), - (infosource, dtifit, [['subject_id', 'base_name']]), - (bet, dtifit, [('mask_file', 'mask')]) - ]) + (fslroi, bet, [('roi_file', 'in_file')]), + (eddycorrect, dtifit, [('outputnode.eddy_corrected', 'dwi')]), + (infosource, dtifit, [['subject_id', 'base_name']]), + (bet, dtifit, [('mask_file', 'mask')]) +]) """ @@ -223,9 +223,9 @@ tractography.add_nodes([bedpostx, flirt]) tractography.connect([(bedpostx, probtrackx, [('outputnode.thsamples', 'thsamples'), - ('outputnode.phsamples', 'phsamples'), - ('outputnode.fsamples', 'fsamples') - ]), + ('outputnode.phsamples', 'phsamples'), + ('outputnode.fsamples', 'fsamples') + ]), (probtrackx, findthebiggest, [('targets', 'in_files')]), (flirt, probtrackx, [('out_matrix_file', 'xfm')]) ]) @@ -252,24 +252,24 @@ def getstripdir(subject_id): dwiproc = pe.Workflow(name="dwiproc") dwiproc.base_dir = os.path.abspath('fsl_dti_tutorial') dwiproc.connect([ - (infosource, datasource, [('subject_id', 'subject_id')]), - (datasource, computeTensor, [('dwi', 'fslroi.in_file'), - ('bvals', 'dtifit.bvals'), - ('bvecs', 'dtifit.bvecs'), - ('dwi', 'eddycorrect.inputnode.in_file')]), - (datasource, tractography, [('bvals', 'bedpostx.inputnode.bvals'), - ('bvecs', 'bedpostx.inputnode.bvecs'), - ('seed_file', 'probtrackx.seed'), - ('target_masks', 'probtrackx.target_masks') - ]), - (computeTensor, tractography, [('eddycorrect.outputnode.eddy_corrected', 'bedpostx.inputnode.dwi'), - ('bet.mask_file', 'bedpostx.inputnode.mask'), - ('bet.mask_file', 'probtrackx.mask'), - ('fslroi.roi_file', 'flirt.reference')]), - (infosource, datasink, [('subject_id', 'container'), - (('subject_id', getstripdir), 'strip_dir')]), - (tractography, datasink, [('findthebiggest.out_file', 'fbiggest.@biggestsegmentation')]) - ]) + (infosource, datasource, [('subject_id', 'subject_id')]), + (datasource, computeTensor, [('dwi', 'fslroi.in_file'), + ('bvals', 'dtifit.bvals'), + ('bvecs', 'dtifit.bvecs'), + ('dwi', 'eddycorrect.inputnode.in_file')]), + (datasource, tractography, [('bvals', 'bedpostx.inputnode.bvals'), + ('bvecs', 'bedpostx.inputnode.bvecs'), + ('seed_file', 'probtrackx.seed'), + ('target_masks', 'probtrackx.target_masks') + ]), + (computeTensor, tractography, [('eddycorrect.outputnode.eddy_corrected', 'bedpostx.inputnode.dwi'), + ('bet.mask_file', 'bedpostx.inputnode.mask'), + ('bet.mask_file', 'probtrackx.mask'), + ('fslroi.roi_file', 'flirt.reference')]), + (infosource, datasink, [('subject_id', 'container'), + (('subject_id', getstripdir), 'strip_dir')]), + (tractography, datasink, [('findthebiggest.out_file', 'fbiggest.@biggestsegmentation')]) +]) if __name__ == '__main__': dwiproc.run() diff --git a/examples/dmri_mrtrix_dti.py b/examples/dmri_mrtrix_dti.py index 5d7c7336c4..36b8f5508e 100755 --- a/examples/dmri_mrtrix_dti.py +++ b/examples/dmri_mrtrix_dti.py @@ -250,12 +250,12 @@ dwiproc = pe.Workflow(name="dwiproc") dwiproc.base_dir = os.path.abspath('dmri_mrtrix_dti') dwiproc.connect([ - (infosource, datasource, [('subject_id', 'subject_id')]), - (datasource, tractography, [('dwi', 'inputnode.dwi'), - ('bvals', 'inputnode.bvals'), - ('bvecs', 'inputnode.bvecs') - ]) - ]) + (infosource, datasource, [('subject_id', 'subject_id')]), + (datasource, tractography, [('dwi', 'inputnode.dwi'), + ('bvals', 'inputnode.bvals'), + ('bvecs', 'inputnode.bvecs') + ]) +]) if __name__ == '__main__': dwiproc.run() diff --git a/examples/dmri_preprocessing.py b/examples/dmri_preprocessing.py index 22676d6093..99a8998113 100644 --- a/examples/dmri_preprocessing.py +++ b/examples/dmri_preprocessing.py @@ -81,7 +81,7 @@ """ datasource = pe.Node(nio.DataGrabber(infields=['subject_id'], - outfields=list(info.keys())), name='datasource') + outfields=list(info.keys())), name='datasource') datasource.inputs.template = "%s/%s" @@ -100,7 +100,7 @@ """ inputnode = pe.Node(niu.IdentityInterface(fields=["dwi", "bvecs", "bvals", - "dwi_rev"]), name="inputnode") + "dwi_rev"]), name="inputnode") """ @@ -155,14 +155,14 @@ wf = pe.Workflow(name="dMRI_Preprocessing") wf.base_dir = os.path.abspath('preprocessing_dmri_tutorial') wf.connect([ - (infosource, datasource, [('subject_id', 'subject_id')]), - (datasource, prep, [('dwi', 'inputnode.in_file'), - ('dwi_rev', 'inputnode.alt_file'), - ('bvals', 'inputnode.in_bval'), - ('bvecs', 'inputnode.in_bvec')]), - (prep, bias, [('outputnode.out_file', 'inputnode.in_file'), - ('outputnode.out_mask', 'inputnode.in_mask')]), - (datasource, bias, [('bvals', 'inputnode.in_bval')]) + (infosource, datasource, [('subject_id', 'subject_id')]), + (datasource, prep, [('dwi', 'inputnode.in_file'), + ('dwi_rev', 'inputnode.alt_file'), + ('bvals', 'inputnode.in_bval'), + ('bvecs', 'inputnode.in_bvec')]), + (prep, bias, [('outputnode.out_file', 'inputnode.in_file'), + ('outputnode.out_mask', 'inputnode.in_mask')]), + (datasource, bias, [('bvals', 'inputnode.in_bval')]) ]) diff --git a/examples/fmri_ants_openfmri.py b/examples/fmri_ants_openfmri.py index 875934faac..8c9cbdcdd0 100755 --- a/examples/fmri_ants_openfmri.py +++ b/examples/fmri_ants_openfmri.py @@ -903,7 +903,7 @@ def merge_files(copes, varcopes, zstats): [('copes', 'copes'), ('varcopes', 'varcopes'), ('zstats', 'zstats'), - ])]) + ])]) wf.connect(mergefunc, 'out_files', registration, 'inputspec.source_files') def split_files(in_files, splits): @@ -1007,7 +1007,7 @@ def get_subs(subject_id, conds, run_id, model_id, task_id): [('design_cov', 'qa.model'), ('design_image', 'qa.model.@matrix_image'), ('design_file', 'qa.model.@matrix'), - ])]) + ])]) wf.connect([(preproc, datasink, [('outputspec.motion_parameters', 'qa.motion'), ('outputspec.motion_plots', diff --git a/examples/fmri_freesurfer_smooth.py b/examples/fmri_freesurfer_smooth.py index ce8be2ff98..06c9eef847 100755 --- a/examples/fmri_freesurfer_smooth.py +++ b/examples/fmri_freesurfer_smooth.py @@ -177,7 +177,7 @@ (realign, ApplyVolTransform, [('mean_image', 'source_file')]), (ApplyVolTransform, Threshold, [('transformed_file', 'in_file')]), (realign, art, [('realignment_parameters', 'realignment_parameters'), - ('realigned_files', 'realigned_files')]), + ('realigned_files', 'realigned_files')]), (Threshold, art, [('binary_file', 'mask_file')]), (realign, volsmooth, [('realigned_files', 'in_files')]), (realign, surfsmooth, [('realigned_files', 'in_file')]), @@ -227,9 +227,9 @@ volanalysis.connect([(modelspec, level1design, [('session_info', 'session_info')]), (level1design, level1estimate, [('spm_mat_file', 'spm_mat_file')]), (level1estimate, contrastestimate, [('spm_mat_file', 'spm_mat_file'), - ('beta_images', 'beta_images'), - ('residual_image', 'residual_image')]), - ]) + ('beta_images', 'beta_images'), + ('residual_image', 'residual_image')]), + ]) """ Set up surface analysis workflow @@ -327,13 +327,13 @@ l1pipeline = pe.Workflow(name='firstlevel') l1pipeline.connect([(inputnode, preproc, [('func', 'realign.in_files'), - ('subject_id', 'surfregister.subject_id'), - ('subject_id', 'fssource.subject_id'), - ]), + ('subject_id', 'surfregister.subject_id'), + ('subject_id', 'fssource.subject_id'), + ]), (inputnode, volanalysis, [('session_info', 'modelspec.subject_info'), - ('contrasts', 'contrastestimate.contrasts')]), - (inputnode, surfanalysis, [('session_info', 'modelspec.subject_info'), ('contrasts', 'contrastestimate.contrasts')]), + (inputnode, surfanalysis, [('session_info', 'modelspec.subject_info'), + ('contrasts', 'contrastestimate.contrasts')]), ]) # attach volume and surface model specification and estimation components @@ -521,8 +521,8 @@ def subjectinfo(subject_id): level1.connect([(infosource, datasource, [('subject_id', 'subject_id')]), (datasource, l1pipeline, [('func', 'inputnode.func')]), (infosource, l1pipeline, [('subject_id', 'inputnode.subject_id'), - (('subject_id', subjectinfo), - 'inputnode.session_info')]), + (('subject_id', subjectinfo), + 'inputnode.session_info')]), ]) @@ -544,11 +544,11 @@ def getsubs(subject_id): # store relevant outputs from various stages of the 1st level analysis level1.connect([(infosource, datasink, [('subject_id', 'container'), - (('subject_id', getsubs), 'substitutions') - ]), + (('subject_id', getsubs), 'substitutions') + ]), (l1pipeline, datasink, [('surfanalysis.contrastestimate.con_images', 'contrasts'), - ('preproc.surfregister.out_reg_file', 'registrations'), - ]) + ('preproc.surfregister.out_reg_file', 'registrations'), + ]) ]) diff --git a/examples/fmri_fsl.py b/examples/fmri_fsl.py index df1bb4bf03..8c67fe7191 100755 --- a/examples/fmri_fsl.py +++ b/examples/fmri_fsl.py @@ -402,20 +402,20 @@ def getinormscale(medianvals): conestimate = pe.MapNode(interface=fsl.ContrastMgr(), name='conestimate', iterfield=['tcon_file', 'param_estimates', - 'sigmasquareds', 'corrections', - 'dof_file']) + 'sigmasquareds', 'corrections', + 'dof_file']) modelfit.connect([ - (modelspec, level1design, [('session_info', 'session_info')]), - (level1design, modelgen, [('fsf_files', 'fsf_file'), - ('ev_files', 'ev_files')]), - (modelgen, modelestimate, [('design_file', 'design_file')]), - (modelgen, conestimate, [('con_file', 'tcon_file')]), - (modelestimate, conestimate, [('param_estimates', 'param_estimates'), - ('sigmasquareds', 'sigmasquareds'), - ('corrections', 'corrections'), - ('dof_file', 'dof_file')]), - ]) + (modelspec, level1design, [('session_info', 'session_info')]), + (level1design, modelgen, [('fsf_files', 'fsf_file'), + ('ev_files', 'ev_files')]), + (modelgen, modelestimate, [('design_file', 'design_file')]), + (modelgen, conestimate, [('con_file', 'tcon_file')]), + (modelestimate, conestimate, [('param_estimates', 'param_estimates'), + ('sigmasquareds', 'sigmasquareds'), + ('corrections', 'corrections'), + ('dof_file', 'dof_file')]), +]) """ Set up fixed-effects workflow @@ -431,8 +431,8 @@ def getinormscale(medianvals): """ copemerge = pe.MapNode(interface=fsl.Merge(dimension='t'), - iterfield=['in_files'], - name="copemerge") + iterfield=['in_files'], + name="copemerge") varcopemerge = pe.MapNode(interface=fsl.Merge(dimension='t'), iterfield=['in_files'], @@ -456,8 +456,8 @@ def getinormscale(medianvals): fixed_fx.connect([(copemerge, flameo, [('merged_file', 'cope_file')]), (varcopemerge, flameo, [('merged_file', 'var_cope_file')]), (level2model, flameo, [('design_mat', 'design_file'), - ('design_con', 't_con_file'), - ('design_grp', 'cov_split_file')]), + ('design_con', 't_con_file'), + ('design_grp', 'cov_split_file')]), ]) @@ -487,9 +487,9 @@ def num_copes(files): ('highpass.out_file', 'modelestimate.in_file')]), (preproc, fixed_fx, [('coregister.out_file', 'flameo.mask_file')]), (modelfit, fixed_fx, [(('conestimate.copes', sort_copes), 'copemerge.in_files'), - (('conestimate.varcopes', sort_copes), 'varcopemerge.in_files'), - (('conestimate.copes', num_copes), 'l2model.num_copes'), - ]) + (('conestimate.varcopes', sort_copes), 'varcopemerge.in_files'), + (('conestimate.copes', num_copes), 'l2model.num_copes'), + ]) ]) diff --git a/examples/fmri_nipy_glm.py b/examples/fmri_nipy_glm.py index 5dfbce03d4..ca149a248e 100755 --- a/examples/fmri_nipy_glm.py +++ b/examples/fmri_nipy_glm.py @@ -245,7 +245,7 @@ def subjectinfo(subject_id): (datasource, realign, [('func', 'in_files')]), (realign, compute_mask, [('mean_image', 'mean_volume')]), (realign, coregister, [('mean_image', 'source'), - ('realigned_files', 'apply_to_files')]), + ('realigned_files', 'apply_to_files')]), (datasource, coregister, [('struct', 'target')]), (coregister, smooth, [('coregistered_files', 'in_files')]), (realign, modelspec, [('realignment_parameters', 'realignment_parameters')]), @@ -264,7 +264,7 @@ def subjectinfo(subject_id): ("axis", "axis"), ("constants", "constants"), ("reg_names", "reg_names")]) - ]) + ]) if __name__ == '__main__': l1pipeline.run() diff --git a/examples/fmri_openfmri.py b/examples/fmri_openfmri.py index dddfcda605..af41f11833 100755 --- a/examples/fmri_openfmri.py +++ b/examples/fmri_openfmri.py @@ -332,7 +332,7 @@ def merge_files(copes, varcopes, zstats): [('copes', 'copes'), ('varcopes', 'varcopes'), ('zstats', 'zstats'), - ])]) + ])]) wf.connect(mergefunc, 'out_files', registration, 'inputspec.source_files') def split_files(in_files, splits): diff --git a/examples/fmri_spm.py b/examples/fmri_spm.py index a4db27ff09..7d3f735a0c 100755 --- a/examples/fmri_spm.py +++ b/examples/fmri_spm.py @@ -271,13 +271,13 @@ def subjectinfo(subject_id): l1pipeline.connect([(infosource, datasource, [('subject_id', 'subject_id')]), (datasource, realign, [('func', 'in_files')]), (realign, coregister, [('mean_image', 'source'), - ('realigned_files', 'apply_to_files')]), + ('realigned_files', 'apply_to_files')]), (datasource, coregister, [('struct', 'target')]), (datasource, normalize, [('struct', 'source')]), (coregister, normalize, [('coregistered_files', 'apply_to_files')]), (normalize, smooth, [('normalized_files', 'in_files')]), (infosource, modelspec, [(('subject_id', subjectinfo), - 'subject_info')]), + 'subject_info')]), (realign, modelspec, [('realignment_parameters', 'realignment_parameters')]), (smooth, modelspec, [('smoothed_files', 'functional_runs')]), (normalize, skullstrip, [('normalized_source', 'in_file')]), @@ -289,9 +289,9 @@ def subjectinfo(subject_id): (skullstrip, level1design, [('mask_file', 'mask_image')]), (level1design, level1estimate, [('spm_mat_file', 'spm_mat_file')]), (level1estimate, contrastestimate, [('spm_mat_file', 'spm_mat_file'), - ('beta_images', 'beta_images'), - ('residual_image', 'residual_image')]), - ]) + ('beta_images', 'beta_images'), + ('residual_image', 'residual_image')]), + ]) """ @@ -324,19 +324,19 @@ def getstripdir(subject_id): # store relevant outputs from various stages of the 1st level analysis l1pipeline.connect([(infosource, datasink, [('subject_id', 'container'), - (('subject_id', getstripdir), 'strip_dir')]), + (('subject_id', getstripdir), 'strip_dir')]), (realign, datasink, [('mean_image', 'realign.@mean'), - ('realignment_parameters', 'realign.@param')]), + ('realignment_parameters', 'realign.@param')]), (art, datasink, [('outlier_files', 'art.@outliers'), - ('statistic_files', 'art.@stats')]), + ('statistic_files', 'art.@stats')]), (level1design, datasink, [('spm_mat_file', 'model.pre-estimate')]), (level1estimate, datasink, [('spm_mat_file', 'model.@spm'), - ('beta_images', 'model.@beta'), - ('mask_image', 'model.@mask'), - ('residual_image', 'model.@res'), - ('RPVimage', 'model.@rpv')]), + ('beta_images', 'model.@beta'), + ('mask_image', 'model.@mask'), + ('residual_image', 'model.@res'), + ('RPVimage', 'model.@rpv')]), (contrastestimate, datasink, [('con_images', 'contrasts.@con'), - ('spmT_images', 'contrasts.@T')]), + ('spmT_images', 'contrasts.@T')]), ]) @@ -385,8 +385,8 @@ def getstripdir(subject_id): l2pipeline.connect([(l2source, onesamplettestdes, [('outfiles', 'in_files')]), (onesamplettestdes, l2estimate, [('spm_mat_file', 'spm_mat_file')]), (l2estimate, l2conestimate, [('spm_mat_file', 'spm_mat_file'), - ('beta_images', 'beta_images'), - ('residual_image', 'residual_image')]), + ('beta_images', 'beta_images'), + ('residual_image', 'residual_image')]), ]) """ diff --git a/examples/fmri_spm_auditory.py b/examples/fmri_spm_auditory.py index a1a413d751..9933277f0f 100755 --- a/examples/fmri_spm_auditory.py +++ b/examples/fmri_spm_auditory.py @@ -187,11 +187,11 @@ def get_vox_dims(volume): l1analysis.connect([(modelspec, level1design, [('session_info', 'session_info')]), (level1design, level1estimate, [('spm_mat_file', 'spm_mat_file')]), (level1estimate, contrastestimate, [('spm_mat_file', 'spm_mat_file'), - ('beta_images', 'beta_images'), - ('residual_image', 'residual_image')]), + ('beta_images', 'beta_images'), + ('residual_image', 'residual_image')]), (contrastestimate, threshold, [('spm_mat_file', 'spm_mat_file'), - ('spmT_images', 'stat_image')]), - ]) + ('spmT_images', 'stat_image')]), + ]) """ Preproc + Analysis pipeline @@ -376,9 +376,9 @@ def getstripdir(subject_id): # store relevant outputs from various stages of the 1st level analysis level1.connect([(infosource, datasink, [('subject_id', 'container'), - (('subject_id', getstripdir), 'strip_dir')]), + (('subject_id', getstripdir), 'strip_dir')]), (l1pipeline, datasink, [('analysis.contrastestimate.con_images', 'contrasts.@con'), - ('analysis.contrastestimate.spmT_images', 'contrasts.@T')]), + ('analysis.contrastestimate.spmT_images', 'contrasts.@T')]), ]) diff --git a/examples/fmri_spm_dartel.py b/examples/fmri_spm_dartel.py index 529c541732..a2e7d7fccc 100755 --- a/examples/fmri_spm_dartel.py +++ b/examples/fmri_spm_dartel.py @@ -113,7 +113,7 @@ normalize_struct.inputs.fwhm = 2 preproc.connect([(realign, coregister, [('mean_image', 'source'), - ('realigned_files', 'apply_to_files')]), + ('realigned_files', 'apply_to_files')]), (coregister, normalize_and_smooth_func, [('coregistered_files', 'apply_to_files')]), (normalize_struct, skullstrip, [('normalized_files', 'in_file')]), (realign, art, [('realignment_parameters', 'realignment_parameters')]), @@ -183,12 +183,12 @@ l1analysis.connect([(modelspec, level1design, [('session_info', 'session_info')]), (level1design, level1estimate, [('spm_mat_file', 'spm_mat_file')]), (level1estimate, contrastestimate, [('spm_mat_file', 'spm_mat_file'), - ('beta_images', 'beta_images'), - ('residual_image', 'residual_image')]), + ('beta_images', 'beta_images'), + ('residual_image', 'residual_image')]), (contrastestimate, selectcontrast, [('spmT_images', 'inlist')]), (selectcontrast, overlaystats, [('out', 'stat_image')]), (overlaystats, slicestats, [('out_file', 'in_file')]) - ]) + ]) """ Preproc + Analysis pipeline @@ -404,8 +404,8 @@ def subjectinfo(subject_id): (infosource, datasource, [('subject_id', 'subject_id')]), (datasource, l1pipeline, [('func', 'preproc.realign.in_files'), - ('struct', 'preproc.coregister.target'), - ('struct', 'preproc.normalize_struct.apply_to_files')]), + ('struct', 'preproc.coregister.target'), + ('struct', 'preproc.normalize_struct.apply_to_files')]), (dartel_workflow, l1pipeline, [('outputspec.template_file', 'preproc.normalize_struct.template_file'), ('outputspec.template_file', 'preproc.normalize_and_smooth_func.template_file')]), (infosource, pick_flow, [('subject_id', 'subject_id')]), @@ -413,7 +413,7 @@ def subjectinfo(subject_id): (pick_flow, l1pipeline, [('dartel_flow_field', 'preproc.normalize_struct.flowfield_files'), ('dartel_flow_field', 'preproc.normalize_and_smooth_func.flowfield_files')]), (infosource, l1pipeline, [(('subject_id', subjectinfo), - 'analysis.modelspec.subject_info')]), + 'analysis.modelspec.subject_info')]), ]) @@ -450,11 +450,11 @@ def getstripdir(subject_id): # store relevant outputs from various stages of the 1st level analysis level1.connect([(infosource, datasink, [('subject_id', 'container'), - (('subject_id', getstripdir), 'strip_dir')]), + (('subject_id', getstripdir), 'strip_dir')]), (l1pipeline, datasink, [('analysis.contrastestimate.con_images', 'contrasts.@con'), - ('analysis.contrastestimate.spmT_images', 'contrasts.@T')]), + ('analysis.contrastestimate.spmT_images', 'contrasts.@T')]), (infosource, report, [('subject_id', 'container'), - (('subject_id', getstripdir), 'strip_dir')]), + (('subject_id', getstripdir), 'strip_dir')]), (l1pipeline, report, [('analysis.slicestats.out_file', '@report')]), ]) @@ -519,8 +519,8 @@ def getstripdir(subject_id): l2pipeline.connect([(l2source, onesamplettestdes, [('outfiles', 'in_files')]), (onesamplettestdes, l2estimate, [('spm_mat_file', 'spm_mat_file')]), (l2estimate, l2conestimate, [('spm_mat_file', 'spm_mat_file'), - ('beta_images', 'beta_images'), - ('residual_image', 'residual_image')]), + ('beta_images', 'beta_images'), + ('residual_image', 'residual_image')]), ]) """ diff --git a/examples/fmri_spm_face.py b/examples/fmri_spm_face.py index 532ddf0a33..7f918aafa7 100755 --- a/examples/fmri_spm_face.py +++ b/examples/fmri_spm_face.py @@ -182,11 +182,11 @@ def pickfirst(l): l1analysis.connect([(modelspec, level1design, [('session_info', 'session_info')]), (level1design, level1estimate, [('spm_mat_file', 'spm_mat_file')]), (level1estimate, contrastestimate, [('spm_mat_file', 'spm_mat_file'), - ('beta_images', 'beta_images'), - ('residual_image', 'residual_image')]), + ('beta_images', 'beta_images'), + ('residual_image', 'residual_image')]), (contrastestimate, threshold, [('spm_mat_file', 'spm_mat_file'), - (('spmT_images', pickfirst), 'stat_image')]), - ]) + (('spmT_images', pickfirst), 'stat_image')]), + ]) """ Preproc + Analysis pipeline @@ -402,7 +402,7 @@ def makelist(item): l1pipeline.connect([(preproc, paramanalysis, [('realign.realignment_parameters', 'modelspec.realignment_parameters'), (('smooth.smoothed_files', makelist), - 'modelspec.functional_runs')])]) + 'modelspec.functional_runs')])]) """ Setup the pipeline @@ -432,7 +432,7 @@ def makelist(item): level1.connect([(infosource, datasource, [('subject_id', 'subject_id')]), (datasource, l1pipeline, [('struct', 'preproc.coregister.source'), - ('func', 'preproc.realign.in_files')]) + ('func', 'preproc.realign.in_files')]) ]) @@ -466,11 +466,11 @@ def getstripdir(subject_id): # store relevant outputs from various stages of the 1st level analysis level1.connect([(infosource, datasink, [('subject_id', 'container'), - (('subject_id', getstripdir), 'strip_dir')]), + (('subject_id', getstripdir), 'strip_dir')]), (l1pipeline, datasink, [('analysis.contrastestimate.con_images', 'contrasts.@con'), - ('analysis.contrastestimate.spmT_images', 'contrasts.@T'), - ('paramanalysis.contrastestimate.con_images', 'paramcontrasts.@con'), - ('paramanalysis.contrastestimate.spmT_images', 'paramcontrasts.@T')]), + ('analysis.contrastestimate.spmT_images', 'contrasts.@T'), + ('paramanalysis.contrastestimate.con_images', 'paramcontrasts.@con'), + ('paramanalysis.contrastestimate.spmT_images', 'paramcontrasts.@T')]), ]) diff --git a/examples/fmri_spm_nested.py b/examples/fmri_spm_nested.py index 2dc49c0399..b73b6b8c2d 100755 --- a/examples/fmri_spm_nested.py +++ b/examples/fmri_spm_nested.py @@ -118,7 +118,7 @@ smooth.iterables = ('fwhm', fwhmlist) preproc.connect([(realign, coregister, [('mean_image', 'source'), - ('realigned_files', 'apply_to_files')]), + ('realigned_files', 'apply_to_files')]), (coregister, normalize, [('coregistered_files', 'apply_to_files')]), (normalize, smooth, [('normalized_files', 'in_files')]), (normalize, skullstrip, [('normalized_source', 'in_file')]), @@ -189,12 +189,12 @@ l1analysis.connect([(modelspec, level1design, [('session_info', 'session_info')]), (level1design, level1estimate, [('spm_mat_file', 'spm_mat_file')]), (level1estimate, contrastestimate, [('spm_mat_file', 'spm_mat_file'), - ('beta_images', 'beta_images'), - ('residual_image', 'residual_image')]), + ('beta_images', 'beta_images'), + ('residual_image', 'residual_image')]), (contrastestimate, selectcontrast, [('spmT_images', 'inlist')]), (selectcontrast, overlaystats, [('out', 'stat_image')]), (overlaystats, slicestats, [('out_file', 'in_file')]) - ]) + ]) """ Preproc + Analysis pipeline @@ -363,10 +363,10 @@ def subjectinfo(subject_id): level1.connect([(infosource, datasource, [('subject_id', 'subject_id')]), (datasource, l1pipeline, [('func', 'preproc.realign.in_files'), - ('struct', 'preproc.coregister.target'), - ('struct', 'preproc.normalize.source')]), + ('struct', 'preproc.coregister.target'), + ('struct', 'preproc.normalize.source')]), (infosource, l1pipeline, [(('subject_id', subjectinfo), - 'analysis.modelspec.subject_info')]), + 'analysis.modelspec.subject_info')]), ]) @@ -403,11 +403,11 @@ def getstripdir(subject_id): # store relevant outputs from various stages of the 1st level analysis level1.connect([(infosource, datasink, [('subject_id', 'container'), - (('subject_id', getstripdir), 'strip_dir')]), + (('subject_id', getstripdir), 'strip_dir')]), (l1pipeline, datasink, [('analysis.contrastestimate.con_images', 'contrasts.@con'), - ('analysis.contrastestimate.spmT_images', 'contrasts.@T')]), + ('analysis.contrastestimate.spmT_images', 'contrasts.@T')]), (infosource, report, [('subject_id', 'container'), - (('subject_id', getstripdir), 'strip_dir')]), + (('subject_id', getstripdir), 'strip_dir')]), (l1pipeline, report, [('analysis.slicestats.out_file', '@report')]), ]) @@ -472,8 +472,8 @@ def getstripdir(subject_id): l2pipeline.connect([(l2source, onesamplettestdes, [('outfiles', 'in_files')]), (onesamplettestdes, l2estimate, [('spm_mat_file', 'spm_mat_file')]), (l2estimate, l2conestimate, [('spm_mat_file', 'spm_mat_file'), - ('beta_images', 'beta_images'), - ('residual_image', 'residual_image')]), + ('beta_images', 'beta_images'), + ('residual_image', 'residual_image')]), ]) """ diff --git a/examples/frontiers_paper/smoothing_comparison.py b/examples/frontiers_paper/smoothing_comparison.py index d4921142a8..b16b229f6d 100644 --- a/examples/frontiers_paper/smoothing_comparison.py +++ b/examples/frontiers_paper/smoothing_comparison.py @@ -28,8 +28,8 @@ iter_smoothing_method = pe.Node(interface=util.IdentityInterface(fields=["smoothing_method"]), name="iter_smoothing_method") iter_smoothing_method.iterables = [('smoothing_method', ['isotropic_voxel', - 'anisotropic_voxel', - 'isotropic_surface'])] + 'anisotropic_voxel', + 'isotropic_surface'])] realign = pe.Node(interface=spm.Realign(), name="realign") realign.inputs.register_to_mean = True diff --git a/examples/smri_ants_build_template.py b/examples/smri_ants_build_template.py index 6b14550f0f..21603c956c 100644 --- a/examples/smri_ants_build_template.py +++ b/examples/smri_ants_build_template.py @@ -39,13 +39,13 @@ print(mydatadir) MyFileURLs = [ - ('http://slicer.kitware.com/midas3/download?bitstream=13121', '01_T1_half.nii.gz'), - ('http://slicer.kitware.com/midas3/download?bitstream=13122', '02_T1_half.nii.gz'), - ('http://slicer.kitware.com/midas3/download?bitstream=13124', '03_T1_half.nii.gz'), - ('http://slicer.kitware.com/midas3/download?bitstream=13128', '01_T1_inv_half.nii.gz'), - ('http://slicer.kitware.com/midas3/download?bitstream=13123', '02_T1_inv_half.nii.gz'), - ('http://slicer.kitware.com/midas3/download?bitstream=13125', '03_T1_inv_half.nii.gz'), - ] + ('http://slicer.kitware.com/midas3/download?bitstream=13121', '01_T1_half.nii.gz'), + ('http://slicer.kitware.com/midas3/download?bitstream=13122', '02_T1_half.nii.gz'), + ('http://slicer.kitware.com/midas3/download?bitstream=13124', '03_T1_half.nii.gz'), + ('http://slicer.kitware.com/midas3/download?bitstream=13128', '01_T1_inv_half.nii.gz'), + ('http://slicer.kitware.com/midas3/download?bitstream=13123', '02_T1_inv_half.nii.gz'), + ('http://slicer.kitware.com/midas3/download?bitstream=13125', '03_T1_inv_half.nii.gz'), +] for tt in MyFileURLs: myURL = tt[0] localFilename = os.path.join(mydatadir, tt[1]) diff --git a/examples/smri_ants_registration.py b/examples/smri_ants_registration.py index ca49b56aa0..f2558d560d 100644 --- a/examples/smri_ants_registration.py +++ b/examples/smri_ants_registration.py @@ -34,9 +34,9 @@ print(mydatadir) MyFileURLs = [ - ('http://slicer.kitware.com/midas3/download?bitstream=13121', '01_T1_half.nii.gz'), - ('http://slicer.kitware.com/midas3/download?bitstream=13122', '02_T1_half.nii.gz'), - ] + ('http://slicer.kitware.com/midas3/download?bitstream=13121', '01_T1_half.nii.gz'), + ('http://slicer.kitware.com/midas3/download?bitstream=13122', '02_T1_half.nii.gz'), +] for tt in MyFileURLs: myURL = tt[0] localFilename = os.path.join(mydatadir, tt[1]) diff --git a/examples/smri_antsregistration_build_template.py b/examples/smri_antsregistration_build_template.py index 46cd680599..ad4e0470ef 100644 --- a/examples/smri_antsregistration_build_template.py +++ b/examples/smri_antsregistration_build_template.py @@ -39,13 +39,13 @@ print(mydatadir) MyFileURLs = [ - ('http://slicer.kitware.com/midas3/download?bitstream=13121', '01_T1_half.nii.gz'), - ('http://slicer.kitware.com/midas3/download?bitstream=13122', '02_T1_half.nii.gz'), - ('http://slicer.kitware.com/midas3/download?bitstream=13124', '03_T1_half.nii.gz'), - ('http://slicer.kitware.com/midas3/download?bitstream=13128', '01_T1_inv_half.nii.gz'), - ('http://slicer.kitware.com/midas3/download?bitstream=13123', '02_T1_inv_half.nii.gz'), - ('http://slicer.kitware.com/midas3/download?bitstream=13125', '03_T1_inv_half.nii.gz'), - ] + ('http://slicer.kitware.com/midas3/download?bitstream=13121', '01_T1_half.nii.gz'), + ('http://slicer.kitware.com/midas3/download?bitstream=13122', '02_T1_half.nii.gz'), + ('http://slicer.kitware.com/midas3/download?bitstream=13124', '03_T1_half.nii.gz'), + ('http://slicer.kitware.com/midas3/download?bitstream=13128', '01_T1_inv_half.nii.gz'), + ('http://slicer.kitware.com/midas3/download?bitstream=13123', '02_T1_inv_half.nii.gz'), + ('http://slicer.kitware.com/midas3/download?bitstream=13125', '03_T1_inv_half.nii.gz'), +] for tt in MyFileURLs: myURL = tt[0] localFilename = os.path.join(mydatadir, tt[1]) @@ -108,7 +108,7 @@ InitialTemplateInputs = [mdict['T1'] for mdict in ListOfImagesDictionaries] datasource = pe.Node(interface=util.IdentityInterface(fields=['InitialTemplateInputs', 'ListOfImagesDictionaries', - 'registrationImageTypes', 'interpolationMapping']), + 'registrationImageTypes', 'interpolationMapping']), run_without_submitting=True, name='InputImages') datasource.inputs.InitialTemplateInputs = InitialTemplateInputs diff --git a/examples/workshop_dartmouth_2010.py b/examples/workshop_dartmouth_2010.py index 779fec9045..1c9c587ae9 100644 --- a/examples/workshop_dartmouth_2010.py +++ b/examples/workshop_dartmouth_2010.py @@ -133,8 +133,8 @@ motion_correct_and_smooth = pe.Workflow(name="motion_correct_and_smooth") motion_correct_and_smooth.base_dir = os.path.abspath('.') # define where will be the root folder for the workflow motion_correct_and_smooth.connect([ - (motion_correct, smooth, [('out_file', 'in_file')]) - ]) + (motion_correct, smooth, [('out_file', 'in_file')]) +]) # we are connecting 'out_file' output of motion_correct to 'in_file' input of smooth motion_correct_and_smooth.run() @@ -154,8 +154,8 @@ demean = pe.Workflow(name="demean") demean.base_dir = os.path.abspath('.') demean.connect([ - (calc_mean, subtract, [('out_file', 'in_file2')]) - ]) + (calc_mean, subtract, [('out_file', 'in_file2')]) +]) demean.inputs.calc_mean.in_file = os.path.abspath('data/s1/f3.nii') demean.inputs.subtract.in_file = os.path.abspath('data/s1/f3.nii') @@ -216,9 +216,9 @@ preprocess = pe.Workflow(name='preprocout') preprocess.base_dir = os.path.abspath('.') preprocess.connect([ - (preproc, datasink, [('meanfunc2.out_file', 'meanfunc'), - ('maskfunc3.out_file', 'funcruns')]) - ]) + (preproc, datasink, [('meanfunc2.out_file', 'meanfunc'), + ('maskfunc3.out_file', 'funcruns')]) +]) preprocess.run() """ diff --git a/nipype/__init__.py b/nipype/__init__.py index bc86315987..86a75a37ca 100644 --- a/nipype/__init__.py +++ b/nipype/__init__.py @@ -55,7 +55,7 @@ def _test_local_install(): imported locally is a bad idea. """ if os.getcwd() == os.sep.join( - os.path.abspath(__file__).split(os.sep)[:-2]): + os.path.abspath(__file__).split(os.sep)[:-2]): import warnings warnings.warn('Running the tests from the install directory may ' 'trigger some failures') diff --git a/nipype/algorithms/metrics.py b/nipype/algorithms/metrics.py index 91e4695058..e2e67bc952 100644 --- a/nipype/algorithms/metrics.py +++ b/nipype/algorithms/metrics.py @@ -360,9 +360,9 @@ def _list_outputs(self): class FuzzyOverlapInputSpec(BaseInterfaceInputSpec): in_ref = InputMultiPath(File(exists=True), mandatory=True, - desc='Reference image. Requires the same dimensions as in_tst.') + desc='Reference image. Requires the same dimensions as in_tst.') in_tst = InputMultiPath(File(exists=True), mandatory=True, - desc='Test image. Requires the same dimensions as in_ref.') + desc='Test image. Requires the same dimensions as in_ref.') weighting = traits.Enum('none', 'volume', 'squared_vol', usedefault=True, desc=('\'none\': no class-overlap weighting is ' 'performed. \'volume\': computed class-' diff --git a/nipype/algorithms/modelgen.py b/nipype/algorithms/modelgen.py index 346000c39e..26439e5951 100644 --- a/nipype/algorithms/modelgen.py +++ b/nipype/algorithms/modelgen.py @@ -316,10 +316,10 @@ def _generate_standard_design(self, infolist, sessinfo[i]['cond'][cid]['amplitudes'] = \ info.amplitudes[cid] if hasattr(info, 'tmod') and info.tmod and \ - len(info.tmod) > cid: + len(info.tmod) > cid: sessinfo[i]['cond'][cid]['tmod'] = info.tmod[cid] if hasattr(info, 'pmod') and info.pmod and \ - len(info.pmod) > cid: + len(info.pmod) > cid: if info.pmod[cid]: sessinfo[i]['cond'][cid]['pmod'] = [] for j, name in enumerate(info.pmod[cid].name): @@ -335,7 +335,7 @@ def _generate_standard_design(self, infolist, for j, r in enumerate(info.regressors): sessinfo[i]['regress'].insert(j, dict(name='', val=[])) if hasattr(info, 'regressor_names') and \ - info.regressor_names is not None: + info.regressor_names is not None: sessinfo[i]['regress'][j]['name'] = \ info.regressor_names[j] else: @@ -476,12 +476,12 @@ def _concatenate_info(self, infolist): for j, val in enumerate(info.onsets): if self.inputs.input_units == 'secs': onsets = np.array(info.onsets[j]) +\ - self.inputs.time_repetition * \ - sum(nscans[0:(i + 1)]) + self.inputs.time_repetition * \ + sum(nscans[0:(i + 1)]) infoout.onsets[j].extend(onsets.tolist()) else: onsets = np.array(info.onsets[j]) + \ - sum(nscans[0:(i + 1)]) + sum(nscans[0:(i + 1)]) infoout.onsets[j].extend(onsets.tolist()) for j, val in enumerate(info.durations): if len(info.onsets[j]) > 1 and len(val) == 1: @@ -561,7 +561,7 @@ class SpecifySparseModelInputSpec(SpecifyModelInputSpec): time_acquisition = traits.Float(0, mandatory=True, desc="Time in seconds to acquire a single image volume") volumes_in_cluster = traits.Range(1, usedefault=True, - desc="Number of scan volumes in a cluster") + desc="Number of scan volumes in a cluster") model_hrf = traits.Bool(desc="model sparse events with hrf") stimuli_as_impulses = traits.Bool(True, desc="Treat each stimulus to be impulse like.", diff --git a/nipype/algorithms/rapidart.py b/nipype/algorithms/rapidart.py index 69ea3b90d8..435b3c99e5 100644 --- a/nipype/algorithms/rapidart.py +++ b/nipype/algorithms/rapidart.py @@ -119,11 +119,11 @@ def _calc_norm(mc, use_differences, source, brain_pts=None): all_pts)[0:3, :].ravel() if brain_pts is not None: displacement[i, :] = \ - np.sqrt(np.sum(np.power(np.reshape(newpos[i, :], - (3, all_pts.shape[1])) - - all_pts[0:3, :], - 2), - axis=0)) + np.sqrt(np.sum(np.power(np.reshape(newpos[i, :], + (3, all_pts.shape[1])) - + all_pts[0:3, :], + 2), + axis=0)) # np.savez('displacement.npz', newpos=newpos, pts=all_pts) normdata = np.zeros(mc.shape[0]) if use_differences: @@ -131,8 +131,8 @@ def _calc_norm(mc, use_differences, source, brain_pts=None): np.diff(newpos, n=1, axis=0)), axis=0) for i in range(newpos.shape[0]): normdata[i] = \ - np.max(np.sqrt(np.sum(np.reshape(np.power(np.abs(newpos[i, :]), 2), - (3, all_pts.shape[1])), axis=0))) + np.max(np.sqrt(np.sum(np.reshape(np.power(np.abs(newpos[i, :]), 2), + (3, all_pts.shape[1])), axis=0))) else: newpos = np.abs(signal.detrend(newpos, axis=0, type='constant')) normdata = np.sqrt(np.mean(np.power(newpos, 2), axis=1)) @@ -319,7 +319,7 @@ def _list_outputs(self): for i, f in enumerate(filename_to_list(self.inputs.realigned_files)): (outlierfile, intensityfile, statsfile, normfile, plotfile, displacementfile, maskfile) = \ - self._get_output_filenames(f, os.getcwd()) + self._get_output_filenames(f, os.getcwd()) outputs['outlier_files'].insert(i, outlierfile) outputs['intensity_files'].insert(i, intensityfile) outputs['statistic_files'].insert(i, statsfile) @@ -514,13 +514,13 @@ def _detect_outliers_core(self, imgfile, motionfile, runidx, cwd=None): 'min': np.min(mc_in, axis=0).tolist(), 'max': np.max(mc_in, axis=0).tolist(), 'std': np.std(mc_in, axis=0).tolist()}, - ]}, + ]}, {'intensity': [{'using differences': self.inputs.use_differences[1]}, {'mean': np.mean(gz, axis=0).tolist(), 'min': np.min(gz, axis=0).tolist(), 'max': np.max(gz, axis=0).tolist(), 'std': np.std(gz, axis=0).tolist()}, - ]}, + ]}, ] if self.inputs.use_norm: stats.insert(3, {'motion_norm': @@ -528,7 +528,7 @@ def _detect_outliers_core(self, imgfile, motionfile, runidx, cwd=None): 'min': np.min(normval, axis=0).tolist(), 'max': np.max(normval, axis=0).tolist(), 'std': np.std(normval, axis=0).tolist(), - }}) + }}) save_json(statsfile, stats) def _run_interface(self, runtime): diff --git a/nipype/fixes/numpy/testing/nosetester.py b/nipype/fixes/numpy/testing/nosetester.py index 5c392b63bd..22c8d1a5ef 100644 --- a/nipype/fixes/numpy/testing/nosetester.py +++ b/nipype/fixes/numpy/testing/nosetester.py @@ -237,7 +237,7 @@ def prepare_test_args(self, label='fast', verbose=1, extra_argv=None, # our way of doing coverage if coverage: argv += ['--cover-package=%s' % self.package_name, '--with-coverage', - '--cover-tests', '--cover-inclusive', '--cover-erase'] + '--cover-tests', '--cover-inclusive', '--cover-erase'] # construct list of plugins import nose.plugins.builtin from .noseclasses import KnownFailure, Unplugger diff --git a/nipype/interfaces/ants/legacy.py b/nipype/interfaces/ants/legacy.py index 3482f91fe5..313019b08e 100644 --- a/nipype/interfaces/ants/legacy.py +++ b/nipype/interfaces/ants/legacy.py @@ -251,7 +251,7 @@ def _list_outputs(self): outputs['template_files'].append(os.path.realpath(file_)) outputs['final_template_file'] = \ os.path.realpath('%stemplate.nii.gz' % - self.inputs.out_prefix) + self.inputs.out_prefix) outputs['subject_outfiles'] = [] for filename in self.inputs.in_files: _, base, _ = split_filename(filename) diff --git a/nipype/interfaces/ants/registration.py b/nipype/interfaces/ants/registration.py index aa2e1494e3..d60ab96411 100644 --- a/nipype/interfaces/ants/registration.py +++ b/nipype/interfaces/ants/registration.py @@ -329,9 +329,9 @@ class RegistrationInputSpec(ANTSCommandInputSpec): traits.Float()), traits.Tuple(traits.Float(), # gdf & syn traits.Float( - ), - traits.Float( - )), + ), + traits.Float( + )), traits.Tuple(traits.Float(), # BSplineSyn traits.Int(), traits.Int(), @@ -607,7 +607,7 @@ def _formatRegistration(self): if isdefined(self.inputs.sigma_units): retval.append('--smoothing-sigmas %s%s' % (self._antsJoinList(self.inputs.smoothing_sigmas[ - ii]), + ii]), self.inputs.sigma_units[ii])) else: retval.append('--smoothing-sigmas %s' % diff --git a/nipype/interfaces/ants/visualization.py b/nipype/interfaces/ants/visualization.py index 635c4be7f5..6780b79d8b 100644 --- a/nipype/interfaces/ants/visualization.py +++ b/nipype/interfaces/ants/visualization.py @@ -16,22 +16,22 @@ class ConvertScalarImageToRGBInputSpec(ANTSCommandInputSpec): dimension = traits.Enum(3, 2, argstr='%d', usedefault=True, - desc='image dimension (2 or 3)', mandatory=True, - position=0) + desc='image dimension (2 or 3)', mandatory=True, + position=0) input_image = File(argstr='%s', exists=True, - desc='Main input is a 3-D grayscale image.', mandatory=True, - position=1) + desc='Main input is a 3-D grayscale image.', mandatory=True, + position=1) output_image = traits.Str('rgb.nii.gz', argstr='%s', usedefault=True, - desc=('rgb output image'), position=2) + desc=('rgb output image'), position=2) mask_image = File('none', argstr='%s', exists=True, - desc='mask image', position=3, usedefault=True) + desc='mask image', position=3, usedefault=True) colormap = traits.Str(argstr='%s', usedefault=True, - desc=('Possible colormaps: grey, red, green, ' - 'blue, copper, jet, hsv, spring, summer, ' - 'autumn, winter, hot, cool, overunder, custom ' - ), mandatory=True, position=4) + desc=('Possible colormaps: grey, red, green, ' + 'blue, copper, jet, hsv, spring, summer, ' + 'autumn, winter, hot, cool, overunder, custom ' + ), mandatory=True, position=4) custom_color_map_file = traits.Str('none', argstr='%s', usedefault=True, - desc='custom color map file', position=5) + desc='custom color map file', position=5) minimum_input = traits.Int(argstr='%d', desc='minimum input', mandatory=True, position=6) maximum_input = traits.Int(argstr='%d', desc='maximum input', @@ -79,27 +79,27 @@ class CreateTiledMosaicInputSpec(ANTSCommandInputSpec): desc='Main input is a 3-D grayscale image.', mandatory=True) rgb_image = File(argstr='-r %s', exists=True, - desc=('An optional Rgb image can be added as an overlay.' + desc=('An optional Rgb image can be added as an overlay.' 'It must have the same image' 'geometry as the input grayscale image.'), - mandatory=True) + mandatory=True) mask_image = File(argstr='-x %s', exists=True, desc='Specifies the ROI of the RGB voxels used.') alpha_value = traits.Float(argstr='-a %.2f', desc=('If an Rgb image is provided, render the overlay ' - 'using the specified alpha parameter.')) + 'using the specified alpha parameter.')) output_image = traits.Str('output.png', argstr='-o %s', desc='The output consists of the tiled mosaic image.', usedefault=True) tile_geometry = traits.Str(argstr='-t %s', desc=( - 'The tile geometry specifies the number of rows and columns' - 'in the output image. For example, if the user specifies "5x10", ' - 'then 5 rows by 10 columns of slices are rendered. If R < 0 and C > ' - '0 (or vice versa), the negative value is selected' - 'based on direction.')) + 'The tile geometry specifies the number of rows and columns' + 'in the output image. For example, if the user specifies "5x10", ' + 'then 5 rows by 10 columns of slices are rendered. If R < 0 and C > ' + '0 (or vice versa), the negative value is selected' + 'based on direction.')) direction = traits.Int(argstr='-d %d', desc=('Specifies the direction of ' - 'the slices. If no direction is specified, the ' - 'direction with the coarsest spacing is chosen.')) + 'the slices. If no direction is specified, the ' + 'direction with the coarsest spacing is chosen.')) pad_or_crop = traits.Str(argstr='-p %s', desc='argument passed to -p flag:' '[padVoxelWidth,]' @@ -115,7 +115,7 @@ class CreateTiledMosaicInputSpec(ANTSCommandInputSpec): ) slices = traits.Str(argstr='-s %s', desc=('Number of slices to increment Slice1xSlice2xSlice3' - '[numberOfSlicesToIncrement,,]')) + '[numberOfSlicesToIncrement,,]')) flip_slice = traits.Str(argstr='-f %s', desc=('flipXxflipY')) permute_axes = traits.Bool(argstr='-g', desc='doPermute' diff --git a/nipype/interfaces/base.py b/nipype/interfaces/base.py index 1129610990..f37f65fda7 100644 --- a/nipype/interfaces/base.py +++ b/nipype/interfaces/base.py @@ -1501,7 +1501,7 @@ def _run_interface(self, runtime, correct_return_codes=[0]): runtime = run_command(runtime, output=self.inputs.terminal_output, redirect_x=self._redirect_x) if runtime.returncode is None or \ - runtime.returncode not in correct_return_codes: + runtime.returncode not in correct_return_codes: self.raise_exception(runtime) return runtime diff --git a/nipype/interfaces/camino/convert.py b/nipype/interfaces/camino/convert.py index 0c88ff665a..cdde8a2b88 100644 --- a/nipype/interfaces/camino/convert.py +++ b/nipype/interfaces/camino/convert.py @@ -188,13 +188,13 @@ class ProcStreamlinesInputSpec(StdOutCommandLineInputSpec): desc='data file') maxtractpoints = traits.Int(argstr='-maxtractpoints %d', units='NA', - desc="maximum number of tract points") + desc="maximum number of tract points") mintractpoints = traits.Int(argstr='-mintractpoints %d', units='NA', - desc="minimum number of tract points") + desc="minimum number of tract points") maxtractlength = traits.Int(argstr='-maxtractlength %d', units='mm', - desc="maximum length of tracts") + desc="maximum length of tracts") mintractlength = traits.Int(argstr='-mintractlength %d', units='mm', - desc="minimum length of tracts") + desc="minimum length of tracts") datadims = traits.List(traits.Int, desc='data dimensions in voxels', argstr='-datadims %s', minlen=3, maxlen=3, units='voxels') diff --git a/nipype/interfaces/freesurfer/utils.py b/nipype/interfaces/freesurfer/utils.py index f816a38a99..5bc417d3ba 100644 --- a/nipype/interfaces/freesurfer/utils.py +++ b/nipype/interfaces/freesurfer/utils.py @@ -633,7 +633,7 @@ def _format_arg(self, name, spec, value): def _run_interface(self, runtime): if not isdefined(self.inputs.screenshot_stem): stem = "%s_%s_%s" % ( - self.inputs.subject_id, self.inputs.hemi, self.inputs.surface) + self.inputs.subject_id, self.inputs.hemi, self.inputs.surface) else: stem = self.inputs.screenshot_stem stem_args = self.inputs.stem_template_args diff --git a/nipype/interfaces/fsl/dti.py b/nipype/interfaces/fsl/dti.py index b8db4a63b2..f9a0e47789 100644 --- a/nipype/interfaces/fsl/dti.py +++ b/nipype/interfaces/fsl/dti.py @@ -177,9 +177,9 @@ class FSLXCommandOutputSpec(TraitedSpec): mean_fsamples = OutputMultiPath(File(exists=True), desc=('Mean of ' 'distribution on f anisotropy')) mean_S0samples = File(exists=True, desc=('Mean of distribution on T2w' - 'baseline signal intensity S0')) + 'baseline signal intensity S0')) mean_tausamples = File(exists=True, desc=('Mean of distribution on ' - 'tau samples (only with rician noise)')) + 'tau samples (only with rician noise)')) phsamples = OutputMultiPath(File(exists=True), desc=('phi samples, per fiber')) thsamples = OutputMultiPath(File(exists=True), desc=('theta samples, per fiber')) @@ -273,7 +273,7 @@ class BEDPOSTX5OutputSpec(TraitedSpec): mean_fsamples = OutputMultiPath(File(exists=True), desc=('Mean of ' 'distribution on f anisotropy')) mean_S0samples = File(exists=True, desc=('Mean of distribution on T2w' - 'baseline signal intensity S0')) + 'baseline signal intensity S0')) mean_phsamples = OutputMultiPath(File(exists=True), desc=('Mean of ' 'distribution on phi')) mean_thsamples = OutputMultiPath(File(exists=True), desc=('Mean of ' @@ -534,7 +534,7 @@ class BEDPOSTX4OutputSpec(TraitedSpec): 'bedpostx output files for this subject') xfms_directory = Directory(exists=True, desc='path/name of directory with the ' + - 'tranformation matrices') + 'tranformation matrices') merged_thsamples = traits.List(File(exists=True), desc='a list of path/name of 4D volume ' + 'with samples from the distribution ' + @@ -841,9 +841,9 @@ def _list_outputs(self): outputs['fdt_paths'] = [] for seed in self.inputs.seed: outputs['fdt_paths'].append( - os.path.abspath( - self._gen_fname("fdt_paths_%s" % ("_".join([str(s) for s in seed])), - cwd=out_dir, suffix=''))) + os.path.abspath( + self._gen_fname("fdt_paths_%s" % ("_".join([str(s) for s in seed])), + cwd=out_dir, suffix=''))) else: outputs['fdt_paths'] = os.path.abspath(self._gen_fname("fdt_paths", cwd=out_dir, suffix='')) @@ -853,13 +853,13 @@ def _list_outputs(self): outputs['targets'] = [] for target in self.inputs.target_masks: outputs['targets'].append(os.path.abspath( - self._gen_fname('seeds_to_' + os.path.split(target)[1], - cwd=out_dir, - suffix=''))) + self._gen_fname('seeds_to_' + os.path.split(target)[1], + cwd=out_dir, + suffix=''))) if isdefined(self.inputs.verbose) and self.inputs.verbose == 2: outputs['particle_files'] = [os.path.abspath( - os.path.join(out_dir, 'particle%d' % i)) - for i in range(self.inputs.n_samples)] + os.path.join(out_dir, 'particle%d' % i)) + for i in range(self.inputs.n_samples)] return outputs def _gen_filename(self, name): @@ -955,7 +955,7 @@ def _list_outputs(self): if isdefined(self.inputs.omatrix2): outputs['lookup_tractspace'] = \ - os.path.abspath(os.path.join(out_dir, 'lookup_tractspace_fdt_matrix2.nii.gz')) + os.path.abspath(os.path.join(out_dir, 'lookup_tractspace_fdt_matrix2.nii.gz')) outputs['matrix2_dot'] = os.path.abspath(os.path.join(out_dir, 'fdt_matrix2.dot')) if isdefined(self.inputs.omatrix3): diff --git a/nipype/interfaces/fsl/tests/test_FILMGLS.py b/nipype/interfaces/fsl/tests/test_FILMGLS.py index 8e55381660..8fe231cf79 100644 --- a/nipype/interfaces/fsl/tests/test_FILMGLS.py +++ b/nipype/interfaces/fsl/tests/test_FILMGLS.py @@ -43,7 +43,7 @@ def test_filmgls(): threshold=dict(usedefault=True, argstr='--thr=%f',), tukey_window=dict(xor=['autocorr_estimate_only', 'fit_armodel', 'tukey_window', 'multitaper_product', 'use_pava', 'autocorr_noestimate'], argstr='--tukey=%d',), use_pava=dict(argstr='--pava',), - ) + ) instance = FILMGLS() if isinstance(instance.inputs, FILMGLSInputSpec): for key, metadata in list(input_map.items()): diff --git a/nipype/interfaces/fsl/tests/test_dti.py b/nipype/interfaces/fsl/tests/test_dti.py index 077bc8c444..2c02481090 100644 --- a/nipype/interfaces/fsl/tests/test_dti.py +++ b/nipype/interfaces/fsl/tests/test_dti.py @@ -99,9 +99,9 @@ def test_dtifit2(): yield assert_equal, dti.cmdline, \ 'dtifit -k %s -o foo.dti.nii -m %s -r %s -b %s -Z 50 -z 10' % (filelist[0], - filelist[1], - filelist[0], - filelist[1]) + filelist[1], + filelist[0], + filelist[1]) clean_directory(outdir, cwd) @@ -380,12 +380,12 @@ def test_Vec_reg(): # test arguments for opt_map opt_map = {'verbose': ('-v', True), - 'helpDoc': ('-h', True), - 'tensor': ('--tensor', True), - 'affineTmat': ('-t Tmat', 'Tmat'), - 'warpFile': ('-w wrpFile', 'wrpFile'), - 'interpolation': ('--interp=sinc', 'sinc'), - 'brainMask': ('-m mask', 'mask')} + 'helpDoc': ('-h', True), + 'tensor': ('--tensor', True), + 'affineTmat': ('-t Tmat', 'Tmat'), + 'warpFile': ('-w wrpFile', 'wrpFile'), + 'interpolation': ('--interp=sinc', 'sinc'), + 'brainMask': ('-m mask', 'mask')} for name, settings in list(opt_map.items()): vrg4 = fsl.VecReg(infile='infile', outfile='outfile', @@ -460,7 +460,7 @@ def test_tbss_skeleton(): # Now we get a command line yield assert_equal, bones.cmdline, \ "tbss_skeleton -i a.nii -p 0.200 b.nii %s b.nii %s" % (Info.standard_image("LowerCingulum_1mm.nii.gz"), - os.path.join(newdir, "b_skeletonised.nii")) + os.path.join(newdir, "b_skeletonised.nii")) # Can we specify a mask? bones.inputs.use_cingulum_mask = Undefined @@ -494,7 +494,7 @@ def test_distancemap(): mapper.inputs.local_max_file = True yield assert_equal, mapper.cmdline, \ "distancemap --out=%s --in=a.nii --localmax=%s" % (os.path.join(newdir, "a_dstmap.nii"), - os.path.join(newdir, "a_lclmax.nii")) + os.path.join(newdir, "a_lclmax.nii")) # And call it whatever we want mapper.inputs.local_max_file = "max.nii" diff --git a/nipype/interfaces/fsl/tests/test_epi.py b/nipype/interfaces/fsl/tests/test_epi.py index 297e2e0429..4f2b0ed2c3 100644 --- a/nipype/interfaces/fsl/tests/test_epi.py +++ b/nipype/interfaces/fsl/tests/test_epi.py @@ -10,7 +10,7 @@ import nibabel as nb from nipype.testing import (assert_equal, assert_not_equal, - assert_raises, skipif) + assert_raises, skipif) import nipype.interfaces.fsl.epi as fsl from nipype.interfaces.fsl import no_fsl diff --git a/nipype/interfaces/fsl/utils.py b/nipype/interfaces/fsl/utils.py index 7d173a4754..c98141dfd1 100644 --- a/nipype/interfaces/fsl/utils.py +++ b/nipype/interfaces/fsl/utils.py @@ -1292,7 +1292,7 @@ def _list_outputs(self): if not isdefined(outputs['out_file']) and \ isdefined(self.inputs.in_file): outputs['out_file'] = self._gen_fname(self.inputs.in_file, - suffix='_sigloss') + suffix='_sigloss') return outputs def _gen_filename(self, name): @@ -1686,7 +1686,7 @@ class ConvertWarpInputSpec(FSLCommandInputSpec): 'of subjects.')) midmat = File(exists=True, argstr="--midmat=%s", - desc="Name of file containing mid-warp-affine transform") + desc="Name of file containing mid-warp-affine transform") warp2 = File(exists=True, argstr='--warp2=%s', desc=('Name of file containing secondary warp-fields/coefficients (after warp1/midmat but before postmat). This could e.g. be a ' diff --git a/nipype/interfaces/io.py b/nipype/interfaces/io.py index 616dced6d9..ed5c0b5f9f 100644 --- a/nipype/interfaces/io.py +++ b/nipype/interfaces/io.py @@ -1156,8 +1156,7 @@ def _run_interface(self, runtime): full_path = os.path.join(curr_dir, infile) self._match_path(full_path) if (self.inputs.unpack_single and - len(self.result['out_paths']) == 1 - ): + len(self.result['out_paths']) == 1): for key, vals in self.result.items(): self.result[key] = vals[0] else: @@ -1578,7 +1577,7 @@ class XNATSinkInputSpec(DynamicTraitedSpec, BaseInterfaceInputSpec): desc=('Option to share the subjects from the original project' 'instead of creating new ones when possible - the created ' 'experiments are then shared back to the original project' - ), + ), usedefault=True) def __setattr__(self, key, value): diff --git a/nipype/interfaces/matlab.py b/nipype/interfaces/matlab.py index 09f6002d55..fe9d4457a6 100644 --- a/nipype/interfaces/matlab.py +++ b/nipype/interfaces/matlab.py @@ -32,7 +32,7 @@ class MatlabInputSpec(CommandLineInputSpec): """ Basic expected inputs to Matlab interface """ script = traits.Str(argstr='-r \"%s;exit\"', desc='m-code to run', - mandatory=True, position=-1) + mandatory=True, position=-1) uses_mcr = traits.Bool(desc='use MCR interface', xor=['nodesktop', 'nosplash', 'single_comp_thread'], @@ -51,7 +51,7 @@ class MatlabInputSpec(CommandLineInputSpec): nohash=True) # non-commandline options mfile = traits.Bool(True, desc='Run m-code using m-file', - usedefault=True) + usedefault=True) script_file = File('pyscript.m', usedefault=True, desc='Name of file to write m-code to') paths = InputMultiPath(Directory(), desc='Paths to add to matlabpath') diff --git a/nipype/interfaces/mrtrix/convert.py b/nipype/interfaces/mrtrix/convert.py index 4a12112538..711ea2107b 100644 --- a/nipype/interfaces/mrtrix/convert.py +++ b/nipype/interfaces/mrtrix/convert.py @@ -118,9 +118,9 @@ def track_gen(track_points): if not n_streams == stream_count: raise HeaderError( 'Expecting %s points, found only %s' % ( - stream_count, n_streams)) + stream_count, n_streams)) iflogger.error('Expecting %s points, found only %s' % ( - stream_count, n_streams)) + stream_count, n_streams)) break pts = np.ndarray( shape=(n_pts, pt_cols), diff --git a/nipype/interfaces/nipy/model.py b/nipype/interfaces/nipy/model.py index 637ec3e6c7..7fba0b26c7 100644 --- a/nipype/interfaces/nipy/model.py +++ b/nipype/interfaces/nipy/model.py @@ -39,8 +39,8 @@ class FitGLMInputSpec(BaseInterfaceInputSpec): "With Derivative' or 'FIR'"), usedefault=True) drift_model = traits.Enum("Cosine", "Polynomial", "Blank", desc=("string that specifies the desired drift " - "model, to be chosen among 'Polynomial', " - "'Cosine', 'Blank'"), usedefault=True) + "model, to be chosen among 'Polynomial', " + "'Cosine', 'Blank'"), usedefault=True) TR = traits.Float(mandatory=True) model = traits.Enum("ar1", "spherical", desc=("autoregressive mode is available only for the " @@ -148,8 +148,8 @@ def _run_interface(self, runtime): if self.inputs.normalize_design_matrix: for i in range(len(self._reg_names) - 1): design_matrix[:, i] = ((design_matrix[:, i] - - design_matrix[:, i].mean()) / - design_matrix[:, i].std()) + design_matrix[:, i].mean()) / + design_matrix[:, i].std()) if self.inputs.plot_design_matrix: import pylab diff --git a/nipype/interfaces/nitime/tests/test_nitime.py b/nipype/interfaces/nitime/tests/test_nitime.py index c55c2b1aa9..a5bfe177bf 100644 --- a/nipype/interfaces/nitime/tests/test_nitime.py +++ b/nipype/interfaces/nitime/tests/test_nitime.py @@ -63,8 +63,8 @@ def test_coherence_analysis(): T.metadata['roi'] = roi_names C = nta.CoherenceAnalyzer(T, method=dict(this_method='welch', - NFFT=CA.inputs.NFFT, - n_overlap=CA.inputs.n_overlap)) + NFFT=CA.inputs.NFFT, + n_overlap=CA.inputs.n_overlap)) freq_idx = np.where((C.frequencies > CA.inputs.frequency_range[0]) * (C.frequencies < CA.inputs.frequency_range[1]))[0] diff --git a/nipype/interfaces/spm/utils.py b/nipype/interfaces/spm/utils.py index 5c6da67080..29682171cc 100644 --- a/nipype/interfaces/spm/utils.py +++ b/nipype/interfaces/spm/utils.py @@ -42,9 +42,9 @@ def _list_outputs(self): class CalcCoregAffineInputSpec(SPMCommandInputSpec): target = File(exists=True, mandatory=True, - desc='target for generating affine transform') + desc='target for generating affine transform') moving = File(exists=True, mandatory=True, copyfile=False, - desc='volume transform can be applied to register with target') + desc='volume transform can be applied to register with target') mat = File(desc='Filename used to store affine matrix') invmat = File(desc='Filename used to store inverse affine matrix') @@ -109,9 +109,9 @@ def _make_matlab_command(self, _): M = inv(M); save('%s','M') """ % (self.inputs.target, - self.inputs.moving, - self.inputs.mat, - self.inputs.invmat) + self.inputs.moving, + self.inputs.mat, + self.inputs.invmat) return script def _list_outputs(self): @@ -123,9 +123,9 @@ def _list_outputs(self): class ApplyTransformInputSpec(SPMCommandInputSpec): in_file = File(exists=True, mandatory=True, copyfile=True, - desc='file to apply transform to, (only updates header)') + desc='file to apply transform to, (only updates header)') mat = File(exists=True, mandatory=True, - desc='file holding transform to apply') + desc='file holding transform to apply') out_file = File(desc="output file name for transformed data", genfile=True) @@ -167,8 +167,8 @@ def _make_matlab_command(self, _): spm_write_vol(V,X); """ % (self.inputs.in_file, - self.inputs.out_file, - self.inputs.mat) + self.inputs.out_file, + self.inputs.mat) # img_space = spm_get_space(infile); # spm_get_space(infile, transform.M * img_space); return script @@ -188,9 +188,9 @@ def _gen_outfilename(self): class ResliceInputSpec(SPMCommandInputSpec): in_file = File(exists=True, mandatory=True, - desc='file to apply transform to, (only updates header)') + desc='file to apply transform to, (only updates header)') space_defining = File(exists=True, mandatory=True, - desc='Volume defining space to slice in_file into') + desc='Volume defining space to slice in_file into') interp = traits.Range(low=0, high=7, usedefault=True, desc='degree of b-spline used for interpolation' @@ -223,8 +223,8 @@ def _make_matlab_command(self, _): invols = spm_vol(infiles); spm_reslice(invols, flags); """ % (self.inputs.interp, - self.inputs.space_defining, - self.inputs.in_file) + self.inputs.space_defining, + self.inputs.in_file) return script def _list_outputs(self): diff --git a/nipype/interfaces/tests/test_io.py b/nipype/interfaces/tests/test_io.py index 495ebbf773..8b5df0a7ce 100644 --- a/nipype/interfaces/tests/test_io.py +++ b/nipype/interfaces/tests/test_io.py @@ -201,7 +201,7 @@ def test_datasink_substitutions(): ds.run() yield assert_equal, \ sorted([os.path.basename(x) for - x in glob.glob(os.path.join(outdir, '*'))]), \ + x in glob.glob(os.path.join(outdir, '*'))]), \ ['!-yz-b.n', 'ABABAB.n'] # so we got re used 2nd and both patterns shutil.rmtree(indir) shutil.rmtree(outdir) @@ -250,7 +250,7 @@ def test_s3datasink_substitutions(): ds.run() yield assert_equal, \ sorted([os.path.basename(x) for - x in glob.glob(os.path.join(outdir, '*'))]), \ + x in glob.glob(os.path.join(outdir, '*'))]), \ ['!-yz-b.n', 'ABABAB.n'] # so we got re used 2nd and both patterns bkt = conn.get_bucket(ds.inputs.bucket) diff --git a/nipype/interfaces/traits_extension.py b/nipype/interfaces/traits_extension.py index 1a6e804f05..49af1db164 100644 --- a/nipype/interfaces/traits_extension.py +++ b/nipype/interfaces/traits_extension.py @@ -35,7 +35,7 @@ class BaseFile (traits.BaseStr): info_text = 'a file name' def __init__(self, value='', filter=None, auto_set=False, - entries=0, exists=False, **metadata): + entries=0, exists=False, **metadata): """ Creates a File trait. Parameters @@ -86,7 +86,7 @@ class File (BaseFile): """ def __init__(self, value='', filter=None, auto_set=False, - entries=0, exists=False, **metadata): + entries=0, exists=False, **metadata): """ Creates a File trait. Parameters @@ -112,7 +112,7 @@ def __init__(self, value='', filter=None, auto_set=False, fast_validate = (11, str) super(File, self).__init__(value, filter, auto_set, entries, exists, - **metadata) + **metadata) # ------------------------------------------------------------------------------- # 'BaseDirectory' and 'Directory' traits: @@ -127,7 +127,7 @@ class BaseDirectory (traits.BaseStr): info_text = 'a directory name' def __init__(self, value='', auto_set=False, entries=0, - exists=False, **metadata): + exists=False, **metadata): """ Creates a BaseDirectory trait. Parameters @@ -175,7 +175,7 @@ class Directory (BaseDirectory): """ def __init__(self, value='', auto_set=False, entries=0, - exists=False, **metadata): + exists=False, **metadata): """ Creates a Directory trait. Parameters @@ -199,7 +199,7 @@ def __init__(self, value='', auto_set=False, entries=0, self.fast_validate = (11, str) super(Directory, self).__init__(value, auto_set, entries, exists, - **metadata) + **metadata) """ diff --git a/nipype/pipeline/plugins/base.py b/nipype/pipeline/plugins/base.py index 511548b81e..7d9ae77c2b 100644 --- a/nipype/pipeline/plugins/base.py +++ b/nipype/pipeline/plugins/base.py @@ -233,7 +233,7 @@ def run(self, graph, config, updatehash=False): # setup polling - TODO: change to threaded model notrun = [] while np.any(self.proc_done == False) | \ - np.any(self.proc_pending == True): + np.any(self.proc_pending == True): toappend = [] # trigger callbacks for any pending results while self.pending_tasks: @@ -371,12 +371,9 @@ def _send_procs_to_workers(self, updatehash=False, graph=None): hash_exists, _, _, _ = self.procs[ jobid].hash_exists() logger.debug('Hash exists %s' % str(hash_exists)) - if (hash_exists and - (self.procs[jobid].overwrite == False or - (self.procs[jobid].overwrite == None and - not self.procs[jobid]._interface.always_run) - ) - ): + if (hash_exists and (self.procs[jobid].overwrite is False or + (self.procs[jobid].overwrite is None and not + self.procs[jobid]._interface.always_run))): continue_with_submission = False self._task_finished_cb(jobid) self._remove_node_dirs() diff --git a/nipype/pipeline/plugins/dagman.py b/nipype/pipeline/plugins/dagman.py index 7b9ca27282..4f89a13ce6 100644 --- a/nipype/pipeline/plugins/dagman.py +++ b/nipype/pipeline/plugins/dagman.py @@ -114,9 +114,9 @@ def _submit_graph(self, pyfiles, dependencies, nodes): "wrapper_args"]) # add required slots to the template template = '%s\n%s\n%s\nqueue\n' % ( - '%(initial_specs)s', - template, - '%(override_specs)s') + '%(initial_specs)s', + template, + '%(override_specs)s') batch_dir, name = os.path.split(pyscript) name = '.'.join(name.split('.')[:-1]) specs = dict( @@ -126,13 +126,13 @@ def _submit_graph(self, pyfiles, dependencies, nodes): nodescript=pyscript, basename=os.path.join(batch_dir, name), override_specs=override_specs - ) + ) if wrapper_cmd is not None: specs['executable'] = wrapper_cmd specs['nodescript'] = \ '%s %s %s' % (wrapper_args % specs, # give access to variables - sys.executable, - pyscript) + sys.executable, + pyscript) submitspec = template % specs # write submit spec for this job submitfile = os.path.join(batch_dir, diff --git a/nipype/pipeline/plugins/ipythonx.py b/nipype/pipeline/plugins/ipythonx.py index db7c467d60..7eca73e0ea 100644 --- a/nipype/pipeline/plugins/ipythonx.py +++ b/nipype/pipeline/plugins/ipythonx.py @@ -65,7 +65,7 @@ def _submit_job(self, node, updatehash=False): """ task = self.ipyclient.StringTask(cmdstr, push=dict(task=node, - updatehash=updatehash), + updatehash=updatehash), pull=['result', 'traceback']) return self.taskclient.run(task, block=False) diff --git a/nipype/pipeline/plugins/sgegraph.py b/nipype/pipeline/plugins/sgegraph.py index 10fde4d0e2..efc77ce3e8 100644 --- a/nipype/pipeline/plugins/sgegraph.py +++ b/nipype/pipeline/plugins/sgegraph.py @@ -17,9 +17,9 @@ def node_completed_status(checknode): """ """ TODO: place this in the base.py file and refactor """ node_state_does_not_require_overwrite = (checknode.overwrite is False or - (checknode.overwrite is None and not - checknode._interface.always_run) - ) + (checknode.overwrite is None and not + checknode._interface.always_run) + ) hash_exists = False try: hash_exists, _, _, _ = checknode.hash_exists() diff --git a/nipype/pipeline/plugins/slurmgraph.py b/nipype/pipeline/plugins/slurmgraph.py index 0733412d38..3c0bc62aaf 100644 --- a/nipype/pipeline/plugins/slurmgraph.py +++ b/nipype/pipeline/plugins/slurmgraph.py @@ -17,9 +17,9 @@ def node_completed_status(checknode): """ """ TODO: place this in the base.py file and refactor """ node_state_does_not_require_overwrite = (checknode.overwrite is False or - (checknode.overwrite is None and not - checknode._interface.always_run) - ) + (checknode.overwrite is None and not + checknode._interface.always_run) + ) hash_exists = False try: hash_exists, _, _, _ = checknode.hash_exists() diff --git a/nipype/utils/config.py b/nipype/utils/config.py index 12e7e4cae0..bd7ab032ef 100644 --- a/nipype/utils/config.py +++ b/nipype/utils/config.py @@ -87,11 +87,11 @@ def __init__(self, *args, **kwargs): if os.path.exists(old_config_file): if os.path.exists(new_config_file): msg = ("Detected presence of both old (%s, used by versions " - "< 0.5.2) and new (%s) config files. This version will " - "proceed with the new one. We advise to merge settings " - "and remove old config file if you are not planning to " - "use previous releases of nipype.") % (old_config_file, - new_config_file) + "< 0.5.2) and new (%s) config files. This version will " + "proceed with the new one. We advise to merge settings " + "and remove old config file if you are not planning to " + "use previous releases of nipype.") % (old_config_file, + new_config_file) warn(msg) else: warn("Moving old config file from: %s to %s" % (old_config_file, diff --git a/nipype/utils/docparse.py b/nipype/utils/docparse.py index c08cbdcad0..d95adb40bf 100644 --- a/nipype/utils/docparse.py +++ b/nipype/utils/docparse.py @@ -288,8 +288,8 @@ def _parse_doc(doc, style=['--']): for line in doclist: linelist = line.split() flag = [item for i, item in enumerate(linelist) if i < 2 and - any([item.startswith(s) for s in style]) and - len(item) > 1] + any([item.startswith(s) for s in style]) and + len(item) > 1] if flag: if len(flag) == 1: style_idx = [flag[0].startswith(s) for s in style].index(True) diff --git a/nipype/utils/nipype2boutiques.py b/nipype/utils/nipype2boutiques.py index e0931db165..49fc1d755d 100644 --- a/nipype/utils/nipype2boutiques.py +++ b/nipype/utils/nipype2boutiques.py @@ -236,10 +236,10 @@ def get_unique_value(type, id): assuming id is unique. ''' return { - "File": os.path.abspath(create_tempfile()), - "Boolean": True, - "Number": abs(hash(id)), # abs in case input param must be positive... - "String": id + "File": os.path.abspath(create_tempfile()), + "Boolean": True, + "Number": abs(hash(id)), # abs in case input param must be positive... + "String": id }[type] diff --git a/nipype/workflows/dmri/camino/connectivity_mapping.py b/nipype/workflows/dmri/camino/connectivity_mapping.py index 7cbb1ba996..a0838b4468 100644 --- a/nipype/workflows/dmri/camino/connectivity_mapping.py +++ b/nipype/workflows/dmri/camino/connectivity_mapping.py @@ -346,7 +346,7 @@ def create_connectivity_pipeline(name="connectivity"): mapping.connect([(dtifit, fa, [("tensor_fitted", "in_file")])]) mapping.connect([(fa, analyzeheader_fa, [("fa", "in_file")])]) mapping.connect([(inputnode_within, analyzeheader_fa, [(('dwi', get_vox_dims), 'voxel_dims'), - (('dwi', get_data_dims), 'data_dims')])]) + (('dwi', get_data_dims), 'data_dims')])]) mapping.connect([(fa, fa2nii, [('fa', 'data_file')])]) mapping.connect([(inputnode_within, fa2nii, [(('dwi', get_affine), 'affine')])]) mapping.connect([(analyzeheader_fa, fa2nii, [('header', 'header_file')])]) @@ -354,7 +354,7 @@ def create_connectivity_pipeline(name="connectivity"): mapping.connect([(dtifit, trace, [("tensor_fitted", "in_file")])]) mapping.connect([(trace, analyzeheader_trace, [("trace", "in_file")])]) mapping.connect([(inputnode_within, analyzeheader_trace, [(('dwi', get_vox_dims), 'voxel_dims'), - (('dwi', get_data_dims), 'data_dims')])]) + (('dwi', get_data_dims), 'data_dims')])]) mapping.connect([(trace, trace2nii, [('trace', 'data_file')])]) mapping.connect([(inputnode_within, trace2nii, [(('dwi', get_affine), 'affine')])]) mapping.connect([(analyzeheader_trace, trace2nii, [('header', 'header_file')])]) @@ -371,7 +371,7 @@ def create_connectivity_pipeline(name="connectivity"): (camino2trackvis, trk2camino, [['trackvis', 'in_file']]) ]) mapping.connect([(inputnode_within, camino2trackvis, [(('dwi', get_vox_dims), 'voxel_dims'), - (('dwi', get_data_dims), 'data_dims')])]) + (('dwi', get_data_dims), 'data_dims')])]) """ Here the CMTK connectivity mapping nodes are connected. @@ -451,16 +451,16 @@ def create_connectivity_pipeline(name="connectivity"): inputnode = pe.Node(interface=util.IdentityInterface(fields=["subject_id", "dwi", "bvecs", "bvals", "subjects_dir", "resolution_network_file"]), name="inputnode") outputnode = pe.Node(interface=util.IdentityInterface(fields=["fa", - "struct", - "trace", - "tracts", - "connectome", - "cmatrix", - "networks", - "rois", - "mean_fiber_length", - "fiber_length_std", - "tensors"]), + "struct", + "trace", + "tracts", + "connectome", + "cmatrix", + "networks", + "rois", + "mean_fiber_length", + "fiber_length_std", + "tensors"]), name="outputnode") connectivity = pe.Workflow(name="connectivity") @@ -485,6 +485,6 @@ def create_connectivity_pipeline(name="connectivity"): ("mri_convert_Brain.out_file", "struct"), ("trace2nii.nifti_file", "trace"), ("dtifit.tensor_fitted", "tensors")]) - ]) + ]) return connectivity diff --git a/nipype/workflows/dmri/camino/diffusion.py b/nipype/workflows/dmri/camino/diffusion.py index 3e176491f0..1c5c174e2d 100644 --- a/nipype/workflows/dmri/camino/diffusion.py +++ b/nipype/workflows/dmri/camino/diffusion.py @@ -153,7 +153,7 @@ def create_camino_dti_pipeline(name="dtiproc"): tractography.connect([(inputnode1, image2voxel, [("dwi", "in_file")]), (inputnode1, fsl2scheme, [("bvecs", "bvec_file"), ("bvals", "bval_file")]) - ]) + ]) """ Tensor fitting @@ -161,7 +161,7 @@ def create_camino_dti_pipeline(name="dtiproc"): tractography.connect([(image2voxel, dtifit, [['voxel_order', 'in_file']]), (fsl2scheme, dtifit, [['scheme', 'scheme_file']]) - ]) + ]) """ Workflow for applying DT streamline tractogpahy @@ -198,7 +198,7 @@ def create_camino_dti_pipeline(name="dtiproc"): tractography.connect([(dtifit, fa, [("tensor_fitted", "in_file")])]) tractography.connect([(fa, analyzeheader_fa, [("fa", "in_file")])]) tractography.connect([(inputnode1, analyzeheader_fa, [(('dwi', get_vox_dims), 'voxel_dims'), - (('dwi', get_data_dims), 'data_dims')])]) + (('dwi', get_data_dims), 'data_dims')])]) tractography.connect([(fa, fa2nii, [('fa', 'data_file')])]) tractography.connect([(inputnode1, fa2nii, [(('dwi', get_affine), 'affine')])]) tractography.connect([(analyzeheader_fa, fa2nii, [('header', 'header_file')])]) @@ -206,7 +206,7 @@ def create_camino_dti_pipeline(name="dtiproc"): tractography.connect([(dtifit, trace, [("tensor_fitted", "in_file")])]) tractography.connect([(trace, analyzeheader_trace, [("trace", "in_file")])]) tractography.connect([(inputnode1, analyzeheader_trace, [(('dwi', get_vox_dims), 'voxel_dims'), - (('dwi', get_data_dims), 'data_dims')])]) + (('dwi', get_data_dims), 'data_dims')])]) tractography.connect([(trace, trace2nii, [('trace', 'data_file')])]) tractography.connect([(inputnode1, trace2nii, [(('dwi', get_affine), 'affine')])]) tractography.connect([(analyzeheader_trace, trace2nii, [('header', 'header_file')])]) @@ -216,18 +216,18 @@ def create_camino_dti_pipeline(name="dtiproc"): tractography.connect([(trackpico, cam2trk_pico, [('tracked', 'in_file')])]) tractography.connect([(trackdt, cam2trk_dt, [('tracked', 'in_file')])]) tractography.connect([(inputnode1, cam2trk_pico, [(('dwi', get_vox_dims), 'voxel_dims'), - (('dwi', get_data_dims), 'data_dims')])]) + (('dwi', get_data_dims), 'data_dims')])]) tractography.connect([(inputnode1, cam2trk_dt, [(('dwi', get_vox_dims), 'voxel_dims'), - (('dwi', get_data_dims), 'data_dims')])]) + (('dwi', get_data_dims), 'data_dims')])]) inputnode = pe.Node(interface=util.IdentityInterface(fields=["dwi", "bvecs", "bvals"]), name="inputnode") outputnode = pe.Node(interface=util.IdentityInterface(fields=["fa", - "trace", - "tracts_pico", - "tracts_dt", - "tensors"]), + "trace", + "tracts_pico", + "tracts_dt", + "tensors"]), name="outputnode") workflow = pe.Workflow(name=name) @@ -242,6 +242,6 @@ def create_camino_dti_pipeline(name="dtiproc"): ("fa2nii.nifti_file", "fa"), ("trace2nii.nifti_file", "trace"), ("dtifit.tensor_fitted", "tensors")]) - ]) + ]) return workflow diff --git a/nipype/workflows/dmri/camino/group_connectivity.py b/nipype/workflows/dmri/camino/group_connectivity.py index e61d1273ca..1f323bda3d 100644 --- a/nipype/workflows/dmri/camino/group_connectivity.py +++ b/nipype/workflows/dmri/camino/group_connectivity.py @@ -83,7 +83,7 @@ def create_group_connectivity_pipeline(group_list, group_id, data_dir, subjects_ l1pipeline.connect([(datasource, conmapper, [("dwi", "inputnode.dwi"), ("bvals", "inputnode.bvals"), ("bvecs", "inputnode.bvecs"), - ])]) + ])]) l1pipeline.connect([(conmapper, datasink, [("outputnode.connectome", "@l1output.cff"), ("outputnode.fa", "@l1output.fa"), ("outputnode.tracts", "@l1output.tracts"), diff --git a/nipype/workflows/dmri/connectivity/group_connectivity.py b/nipype/workflows/dmri/connectivity/group_connectivity.py index f0c3e7c67b..e4651febd9 100644 --- a/nipype/workflows/dmri/connectivity/group_connectivity.py +++ b/nipype/workflows/dmri/connectivity/group_connectivity.py @@ -129,9 +129,9 @@ def create_merge_networks_by_group_workflow(group_list, group_id, data_dir, subj [(group_infosource, l2infosource, [('group_id', 'group_id')])]) l2pipeline.connect([ - (l2infosource, l2source, [('group_id', 'group_id')]), - (l2source, l2inputnode, [('CFFfiles', 'CFFfiles')]), - ]) + (l2infosource, l2source, [('group_id', 'group_id')]), + (l2source, l2inputnode, [('CFFfiles', 'CFFfiles')]), + ]) l2pipeline.connect( [(l2inputnode, MergeCNetworks, [('CFFfiles', 'in_files')])]) @@ -210,14 +210,14 @@ def create_merge_network_results_by_group_workflow(group_list, group_id, data_di [(group_infosource, l2infosource, [('group_id', 'group_id')])]) l2pipeline.connect([ - (l2infosource, l2source, [('group_id', 'group_id')]), - (l2source, l2inputnode, [('CFFfiles', 'CFFfiles')]), - (l2source, l2inputnode, [( - 'CSVmatrices', 'CSVmatrices')]), - (l2source, l2inputnode, [('CSVnodal', 'CSVnodal')]), - (l2source, l2inputnode, [('CSVglobal', 'CSVglobal')]), - (l2source, l2inputnode, [('CSVfibers', 'CSVfibers')]), - ]) + (l2infosource, l2source, [('group_id', 'group_id')]), + (l2source, l2inputnode, [('CFFfiles', 'CFFfiles')]), + (l2source, l2inputnode, [( + 'CSVmatrices', 'CSVmatrices')]), + (l2source, l2inputnode, [('CSVnodal', 'CSVnodal')]), + (l2source, l2inputnode, [('CSVglobal', 'CSVglobal')]), + (l2source, l2inputnode, [('CSVfibers', 'CSVfibers')]), + ]) l2pipeline.connect( [(l2inputnode, MergeCNetworks, [('CFFfiles', 'in_files')])]) @@ -337,9 +337,9 @@ def create_merge_group_networks_workflow(group_list, data_dir, subjects_dir, out l3pipeline = pe.Workflow(name="l3output") l3pipeline.base_dir = output_dir l3pipeline.connect([ - (l3infosource, l3source, [('group_id', 'group_id')]), - (l3source, l3inputnode, [('CFFfiles', 'Group_CFFs')]), - ]) + (l3infosource, l3source, [('group_id', 'group_id')]), + (l3source, l3inputnode, [('CFFfiles', 'Group_CFFs')]), + ]) l3pipeline.connect( [(l3inputnode, MergeCNetworks_grp, [('Group_CFFs', 'in_files')])]) @@ -400,12 +400,12 @@ def create_merge_group_network_results_workflow(group_list, data_dir, subjects_d l3pipeline = pe.Workflow(name="l3output") l3pipeline.base_dir = output_dir l3pipeline.connect([ - (l3infosource, l3source, [('group_id', 'group_id')]), - (l3source, l3inputnode, [('CFFfiles', 'Group_CFFs')]), - (l3source, l3inputnode, [('CSVnodemetrics', 'Group_CSVnodemetrics')]), - (l3source, l3inputnode, [('CSVglobalmetrics', 'Group_CSVglobalmetrics')]), - (l3source, l3inputnode, [('CSVmatrices', 'Group_CSVmatrices')]), - ]) + (l3infosource, l3source, [('group_id', 'group_id')]), + (l3source, l3inputnode, [('CFFfiles', 'Group_CFFs')]), + (l3source, l3inputnode, [('CSVnodemetrics', 'Group_CSVnodemetrics')]), + (l3source, l3inputnode, [('CSVglobalmetrics', 'Group_CSVglobalmetrics')]), + (l3source, l3inputnode, [('CSVmatrices', 'Group_CSVmatrices')]), + ]) l3pipeline.connect([(l3inputnode, MergeCNetworks_grp, [('Group_CFFs', 'in_files')])]) l3pipeline.connect([(MergeCNetworks_grp, l3datasink, [('connectome_file', '@l3output')])]) @@ -494,17 +494,17 @@ def create_average_networks_by_group_workflow(group_list, data_dir, subjects_dir l4pipeline = pe.Workflow(name="l4output") l4pipeline.base_dir = output_dir l4pipeline.connect([ - (l4infosource, l4source_grp1, [('group_id1', 'group_id')]), - (l4infosource, l4source_grp2, [('group_id2', 'group_id')]), - (l4source_grp1, l4inputnode, [('CMatrices', 'CMatrices_grp1')]), - (l4source_grp2, l4inputnode, [('CMatrices', 'CMatrices_grp2')]), - (l4source_grp1, l4inputnode, [('networks', 'networks_grp1')]), - (l4source_grp2, l4inputnode, [('networks', 'networks_grp2')]), - (l4source_grp1, l4inputnode, [('fibmean', 'fibmean_grp1')]), - (l4source_grp2, l4inputnode, [('fibmean', 'fibmean_grp2')]), - (l4source_grp1, l4inputnode, [('fibdev', 'fibdev_grp1')]), - (l4source_grp2, l4inputnode, [('fibdev', 'fibdev_grp2')]), - ]) + (l4infosource, l4source_grp1, [('group_id1', 'group_id')]), + (l4infosource, l4source_grp2, [('group_id2', 'group_id')]), + (l4source_grp1, l4inputnode, [('CMatrices', 'CMatrices_grp1')]), + (l4source_grp2, l4inputnode, [('CMatrices', 'CMatrices_grp2')]), + (l4source_grp1, l4inputnode, [('networks', 'networks_grp1')]), + (l4source_grp2, l4inputnode, [('networks', 'networks_grp2')]), + (l4source_grp1, l4inputnode, [('fibmean', 'fibmean_grp1')]), + (l4source_grp2, l4inputnode, [('fibmean', 'fibmean_grp2')]), + (l4source_grp1, l4inputnode, [('fibdev', 'fibdev_grp1')]), + (l4source_grp2, l4inputnode, [('fibdev', 'fibdev_grp2')]), + ]) l4pipeline.connect([(l4inputnode, average_networks_grp1, [('networks_grp1', 'in_files')])]) l4pipeline.connect([(l4infosource, average_networks_grp1, [('group_id1', 'group_id')])]) diff --git a/nipype/workflows/dmri/connectivity/nx.py b/nipype/workflows/dmri/connectivity/nx.py index 804f77ec84..4fe2f89141 100644 --- a/nipype/workflows/dmri/connectivity/nx.py +++ b/nipype/workflows/dmri/connectivity/nx.py @@ -83,7 +83,7 @@ def create_networkx_pipeline(name="networkx", extra_column_heading="subject"): pipeline.connect([(ntwkMetrics, mergeNetworks, [("gpickled_network_files", "in2")])]) outputnode = pe.Node(interface=util.IdentityInterface(fields=["network_files", - "csv_files", "matlab_files", "node_csv", "global_csv"]), + "csv_files", "matlab_files", "node_csv", "global_csv"]), name="outputnode") pipeline.connect([(MergeCSVFiles_node, outputnode, [("csv_file", "node_csv")])]) diff --git a/nipype/workflows/dmri/dipy/denoise.py b/nipype/workflows/dmri/dipy/denoise.py index 6519584783..183756a1cc 100644 --- a/nipype/workflows/dmri/dipy/denoise.py +++ b/nipype/workflows/dmri/dipy/denoise.py @@ -30,18 +30,18 @@ def nlmeans_pipeline(name='Denoise', name='outputnode') nmask = pe.Node(niu.Function(input_names=['in_file', 'in_mask'], - output_names=['out_file'], function=bg_mask), + output_names=['out_file'], function=bg_mask), name='NoiseMsk') nlmeans = pe.Node(dipy.Denoise(**params), name='NLMeans') wf = pe.Workflow(name=name) wf.connect([ - (inputnode, nmask, [('in_file', 'in_file'), - ('in_mask', 'in_mask')]), - (inputnode, nlmeans, [('in_file', 'in_file'), - ('in_mask', 'in_mask')]), - (nmask, nlmeans, [('out_file', 'noise_mask')]), - (nlmeans, outputnode, [('out_file', 'out_file')]) + (inputnode, nmask, [('in_file', 'in_file'), + ('in_mask', 'in_mask')]), + (inputnode, nlmeans, [('in_file', 'in_file'), + ('in_mask', 'in_mask')]), + (nmask, nlmeans, [('out_file', 'noise_mask')]), + (nlmeans, outputnode, [('out_file', 'out_file')]) ]) return wf diff --git a/nipype/workflows/dmri/fsl/epi.py b/nipype/workflows/dmri/fsl/epi.py index 01a454f82d..b8d3696db0 100644 --- a/nipype/workflows/dmri/fsl/epi.py +++ b/nipype/workflows/dmri/fsl/epi.py @@ -89,7 +89,7 @@ def create_dmri_preprocessing(name='dMRI_preprocessing', use_fieldmap=True, fiel if use_fieldmap: # we have a fieldmap, so lets use it (yay!) susceptibility = create_epidewarp_pipeline( - fieldmap_registration=fieldmap_registration) + fieldmap_registration=fieldmap_registration) pipeline.connect([ (inputnode, motion, [('in_file', 'inputnode.in_file'), @@ -250,14 +250,14 @@ def create_eddy_correct_pipeline(name='eddy_correct'): name='outputnode') pipeline.connect([ - (inputnode, split, [('in_file', 'in_file')]), - (split, pick_ref, [('out_files', 'inlist')]), - (inputnode, pick_ref, [('ref_num', 'index')]), - (split, coregistration, [('out_files', 'in_file')]), - (pick_ref, coregistration, [('out', 'reference')]), - (coregistration, merge, [('out_file', 'in_files')]), - (merge, outputnode, [('merged_file', 'eddy_corrected')]) - ]) + (inputnode, split, [('in_file', 'in_file')]), + (split, pick_ref, [('out_files', 'inlist')]), + (inputnode, pick_ref, [('ref_num', 'index')]), + (split, coregistration, [('out_files', 'in_file')]), + (pick_ref, coregistration, [('out', 'reference')]), + (coregistration, merge, [('out_file', 'in_files')]), + (merge, outputnode, [('merged_file', 'eddy_corrected')]) + ]) return pipeline @@ -366,27 +366,27 @@ def fieldmap_correction(name='fieldmap_correction', nocheck=False): name='outputnode') pipeline.connect([ - (inputnode, select_mag, [('fieldmap_mag', 'in_file')]), - (inputnode, fslprep, [('fieldmap_pha', 'in_phase'), ('te_diff', 'delta_TE')]), - (inputnode, mask_mag, [('in_mask', 'mask_file')]), - (select_mag, mask_mag, [('roi_file', 'in_file')]), - (mask_mag, fslprep, [('out_file', 'in_magnitude')]), - (fslprep, vsm, [('out_fieldmap', 'phasemap_in_file')]), - (inputnode, vsm, [('fieldmap_mag', 'in_file'), - ('encoding_direction', 'unwarp_direction'), - (('te_diff', _ms2sec), 'asym_se_time'), - ('vsm_sigma', 'smooth2d'), - (('epi_echospacing', _ms2sec), 'dwell_time')]), - (mask_mag, vsm, [('out_file', 'mask_file')]), - (inputnode, dwi_split, [('in_file', 'in_file')]), - (dwi_split, dwi_applyxfm, [('out_files', 'in_file')]), - (mask_mag, dwi_applyxfm, [('out_file', 'mask_file')]), - (vsm, dwi_applyxfm, [('shift_out_file', 'shift_in_file')]), - (inputnode, dwi_applyxfm, [('encoding_direction', 'unwarp_direction')]), - (dwi_applyxfm, dwi_merge, [('unwarped_file', 'in_files')]), - (dwi_merge, outputnode, [('merged_file', 'epi_corrected')]), - (vsm, outputnode, [('shift_out_file', 'out_vsm')]) - ]) + (inputnode, select_mag, [('fieldmap_mag', 'in_file')]), + (inputnode, fslprep, [('fieldmap_pha', 'in_phase'), ('te_diff', 'delta_TE')]), + (inputnode, mask_mag, [('in_mask', 'mask_file')]), + (select_mag, mask_mag, [('roi_file', 'in_file')]), + (mask_mag, fslprep, [('out_file', 'in_magnitude')]), + (fslprep, vsm, [('out_fieldmap', 'phasemap_in_file')]), + (inputnode, vsm, [('fieldmap_mag', 'in_file'), + ('encoding_direction', 'unwarp_direction'), + (('te_diff', _ms2sec), 'asym_se_time'), + ('vsm_sigma', 'smooth2d'), + (('epi_echospacing', _ms2sec), 'dwell_time')]), + (mask_mag, vsm, [('out_file', 'mask_file')]), + (inputnode, dwi_split, [('in_file', 'in_file')]), + (dwi_split, dwi_applyxfm, [('out_files', 'in_file')]), + (mask_mag, dwi_applyxfm, [('out_file', 'mask_file')]), + (vsm, dwi_applyxfm, [('shift_out_file', 'shift_in_file')]), + (inputnode, dwi_applyxfm, [('encoding_direction', 'unwarp_direction')]), + (dwi_applyxfm, dwi_merge, [('unwarped_file', 'in_files')]), + (dwi_merge, outputnode, [('merged_file', 'epi_corrected')]), + (vsm, outputnode, [('shift_out_file', 'out_vsm')]) + ]) return pipeline @@ -444,12 +444,12 @@ def topup_correction(name='topup_correction'): ) outputnode = pe.Node(niu.IdentityInterface( - fields=['out_fieldcoef', - 'out_movpar', - 'out_enc_file', - 'epi_corrected' - ]), name='outputnode' - ) + fields=['out_fieldcoef', + 'out_movpar', + 'out_enc_file', + 'epi_corrected' + ]), name='outputnode' + ) b0_dir = pe.Node(fsl.ExtractROI(t_size=1), name='b0_1') b0_rev = pe.Node(fsl.ExtractROI(t_size=1), name='b0_2') @@ -461,21 +461,21 @@ def topup_correction(name='topup_correction'): applytopup = pe.Node(fsl.ApplyTOPUP(in_index=[1, 2]), name='applytopup') pipeline.connect([ - (inputnode, b0_dir, [('in_file_dir', 'in_file'), ('ref_num', 't_min')]), - (inputnode, b0_rev, [('in_file_rev', 'in_file'), ('ref_num', 't_min')]), - (inputnode, combin2, [('in_file_dir', 'in1'), ('in_file_rev', 'in2')]), - (b0_dir, combin, [('roi_file', 'in1')]), - (b0_rev, combin, [('roi_file', 'in2')]), - (combin, merged, [('out', 'in_files')]), - (merged, topup, [('merged_file', 'in_file')]), - (inputnode, topup, [('encoding_direction', 'encoding_direction'), ('readout_times', 'readout_times')]), - (topup, applytopup, [('out_fieldcoef', 'in_topup_fieldcoef'), ('out_movpar', 'in_topup_movpar'), - ('out_enc_file', 'encoding_file')]), - (combin2, applytopup, [('out', 'in_files')]), - (topup, outputnode, [('out_fieldcoef', 'out_fieldcoef'), ('out_movpar', 'out_movpar'), - ('out_enc_file', 'out_enc_file')]), - (applytopup, outputnode, [('out_corrected', 'epi_corrected')]) - ]) + (inputnode, b0_dir, [('in_file_dir', 'in_file'), ('ref_num', 't_min')]), + (inputnode, b0_rev, [('in_file_rev', 'in_file'), ('ref_num', 't_min')]), + (inputnode, combin2, [('in_file_dir', 'in1'), ('in_file_rev', 'in2')]), + (b0_dir, combin, [('roi_file', 'in1')]), + (b0_rev, combin, [('roi_file', 'in2')]), + (combin, merged, [('out', 'in_files')]), + (merged, topup, [('merged_file', 'in_file')]), + (inputnode, topup, [('encoding_direction', 'encoding_direction'), ('readout_times', 'readout_times')]), + (topup, applytopup, [('out_fieldcoef', 'in_topup_fieldcoef'), ('out_movpar', 'in_topup_movpar'), + ('out_enc_file', 'encoding_file')]), + (combin2, applytopup, [('out', 'in_files')]), + (topup, outputnode, [('out_fieldcoef', 'out_fieldcoef'), ('out_movpar', 'out_movpar'), + ('out_enc_file', 'out_enc_file')]), + (applytopup, outputnode, [('out_corrected', 'epi_corrected')]) + ]) return pipeline @@ -641,26 +641,26 @@ def create_epidewarp_pipeline(name='epidewarp', fieldmap_registration=False): interp='nearestneighbour'), name='msk_apply_xfm') pipeline.connect([ - (inputnode, select_epi, [('in_file', 'in_file'), ('ref_num', 't_min')]), - (select_epi, vsm_reg, [('roi_file', 'reference')]), - (vsm, vsm_fwd, [('shift_out_file', 'shift_in_file')]), - (mask_mag_dil, vsm_fwd, [('out_file', 'mask_file')]), - (inputnode, vsm_fwd, [('fieldmap_mag', 'in_file')]), - (vsm_fwd, vsm_reg, [('warped_file', 'in_file')]), - (vsm_reg, msk_applyxfm, [('out_matrix_file', 'in_matrix_file')]), - (select_epi, msk_applyxfm, [('roi_file', 'reference')]), - (mask_mag_dil, msk_applyxfm, [('out_file', 'in_file')]), - (vsm_reg, vsm_applyxfm, [('out_matrix_file', 'in_matrix_file')]), - (select_epi, vsm_applyxfm, [('roi_file', 'reference')]), - (vsm_mean, vsm_applyxfm, [('out_file', 'in_file')]), - (msk_applyxfm, dwi_applyxfm, [('out_file', 'mask_file')]), - (vsm_applyxfm, dwi_applyxfm, [('out_file', 'shift_in_file')]) - ]) + (inputnode, select_epi, [('in_file', 'in_file'), ('ref_num', 't_min')]), + (select_epi, vsm_reg, [('roi_file', 'reference')]), + (vsm, vsm_fwd, [('shift_out_file', 'shift_in_file')]), + (mask_mag_dil, vsm_fwd, [('out_file', 'mask_file')]), + (inputnode, vsm_fwd, [('fieldmap_mag', 'in_file')]), + (vsm_fwd, vsm_reg, [('warped_file', 'in_file')]), + (vsm_reg, msk_applyxfm, [('out_matrix_file', 'in_matrix_file')]), + (select_epi, msk_applyxfm, [('roi_file', 'reference')]), + (mask_mag_dil, msk_applyxfm, [('out_file', 'in_file')]), + (vsm_reg, vsm_applyxfm, [('out_matrix_file', 'in_matrix_file')]), + (select_epi, vsm_applyxfm, [('roi_file', 'reference')]), + (vsm_mean, vsm_applyxfm, [('out_file', 'in_file')]), + (msk_applyxfm, dwi_applyxfm, [('out_file', 'mask_file')]), + (vsm_applyxfm, dwi_applyxfm, [('out_file', 'shift_in_file')]) + ]) else: pipeline.connect([ - (mask_mag_dil, dwi_applyxfm, [('out_file', 'mask_file')]), - (vsm_mean, dwi_applyxfm, [('out_file', 'shift_in_file')]) - ]) + (mask_mag_dil, dwi_applyxfm, [('out_file', 'mask_file')]), + (vsm_mean, dwi_applyxfm, [('out_file', 'shift_in_file')]) + ]) return pipeline diff --git a/nipype/workflows/dmri/fsl/tbss.py b/nipype/workflows/dmri/fsl/tbss.py index 792263e370..504334c2d3 100644 --- a/nipype/workflows/dmri/fsl/tbss.py +++ b/nipype/workflows/dmri/fsl/tbss.py @@ -77,7 +77,7 @@ def create_tbss_1_preproc(name='tbss_1_preproc'): (getmask1, getmask2, [("out_file", "in_file"), ("out_file", "operand_files")]), (prepfa, slicer, [('out_file', 'in_file')]), - ]) + ]) # Define the outputnode outputnode = pe.Node(interface=util.IdentityInterface(fields=["fa_list", @@ -85,10 +85,10 @@ def create_tbss_1_preproc(name='tbss_1_preproc'): "slices"]), name="outputnode") tbss1.connect([ - (prepfa, outputnode, [("out_file", "fa_list")]), - (getmask2, outputnode, [("out_file", "mask_list")]), - (slicer, outputnode, [('out_file', 'slices')]) - ]) + (prepfa, outputnode, [("out_file", "fa_list")]), + (getmask2, outputnode, [("out_file", "mask_list")]), + (slicer, outputnode, [('out_file', 'slices')]) + ]) return tbss1 @@ -152,7 +152,7 @@ def create_tbss_2_reg(name="tbss_2_reg"): ("mask_list", "inmask_file"), ("target", "ref_file")]), (flirt, fnirt, [("out_matrix_file", "affine_file")]), - ]) + ]) # Define the outputnode outputnode = pe.Node(interface=util.IdentityInterface(fields=['field_list']), @@ -160,7 +160,7 @@ def create_tbss_2_reg(name="tbss_2_reg"): tbss2.connect([ (fnirt, outputnode, [('fieldcoeff_file', 'field_list')]) - ]) + ]) return tbss2 @@ -228,7 +228,7 @@ def create_tbss_3_postreg(name='tbss_3_postreg', estimate_skeleton=True): (mergefa, groupmask, [("merged_file", "in_file")]), (mergefa, maskgroup, [("merged_file", "in_file")]), (groupmask, maskgroup, [("out_file", "in_file2")]), - ]) + ]) # Create outputnode outputnode = pe.Node(interface=util.IdentityInterface(fields=['groupmask', @@ -247,13 +247,13 @@ def create_tbss_3_postreg(name='tbss_3_postreg', estimate_skeleton=True): makeskeleton = pe.Node(fsl.TractSkeleton(skeleton_file=True), name="makeskeleton") tbss3.connect([ - (maskgroup, meanfa, [("out_file", "in_file")]), - (meanfa, makeskeleton, [("out_file", "in_file")]), - (groupmask, outputnode, [('out_file', 'groupmask')]), - (makeskeleton, outputnode, [('skeleton_file', 'skeleton_file')]), - (meanfa, outputnode, [('out_file', 'meanfa_file')]), - (maskgroup, outputnode, [('out_file', 'mergefa_file')]) - ]) + (maskgroup, meanfa, [("out_file", "in_file")]), + (meanfa, makeskeleton, [("out_file", "in_file")]), + (groupmask, outputnode, [('out_file', 'groupmask')]), + (makeskeleton, outputnode, [('skeleton_file', 'skeleton_file')]), + (meanfa, outputnode, [('out_file', 'meanfa_file')]), + (maskgroup, outputnode, [('out_file', 'mergefa_file')]) + ]) else: # $FSLDIR/bin/fslmaths $FSLDIR/data/standard/FMRIB58_FA_1mm -mas mean_FA_mask mean_FA maskstd = pe.Node(fsl.ImageMaths(op_string="-mas", @@ -271,18 +271,18 @@ def create_tbss_3_postreg(name='tbss_3_postreg', estimate_skeleton=True): name="maskgroup2") tbss3.connect([ - (groupmask, maskstd, [("out_file", "in_file2")]), - (maskstd, binmaskstd, [("out_file", "in_file")]), - (maskgroup, maskgroup2, [("out_file", "in_file")]), - (binmaskstd, maskgroup2, [("out_file", "in_file2")]) + (groupmask, maskstd, [("out_file", "in_file2")]), + (maskstd, binmaskstd, [("out_file", "in_file")]), + (maskgroup, maskgroup2, [("out_file", "in_file")]), + (binmaskstd, maskgroup2, [("out_file", "in_file2")]) ]) outputnode.inputs.skeleton_file = fsl.Info.standard_image("FMRIB58_FA-skeleton_1mm.nii.gz") tbss3.connect([ - (binmaskstd, outputnode, [('out_file', 'groupmask')]), - (maskstd, outputnode, [('out_file', 'meanfa_file')]), - (maskgroup2, outputnode, [('out_file', 'mergefa_file')]) - ]) + (binmaskstd, outputnode, [('out_file', 'groupmask')]), + (maskstd, outputnode, [('out_file', 'meanfa_file')]), + (maskgroup2, outputnode, [('out_file', 'mergefa_file')]) + ]) return tbss3 @@ -329,8 +329,8 @@ def create_tbss_4_prestats(name='tbss_4_prestats'): # Mask the skeleton at the threshold skeletonmask = pe.Node(fsl.ImageMaths( - suffix="_mask"), - name="skeletonmask") + suffix="_mask"), + name="skeletonmask") # Invert the brainmask then add in the tract skeleton invertmask = pe.Node(fsl.ImageMaths(suffix="_inv", @@ -360,7 +360,7 @@ def create_tbss_4_prestats(name='tbss_4_prestats'): (skeletonmask, invertmask, [("out_file", "in_file2")]), (invertmask, distancemap, [("out_file", "in_file")]), (distancemap, projectfa, [("distance_map", "distance_map")]), - ]) + ]) # Create the outputnode outputnode = pe.Node(interface=util.IdentityInterface(fields=['projectedfa_file', @@ -370,12 +370,12 @@ def create_tbss_4_prestats(name='tbss_4_prestats'): name='outputnode') tbss4.connect([ - (projectfa, outputnode, [('projected_data', 'projectedfa_file'), - ('skeleton_file', 'skeleton_file') - ]), - (distancemap, outputnode, [('distance_map', 'distance_map')]), - (skeletonmask, outputnode, [('out_file', 'skeleton_mask')]) - ]) + (projectfa, outputnode, [('projected_data', 'projectedfa_file'), + ('skeleton_file', 'skeleton_file') + ]), + (distancemap, outputnode, [('distance_map', 'distance_map')]), + (skeletonmask, outputnode, [('out_file', 'skeleton_mask')]) + ]) return tbss4 @@ -420,20 +420,20 @@ def create_tbss_all(name='tbss_all', estimate_skeleton=True): tbss_all = pe.Workflow(name=name) tbss_all.connect([ - (inputnode, tbss1, [('fa_list', 'inputnode.fa_list')]), - (inputnode, tbss4, [('skeleton_thresh', 'inputnode.skeleton_thresh')]), - - (tbss1, tbss2, [('outputnode.fa_list', 'inputnode.fa_list'), - ('outputnode.mask_list', 'inputnode.mask_list')]), - (tbss1, tbss3, [('outputnode.fa_list', 'inputnode.fa_list')]), - (tbss2, tbss3, [('outputnode.field_list', 'inputnode.field_list')]), - (tbss3, tbss4, [ - ('outputnode.groupmask', 'inputnode.groupmask'), - ('outputnode.skeleton_file', 'inputnode.skeleton_file'), - ('outputnode.meanfa_file', 'inputnode.meanfa_file'), - ('outputnode.mergefa_file', 'inputnode.mergefa_file') - ]) - ]) + (inputnode, tbss1, [('fa_list', 'inputnode.fa_list')]), + (inputnode, tbss4, [('skeleton_thresh', 'inputnode.skeleton_thresh')]), + + (tbss1, tbss2, [('outputnode.fa_list', 'inputnode.fa_list'), + ('outputnode.mask_list', 'inputnode.mask_list')]), + (tbss1, tbss3, [('outputnode.fa_list', 'inputnode.fa_list')]), + (tbss2, tbss3, [('outputnode.field_list', 'inputnode.field_list')]), + (tbss3, tbss4, [ + ('outputnode.groupmask', 'inputnode.groupmask'), + ('outputnode.skeleton_file', 'inputnode.skeleton_file'), + ('outputnode.meanfa_file', 'inputnode.meanfa_file'), + ('outputnode.mergefa_file', 'inputnode.mergefa_file') + ]) + ]) # Define the outputnode outputnode = pe.Node(interface=util.IdentityInterface(fields=['groupmask', @@ -446,47 +446,47 @@ def create_tbss_all(name='tbss_all', estimate_skeleton=True): 'distance_map']), name='outputnode') outputall_node = pe.Node(interface=util.IdentityInterface( - fields=['fa_list1', - 'mask_list1', - 'field_list2', - 'groupmask3', - 'skeleton_file3', - 'meanfa_file3', - 'mergefa_file3', - 'projectedfa_file4', - 'skeleton_mask4', - 'distance_map4']), - name='outputall_node') + fields=['fa_list1', + 'mask_list1', + 'field_list2', + 'groupmask3', + 'skeleton_file3', + 'meanfa_file3', + 'mergefa_file3', + 'projectedfa_file4', + 'skeleton_mask4', + 'distance_map4']), + name='outputall_node') tbss_all.connect([ - (tbss3, outputnode, [('outputnode.meanfa_file', 'meanfa_file'), - ('outputnode.mergefa_file', 'mergefa_file'), - ('outputnode.groupmask', 'groupmask'), - ('outputnode.skeleton_file', 'skeleton_file3'), - ]), - (tbss4, outputnode, [('outputnode.projectedfa_file', 'projectedfa_file'), - ('outputnode.skeleton_file', 'skeleton_file4'), - ('outputnode.skeleton_mask', 'skeleton_mask'), - ('outputnode.distance_map', 'distance_map'), - ]), - - (tbss1, outputall_node, [('outputnode.fa_list', 'fa_list1'), - ('outputnode.mask_list', 'mask_list1'), - ]), - (tbss2, outputall_node, [('outputnode.field_list', 'field_list2'), - ]), - (tbss3, outputall_node, [ - ('outputnode.meanfa_file', 'meanfa_file3'), - ('outputnode.mergefa_file', 'mergefa_file3'), - ('outputnode.groupmask', 'groupmask3'), - ('outputnode.skeleton_file', 'skeleton_file3'), - ]), - (tbss4, outputall_node, [ - ('outputnode.projectedfa_file', 'projectedfa_file4'), - ('outputnode.skeleton_mask', 'skeleton_mask4'), - ('outputnode.distance_map', 'distance_map4'), - ]), - ]) + (tbss3, outputnode, [('outputnode.meanfa_file', 'meanfa_file'), + ('outputnode.mergefa_file', 'mergefa_file'), + ('outputnode.groupmask', 'groupmask'), + ('outputnode.skeleton_file', 'skeleton_file3'), + ]), + (tbss4, outputnode, [('outputnode.projectedfa_file', 'projectedfa_file'), + ('outputnode.skeleton_file', 'skeleton_file4'), + ('outputnode.skeleton_mask', 'skeleton_mask'), + ('outputnode.distance_map', 'distance_map'), + ]), + + (tbss1, outputall_node, [('outputnode.fa_list', 'fa_list1'), + ('outputnode.mask_list', 'mask_list1'), + ]), + (tbss2, outputall_node, [('outputnode.field_list', 'field_list2'), + ]), + (tbss3, outputall_node, [ + ('outputnode.meanfa_file', 'meanfa_file3'), + ('outputnode.mergefa_file', 'mergefa_file3'), + ('outputnode.groupmask', 'groupmask3'), + ('outputnode.skeleton_file', 'skeleton_file3'), + ]), + (tbss4, outputall_node, [ + ('outputnode.projectedfa_file', 'projectedfa_file4'), + ('outputnode.skeleton_mask', 'skeleton_mask4'), + ('outputnode.distance_map', 'distance_map4'), + ]), + ]) return tbss_all @@ -555,29 +555,29 @@ def create_tbss_non_FA(name='tbss_non_FA'): tbss_non_FA = pe.Workflow(name=name) tbss_non_FA.connect([ - (inputnode, applywarp, [('file_list', 'in_file'), - ('field_list', 'field_file'), - ]), - (applywarp, merge, [("out_file", "in_files")]), + (inputnode, applywarp, [('file_list', 'in_file'), + ('field_list', 'field_file'), + ]), + (applywarp, merge, [("out_file", "in_files")]), - (merge, maskgroup, [("merged_file", "in_file")]), + (merge, maskgroup, [("merged_file", "in_file")]), - (inputnode, maskgroup, [('groupmask', 'in_file2')]), + (inputnode, maskgroup, [('groupmask', 'in_file2')]), - (maskgroup, projectfa, [('out_file', 'alt_data_file')]), - (inputnode, projectfa, [('skeleton_thresh', 'threshold'), - ("meanfa_file", "in_file"), - ("distance_map", "distance_map"), - ("all_FA_file", 'data_file') - ]), - ]) + (maskgroup, projectfa, [('out_file', 'alt_data_file')]), + (inputnode, projectfa, [('skeleton_thresh', 'threshold'), + ("meanfa_file", "in_file"), + ("distance_map", "distance_map"), + ("all_FA_file", 'data_file') + ]), + ]) # Define the outputnode outputnode = pe.Node(interface=util.IdentityInterface( - fields=['projected_nonFA_file']), - name='outputnode') + fields=['projected_nonFA_file']), + name='outputnode') tbss_non_FA.connect([ - (projectfa, outputnode, [('projected_data', 'projected_nonFA_file'), - ]), - ]) + (projectfa, outputnode, [('projected_data', 'projected_nonFA_file'), + ]), + ]) return tbss_non_FA diff --git a/nipype/workflows/dmri/mrtrix/connectivity_mapping.py b/nipype/workflows/dmri/mrtrix/connectivity_mapping.py index 63a40fd013..1bf1d53cc6 100644 --- a/nipype/workflows/dmri/mrtrix/connectivity_mapping.py +++ b/nipype/workflows/dmri/mrtrix/connectivity_mapping.py @@ -516,25 +516,25 @@ def create_connectivity_pipeline(name="connectivity", parcellation_name='scale50 inputnode = pe.Node(interface=util.IdentityInterface(fields=["subject_id", "dwi", "bvecs", "bvals", "subjects_dir"]), name="inputnode") outputnode = pe.Node(interface=util.IdentityInterface(fields=["fa", - "struct", - "tracts", - "tracks2prob", - "connectome", - "nxstatscff", - "nxmatlab", - "nxcsv", - "fiber_csv", - "cmatrices_csv", - "nxmergedcsv", - "cmatrix", - "networks", - "filtered_tracts", - "rois", - "odfs", - "tdi", - "mean_fiber_length", - "median_fiber_length", - "fiber_length_std"]), + "struct", + "tracts", + "tracks2prob", + "connectome", + "nxstatscff", + "nxmatlab", + "nxcsv", + "fiber_csv", + "cmatrices_csv", + "nxmergedcsv", + "cmatrix", + "networks", + "filtered_tracts", + "rois", + "odfs", + "tdi", + "mean_fiber_length", + "median_fiber_length", + "fiber_length_std"]), name="outputnode") connectivity = pe.Workflow(name="connectivity") @@ -564,7 +564,7 @@ def create_connectivity_pipeline(name="connectivity", parcellation_name='scale50 ("mri_convert_Brain.out_file", "struct"), ("MRconvert_fa.converted", "fa"), ("MRconvert_tracks2prob.converted", "tracks2prob")]) - ]) + ]) connectivity.connect([(cmats_to_csv, outputnode, [("outputnode.csv_file", "cmatrices_csv")])]) connectivity.connect([(networkx, outputnode, [("outputnode.csv_files", "nxcsv")])]) diff --git a/nipype/workflows/dmri/mrtrix/diffusion.py b/nipype/workflows/dmri/mrtrix/diffusion.py index 52ac4692bd..86d098011b 100644 --- a/nipype/workflows/dmri/mrtrix/diffusion.py +++ b/nipype/workflows/dmri/mrtrix/diffusion.py @@ -36,8 +36,8 @@ def create_mrtrix_dti_pipeline(name="dtiproc", tractography_type='probabilistic' """ inputnode = pe.Node(interface=util.IdentityInterface(fields=["dwi", - "bvecs", - "bvals"]), + "bvecs", + "bvals"]), name="inputnode") bet = pe.Node(interface=fsl.BET(), name="bet") diff --git a/nipype/workflows/dmri/mrtrix/group_connectivity.py b/nipype/workflows/dmri/mrtrix/group_connectivity.py index 37ff71409d..b308e17137 100644 --- a/nipype/workflows/dmri/mrtrix/group_connectivity.py +++ b/nipype/workflows/dmri/mrtrix/group_connectivity.py @@ -102,7 +102,7 @@ def create_group_connectivity_pipeline(group_list, group_id, data_dir, subjects_ l1pipeline.connect([(datasource, conmapper, [("dwi", "inputnode.dwi"), ("bvals", "inputnode.bvals"), ("bvecs", "inputnode.bvecs"), - ])]) + ])]) l1pipeline.connect([(conmapper, datasink, [("outputnode.connectome", "@l1output.cff"), ("outputnode.nxstatscff", "@l1output.nxstatscff"), ("outputnode.nxmatlab", "@l1output.nxmatlab"), diff --git a/nipype/workflows/fmri/fsl/estimate.py b/nipype/workflows/fmri/fsl/estimate.py index 79e14a68d3..ef2a3c44d0 100644 --- a/nipype/workflows/fmri/fsl/estimate.py +++ b/nipype/workflows/fmri/fsl/estimate.py @@ -132,7 +132,7 @@ def create_modelfit_workflow(name='modelfit', f_contrasts=False): (merge_contrasts, outputspec, [('out', 'zfiles')]), (modelestimate, outputspec, [('param_estimates', 'parameter_estimates'), ('dof_file', 'dof_file')]), - ]) + ]) if version < 507: modelfit.connect([ (modelgen, conestimate, [('con_file', 'tcon_file'), @@ -145,7 +145,7 @@ def create_modelfit_workflow(name='modelfit', f_contrasts=False): ('zfstats', 'in2')]), (conestimate, outputspec, [('copes', 'copes'), ('varcopes', 'varcopes')]), - ]) + ]) else: modelfit.connect([ (modelgen, modelestimate, [('con_file', 'tcon_file'), @@ -154,7 +154,7 @@ def create_modelfit_workflow(name='modelfit', f_contrasts=False): ('zfstats', 'in2')]), (modelestimate, outputspec, [('copes', 'copes'), ('varcopes', 'varcopes')]), - ]) + ]) return modelfit diff --git a/nipype/workflows/fmri/spm/preprocess.py b/nipype/workflows/fmri/spm/preprocess.py index dc190abf39..34060fc6d3 100644 --- a/nipype/workflows/fmri/spm/preprocess.py +++ b/nipype/workflows/fmri/spm/preprocess.py @@ -95,8 +95,8 @@ def create_spm_preproc(name='preproc'): save_plot=True), name='artdetect') workflow.connect([(inputnode, artdetect, [('norm_threshold', 'norm_threshold'), - ('zintensity_threshold', - 'zintensity_threshold')])]) + ('zintensity_threshold', + 'zintensity_threshold')])]) workflow.connect([(realign, artdetect, [('realigned_files', 'realigned_files'), ('realignment_parameters', 'realignment_parameters')])]) @@ -117,15 +117,15 @@ def create_spm_preproc(name='preproc'): ]), name="outputspec") workflow.connect([ - (maskflow, outputnode, [("outputspec.reg_file", "reg_file")]), - (maskflow, outputnode, [("outputspec.reg_cost", "reg_cost")]), - (maskflow, outputnode, [(("outputspec.mask_file", poplist), "mask_file")]), - (realign, outputnode, [('realignment_parameters', 'realignment_parameters')]), - (smooth, outputnode, [('smoothed_files', 'smoothed_files')]), - (artdetect, outputnode, [('outlier_files', 'outlier_files'), - ('statistic_files', 'outlier_stats'), - ('plot_files', 'outlier_plots')]) - ]) + (maskflow, outputnode, [("outputspec.reg_file", "reg_file")]), + (maskflow, outputnode, [("outputspec.reg_cost", "reg_cost")]), + (maskflow, outputnode, [(("outputspec.mask_file", poplist), "mask_file")]), + (realign, outputnode, [('realignment_parameters', 'realignment_parameters')]), + (smooth, outputnode, [('smoothed_files', 'smoothed_files')]), + (artdetect, outputnode, [('outlier_files', 'outlier_files'), + ('statistic_files', 'outlier_stats'), + ('plot_files', 'outlier_plots')]) + ]) return workflow @@ -303,8 +303,8 @@ def get2classes(dartel_files): ]), name="outputspec") workflow.connect([ - (dartel, outputnode, [('final_template_file', 'template_file'), - ('dartel_flow_fields', 'flow_fields')]), - ]) + (dartel, outputnode, [('final_template_file', 'template_file'), + ('dartel_flow_fields', 'flow_fields')]), + ]) return workflow diff --git a/nipype/workflows/rsfmri/fsl/resting.py b/nipype/workflows/rsfmri/fsl/resting.py index 5939c8707d..8826a7ed9d 100644 --- a/nipype/workflows/rsfmri/fsl/resting.py +++ b/nipype/workflows/rsfmri/fsl/resting.py @@ -71,9 +71,9 @@ def create_realign_flow(name='realign'): ]), name='inputspec') outputnode = pe.Node(interface=util.IdentityInterface(fields=[ - 'realigned_file', - ]), - name='outputspec') + 'realigned_file', + ]), + name='outputspec') realigner = pe.Node(fsl.MCFLIRT(save_mats=True, stats_imgs=True), name='realigner') splitter = pe.Node(fsl.Split(dimension='t'), name='splitter') @@ -136,10 +136,10 @@ def create_resting_preproc(name='restpreproc'): ]), name='inputspec') outputnode = pe.Node(interface=util.IdentityInterface(fields=[ - 'noise_mask_file', - 'filtered_file', - ]), - name='outputspec') + 'noise_mask_file', + 'filtered_file', + ]), + name='outputspec') slicetimer = pe.Node(fsl.SliceTimer(), name='slicetimer') realigner = create_realign_flow() tsnr = pe.Node(TSNR(regress_poly=2), name='tsnr') diff --git a/nipype/workflows/smri/ants/ANTSBuildTemplate.py b/nipype/workflows/smri/ants/ANTSBuildTemplate.py index e59cf670ff..fd92c18a1e 100644 --- a/nipype/workflows/smri/ants/ANTSBuildTemplate.py +++ b/nipype/workflows/smri/ants/ANTSBuildTemplate.py @@ -235,9 +235,9 @@ def ANTSTemplateBuildSingleIterationWF(iterationPhasePrefix=''): ############################################## # Now warp all the ListOfPassiveImagesDictionaries images FlattenTransformAndImagesListNode = pe.Node(Function(function=FlattenTransformAndImagesList, - input_names=['ListOfPassiveImagesDictionaries', 'transformation_series'], - output_names=['flattened_images', 'flattened_transforms', 'flattened_image_nametypes']), - run_without_submitting=True, name="99_FlattenTransformAndImagesList") + input_names=['ListOfPassiveImagesDictionaries', 'transformation_series'], + output_names=['flattened_images', 'flattened_transforms', 'flattened_image_nametypes']), + run_without_submitting=True, name="99_FlattenTransformAndImagesList") TemplateBuildSingleIterationWF.connect(inputSpec, 'ListOfPassiveImagesDictionaries', FlattenTransformAndImagesListNode, 'ListOfPassiveImagesDictionaries') TemplateBuildSingleIterationWF.connect(MakeTransformsLists, 'out', FlattenTransformAndImagesListNode, 'transformation_series') wimtPassivedeformed = pe.MapNode(interface=WarpImageMultiTransform(), @@ -248,15 +248,15 @@ def ANTSTemplateBuildSingleIterationWF(iterationPhasePrefix=''): TemplateBuildSingleIterationWF.connect(FlattenTransformAndImagesListNode, 'flattened_transforms', wimtPassivedeformed, 'transformation_series') RenestDeformedPassiveImagesNode = pe.Node(Function(function=RenestDeformedPassiveImages, - input_names=['deformedPassiveImages', 'flattened_image_nametypes'], - output_names=['nested_imagetype_list', 'outputAverageImageName_list', 'image_type_list']), - run_without_submitting=True, name="99_RenestDeformedPassiveImages") + input_names=['deformedPassiveImages', 'flattened_image_nametypes'], + output_names=['nested_imagetype_list', 'outputAverageImageName_list', 'image_type_list']), + run_without_submitting=True, name="99_RenestDeformedPassiveImages") TemplateBuildSingleIterationWF.connect(wimtPassivedeformed, 'output_image', RenestDeformedPassiveImagesNode, 'deformedPassiveImages') TemplateBuildSingleIterationWF.connect(FlattenTransformAndImagesListNode, 'flattened_image_nametypes', RenestDeformedPassiveImagesNode, 'flattened_image_nametypes') # Now Average All passive input_images deformed images together to create an updated template average AvgDeformedPassiveImages = pe.MapNode(interface=AverageImages(), - iterfield=['images', 'output_average_image'], - name='AvgDeformedPassiveImages') + iterfield=['images', 'output_average_image'], + name='AvgDeformedPassiveImages') AvgDeformedPassiveImages.inputs.dimension = 3 AvgDeformedPassiveImages.inputs.normalize = False TemplateBuildSingleIterationWF.connect(RenestDeformedPassiveImagesNode, "nested_imagetype_list", AvgDeformedPassiveImages, 'images') diff --git a/nipype/workflows/smri/ants/antsRegistrationBuildTemplate.py b/nipype/workflows/smri/ants/antsRegistrationBuildTemplate.py index e1be2d8372..54b61794d8 100644 --- a/nipype/workflows/smri/ants/antsRegistrationBuildTemplate.py +++ b/nipype/workflows/smri/ants/antsRegistrationBuildTemplate.py @@ -17,10 +17,10 @@ from ....interfaces.utility import Function from ....interfaces.ants import ( - Registration, - ApplyTransforms, - AverageImages, MultiplyImages, - AverageAffineTransform) + Registration, + ApplyTransforms, + AverageImages, MultiplyImages, + AverageAffineTransform) def makeListOfOneElement(inputFile): @@ -179,10 +179,10 @@ def antsRegistrationTemplateBuildSingleIterationWF(iterationPhasePrefix=''): TemplateBuildSingleIterationWF = pe.Workflow(name='antsRegistrationTemplateBuildSingleIterationWF_' + str(iterationPhasePrefix)) inputSpec = pe.Node(interface=util.IdentityInterface(fields=[ - 'ListOfImagesDictionaries', 'registrationImageTypes', - 'interpolationMapping', 'fixed_image']), - run_without_submitting=True, - name='inputspec') + 'ListOfImagesDictionaries', 'registrationImageTypes', + 'interpolationMapping', 'fixed_image']), + run_without_submitting=True, + name='inputspec') # HACK: TODO: Need to move all local functions to a common untility file, or at the top of the file so that # they do not change due to re-indenting. Otherwise re-indenting for flow control will trigger # their hash to change. @@ -309,11 +309,11 @@ def antsRegistrationTemplateBuildSingleIterationWF(iterationPhasePrefix=''): ############################################## # Now warp all the ListOfPassiveImagesDictionaries images FlattenTransformAndImagesListNode = pe.Node(Function(function=FlattenTransformAndImagesList, - input_names=['ListOfPassiveImagesDictionaries', 'transforms', - 'invert_transform_flags', 'interpolationMapping'], - output_names=['flattened_images', 'flattened_transforms', 'flattened_invert_transform_flags', - 'flattened_image_nametypes', 'flattened_interpolation_type']), - run_without_submitting=True, name="99_FlattenTransformAndImagesList") + input_names=['ListOfPassiveImagesDictionaries', 'transforms', + 'invert_transform_flags', 'interpolationMapping'], + output_names=['flattened_images', 'flattened_transforms', 'flattened_invert_transform_flags', + 'flattened_image_nametypes', 'flattened_interpolation_type']), + run_without_submitting=True, name="99_FlattenTransformAndImagesList") GetPassiveImagesNode = pe.Node(interface=util.Function(function=GetPassiveImages, input_names=['ListOfImagesDictionaries', 'registrationImageTypes'], @@ -338,17 +338,17 @@ def antsRegistrationTemplateBuildSingleIterationWF(iterationPhasePrefix=''): TemplateBuildSingleIterationWF.connect(FlattenTransformAndImagesListNode, 'flattened_invert_transform_flags', wimtPassivedeformed, 'invert_transform_flags') RenestDeformedPassiveImagesNode = pe.Node(Function(function=RenestDeformedPassiveImages, - input_names=['deformedPassiveImages', 'flattened_image_nametypes', 'interpolationMapping'], - output_names=['nested_imagetype_list', 'outputAverageImageName_list', - 'image_type_list', 'nested_interpolation_type']), - run_without_submitting=True, name="99_RenestDeformedPassiveImages") + input_names=['deformedPassiveImages', 'flattened_image_nametypes', 'interpolationMapping'], + output_names=['nested_imagetype_list', 'outputAverageImageName_list', + 'image_type_list', 'nested_interpolation_type']), + run_without_submitting=True, name="99_RenestDeformedPassiveImages") TemplateBuildSingleIterationWF.connect(inputSpec, 'interpolationMapping', RenestDeformedPassiveImagesNode, 'interpolationMapping') TemplateBuildSingleIterationWF.connect(wimtPassivedeformed, 'output_image', RenestDeformedPassiveImagesNode, 'deformedPassiveImages') TemplateBuildSingleIterationWF.connect(FlattenTransformAndImagesListNode, 'flattened_image_nametypes', RenestDeformedPassiveImagesNode, 'flattened_image_nametypes') # Now Average All passive input_images deformed images together to create an updated template average AvgDeformedPassiveImages = pe.MapNode(interface=AverageImages(), - iterfield=['images', 'output_average_image'], - name='AvgDeformedPassiveImages') + iterfield=['images', 'output_average_image'], + name='AvgDeformedPassiveImages') AvgDeformedPassiveImages.inputs.dimension = 3 AvgDeformedPassiveImages.inputs.normalize = False TemplateBuildSingleIterationWF.connect(RenestDeformedPassiveImagesNode, "nested_imagetype_list", AvgDeformedPassiveImages, 'images') diff --git a/nipype/workflows/smri/freesurfer/bem.py b/nipype/workflows/smri/freesurfer/bem.py index 46c7b2f239..a9b0a0a325 100644 --- a/nipype/workflows/smri/freesurfer/bem.py +++ b/nipype/workflows/smri/freesurfer/bem.py @@ -66,10 +66,10 @@ def create_bem_flow(name='bem', out_format='stl'): """ bemflow.connect([ - (inputnode, watershed_bem, [('subject_id', 'subject_id'), - ('subjects_dir', 'subjects_dir')]), - (watershed_bem, surfconvert, [('mesh_files', 'in_file')]), - ]) + (inputnode, watershed_bem, [('subject_id', 'subject_id'), + ('subjects_dir', 'subjects_dir')]), + (watershed_bem, surfconvert, [('mesh_files', 'in_file')]), + ]) """ Setup an outputnode that defines relevant inputs of the workflow. @@ -78,6 +78,6 @@ def create_bem_flow(name='bem', out_format='stl'): outputnode = pe.Node(niu.IdentityInterface(fields=["meshes"]), name="outputspec") bemflow.connect([ - (surfconvert, outputnode, [("converted", "meshes")]), - ]) + (surfconvert, outputnode, [("converted", "meshes")]), + ]) return bemflow diff --git a/nipype/workflows/smri/freesurfer/utils.py b/nipype/workflows/smri/freesurfer/utils.py index d3abf46160..d225929d4d 100644 --- a/nipype/workflows/smri/freesurfer/utils.py +++ b/nipype/workflows/smri/freesurfer/utils.py @@ -221,11 +221,11 @@ def switch_labels(inverse, transform_output, source_file, label_file): return label_file, transform_output chooser = pe.MapNode(niu.Function(input_names=['inverse', - 'transform_output', - 'source_file', - 'label_file'], + 'transform_output', + 'source_file', + 'label_file'], output_names=['label_file', - 'source_file'], + 'source_file'], function=switch_labels), iterfield=['transform_output', 'source_file'], name='chooser') @@ -247,8 +247,8 @@ def switch_labels(inverse, transform_output, source_file, label_file): ]), name="outputspec") getstats.connect([ - (statnode, outputnode, [("summary_file", "stats_file")]), - ]) + (statnode, outputnode, [("summary_file", "stats_file")]), + ]) return getstats @@ -339,18 +339,18 @@ def create_tessellation_flow(name='tessellate', out_format='stl'): """ tessflow.connect([ - (inputnode, fssource, [('subject_id', 'subject_id'), - ('subjects_dir', 'subjects_dir')]), - (fssource, volconvert, [('aseg', 'in_file')]), - (volconvert, region_list_from_volume_node, [('out_file', 'in_file')]), - (region_list_from_volume_node, tessellate, [('region_list', 'label_value')]), - (region_list_from_volume_node, id_list_from_lookup_table_node, [('region_list', 'region_list')]), - (inputnode, id_list_from_lookup_table_node, [('lookup_file', 'lookup_file')]), - (id_list_from_lookup_table_node, tessellate, [('id_list', 'out_file')]), - (fssource, tessellate, [('aseg', 'in_file')]), - (tessellate, surfconvert, [('surface', 'in_file')]), - (surfconvert, smoother, [('converted', 'in_file1')]), - ]) + (inputnode, fssource, [('subject_id', 'subject_id'), + ('subjects_dir', 'subjects_dir')]), + (fssource, volconvert, [('aseg', 'in_file')]), + (volconvert, region_list_from_volume_node, [('out_file', 'in_file')]), + (region_list_from_volume_node, tessellate, [('region_list', 'label_value')]), + (region_list_from_volume_node, id_list_from_lookup_table_node, [('region_list', 'region_list')]), + (inputnode, id_list_from_lookup_table_node, [('lookup_file', 'lookup_file')]), + (id_list_from_lookup_table_node, tessellate, [('id_list', 'out_file')]), + (fssource, tessellate, [('aseg', 'in_file')]), + (tessellate, surfconvert, [('surface', 'in_file')]), + (surfconvert, smoother, [('converted', 'in_file1')]), + ]) """ Setup an outputnode that defines relevant inputs of the workflow. @@ -365,9 +365,9 @@ def create_tessellation_flow(name='tessellate', out_format='stl'): ]) tessflow.connect([ (stl_to_gifti, outputnode, [("converted", "meshes")]), - ]) + ]) else: tessflow.connect([ (smoother, outputnode, [("mesh_file", "meshes")]), - ]) + ]) return tessflow diff --git a/setup.py b/setup.py index 6341094694..3d81cfe495 100755 --- a/setup.py +++ b/setup.py @@ -181,11 +181,11 @@ def version_getter(pkg_name): if messages is None: messages = {} msgs = { - 'missing': 'Cannot import package "%s" - is it installed?', - 'missing opt': 'Missing optional package "%s"', - 'opt suffix': '; you may get run-time errors', - 'version too old': 'You have version %s of package "%s"' - ' but we need version >= %s', } + 'missing': 'Cannot import package "%s" - is it installed?', + 'missing opt': 'Missing optional package "%s"', + 'opt suffix': '; you may get run-time errors', + 'version too old': 'You have version %s of package "%s"' + ' but we need version >= %s', } msgs.update(messages) status, have_version = _package_status(pkg_name, version, @@ -298,119 +298,119 @@ def main(**extra_args): install_requires=REQUIRES, provides=PROVIDES, packages=['nipype', - 'nipype.algorithms', - 'nipype.algorithms.tests', - 'nipype.caching', - 'nipype.caching.tests', - 'nipype.external', - 'nipype.fixes', - 'nipype.fixes.numpy', - 'nipype.fixes.numpy.testing', - 'nipype.interfaces', - 'nipype.interfaces.afni', - 'nipype.interfaces.afni.tests', - 'nipype.interfaces.ants', - 'nipype.interfaces.ants.tests', - 'nipype.interfaces.camino', - 'nipype.interfaces.camino.tests', - 'nipype.interfaces.camino2trackvis', - 'nipype.interfaces.camino2trackvis.tests', - 'nipype.interfaces.cmtk', - 'nipype.interfaces.cmtk.tests', - 'nipype.interfaces.diffusion_toolkit', - 'nipype.interfaces.diffusion_toolkit.tests', - 'nipype.interfaces.dipy', - 'nipype.interfaces.dipy.tests', - 'nipype.interfaces.elastix', - 'nipype.interfaces.elastix.tests', - 'nipype.interfaces.freesurfer', - 'nipype.interfaces.freesurfer.tests', - 'nipype.interfaces.fsl', - 'nipype.interfaces.fsl.tests', - 'nipype.interfaces.mipav', - 'nipype.interfaces.mipav.tests', - 'nipype.interfaces.mne', - 'nipype.interfaces.mne.tests', - 'nipype.interfaces.mrtrix', - 'nipype.interfaces.mrtrix.tests', - 'nipype.interfaces.nipy', - 'nipype.interfaces.nipy.tests', - 'nipype.interfaces.nitime', - 'nipype.interfaces.nitime.tests', - 'nipype.interfaces.script_templates', - 'nipype.interfaces.semtools', - 'nipype.interfaces.semtools.brains', - 'nipype.interfaces.semtools.brains.tests', - 'nipype.interfaces.semtools.diffusion', - 'nipype.interfaces.semtools.diffusion.tests', - 'nipype.interfaces.semtools.diffusion.tractography', - 'nipype.interfaces.semtools.diffusion.tractography.tests', - 'nipype.interfaces.semtools.filtering', - 'nipype.interfaces.semtools.filtering.tests', - 'nipype.interfaces.semtools.legacy', - 'nipype.interfaces.semtools.legacy.tests', - 'nipype.interfaces.semtools.registration', - 'nipype.interfaces.semtools.registration.tests', - 'nipype.interfaces.semtools.segmentation', - 'nipype.interfaces.semtools.segmentation.tests', - 'nipype.interfaces.semtools.testing', - 'nipype.interfaces.semtools.tests', - 'nipype.interfaces.semtools.utilities', - 'nipype.interfaces.semtools.utilities.tests', - 'nipype.interfaces.slicer', - 'nipype.interfaces.slicer.diffusion', - 'nipype.interfaces.slicer.diffusion.tests', - 'nipype.interfaces.slicer.filtering', - 'nipype.interfaces.slicer.filtering.tests', - 'nipype.interfaces.slicer.legacy', - 'nipype.interfaces.slicer.legacy.diffusion', - 'nipype.interfaces.slicer.legacy.diffusion.tests', - 'nipype.interfaces.slicer.legacy.tests', - 'nipype.interfaces.slicer.quantification', - 'nipype.interfaces.slicer.quantification.tests', - 'nipype.interfaces.slicer.registration', - 'nipype.interfaces.slicer.registration.tests', - 'nipype.interfaces.slicer.segmentation', - 'nipype.interfaces.slicer.segmentation.tests', - 'nipype.interfaces.slicer.tests', - 'nipype.interfaces.spm', - 'nipype.interfaces.spm.tests', - 'nipype.interfaces.tests', - 'nipype.interfaces.vista', - 'nipype.interfaces.vista.tests', - 'nipype.pipeline', - 'nipype.pipeline.plugins', - 'nipype.pipeline.plugins.tests', - 'nipype.pipeline.tests', - 'nipype.testing', - 'nipype.testing.data', - 'nipype.testing.data.bedpostxout', - 'nipype.testing.data.dicomdir', - 'nipype.testing.data.tbss_dir', - 'nipype.utils', - 'nipype.utils.tests', - 'nipype.workflows', - 'nipype.workflows.data', - 'nipype.workflows.dmri', - 'nipype.workflows.dmri.camino', - 'nipype.workflows.dmri.connectivity', - 'nipype.workflows.dmri.dipy', - 'nipype.workflows.dmri.fsl', - 'nipype.workflows.dmri.fsl.tests', - 'nipype.workflows.dmri.mrtrix', - 'nipype.workflows.fmri', - 'nipype.workflows.fmri.fsl', - 'nipype.workflows.fmri.fsl.tests', - 'nipype.workflows.fmri.spm', - 'nipype.workflows.fmri.spm.tests', - 'nipype.workflows.graph', - 'nipype.workflows.misc', - 'nipype.workflows.rsfmri', - 'nipype.workflows.rsfmri.fsl', - 'nipype.workflows.smri', - 'nipype.workflows.smri.ants', - 'nipype.workflows.smri.freesurfer', - 'nipype.workflows.warp'], + 'nipype.algorithms', + 'nipype.algorithms.tests', + 'nipype.caching', + 'nipype.caching.tests', + 'nipype.external', + 'nipype.fixes', + 'nipype.fixes.numpy', + 'nipype.fixes.numpy.testing', + 'nipype.interfaces', + 'nipype.interfaces.afni', + 'nipype.interfaces.afni.tests', + 'nipype.interfaces.ants', + 'nipype.interfaces.ants.tests', + 'nipype.interfaces.camino', + 'nipype.interfaces.camino.tests', + 'nipype.interfaces.camino2trackvis', + 'nipype.interfaces.camino2trackvis.tests', + 'nipype.interfaces.cmtk', + 'nipype.interfaces.cmtk.tests', + 'nipype.interfaces.diffusion_toolkit', + 'nipype.interfaces.diffusion_toolkit.tests', + 'nipype.interfaces.dipy', + 'nipype.interfaces.dipy.tests', + 'nipype.interfaces.elastix', + 'nipype.interfaces.elastix.tests', + 'nipype.interfaces.freesurfer', + 'nipype.interfaces.freesurfer.tests', + 'nipype.interfaces.fsl', + 'nipype.interfaces.fsl.tests', + 'nipype.interfaces.mipav', + 'nipype.interfaces.mipav.tests', + 'nipype.interfaces.mne', + 'nipype.interfaces.mne.tests', + 'nipype.interfaces.mrtrix', + 'nipype.interfaces.mrtrix.tests', + 'nipype.interfaces.nipy', + 'nipype.interfaces.nipy.tests', + 'nipype.interfaces.nitime', + 'nipype.interfaces.nitime.tests', + 'nipype.interfaces.script_templates', + 'nipype.interfaces.semtools', + 'nipype.interfaces.semtools.brains', + 'nipype.interfaces.semtools.brains.tests', + 'nipype.interfaces.semtools.diffusion', + 'nipype.interfaces.semtools.diffusion.tests', + 'nipype.interfaces.semtools.diffusion.tractography', + 'nipype.interfaces.semtools.diffusion.tractography.tests', + 'nipype.interfaces.semtools.filtering', + 'nipype.interfaces.semtools.filtering.tests', + 'nipype.interfaces.semtools.legacy', + 'nipype.interfaces.semtools.legacy.tests', + 'nipype.interfaces.semtools.registration', + 'nipype.interfaces.semtools.registration.tests', + 'nipype.interfaces.semtools.segmentation', + 'nipype.interfaces.semtools.segmentation.tests', + 'nipype.interfaces.semtools.testing', + 'nipype.interfaces.semtools.tests', + 'nipype.interfaces.semtools.utilities', + 'nipype.interfaces.semtools.utilities.tests', + 'nipype.interfaces.slicer', + 'nipype.interfaces.slicer.diffusion', + 'nipype.interfaces.slicer.diffusion.tests', + 'nipype.interfaces.slicer.filtering', + 'nipype.interfaces.slicer.filtering.tests', + 'nipype.interfaces.slicer.legacy', + 'nipype.interfaces.slicer.legacy.diffusion', + 'nipype.interfaces.slicer.legacy.diffusion.tests', + 'nipype.interfaces.slicer.legacy.tests', + 'nipype.interfaces.slicer.quantification', + 'nipype.interfaces.slicer.quantification.tests', + 'nipype.interfaces.slicer.registration', + 'nipype.interfaces.slicer.registration.tests', + 'nipype.interfaces.slicer.segmentation', + 'nipype.interfaces.slicer.segmentation.tests', + 'nipype.interfaces.slicer.tests', + 'nipype.interfaces.spm', + 'nipype.interfaces.spm.tests', + 'nipype.interfaces.tests', + 'nipype.interfaces.vista', + 'nipype.interfaces.vista.tests', + 'nipype.pipeline', + 'nipype.pipeline.plugins', + 'nipype.pipeline.plugins.tests', + 'nipype.pipeline.tests', + 'nipype.testing', + 'nipype.testing.data', + 'nipype.testing.data.bedpostxout', + 'nipype.testing.data.dicomdir', + 'nipype.testing.data.tbss_dir', + 'nipype.utils', + 'nipype.utils.tests', + 'nipype.workflows', + 'nipype.workflows.data', + 'nipype.workflows.dmri', + 'nipype.workflows.dmri.camino', + 'nipype.workflows.dmri.connectivity', + 'nipype.workflows.dmri.dipy', + 'nipype.workflows.dmri.fsl', + 'nipype.workflows.dmri.fsl.tests', + 'nipype.workflows.dmri.mrtrix', + 'nipype.workflows.fmri', + 'nipype.workflows.fmri.fsl', + 'nipype.workflows.fmri.fsl.tests', + 'nipype.workflows.fmri.spm', + 'nipype.workflows.fmri.spm.tests', + 'nipype.workflows.graph', + 'nipype.workflows.misc', + 'nipype.workflows.rsfmri', + 'nipype.workflows.rsfmri.fsl', + 'nipype.workflows.smri', + 'nipype.workflows.smri.ants', + 'nipype.workflows.smri.freesurfer', + 'nipype.workflows.warp'], # The package_data spec has no effect for me (on python 2.6) -- even # changing to data_files doesn't get this stuff included in the source # distribution -- not sure if it has something to do with the magic @@ -418,16 +418,16 @@ def main(**extra_args): # python -- duplicating things into MANIFEST.in but this is admittedly # only a workaround to get things started -- not a solution package_data={'nipype': - [pjoin('testing', 'data', '*'), - pjoin('testing', 'data', 'dicomdir', '*'), - pjoin('testing', 'data', 'bedpostxout', '*'), - pjoin('testing', 'data', 'tbss_dir', '*'), - pjoin('workflows', 'data', '*'), - pjoin('pipeline', 'report_template.html'), - pjoin('external', 'd3.js'), - pjoin('interfaces', 'script_templates', '*'), - pjoin('interfaces', 'tests', 'realign_json.json') - ]}, + [pjoin('testing', 'data', '*'), + pjoin('testing', 'data', 'dicomdir', '*'), + pjoin('testing', 'data', 'bedpostxout', '*'), + pjoin('testing', 'data', 'tbss_dir', '*'), + pjoin('workflows', 'data', '*'), + pjoin('pipeline', 'report_template.html'), + pjoin('external', 'd3.js'), + pjoin('interfaces', 'script_templates', '*'), + pjoin('interfaces', 'tests', 'realign_json.json') + ]}, scripts=glob('bin/*'), cmdclass=cmdclass, **extra_args diff --git a/tools/github.py b/tools/github.py index 3f966383ee..cc6c78e1a8 100644 --- a/tools/github.py +++ b/tools/github.py @@ -94,5 +94,5 @@ def get_file_url(object): shortfile = os.path.join('nipype', filename.split('nipype/')[-1]) uri = 'http://github.com/nipy/nipype/tree/%s/%s#L%d' % \ (info['commit_hash'], - shortfile, lines[1]) + shortfile, lines[1]) return uri From 42b2ae4946adfa31bf3f43b8526ff736e4c9d9dc Mon Sep 17 00:00:00 2001 From: miykael Date: Sun, 1 Nov 2015 11:39:04 +0100 Subject: [PATCH 17/19] FIX: PEP8 - E241 multiple spaces after ',' - 2nd clean up --- examples/dmri_preprocessing.py | 16 +- examples/fmri_fsl.py | 2 +- examples/fmri_fsl_reuse.py | 2 +- examples/test_spm.py | 4 +- nipype/algorithms/icc.py | 2 +- nipype/algorithms/metrics.py | 2 +- nipype/external/provcopy.py | 38 +- nipype/interfaces/afni/preprocess.py | 2 +- nipype/interfaces/camino/__init__.py | 2 +- nipype/interfaces/diffusion_toolkit/dti.py | 24 +- nipype/interfaces/diffusion_toolkit/odf.py | 10 +- nipype/interfaces/fsl/dti.py | 2 +- nipype/interfaces/fsl/tests/test_dti.py | 142 +++---- .../interfaces/fsl/tests/test_preprocess.py | 129 +++--- nipype/interfaces/tests/test_base.py | 4 +- nipype/workflows/dmri/dipy/denoise.py | 12 +- nipype/workflows/dmri/fsl/artifacts.py | 375 +++++++++--------- nipype/workflows/dmri/fsl/dti.py | 56 +-- nipype/workflows/dmri/fsl/epi.py | 132 +++--- nipype/workflows/dmri/fsl/utils.py | 120 +++--- .../workflows/smri/ants/ANTSBuildTemplate.py | 2 +- .../ants/antsRegistrationBuildTemplate.py | 20 +- 22 files changed, 540 insertions(+), 558 deletions(-) diff --git a/examples/dmri_preprocessing.py b/examples/dmri_preprocessing.py index 99a8998113..d814e4facc 100644 --- a/examples/dmri_preprocessing.py +++ b/examples/dmri_preprocessing.py @@ -155,14 +155,14 @@ wf = pe.Workflow(name="dMRI_Preprocessing") wf.base_dir = os.path.abspath('preprocessing_dmri_tutorial') wf.connect([ - (infosource, datasource, [('subject_id', 'subject_id')]), - (datasource, prep, [('dwi', 'inputnode.in_file'), - ('dwi_rev', 'inputnode.alt_file'), - ('bvals', 'inputnode.in_bval'), - ('bvecs', 'inputnode.in_bvec')]), - (prep, bias, [('outputnode.out_file', 'inputnode.in_file'), - ('outputnode.out_mask', 'inputnode.in_mask')]), - (datasource, bias, [('bvals', 'inputnode.in_bval')]) + (infosource, datasource, [('subject_id', 'subject_id')]), + (datasource, prep, [('dwi', 'inputnode.in_file'), + ('dwi_rev', 'inputnode.alt_file'), + ('bvals', 'inputnode.in_bval'), + ('bvecs', 'inputnode.in_bvec')]), + (prep, bias, [('outputnode.out_file', 'inputnode.in_file'), + ('outputnode.out_mask', 'inputnode.in_mask')]), + (datasource, bias, [('bvals', 'inputnode.in_bval')]) ]) diff --git a/examples/fmri_fsl.py b/examples/fmri_fsl.py index 8c67fe7191..d33deaab24 100755 --- a/examples/fmri_fsl.py +++ b/examples/fmri_fsl.py @@ -367,7 +367,7 @@ def getinormscale(medianvals): Use :class:`nipype.algorithms.modelgen.SpecifyModel` to generate design information. """ -modelspec = pe.Node(interface=model.SpecifyModel(), name="modelspec") +modelspec = pe.Node(interface=model.SpecifyModel(), name="modelspec") """ Use :class:`nipype.interfaces.fsl.Level1Design` to generate a run specific fsf diff --git a/examples/fmri_fsl_reuse.py b/examples/fmri_fsl_reuse.py index d5038218b7..272068d229 100755 --- a/examples/fmri_fsl_reuse.py +++ b/examples/fmri_fsl_reuse.py @@ -65,7 +65,7 @@ iterfield=['realigned_files', 'realignment_parameters', 'mask_file'], name="art") -modelspec = pe.Node(interface=model.SpecifyModel(), name="modelspec") +modelspec = pe.Node(interface=model.SpecifyModel(), name="modelspec") level1_workflow.connect([(preproc, art, [('outputspec.motion_parameters', 'realignment_parameters'), diff --git a/examples/test_spm.py b/examples/test_spm.py index da35185329..9a5e1f83aa 100644 --- a/examples/test_spm.py +++ b/examples/test_spm.py @@ -37,7 +37,7 @@ workflow3d.connect([(split, stc, [("out_files", "in_files")]), (stc, realign_estimate, [('timecorrected_files', 'in_files')]), (realign_estimate, realign_write, [('modified_in_files', 'in_files')]), - (stc, realign_estwrite, [('timecorrected_files', 'in_files')]), + (stc, realign_estwrite, [('timecorrected_files', 'in_files')]), (realign_write, smooth, [('realigned_files', 'in_files')])]) workflow3d.run() @@ -71,7 +71,7 @@ workflow4d.connect([(gunzip, stc, [("out_file", "in_files")]), (stc, realign_estimate, [('timecorrected_files', 'in_files')]), (realign_estimate, realign_write, [('modified_in_files', 'in_files')]), - (stc, realign_estwrite, [('timecorrected_files', 'in_files')]), + (stc, realign_estwrite, [('timecorrected_files', 'in_files')]), (realign_write, smooth, [('realigned_files', 'in_files')])]) workflow4d.run() diff --git a/nipype/algorithms/icc.py b/nipype/algorithms/icc.py index f30697d584..98758dfcbf 100644 --- a/nipype/algorithms/icc.py +++ b/nipype/algorithms/icc.py @@ -46,7 +46,7 @@ def _run_interface(self, runtime): for x in range(icc.shape[0]): Y = all_data[x, :, :] - icc[x], subject_var[x], session_var[x], session_F[x], _, _ = ICC_rep_anova(Y) + icc[x], subject_var[x], session_var[x], session_F[x], _, _ = ICC_rep_anova(Y) nim = nb.load(self.inputs.subjects_sessions[0][0]) new_data = np.zeros(nim.get_shape()) diff --git a/nipype/algorithms/metrics.py b/nipype/algorithms/metrics.py index e2e67bc952..746919e06e 100644 --- a/nipype/algorithms/metrics.py +++ b/nipype/algorithms/metrics.py @@ -443,7 +443,7 @@ def _run_interface(self, runtime): weights = weights / np.sum(weights) - setattr(self, '_jaccard', np.sum(weights * self._jaccards)) + setattr(self, '_jaccard', np.sum(weights * self._jaccards)) setattr(self, '_dice', np.sum(weights * self._dices)) diff = np.zeros(diff_im[0].shape) diff --git a/nipype/external/provcopy.py b/nipype/external/provcopy.py index daf234571e..42e250f967 100644 --- a/nipype/external/provcopy.py +++ b/nipype/external/provcopy.py @@ -90,25 +90,25 @@ ) PROV_N_MAP = { - PROV_REC_ENTITY: u'entity', - PROV_REC_ACTIVITY: u'activity', - PROV_REC_GENERATION: u'wasGeneratedBy', - PROV_REC_USAGE: u'used', - PROV_REC_COMMUNICATION: u'wasInformedBy', - PROV_REC_START: u'wasStartedBy', - PROV_REC_END: u'wasEndedBy', - PROV_REC_INVALIDATION: u'wasInvalidatedBy', - PROV_REC_DERIVATION: u'wasDerivedFrom', - PROV_REC_AGENT: u'agent', - PROV_REC_ATTRIBUTION: u'wasAttributedTo', - PROV_REC_ASSOCIATION: u'wasAssociatedWith', - PROV_REC_DELEGATION: u'actedOnBehalfOf', - PROV_REC_INFLUENCE: u'wasInfluencedBy', - PROV_REC_ALTERNATE: u'alternateOf', - PROV_REC_SPECIALIZATION: u'specializationOf', - PROV_REC_MENTION: u'mentionOf', - PROV_REC_MEMBERSHIP: u'hadMember', - PROV_REC_BUNDLE: u'bundle', + PROV_REC_ENTITY: u'entity', + PROV_REC_ACTIVITY: u'activity', + PROV_REC_GENERATION: u'wasGeneratedBy', + PROV_REC_USAGE: u'used', + PROV_REC_COMMUNICATION: u'wasInformedBy', + PROV_REC_START: u'wasStartedBy', + PROV_REC_END: u'wasEndedBy', + PROV_REC_INVALIDATION: u'wasInvalidatedBy', + PROV_REC_DERIVATION: u'wasDerivedFrom', + PROV_REC_AGENT: u'agent', + PROV_REC_ATTRIBUTION: u'wasAttributedTo', + PROV_REC_ASSOCIATION: u'wasAssociatedWith', + PROV_REC_DELEGATION: u'actedOnBehalfOf', + PROV_REC_INFLUENCE: u'wasInfluencedBy', + PROV_REC_ALTERNATE: u'alternateOf', + PROV_REC_SPECIALIZATION: u'specializationOf', + PROV_REC_MENTION: u'mentionOf', + PROV_REC_MEMBERSHIP: u'hadMember', + PROV_REC_BUNDLE: u'bundle', } # # Identifiers for PROV's attributes diff --git a/nipype/interfaces/afni/preprocess.py b/nipype/interfaces/afni/preprocess.py index 215709cd61..96bbaaccae 100644 --- a/nipype/interfaces/afni/preprocess.py +++ b/nipype/interfaces/afni/preprocess.py @@ -1095,7 +1095,7 @@ class AllineateInputSpec(AFNICommandInputSpec): # Non-linear experimental _nwarp_types = ['bilinear', 'cubic', 'quintic', 'heptic', 'nonic', - 'poly3', 'poly5', 'poly7', 'poly9'] # same non-hellenistic + 'poly3', 'poly5', 'poly7', 'poly9'] # same non-hellenistic nwarp = traits.Enum( *_nwarp_types, argstr='-nwarp %s', desc='Experimental nonlinear warping: bilinear or legendre poly.') diff --git a/nipype/interfaces/camino/__init__.py b/nipype/interfaces/camino/__init__.py index ec8a9f4c8e..e3f7271626 100644 --- a/nipype/interfaces/camino/__init__.py +++ b/nipype/interfaces/camino/__init__.py @@ -11,7 +11,7 @@ TrackBayesDirac, TrackDT, TrackBallStick, TrackBootstrap, TrackBedpostxDeter, TrackBedpostxProba, ComputeFractionalAnisotropy, ComputeMeanDiffusivity, - ComputeTensorTrace, ComputeEigensystem, DTMetric) + ComputeTensorTrace, ComputeEigensystem, DTMetric) from .calib import (SFPICOCalibData, SFLUTGen) from .odf import (QBallMX, LinRecon, SFPeaks, MESD) from .utils import ImageStats diff --git a/nipype/interfaces/diffusion_toolkit/dti.py b/nipype/interfaces/diffusion_toolkit/dti.py index 65c02ce725..554f2bf38a 100644 --- a/nipype/interfaces/diffusion_toolkit/dti.py +++ b/nipype/interfaces/diffusion_toolkit/dti.py @@ -92,18 +92,18 @@ def _list_outputs(self): output_type = self.inputs.output_type outputs = self.output_spec().get() - outputs['ADC'] = os.path.abspath(fname_presuffix("", prefix=out_prefix, suffix='_adc.' + output_type)) - outputs['B0'] = os.path.abspath(fname_presuffix("", prefix=out_prefix, suffix='_b0.' + output_type)) - outputs['L1'] = os.path.abspath(fname_presuffix("", prefix=out_prefix, suffix='_e1.' + output_type)) - outputs['L2'] = os.path.abspath(fname_presuffix("", prefix=out_prefix, suffix='_e2.' + output_type)) - outputs['L3'] = os.path.abspath(fname_presuffix("", prefix=out_prefix, suffix='_e3.' + output_type)) - outputs['exp'] = os.path.abspath(fname_presuffix("", prefix=out_prefix, suffix='_exp.' + output_type)) - outputs['FA'] = os.path.abspath(fname_presuffix("", prefix=out_prefix, suffix='_fa.' + output_type)) - outputs['FA_color'] = os.path.abspath(fname_presuffix("", prefix=out_prefix, suffix='_fa_color.' + output_type)) - outputs['tensor'] = os.path.abspath(fname_presuffix("", prefix=out_prefix, suffix='_tensor.' + output_type)) - outputs['V1'] = os.path.abspath(fname_presuffix("", prefix=out_prefix, suffix='_v1.' + output_type)) - outputs['V2'] = os.path.abspath(fname_presuffix("", prefix=out_prefix, suffix='_v2.' + output_type)) - outputs['V3'] = os.path.abspath(fname_presuffix("", prefix=out_prefix, suffix='_v3.' + output_type)) + outputs['ADC'] = os.path.abspath(fname_presuffix("", prefix=out_prefix, suffix='_adc.' + output_type)) + outputs['B0'] = os.path.abspath(fname_presuffix("", prefix=out_prefix, suffix='_b0.' + output_type)) + outputs['L1'] = os.path.abspath(fname_presuffix("", prefix=out_prefix, suffix='_e1.' + output_type)) + outputs['L2'] = os.path.abspath(fname_presuffix("", prefix=out_prefix, suffix='_e2.' + output_type)) + outputs['L3'] = os.path.abspath(fname_presuffix("", prefix=out_prefix, suffix='_e3.' + output_type)) + outputs['exp'] = os.path.abspath(fname_presuffix("", prefix=out_prefix, suffix='_exp.' + output_type)) + outputs['FA'] = os.path.abspath(fname_presuffix("", prefix=out_prefix, suffix='_fa.' + output_type)) + outputs['FA_color'] = os.path.abspath(fname_presuffix("", prefix=out_prefix, suffix='_fa_color.' + output_type)) + outputs['tensor'] = os.path.abspath(fname_presuffix("", prefix=out_prefix, suffix='_tensor.' + output_type)) + outputs['V1'] = os.path.abspath(fname_presuffix("", prefix=out_prefix, suffix='_v1.' + output_type)) + outputs['V2'] = os.path.abspath(fname_presuffix("", prefix=out_prefix, suffix='_v2.' + output_type)) + outputs['V3'] = os.path.abspath(fname_presuffix("", prefix=out_prefix, suffix='_v3.' + output_type)) return outputs diff --git a/nipype/interfaces/diffusion_toolkit/odf.py b/nipype/interfaces/diffusion_toolkit/odf.py index 090ac0a795..b2f0b2c6a7 100644 --- a/nipype/interfaces/diffusion_toolkit/odf.py +++ b/nipype/interfaces/diffusion_toolkit/odf.py @@ -143,12 +143,12 @@ def _list_outputs(self): output_type = self.inputs.output_type outputs = self.output_spec().get() - outputs['B0'] = os.path.abspath(fname_presuffix("", prefix=out_prefix, suffix='_b0.' + output_type)) - outputs['DWI'] = os.path.abspath(fname_presuffix("", prefix=out_prefix, suffix='_dwi.' + output_type)) - outputs['max'] = os.path.abspath(fname_presuffix("", prefix=out_prefix, suffix='_max.' + output_type)) - outputs['ODF'] = os.path.abspath(fname_presuffix("", prefix=out_prefix, suffix='_odf.' + output_type)) + outputs['B0'] = os.path.abspath(fname_presuffix("", prefix=out_prefix, suffix='_b0.' + output_type)) + outputs['DWI'] = os.path.abspath(fname_presuffix("", prefix=out_prefix, suffix='_dwi.' + output_type)) + outputs['max'] = os.path.abspath(fname_presuffix("", prefix=out_prefix, suffix='_max.' + output_type)) + outputs['ODF'] = os.path.abspath(fname_presuffix("", prefix=out_prefix, suffix='_odf.' + output_type)) if isdefined(self.inputs.output_entropy): - outputs['entropy'] = os.path.abspath(fname_presuffix("", prefix=out_prefix, suffix='_entropy.' + output_type)) + outputs['entropy'] = os.path.abspath(fname_presuffix("", prefix=out_prefix, suffix='_entropy.' + output_type)) return outputs diff --git a/nipype/interfaces/fsl/dti.py b/nipype/interfaces/fsl/dti.py index f9a0e47789..84e44e4f7a 100644 --- a/nipype/interfaces/fsl/dti.py +++ b/nipype/interfaces/fsl/dti.py @@ -552,7 +552,7 @@ class BEDPOSTX4OutputSpec(TraitedSpec): desc='a list of path/name of 3D volume with mean of distribution on phi') mean_fsamples = traits.List(File(exists=True), desc='a list of path/name of 3D volume with mean of distribution on f anisotropy') - dyads = traits.List(File(exists=True), desc='a list of path/name of mean of PDD distribution in vector form') + dyads = traits.List(File(exists=True), desc='a list of path/name of mean of PDD distribution in vector form') class BEDPOSTX4(FSLCommand): diff --git a/nipype/interfaces/fsl/tests/test_dti.py b/nipype/interfaces/fsl/tests/test_dti.py index 2c02481090..43a3e4becf 100644 --- a/nipype/interfaces/fsl/tests/test_dti.py +++ b/nipype/interfaces/fsl/tests/test_dti.py @@ -172,40 +172,34 @@ def test_randomise2(): 'randomise -i infile3 -o outfile3' # test arguments for opt_map - opt_map = {'demean_data': ('-D', True), - 'one_sample_gmean': ('-1', True), - 'mask_image': ('-m inp_mask', 'inp_mask'), - 'design_matrix': ('-d design.mat', - 'design.mat'), - 't_contrast': ('-t input.con', - 'input.con'), - 'f_contrast': ('-f input.fts', - 'input.fts'), - 'xchange_block_labels': ('-e design.grp', - 'design.grp'), - 'print_unique_perm': ('-q', True), - 'print_info_parallelMode': ('-Q', True), - 'num_permutations': ('-n 10', 10), - 'vox_pvalus': ('-x', True), - 'fstats_only': ('--fonly', True), - 'thresh_free_cluster': ('-T', True), - 'thresh_free_cluster_2Dopt': ('--T2', True), - 'cluster_thresholding': ('-c 0.20', 0.20), - 'cluster_mass_thresholding': ('-C 0.40', 0.40), - 'fcluster_thresholding': ('-F 0.10', 0.10), - 'fcluster_mass_thresholding': ('-S 0.30', 0.30), - 'variance_smoothing': ('-v 0.20', 0.20), - 'diagnostics_off': ('--quiet', True), - 'output_raw': ('-R', True), - 'output_perm_vect': ('-P', True), - 'int_seed': ('--seed=20', 20), - 'TFCE_height_param': ('--tfce_H=0.11', 0.11), - 'TFCE_extent_param': ('--tfce_E=0.50', 0.50), - 'TFCE_connectivity': ('--tfce_C=0.30', 0.30), - 'list_num_voxel_EVs_pos': ('--vxl=1,2,3,4', - '1,2,3,4'), - 'list_img_voxel_EVs': ('--vxf=6,7,8,9,3', - '6,7,8,9,3')} + opt_map = {'demean_data': ('-D', True), + 'one_sample_gmean': ('-1', True), + 'mask_image': ('-m inp_mask', 'inp_mask'), + 'design_matrix': ('-d design.mat', 'design.mat'), + 't_contrast': ('-t input.con', 'input.con'), + 'f_contrast': ('-f input.fts', 'input.fts'), + 'xchange_block_labels': ('-e design.grp', 'design.grp'), + 'print_unique_perm': ('-q', True), + 'print_info_parallelMode': ('-Q', True), + 'num_permutations': ('-n 10', 10), + 'vox_pvalus': ('-x', True), + 'fstats_only': ('--fonly', True), + 'thresh_free_cluster': ('-T', True), + 'thresh_free_cluster_2Dopt': ('--T2', True), + 'cluster_thresholding': ('-c 0.20', 0.20), + 'cluster_mass_thresholding': ('-C 0.40', 0.40), + 'fcluster_thresholding': ('-F 0.10', 0.10), + 'fcluster_mass_thresholding': ('-S 0.30', 0.30), + 'variance_smoothing': ('-v 0.20', 0.20), + 'diagnostics_off': ('--quiet', True), + 'output_raw': ('-R', True), + 'output_perm_vect': ('-P', True), + 'int_seed': ('--seed=20', 20), + 'TFCE_height_param': ('--tfce_H=0.11', 0.11), + 'TFCE_extent_param': ('--tfce_E=0.50', 0.50), + 'TFCE_connectivity': ('--tfce_C=0.30', 0.30), + 'list_num_voxel_EVs_pos': ('--vxl=1,2,3,4', '1,2,3,4'), + 'list_img_voxel_EVs': ('--vxf=6,7,8,9,3', '6,7,8,9,3')} for name, settings in list(opt_map.items()): rand4 = fsl.Randomise(input_4D='infile', output_rootname='root', @@ -255,42 +249,36 @@ def test_Randomise_parallel(): 'randomise_parallel -i infile3 -o outfile3' # test arguments for opt_map - opt_map = {'demean_data': ('-D', True), - 'one_sample_gmean': ('-1', True), - 'mask_image': ('-m inp_mask', 'inp_mask'), - 'design_matrix': ('-d design.mat', - 'design.mat'), - 't_contrast': ('-t input.con', - 'input.con'), - 'f_contrast': ('-f input.fts', - 'input.fts'), - 'xchange_block_labels': ('-e design.grp', - 'design.grp'), - 'print_unique_perm': ('-q', True), - 'print_info_parallelMode': ('-Q', True), - 'num_permutations': ('-n 10', 10), - 'vox_pvalus': ('-x', True), - 'fstats_only': ('--fonly', True), - 'thresh_free_cluster': ('-T', True), - 'thresh_free_cluster_2Dopt': ('--T2', True), - 'cluster_thresholding': ('-c 0.20', 0.20), - 'cluster_mass_thresholding': ('-C 0.40', 0.40), - 'fcluster_thresholding': ('-F 0.10', 0.10), - 'fcluster_mass_thresholding': ('-S 0.30', 0.30), - 'variance_smoothing': ('-v 0.20', 0.20), - 'diagnostics_off': ('--quiet', True), - 'output_raw': ('-R', True), - 'output_perm_vect': ('-P', True), - 'int_seed': ('--seed=20', 20), - 'TFCE_height_param': ('--tfce_H=0.11', 0.11), - 'TFCE_extent_param': ('--tfce_E=0.50', 0.50), - 'TFCE_connectivity': ('--tfce_C=0.30', 0.30), - 'list_num_voxel_EVs_pos': ('--vxl=' + - repr([1, 2, 3, 4]), - repr([1, 2, 3, 4])), - 'list_img_voxel_EVs': ('--vxf=' + - repr([6, 7, 8, 9, 3]), - repr([6, 7, 8, 9, 3]))} + opt_map = {'demean_data': ('-D', True), + 'one_sample_gmean': ('-1', True), + 'mask_image': ('-m inp_mask', 'inp_mask'), + 'design_matrix': ('-d design.mat', 'design.mat'), + 't_contrast': ('-t input.con', 'input.con'), + 'f_contrast': ('-f input.fts', 'input.fts'), + 'xchange_block_labels': ('-e design.grp', 'design.grp'), + 'print_unique_perm': ('-q', True), + 'print_info_parallelMode': ('-Q', True), + 'num_permutations': ('-n 10', 10), + 'vox_pvalus': ('-x', True), + 'fstats_only': ('--fonly', True), + 'thresh_free_cluster': ('-T', True), + 'thresh_free_cluster_2Dopt': ('--T2', True), + 'cluster_thresholding': ('-c 0.20', 0.20), + 'cluster_mass_thresholding': ('-C 0.40', 0.40), + 'fcluster_thresholding': ('-F 0.10', 0.10), + 'fcluster_mass_thresholding': ('-S 0.30', 0.30), + 'variance_smoothing': ('-v 0.20', 0.20), + 'diagnostics_off': ('--quiet', True), + 'output_raw': ('-R', True), + 'output_perm_vect': ('-P', True), + 'int_seed': ('--seed=20', 20), + 'TFCE_height_param': ('--tfce_H=0.11', 0.11), + 'TFCE_extent_param': ('--tfce_E=0.50', 0.50), + 'TFCE_connectivity': ('--tfce_C=0.30', 0.30), + 'list_num_voxel_EVs_pos': ('--vxl=' + repr([1, 2, 3, 4]), + repr([1, 2, 3, 4])), + 'list_img_voxel_EVs': ('--vxf=' + repr([6, 7, 8, 9, 3]), + repr([6, 7, 8, 9, 3]))} for name, settings in list(opt_map.items()): rand4 = fsl.Randomise_parallel(input_4D='infile', @@ -379,13 +367,13 @@ def test_Vec_reg(): yield assert_equal, results.interface.inputs.affineTmat, 'tmat3.mat' # test arguments for opt_map - opt_map = {'verbose': ('-v', True), - 'helpDoc': ('-h', True), - 'tensor': ('--tensor', True), - 'affineTmat': ('-t Tmat', 'Tmat'), - 'warpFile': ('-w wrpFile', 'wrpFile'), - 'interpolation': ('--interp=sinc', 'sinc'), - 'brainMask': ('-m mask', 'mask')} + opt_map = {'verbose': ('-v', True), + 'helpDoc': ('-h', True), + 'tensor': ('--tensor', True), + 'affineTmat': ('-t Tmat', 'Tmat'), + 'warpFile': ('-w wrpFile', 'wrpFile'), + 'interpolation': ('--interp=sinc', 'sinc'), + 'brainMask': ('-m mask', 'mask')} for name, settings in list(opt_map.items()): vrg4 = fsl.VecReg(infile='infile', outfile='outfile', diff --git a/nipype/interfaces/fsl/tests/test_preprocess.py b/nipype/interfaces/fsl/tests/test_preprocess.py index 8ae16e6c28..1065fad6a5 100644 --- a/nipype/interfaces/fsl/tests/test_preprocess.py +++ b/nipype/interfaces/fsl/tests/test_preprocess.py @@ -74,19 +74,19 @@ def func(): # Our options and some test values for them # Should parallel the opt_map structure in the class for clarity opt_map = { - 'outline': ('-o', True), - 'mask': ('-m', True), - 'skull': ('-s', True), - 'no_output': ('-n', True), - 'frac': ('-f 0.40', 0.4), - 'vertical_gradient': ('-g 0.75', 0.75), - 'radius': ('-r 20', 20), - 'center': ('-c 54 75 80', [54, 75, 80]), - 'threshold': ('-t', True), - 'mesh': ('-e', True), - 'surfaces': ('-A', True) - # 'verbose': ('-v', True), - # 'flags': ('--i-made-this-up', '--i-made-this-up'), + 'outline': ('-o', True), + 'mask': ('-m', True), + 'skull': ('-s', True), + 'no_output': ('-n', True), + 'frac': ('-f 0.40', 0.4), + 'vertical_gradient': ('-g 0.75', 0.75), + 'radius': ('-r 20', 20), + 'center': ('-c 54 75 80', [54, 75, 80]), + 'threshold': ('-t', True), + 'mesh': ('-e', True), + 'surfaces': ('-A', True) + # 'verbose': ('-v', True), + # 'flags': ('--i-made-this-up', '--i-made-this-up'), } # Currently we don't test -R, -S, -B, -Z, -F, -A or -A2 @@ -129,32 +129,31 @@ def test_fast(): # Our options and some test values for them # Should parallel the opt_map structure in the class for clarity - opt_map = {'number_classes': ('-n 4', 4), - 'bias_iters': ('-I 5', 5), - 'bias_lowpass': ('-l 15', 15), - 'img_type': ('-t 2', 2), - 'init_seg_smooth': ('-f 0.035', 0.035), - 'segments': ('-g', True), - 'init_transform': ('-a %s' % (tmp_infile), '%s' % (tmp_infile)), - 'other_priors': ('-A %s %s %s' % (tmp_infile, tmp_infile, - tmp_infile), - (['%s' % (tmp_infile), - '%s' % (tmp_infile), - '%s' % (tmp_infile)])), - 'no_pve': ('--nopve', True), - 'output_biasfield': ('-b', True), + opt_map = {'number_classes': ('-n 4', 4), + 'bias_iters': ('-I 5', 5), + 'bias_lowpass': ('-l 15', 15), + 'img_type': ('-t 2', 2), + 'init_seg_smooth': ('-f 0.035', 0.035), + 'segments': ('-g', True), + 'init_transform': ('-a %s' % (tmp_infile), '%s' % (tmp_infile)), + 'other_priors': ('-A %s %s %s' % (tmp_infile, tmp_infile, + tmp_infile), + (['%s' % (tmp_infile), + '%s' % (tmp_infile), + '%s' % (tmp_infile)])), + 'no_pve': ('--nopve', True), + 'output_biasfield': ('-b', True), 'output_biascorrected': ('-B', True), - 'no_bias': ('-N', True), - 'out_basename': ('-o fasted', 'fasted'), - 'use_priors': ('-P', True), - 'segment_iters': ('-W 14', 14), - 'mixel_smooth': ('-R 0.25', 0.25), - 'iters_afterbias': ('-O 3', 3), - 'hyper': ('-H 0.15', 0.15), - 'verbose': ('-v', True), - 'manual_seg': ('-s %s' % (tmp_infile), - '%s' % (tmp_infile)), - 'probability_maps': ('-p', True), + 'no_bias': ('-N', True), + 'out_basename': ('-o fasted', 'fasted'), + 'use_priors': ('-P', True), + 'segment_iters': ('-W 14', 14), + 'mixel_smooth': ('-R 0.25', 0.25), + 'iters_afterbias': ('-O 3', 3), + 'hyper': ('-H 0.15', 0.15), + 'verbose': ('-v', True), + 'manual_seg': ('-s %s' % (tmp_infile), '%s' % (tmp_infile)), + 'probability_maps': ('-p', True), } # test each of our arguments @@ -299,21 +298,21 @@ def test_mcflirt(): yield assert_equal, frt.cmdline, realcmd opt_map = { - 'cost': ('-cost mutualinfo', 'mutualinfo'), - 'bins': ('-bins 256', 256), - 'dof': ('-dof 6', 6), - 'ref_vol': ('-refvol 2', 2), - 'scaling': ('-scaling 6.00', 6.00), - 'smooth': ('-smooth 1.00', 1.00), - 'rotation': ('-rotation 2', 2), - 'stages': ('-stages 3', 3), - 'init': ('-init %s' % (infile), infile), + 'cost': ('-cost mutualinfo', 'mutualinfo'), + 'bins': ('-bins 256', 256), + 'dof': ('-dof 6', 6), + 'ref_vol': ('-refvol 2', 2), + 'scaling': ('-scaling 6.00', 6.00), + 'smooth': ('-smooth 1.00', 1.00), + 'rotation': ('-rotation 2', 2), + 'stages': ('-stages 3', 3), + 'init': ('-init %s' % (infile), infile), 'use_gradient': ('-gdt', True), - 'use_contour': ('-edge', True), - 'mean_vol': ('-meanvol', True), - 'stats_imgs': ('-stats', True), - 'save_mats': ('-mats', True), - 'save_plots': ('-plots', True), + 'use_contour': ('-edge', True), + 'mean_vol': ('-meanvol', True), + 'stats_imgs': ('-stats', True), + 'save_mats': ('-mats', True), + 'save_plots': ('-plots', True), } for name, settings in list(opt_map.items()): @@ -369,7 +368,7 @@ def test_fnirt(): elif item in ('in_fwhm'): cmd = 'fnirt --in=%s %s=%s --logout=%s '\ '--ref=%s --iout=%s' % (infile, flag, - strval, log, reffile, iout) + strval, log, reffile, iout) elif item.startswith('apply'): cmd = 'fnirt %s=%s '\ '--in=%s '\ @@ -396,17 +395,17 @@ def test_fnirt(): # test files opt_map = { - 'affine_file': ('--aff='), - 'inwarp_file': ('--inwarp='), + 'affine_file': ('--aff='), + 'inwarp_file': ('--inwarp='), 'in_intensitymap_file': ('--intin='), - 'config_file': ('--config='), - 'refmask_file': ('--refmask='), - 'inmask_file': ('--inmask='), - 'field_file': ('--fout='), - 'jacobian_file': ('--jout='), - 'modulatedref_file': ('--refout='), + 'config_file': ('--config='), + 'refmask_file': ('--refmask='), + 'inmask_file': ('--inmask='), + 'field_file': ('--fout='), + 'jacobian_file': ('--jout='), + 'modulatedref_file': ('--refout='), 'out_intensitymap_file': ('--intout='), - 'log_file': ('--logout=')} + 'log_file': ('--logout=')} for name, settings in list(opt_map.items()): fnirt = fsl.FNIRT(in_file=infile, @@ -457,9 +456,9 @@ def test_fnirt(): def test_applywarp(): tmpdir, infile, reffile = setup_flirt() opt_map = { - 'out_file': ('--out=bar.nii', 'bar.nii'), - 'premat': ('--premat=%s' % (reffile), reffile), - 'postmat': ('--postmat=%s' % (reffile), reffile), + 'out_file': ('--out=bar.nii', 'bar.nii'), + 'premat': ('--premat=%s' % (reffile), reffile), + 'postmat': ('--postmat=%s' % (reffile), reffile), } # in_file, ref_file, field_file mandatory diff --git a/nipype/interfaces/tests/test_base.py b/nipype/interfaces/tests/test_base.py index cbfd95f092..d186f64b6b 100644 --- a/nipype/interfaces/tests/test_base.py +++ b/nipype/interfaces/tests/test_base.py @@ -140,7 +140,7 @@ class MyInterface(nib.BaseInterface): myif = MyInterface() yield assert_raises, TypeError, setattr(myif.inputs, 'kung', 10.0) myif.inputs.foo = 1 - yield assert_equal, myif.inputs.foo, 1 + yield assert_equal, myif.inputs.foo, 1 set_bar = lambda: setattr(myif.inputs, 'bar', 1) yield assert_raises, IOError, set_bar yield assert_equal, myif.inputs.foo, 1 @@ -386,7 +386,7 @@ class spec4(nib.TraitedSpec): infields = spec4(moo=nme, doo=[tmp_infile]) hashval2 = infields.get_hashval(hash_method='content') - yield assert_not_equal, hashval1[1], hashval2[1] + yield assert_not_equal, hashval1[1], hashval2[1] os.chdir(pwd) teardown_file(tmpd) diff --git a/nipype/workflows/dmri/dipy/denoise.py b/nipype/workflows/dmri/dipy/denoise.py index 183756a1cc..7b7afc47ee 100644 --- a/nipype/workflows/dmri/dipy/denoise.py +++ b/nipype/workflows/dmri/dipy/denoise.py @@ -36,12 +36,12 @@ def nlmeans_pipeline(name='Denoise', wf = pe.Workflow(name=name) wf.connect([ - (inputnode, nmask, [('in_file', 'in_file'), - ('in_mask', 'in_mask')]), - (inputnode, nlmeans, [('in_file', 'in_file'), - ('in_mask', 'in_mask')]), - (nmask, nlmeans, [('out_file', 'noise_mask')]), - (nlmeans, outputnode, [('out_file', 'out_file')]) + (inputnode, nmask, [('in_file', 'in_file'), + ('in_mask', 'in_mask')]), + (inputnode, nlmeans, [('in_file', 'in_file'), + ('in_mask', 'in_mask')]), + (nmask, nlmeans, [('out_file', 'noise_mask')]), + (nlmeans, outputnode, [('out_file', 'out_file')]) ]) return wf diff --git a/nipype/workflows/dmri/fsl/artifacts.py b/nipype/workflows/dmri/fsl/artifacts.py index 03936c5695..dc7387f0c0 100644 --- a/nipype/workflows/dmri/fsl/artifacts.py +++ b/nipype/workflows/dmri/fsl/artifacts.py @@ -73,36 +73,34 @@ def all_fmb_pipeline(name='hmc_sdc_ecc', fugue_params=dict(smooth3d=2.0)): wf = pe.Workflow(name=name) wf.connect([ - (inputnode, hmc, [('in_file', 'inputnode.in_file'), - ('in_bvec', 'inputnode.in_bvec'), - ('in_bval', 'inputnode.in_bval')]), - (inputnode, list_b0, [('in_bval', 'in_bval')]), - (inputnode, avg_b0_0, [('in_file', 'in_file')]), - (list_b0, avg_b0_0, [('out_idx', 'index')]), - (avg_b0_0, bet_dwi0, [('out_file', 'in_file')]), - (bet_dwi0, hmc, [('mask_file', 'inputnode.in_mask')]), - (hmc, sdc, [ - ('outputnode.out_file', 'inputnode.in_file')]), - (bet_dwi0, sdc, [('mask_file', 'inputnode.in_mask')]), - (inputnode, sdc, [('bmap_pha', 'inputnode.bmap_pha'), - ('bmap_mag', 'inputnode.bmap_mag'), - ('epi_param', 'inputnode.settings')]), - (list_b0, sdc, [('out_idx', 'inputnode.in_ref')]), - (hmc, ecc, [ - ('outputnode.out_xfms', 'inputnode.in_xfms')]), - (inputnode, ecc, [('in_file', 'inputnode.in_file'), - ('in_bval', 'inputnode.in_bval')]), - (bet_dwi0, ecc, [('mask_file', 'inputnode.in_mask')]), - (ecc, avg_b0_1, [('outputnode.out_file', 'in_file')]), - (list_b0, avg_b0_1, [('out_idx', 'index')]), - (avg_b0_1, bet_dwi1, [('out_file', 'in_file')]), - (inputnode, unwarp, [('in_file', 'inputnode.in_dwi')]), - (hmc, unwarp, [('outputnode.out_xfms', 'inputnode.in_hmc')]), - (ecc, unwarp, [('outputnode.out_xfms', 'inputnode.in_ecc')]), - (sdc, unwarp, [('outputnode.out_warp', 'inputnode.in_sdc')]), - (hmc, outputnode, [('outputnode.out_bvec', 'out_bvec')]), - (unwarp, outputnode, [('outputnode.out_file', 'out_file')]), - (bet_dwi1, outputnode, [('mask_file', 'out_mask')]) + (inputnode, hmc, [('in_file', 'inputnode.in_file'), + ('in_bvec', 'inputnode.in_bvec'), + ('in_bval', 'inputnode.in_bval')]), + (inputnode, list_b0, [('in_bval', 'in_bval')]), + (inputnode, avg_b0_0, [('in_file', 'in_file')]), + (list_b0, avg_b0_0, [('out_idx', 'index')]), + (avg_b0_0, bet_dwi0, [('out_file', 'in_file')]), + (bet_dwi0, hmc, [('mask_file', 'inputnode.in_mask')]), + (hmc, sdc, [('outputnode.out_file', 'inputnode.in_file')]), + (bet_dwi0, sdc, [('mask_file', 'inputnode.in_mask')]), + (inputnode, sdc, [('bmap_pha', 'inputnode.bmap_pha'), + ('bmap_mag', 'inputnode.bmap_mag'), + ('epi_param', 'inputnode.settings')]), + (list_b0, sdc, [('out_idx', 'inputnode.in_ref')]), + (hmc, ecc, [('outputnode.out_xfms', 'inputnode.in_xfms')]), + (inputnode, ecc, [('in_file', 'inputnode.in_file'), + ('in_bval', 'inputnode.in_bval')]), + (bet_dwi0, ecc, [('mask_file', 'inputnode.in_mask')]), + (ecc, avg_b0_1, [('outputnode.out_file', 'in_file')]), + (list_b0, avg_b0_1, [('out_idx', 'index')]), + (avg_b0_1, bet_dwi1, [('out_file', 'in_file')]), + (inputnode, unwarp, [('in_file', 'inputnode.in_dwi')]), + (hmc, unwarp, [('outputnode.out_xfms', 'inputnode.in_hmc')]), + (ecc, unwarp, [('outputnode.out_xfms', 'inputnode.in_ecc')]), + (sdc, unwarp, [('outputnode.out_warp', 'inputnode.in_sdc')]), + (hmc, outputnode, [('outputnode.out_bvec', 'out_bvec')]), + (unwarp, outputnode, [('outputnode.out_file', 'out_file')]), + (bet_dwi1, outputnode, [('mask_file', 'out_mask')]) ]) return wf @@ -163,33 +161,31 @@ def all_peb_pipeline(name='hmc_sdc_ecc', wf = pe.Workflow(name=name) wf.connect([ - (inputnode, hmc, [('in_file', 'inputnode.in_file'), - ('in_bvec', 'inputnode.in_bvec'), - ('in_bval', 'inputnode.in_bval')]), - (inputnode, avg_b0_0, [('in_file', 'in_dwi'), - ('in_bval', 'in_bval')]), - (avg_b0_0, bet_dwi0, [('out_file', 'in_file')]), - (bet_dwi0, hmc, [('mask_file', 'inputnode.in_mask')]), - (hmc, sdc, [ - ('outputnode.out_file', 'inputnode.in_file')]), - (bet_dwi0, sdc, [('mask_file', 'inputnode.in_mask')]), - (inputnode, sdc, [('in_bval', 'inputnode.in_bval'), - ('alt_file', 'inputnode.alt_file')]), - (inputnode, ecc, [('in_file', 'inputnode.in_file'), - ('in_bval', 'inputnode.in_bval')]), - (bet_dwi0, ecc, [('mask_file', 'inputnode.in_mask')]), - (hmc, ecc, [ - ('outputnode.out_xfms', 'inputnode.in_xfms')]), - (ecc, avg_b0_1, [('outputnode.out_file', 'in_dwi')]), - (inputnode, avg_b0_1, [('in_bval', 'in_bval')]), - (avg_b0_1, bet_dwi1, [('out_file', 'in_file')]), - (inputnode, unwarp, [('in_file', 'inputnode.in_dwi')]), - (hmc, unwarp, [('outputnode.out_xfms', 'inputnode.in_hmc')]), - (ecc, unwarp, [('outputnode.out_xfms', 'inputnode.in_ecc')]), - (sdc, unwarp, [('outputnode.out_warp', 'inputnode.in_sdc')]), - (hmc, outputnode, [('outputnode.out_bvec', 'out_bvec')]), - (unwarp, outputnode, [('outputnode.out_file', 'out_file')]), - (bet_dwi1, outputnode, [('mask_file', 'out_mask')]) + (inputnode, hmc, [('in_file', 'inputnode.in_file'), + ('in_bvec', 'inputnode.in_bvec'), + ('in_bval', 'inputnode.in_bval')]), + (inputnode, avg_b0_0, [('in_file', 'in_dwi'), + ('in_bval', 'in_bval')]), + (avg_b0_0, bet_dwi0, [('out_file', 'in_file')]), + (bet_dwi0, hmc, [('mask_file', 'inputnode.in_mask')]), + (hmc, sdc, [('outputnode.out_file', 'inputnode.in_file')]), + (bet_dwi0, sdc, [('mask_file', 'inputnode.in_mask')]), + (inputnode, sdc, [('in_bval', 'inputnode.in_bval'), + ('alt_file', 'inputnode.alt_file')]), + (inputnode, ecc, [('in_file', 'inputnode.in_file'), + ('in_bval', 'inputnode.in_bval')]), + (bet_dwi0, ecc, [('mask_file', 'inputnode.in_mask')]), + (hmc, ecc, [('outputnode.out_xfms', 'inputnode.in_xfms')]), + (ecc, avg_b0_1, [('outputnode.out_file', 'in_dwi')]), + (inputnode, avg_b0_1, [('in_bval', 'in_bval')]), + (avg_b0_1, bet_dwi1, [('out_file', 'in_file')]), + (inputnode, unwarp, [('in_file', 'inputnode.in_dwi')]), + (hmc, unwarp, [('outputnode.out_xfms', 'inputnode.in_hmc')]), + (ecc, unwarp, [('outputnode.out_xfms', 'inputnode.in_ecc')]), + (sdc, unwarp, [('outputnode.out_warp', 'inputnode.in_sdc')]), + (hmc, outputnode, [('outputnode.out_bvec', 'out_bvec')]), + (unwarp, outputnode, [('outputnode.out_file', 'out_file')]), + (bet_dwi1, outputnode, [('mask_file', 'out_mask')]) ]) return wf @@ -261,30 +257,29 @@ def _gen_index(in_file): wf = pe.Workflow(name=name) wf.connect([ - (inputnode, avg_b0_0, [('in_file', 'in_dwi'), - ('in_bval', 'in_bval')]), - (avg_b0_0, bet_dwi0, [('out_file', 'in_file')]), - (bet_dwi0, sdc, [('mask_file', 'inputnode.in_mask')]), - (inputnode, sdc, [('in_file', 'inputnode.in_file'), - ('alt_file', 'inputnode.alt_file'), - ('in_bval', 'inputnode.in_bval')]), - (sdc, ecc, [('topup.out_enc_file', 'in_acqp'), - ('topup.out_fieldcoef', - 'in_topup_fieldcoef'), - ('topup.out_movpar', 'in_topup_movpar')]), - (bet_dwi0, ecc, [('mask_file', 'in_mask')]), - (inputnode, ecc, [('in_file', 'in_file'), - (('in_file', _gen_index), 'in_index'), - ('in_bval', 'in_bval'), - ('in_bvec', 'in_bvec')]), - (inputnode, rot_bvec, [('in_bvec', 'in_bvec')]), - (ecc, rot_bvec, [('out_parameter', 'eddy_params')]), - (ecc, avg_b0_1, [('out_corrected', 'in_dwi')]), - (inputnode, avg_b0_1, [('in_bval', 'in_bval')]), - (avg_b0_1, bet_dwi1, [('out_file', 'in_file')]), - (ecc, outputnode, [('out_corrected', 'out_file')]), - (rot_bvec, outputnode, [('out_file', 'out_bvec')]), - (bet_dwi1, outputnode, [('mask_file', 'out_mask')]) + (inputnode, avg_b0_0, [('in_file', 'in_dwi'), + ('in_bval', 'in_bval')]), + (avg_b0_0, bet_dwi0, [('out_file', 'in_file')]), + (bet_dwi0, sdc, [('mask_file', 'inputnode.in_mask')]), + (inputnode, sdc, [('in_file', 'inputnode.in_file'), + ('alt_file', 'inputnode.alt_file'), + ('in_bval', 'inputnode.in_bval')]), + (sdc, ecc, [('topup.out_enc_file', 'in_acqp'), + ('topup.out_fieldcoef', 'in_topup_fieldcoef'), + ('topup.out_movpar', 'in_topup_movpar')]), + (bet_dwi0, ecc, [('mask_file', 'in_mask')]), + (inputnode, ecc, [('in_file', 'in_file'), + (('in_file', _gen_index), 'in_index'), + ('in_bval', 'in_bval'), + ('in_bvec', 'in_bvec')]), + (inputnode, rot_bvec, [('in_bvec', 'in_bvec')]), + (ecc, rot_bvec, [('out_parameter', 'eddy_params')]), + (ecc, avg_b0_1, [('out_corrected', 'in_dwi')]), + (inputnode, avg_b0_1, [('in_bval', 'in_bval')]), + (avg_b0_1, bet_dwi1, [('out_file', 'in_file')]), + (ecc, outputnode, [('out_corrected', 'out_file')]), + (rot_bvec, outputnode, [('out_file', 'out_bvec')]), + (bet_dwi1, outputnode, [('mask_file', 'out_mask')]) ]) return wf @@ -379,20 +374,20 @@ def hmc_pipeline(name='motion_correct'): wf = pe.Workflow(name=name) wf.connect([ - (inputnode, split, [('in_file', 'in_file'), - ('in_bval', 'in_bval'), - ('ref_num', 'ref_num')]), - (inputnode, flirt, [('in_mask', 'inputnode.ref_mask')]), - (split, flirt, [('out_ref', 'inputnode.reference'), - ('out_mov', 'inputnode.in_file'), - ('out_bval', 'inputnode.in_bval')]), - (flirt, insmat, [('outputnode.out_xfms', 'inlist')]), - (split, insmat, [('volid', 'volid')]), - (inputnode, rot_bvec, [('in_bvec', 'in_bvec')]), - (insmat, rot_bvec, [('out', 'in_matrix')]), - (rot_bvec, outputnode, [('out_file', 'out_bvec')]), - (flirt, outputnode, [('outputnode.out_file', 'out_file')]), - (insmat, outputnode, [('out', 'out_xfms')]) + (inputnode, split, [('in_file', 'in_file'), + ('in_bval', 'in_bval'), + ('ref_num', 'ref_num')]), + (inputnode, flirt, [('in_mask', 'inputnode.ref_mask')]), + (split, flirt, [('out_ref', 'inputnode.reference'), + ('out_mov', 'inputnode.in_file'), + ('out_bval', 'inputnode.in_bval')]), + (flirt, insmat, [('outputnode.out_xfms', 'inlist')]), + (split, insmat, [('volid', 'volid')]), + (inputnode, rot_bvec, [('in_bvec', 'in_bvec')]), + (insmat, rot_bvec, [('out', 'in_matrix')]), + (rot_bvec, outputnode, [('out_file', 'out_bvec')]), + (flirt, outputnode, [('outputnode.out_file', 'out_file')]), + (insmat, outputnode, [('out', 'out_xfms')]) ]) return wf @@ -491,27 +486,27 @@ def ecc_pipeline(name='eddy_correct'): wf = pe.Workflow(name=name) wf.connect([ - (inputnode, avg_b0, [('in_file', 'in_dwi'), - ('in_bval', 'in_bval')]), - (inputnode, pick_dws, [('in_file', 'in_dwi'), - ('in_bval', 'in_bval')]), - (inputnode, merge, [('in_file', 'in_dwi'), - ('in_bval', 'in_bval')]), - (inputnode, flirt, [('in_mask', 'inputnode.ref_mask'), - ('in_xfms', 'inputnode.in_xfms'), - ('in_bval', 'inputnode.in_bval')]), - (inputnode, get_mat, [('in_bval', 'in_bval')]), - (avg_b0, flirt, [('out_file', 'inputnode.reference')]), - (pick_dws, flirt, [('out_file', 'inputnode.in_file')]), - (flirt, get_mat, [('outputnode.out_xfms', 'in_xfms')]), - (flirt, mult, [(('outputnode.out_xfms', _xfm_jacobian), - 'operand_value')]), - (flirt, split, [('outputnode.out_file', 'in_file')]), - (split, mult, [('out_files', 'in_file')]), - (mult, thres, [('out_file', 'in_file')]), - (thres, merge, [('out_file', 'in_corrected')]), - (get_mat, outputnode, [('out_files', 'out_xfms')]), - (merge, outputnode, [('out_file', 'out_file')]) + (inputnode, avg_b0, [('in_file', 'in_dwi'), + ('in_bval', 'in_bval')]), + (inputnode, pick_dws, [('in_file', 'in_dwi'), + ('in_bval', 'in_bval')]), + (inputnode, merge, [('in_file', 'in_dwi'), + ('in_bval', 'in_bval')]), + (inputnode, flirt, [('in_mask', 'inputnode.ref_mask'), + ('in_xfms', 'inputnode.in_xfms'), + ('in_bval', 'inputnode.in_bval')]), + (inputnode, get_mat, [('in_bval', 'in_bval')]), + (avg_b0, flirt, [('out_file', 'inputnode.reference')]), + (pick_dws, flirt, [('out_file', 'inputnode.in_file')]), + (flirt, get_mat, [('outputnode.out_xfms', 'in_xfms')]), + (flirt, mult, [(('outputnode.out_xfms', _xfm_jacobian), + 'operand_value')]), + (flirt, split, [('outputnode.out_file', 'in_file')]), + (split, mult, [('out_files', 'in_file')]), + (mult, thres, [('out_file', 'in_file')]), + (thres, merge, [('out_file', 'in_corrected')]), + (get_mat, outputnode, [('out_files', 'out_xfms')]), + (merge, outputnode, [('out_file', 'out_file')]) ]) return wf @@ -644,58 +639,58 @@ def sdc_fmb(name='fmb_correction', interp='Linear', wf = pe.Workflow(name=name) wf.connect([ - (inputnode, r_params, [('settings', 'in_file')]), - (r_params, eff_echo, [('echospacing', 'echospacing'), - ('acc_factor', 'acc_factor')]), - (inputnode, pha2rads, [('bmap_pha', 'in_file')]), - (inputnode, firstmag, [('bmap_mag', 'in_file')]), - (inputnode, baseline, [('in_file', 'in_file'), - ('in_ref', 'index')]), - (firstmag, n4, [('roi_file', 'input_image')]), - (n4, bet, [('output_image', 'in_file')]), - (bet, dilate, [('mask_file', 'in_file')]), - (pha2rads, prelude, [('out_file', 'phase_file')]), - (n4, prelude, [('output_image', 'magnitude_file')]), - (dilate, prelude, [('out_file', 'mask_file')]), - (r_params, rad2rsec, [('delta_te', 'delta_te')]), - (prelude, rad2rsec, [('unwrapped_phase_file', 'in_file')]), - - (baseline, fmm2b0, [('out_file', 'fixed_image')]), - (n4, fmm2b0, [('output_image', 'moving_image')]), - (inputnode, fmm2b0, [('in_mask', 'fixed_image_mask')]), - (dilate, fmm2b0, [('out_file', 'moving_image_mask')]), - - (baseline, applyxfm, [('out_file', 'reference_image')]), - (rad2rsec, applyxfm, [('out_file', 'input_image')]), - (fmm2b0, applyxfm, [ + (inputnode, r_params, [('settings', 'in_file')]), + (r_params, eff_echo, [('echospacing', 'echospacing'), + ('acc_factor', 'acc_factor')]), + (inputnode, pha2rads, [('bmap_pha', 'in_file')]), + (inputnode, firstmag, [('bmap_mag', 'in_file')]), + (inputnode, baseline, [('in_file', 'in_file'), + ('in_ref', 'index')]), + (firstmag, n4, [('roi_file', 'input_image')]), + (n4, bet, [('output_image', 'in_file')]), + (bet, dilate, [('mask_file', 'in_file')]), + (pha2rads, prelude, [('out_file', 'phase_file')]), + (n4, prelude, [('output_image', 'magnitude_file')]), + (dilate, prelude, [('out_file', 'mask_file')]), + (r_params, rad2rsec, [('delta_te', 'delta_te')]), + (prelude, rad2rsec, [('unwrapped_phase_file', 'in_file')]), + + (baseline, fmm2b0, [('out_file', 'fixed_image')]), + (n4, fmm2b0, [('output_image', 'moving_image')]), + (inputnode, fmm2b0, [('in_mask', 'fixed_image_mask')]), + (dilate, fmm2b0, [('out_file', 'moving_image_mask')]), + + (baseline, applyxfm, [('out_file', 'reference_image')]), + (rad2rsec, applyxfm, [('out_file', 'input_image')]), + (fmm2b0, applyxfm, [ ('forward_transforms', 'transforms'), ('forward_invert_flags', 'invert_transform_flags')]), - (applyxfm, pre_fugue, [('output_image', 'fmap_in_file')]), - (inputnode, pre_fugue, [('in_mask', 'mask_file')]), - (pre_fugue, demean, [('fmap_out_file', 'in_file')]), - (inputnode, demean, [('in_mask', 'in_mask')]), - (demean, cleanup, [('out_file', 'inputnode.in_file')]), - (inputnode, cleanup, [('in_mask', 'inputnode.in_mask')]), - (cleanup, addvol, [('outputnode.out_file', 'in_file')]), - (inputnode, vsm, [('in_mask', 'mask_file')]), - (addvol, vsm, [('out_file', 'fmap_in_file')]), - (r_params, vsm, [('delta_te', 'asym_se_time')]), - (eff_echo, vsm, [('eff_echo', 'dwell_time')]), - (inputnode, split, [('in_file', 'in_file')]), - (split, unwarp, [('out_files', 'in_file')]), - (vsm, unwarp, [('shift_out_file', 'shift_in_file')]), - (r_params, unwarp, [ + (applyxfm, pre_fugue, [('output_image', 'fmap_in_file')]), + (inputnode, pre_fugue, [('in_mask', 'mask_file')]), + (pre_fugue, demean, [('fmap_out_file', 'in_file')]), + (inputnode, demean, [('in_mask', 'in_mask')]), + (demean, cleanup, [('out_file', 'inputnode.in_file')]), + (inputnode, cleanup, [('in_mask', 'inputnode.in_mask')]), + (cleanup, addvol, [('outputnode.out_file', 'in_file')]), + (inputnode, vsm, [('in_mask', 'mask_file')]), + (addvol, vsm, [('out_file', 'fmap_in_file')]), + (r_params, vsm, [('delta_te', 'asym_se_time')]), + (eff_echo, vsm, [('eff_echo', 'dwell_time')]), + (inputnode, split, [('in_file', 'in_file')]), + (split, unwarp, [('out_files', 'in_file')]), + (vsm, unwarp, [('shift_out_file', 'shift_in_file')]), + (r_params, unwarp, [ (('enc_dir', _fix_enc_dir), 'unwarp_direction')]), - (unwarp, thres, [('unwarped_file', 'in_file')]), - (thres, merge, [('out_file', 'in_files')]), - (r_params, vsm2dfm, [ + (unwarp, thres, [('unwarped_file', 'in_file')]), + (thres, merge, [('out_file', 'in_files')]), + (r_params, vsm2dfm, [ (('enc_dir', _fix_enc_dir), 'inputnode.enc_dir')]), - (merge, vsm2dfm, [('merged_file', 'inputnode.in_ref')]), - (vsm, vsm2dfm, [('shift_out_file', 'inputnode.in_vsm')]), - (merge, outputnode, [('merged_file', 'out_file')]), - (vsm, outputnode, [('shift_out_file', 'out_vsm')]), - (vsm2dfm, outputnode, [('outputnode.out_warp', 'out_warp')]) + (merge, vsm2dfm, [('merged_file', 'inputnode.in_ref')]), + (vsm, vsm2dfm, [('shift_out_file', 'inputnode.in_vsm')]), + (merge, outputnode, [('merged_file', 'out_file')]), + (vsm, outputnode, [('shift_out_file', 'out_vsm')]), + (vsm2dfm, outputnode, [('outputnode.out_warp', 'out_warp')]) ]) return wf @@ -782,25 +777,25 @@ def sdc_peb(name='peb_correction', wf = pe.Workflow(name=name) wf.connect([ - (inputnode, b0_ref, [('in_file', 'in_file'), - (('ref_num', _checkrnum), 't_min')]), - (inputnode, b0_alt, [('alt_file', 'in_file'), - (('ref_num', _checkrnum), 't_min')]), - (b0_ref, b0_comb, [('roi_file', 'in1')]), - (b0_alt, b0_comb, [('roi_file', 'in2')]), - (b0_comb, b0_merge, [('out', 'in_files')]), - (b0_merge, topup, [('merged_file', 'in_file')]), - (topup, unwarp, [('out_fieldcoef', 'in_topup_fieldcoef'), - ('out_movpar', 'in_topup_movpar'), - ('out_enc_file', 'encoding_file')]), - (inputnode, unwarp, [('in_file', 'in_files')]), - (unwarp, outputnode, [('out_corrected', 'out_file')]), + (inputnode, b0_ref, [('in_file', 'in_file'), + (('ref_num', _checkrnum), 't_min')]), + (inputnode, b0_alt, [('alt_file', 'in_file'), + (('ref_num', _checkrnum), 't_min')]), + (b0_ref, b0_comb, [('roi_file', 'in1')]), + (b0_alt, b0_comb, [('roi_file', 'in2')]), + (b0_comb, b0_merge, [('out', 'in_files')]), + (b0_merge, topup, [('merged_file', 'in_file')]), + (topup, unwarp, [('out_fieldcoef', 'in_topup_fieldcoef'), + ('out_movpar', 'in_topup_movpar'), + ('out_enc_file', 'encoding_file')]), + (inputnode, unwarp, [('in_file', 'in_files')]), + (unwarp, outputnode, [('out_corrected', 'out_file')]), # (b0_ref, scaling, [('roi_file', 'in_file')]), # (scaling, vsm2dfm, [('factor', 'inputnode.scaling')]), - (b0_ref, vsm2dfm, [('roi_file', 'inputnode.in_ref')]), - (topup, vsm2dfm, [('out_field', 'inputnode.in_vsm')]), - (topup, outputnode, [('out_field', 'out_vsm')]), - (vsm2dfm, outputnode, [('outputnode.out_warp', 'out_warp')]) + (b0_ref, vsm2dfm, [('roi_file', 'inputnode.in_ref')]), + (topup, vsm2dfm, [('out_field', 'inputnode.in_vsm')]), + (topup, outputnode, [('out_field', 'out_vsm')]), + (vsm2dfm, outputnode, [('outputnode.out_warp', 'out_warp')]) ]) return wf @@ -850,16 +845,16 @@ def remove_bias(name='bias_correct'): wf = pe.Workflow(name=name) wf.connect([ - (inputnode, avg_b0, [('in_file', 'in_dwi'), - ('in_bval', 'in_bval')]), - (avg_b0, n4, [('out_file', 'input_image')]), - (inputnode, n4, [('in_mask', 'mask_image')]), - (inputnode, split, [('in_file', 'in_file')]), - (n4, mult, [('bias_image', 'operand_files')]), - (split, mult, [('out_files', 'in_file')]), - (mult, thres, [('out_file', 'in_file')]), - (thres, merge, [('out_file', 'in_files')]), - (merge, outputnode, [('merged_file', 'out_file')]) + (inputnode, avg_b0, [('in_file', 'in_dwi'), + ('in_bval', 'in_bval')]), + (avg_b0, n4, [('out_file', 'input_image')]), + (inputnode, n4, [('in_mask', 'mask_image')]), + (inputnode, split, [('in_file', 'in_file')]), + (n4, mult, [('bias_image', 'operand_files')]), + (split, mult, [('out_files', 'in_file')]), + (mult, thres, [('out_file', 'in_file')]), + (thres, merge, [('out_file', 'in_files')]), + (merge, outputnode, [('merged_file', 'out_file')]) ]) return wf diff --git a/nipype/workflows/dmri/fsl/dti.py b/nipype/workflows/dmri/fsl/dti.py index b3427645b8..c12238786d 100644 --- a/nipype/workflows/dmri/fsl/dti.py +++ b/nipype/workflows/dmri/fsl/dti.py @@ -74,14 +74,14 @@ def create_bedpostx_pipeline(name='bedpostx', params={'n_fibres': 2, 'fudge': 1, wf = pe.Workflow(name=name) wf.connect([ - (inputnode, slice_dwi, [('dwi', 'in_file')]), - (inputnode, slice_msk, [('mask', 'in_file')]), - (slice_dwi, mask_dwi, [('out_files', 'in_file')]), - (slice_msk, mask_dwi, [('out_files', 'in_file2')]), - (slice_dwi, xfibres, [('out_files', 'dwi')]), - (mask_dwi, xfibres, [('out_file', 'mask')]), - (inputnode, xfibres, [('bvecs', 'bvecs'), - ('bvals', 'bvals')]), + (inputnode, slice_dwi, [('dwi', 'in_file')]), + (inputnode, slice_msk, [('mask', 'in_file')]), + (slice_dwi, mask_dwi, [('out_files', 'in_file')]), + (slice_msk, mask_dwi, [('out_files', 'in_file2')]), + (slice_dwi, xfibres, [('out_files', 'dwi')]), + (mask_dwi, xfibres, [('out_file', 'mask')]), + (inputnode, xfibres, [('bvecs', 'bvecs'), + ('bvals', 'bvals')]), (inputnode, make_dyads, [('mask', 'mask')]) ]) @@ -119,10 +119,10 @@ def merge_and_mean(name='mm'): wf = pe.Workflow(name=name) wf.connect([ - (inputnode, merge, [(('in_files', transpose), 'in_files')]), - (merge, mean, [('merged_file', 'in_file')]), + (inputnode, merge, [(('in_files', transpose), 'in_files')]), + (merge, mean, [('merged_file', 'in_file')]), (merge, outputnode, [('merged_file', 'merged')]), - (mean, outputnode, [('out_file', 'mean')]) + (mean, outputnode, [('out_file', 'mean')]) ]) return wf @@ -190,18 +190,18 @@ def bedpostx_parallel(name='bedpostx_parallel', wf = pe.Workflow(name=name) wf.connect([ - (inputnode, slice_dwi, [('dwi', 'in_file'), - ('mask', 'in_mask')]), - (slice_dwi, xfibres, [('out_files', 'dwi'), - ('out_masks', 'mask')]), - (inputnode, xfibres, [('bvecs', 'bvecs'), - ('bvals', 'bvals')]), - (inputnode, mrg_dyads, [('mask', 'in_reference')]), - (xfibres, mrg_dyads, [(('dyads', transpose), 'in_files')]), - (slice_dwi, mrg_dyads, [('out_index', 'in_index')]), - (inputnode, mrg_fsamp, [('mask', 'in_reference')]), - (xfibres, mrg_fsamp, [(('mean_fsamples', transpose), 'in_files')]), - (slice_dwi, mrg_fsamp, [('out_index', 'in_index')]), + (inputnode, slice_dwi, [('dwi', 'in_file'), + ('mask', 'in_mask')]), + (slice_dwi, xfibres, [('out_files', 'dwi'), + ('out_masks', 'mask')]), + (inputnode, xfibres, [('bvecs', 'bvecs'), + ('bvals', 'bvals')]), + (inputnode, mrg_dyads, [('mask', 'in_reference')]), + (xfibres, mrg_dyads, [(('dyads', transpose), 'in_files')]), + (slice_dwi, mrg_dyads, [('out_index', 'in_index')]), + (inputnode, mrg_fsamp, [('mask', 'in_reference')]), + (xfibres, mrg_fsamp, [(('mean_fsamples', transpose), 'in_files')]), + (slice_dwi, mrg_fsamp, [('out_index', 'in_index')]), (mrg_dyads, outputnode, [('merged_file', 'dyads')]), (mrg_fsamp, outputnode, [('merged_file', 'fsamples')]) ]) @@ -247,11 +247,11 @@ def merge_and_mean_parallel(name='mm'): wf = pe.Workflow(name=name) wf.connect([ - (inputnode, merge, [(('in_files', transpose), 'in_files'), - ('in_reference', 'in_reference'), - ('in_index', 'in_index')]), - (merge, mean, [('merged_file', 'in_file')]), + (inputnode, merge, [(('in_files', transpose), 'in_files'), + ('in_reference', 'in_reference'), + ('in_index', 'in_index')]), + (merge, mean, [('merged_file', 'in_file')]), (merge, outputnode, [('merged_file', 'merged')]), - (mean, outputnode, [('out_file', 'mean')]) + (mean, outputnode, [('out_file', 'mean')]) ]) return wf diff --git a/nipype/workflows/dmri/fsl/epi.py b/nipype/workflows/dmri/fsl/epi.py index b8d3696db0..bfeb2afeb9 100644 --- a/nipype/workflows/dmri/fsl/epi.py +++ b/nipype/workflows/dmri/fsl/epi.py @@ -366,26 +366,26 @@ def fieldmap_correction(name='fieldmap_correction', nocheck=False): name='outputnode') pipeline.connect([ - (inputnode, select_mag, [('fieldmap_mag', 'in_file')]), - (inputnode, fslprep, [('fieldmap_pha', 'in_phase'), ('te_diff', 'delta_TE')]), - (inputnode, mask_mag, [('in_mask', 'mask_file')]), - (select_mag, mask_mag, [('roi_file', 'in_file')]), - (mask_mag, fslprep, [('out_file', 'in_magnitude')]), - (fslprep, vsm, [('out_fieldmap', 'phasemap_in_file')]), - (inputnode, vsm, [('fieldmap_mag', 'in_file'), - ('encoding_direction', 'unwarp_direction'), - (('te_diff', _ms2sec), 'asym_se_time'), - ('vsm_sigma', 'smooth2d'), - (('epi_echospacing', _ms2sec), 'dwell_time')]), - (mask_mag, vsm, [('out_file', 'mask_file')]), - (inputnode, dwi_split, [('in_file', 'in_file')]), - (dwi_split, dwi_applyxfm, [('out_files', 'in_file')]), - (mask_mag, dwi_applyxfm, [('out_file', 'mask_file')]), - (vsm, dwi_applyxfm, [('shift_out_file', 'shift_in_file')]), - (inputnode, dwi_applyxfm, [('encoding_direction', 'unwarp_direction')]), - (dwi_applyxfm, dwi_merge, [('unwarped_file', 'in_files')]), - (dwi_merge, outputnode, [('merged_file', 'epi_corrected')]), - (vsm, outputnode, [('shift_out_file', 'out_vsm')]) + (inputnode, select_mag, [('fieldmap_mag', 'in_file')]), + (inputnode, fslprep, [('fieldmap_pha', 'in_phase'), ('te_diff', 'delta_TE')]), + (inputnode, mask_mag, [('in_mask', 'mask_file')]), + (select_mag, mask_mag, [('roi_file', 'in_file')]), + (mask_mag, fslprep, [('out_file', 'in_magnitude')]), + (fslprep, vsm, [('out_fieldmap', 'phasemap_in_file')]), + (inputnode, vsm, [('fieldmap_mag', 'in_file'), + ('encoding_direction', 'unwarp_direction'), + (('te_diff', _ms2sec), 'asym_se_time'), + ('vsm_sigma', 'smooth2d'), + (('epi_echospacing', _ms2sec), 'dwell_time')]), + (mask_mag, vsm, [('out_file', 'mask_file')]), + (inputnode, dwi_split, [('in_file', 'in_file')]), + (dwi_split, dwi_applyxfm, [('out_files', 'in_file')]), + (mask_mag, dwi_applyxfm, [('out_file', 'mask_file')]), + (vsm, dwi_applyxfm, [('shift_out_file', 'shift_in_file')]), + (inputnode, dwi_applyxfm, [('encoding_direction', 'unwarp_direction')]), + (dwi_applyxfm, dwi_merge, [('unwarped_file', 'in_files')]), + (dwi_merge, outputnode, [('merged_file', 'epi_corrected')]), + (vsm, outputnode, [('shift_out_file', 'out_vsm')]) ]) return pipeline @@ -461,19 +461,19 @@ def topup_correction(name='topup_correction'): applytopup = pe.Node(fsl.ApplyTOPUP(in_index=[1, 2]), name='applytopup') pipeline.connect([ - (inputnode, b0_dir, [('in_file_dir', 'in_file'), ('ref_num', 't_min')]), - (inputnode, b0_rev, [('in_file_rev', 'in_file'), ('ref_num', 't_min')]), - (inputnode, combin2, [('in_file_dir', 'in1'), ('in_file_rev', 'in2')]), - (b0_dir, combin, [('roi_file', 'in1')]), - (b0_rev, combin, [('roi_file', 'in2')]), - (combin, merged, [('out', 'in_files')]), - (merged, topup, [('merged_file', 'in_file')]), - (inputnode, topup, [('encoding_direction', 'encoding_direction'), ('readout_times', 'readout_times')]), - (topup, applytopup, [('out_fieldcoef', 'in_topup_fieldcoef'), ('out_movpar', 'in_topup_movpar'), - ('out_enc_file', 'encoding_file')]), - (combin2, applytopup, [('out', 'in_files')]), - (topup, outputnode, [('out_fieldcoef', 'out_fieldcoef'), ('out_movpar', 'out_movpar'), - ('out_enc_file', 'out_enc_file')]), + (inputnode, b0_dir, [('in_file_dir', 'in_file'), ('ref_num', 't_min')]), + (inputnode, b0_rev, [('in_file_rev', 'in_file'), ('ref_num', 't_min')]), + (inputnode, combin2, [('in_file_dir', 'in1'), ('in_file_rev', 'in2')]), + (b0_dir, combin, [('roi_file', 'in1')]), + (b0_rev, combin, [('roi_file', 'in2')]), + (combin, merged, [('out', 'in_files')]), + (merged, topup, [('merged_file', 'in_file')]), + (inputnode, topup, [('encoding_direction', 'encoding_direction'), ('readout_times', 'readout_times')]), + (topup, applytopup, [('out_fieldcoef', 'in_topup_fieldcoef'), ('out_movpar', 'in_topup_movpar'), + ('out_enc_file', 'encoding_file')]), + (combin2, applytopup, [('out', 'in_files')]), + (topup, outputnode, [('out_fieldcoef', 'out_fieldcoef'), ('out_movpar', 'out_movpar'), + ('out_enc_file', 'out_enc_file')]), (applytopup, outputnode, [('out_corrected', 'epi_corrected')]) ]) @@ -596,26 +596,26 @@ def create_epidewarp_pipeline(name='epidewarp', fieldmap_registration=False): name='outputnode') pipeline.connect([ - (inputnode, dwell_time, [('epi_echospacing', 'dwell_time'), ('pi_accel_factor', 'pi_factor'), ('epi_rev_encoding', 'is_reverse_encoding')]), - (inputnode, select_mag, [('fieldmap_mag', 'in_file')]), - (inputnode, norm_pha, [('fieldmap_pha', 'in_file')]), - (select_mag, mask_mag, [('roi_file', 'in_file')]), - (mask_mag, mask_mag_dil, [('mask_file', 'in_file')]), - (select_mag, prelude, [('roi_file', 'magnitude_file')]), - (norm_pha, prelude, [('out_file', 'phase_file')]), - (mask_mag_dil, prelude, [('out_file', 'mask_file')]), - (prelude, fill_phase, [('unwrapped_phase_file', 'in_file')]), - (inputnode, vsm, [('fieldmap_mag', 'in_file')]), - (fill_phase, vsm, [('out_file', 'phasemap_in_file')]), - (inputnode, vsm, [(('te_diff', _ms2sec), 'asym_se_time'), ('vsm_sigma', 'smooth2d')]), - (dwell_time, vsm, [(('dwell_time', _ms2sec), 'dwell_time')]), - (mask_mag_dil, vsm, [('out_file', 'mask_file')]), - (mask_mag_dil, vsm_mean, [('out_file', 'mask_file')]), - (vsm, vsm_mean, [('unwarped_file', 'in_unwarped'), ('shift_out_file', 'in_file')]), - (inputnode, dwi_split, [('in_file', 'in_file')]), - (dwi_split, dwi_applyxfm, [('out_files', 'in_file')]), - (dwi_applyxfm, dwi_merge, [('unwarped_file', 'in_files')]), - (dwi_merge, outputnode, [('merged_file', 'epi_corrected')]) + (inputnode, dwell_time, [('epi_echospacing', 'dwell_time'), ('pi_accel_factor', 'pi_factor'), ('epi_rev_encoding', 'is_reverse_encoding')]), + (inputnode, select_mag, [('fieldmap_mag', 'in_file')]), + (inputnode, norm_pha, [('fieldmap_pha', 'in_file')]), + (select_mag, mask_mag, [('roi_file', 'in_file')]), + (mask_mag, mask_mag_dil, [('mask_file', 'in_file')]), + (select_mag, prelude, [('roi_file', 'magnitude_file')]), + (norm_pha, prelude, [('out_file', 'phase_file')]), + (mask_mag_dil, prelude, [('out_file', 'mask_file')]), + (prelude, fill_phase, [('unwrapped_phase_file', 'in_file')]), + (inputnode, vsm, [('fieldmap_mag', 'in_file')]), + (fill_phase, vsm, [('out_file', 'phasemap_in_file')]), + (inputnode, vsm, [(('te_diff', _ms2sec), 'asym_se_time'), ('vsm_sigma', 'smooth2d')]), + (dwell_time, vsm, [(('dwell_time', _ms2sec), 'dwell_time')]), + (mask_mag_dil, vsm, [('out_file', 'mask_file')]), + (mask_mag_dil, vsm_mean, [('out_file', 'mask_file')]), + (vsm, vsm_mean, [('unwarped_file', 'in_unwarped'), ('shift_out_file', 'in_file')]), + (inputnode, dwi_split, [('in_file', 'in_file')]), + (dwi_split, dwi_applyxfm, [('out_files', 'in_file')]), + (dwi_applyxfm, dwi_merge, [('unwarped_file', 'in_files')]), + (dwi_merge, outputnode, [('merged_file', 'epi_corrected')]) ]) if fieldmap_registration: @@ -631,7 +631,7 @@ def create_epidewarp_pipeline(name='epidewarp', fieldmap_registration=False): # vsmmag_name, mask_name ), log ) # Forward Map vsm_fwd = pe.Node(fsl.FUGUE( forward_warping=True), name='vsm_fwd') - vsm_reg = pe.Node(fsl.FLIRT(bins=256, cost='corratio', dof=6, interp='spline', searchr_x=[ + vsm_reg = pe.Node(fsl.FLIRT(bins=256, cost='corratio', dof=6, interp='spline', searchr_x=[ -10, 10], searchr_y=[-10, 10], searchr_z=[-10, 10]), name='vsm_registration') # 'flirt -in %s -ref %s -out %s -init %s -applyxfm' % ( vsmmag_name, ref_epi, vsmmag_name, magfw_mat_out ) vsm_applyxfm = pe.Node(fsl.ApplyXfm( @@ -641,25 +641,25 @@ def create_epidewarp_pipeline(name='epidewarp', fieldmap_registration=False): interp='nearestneighbour'), name='msk_apply_xfm') pipeline.connect([ - (inputnode, select_epi, [('in_file', 'in_file'), ('ref_num', 't_min')]), - (select_epi, vsm_reg, [('roi_file', 'reference')]), - (vsm, vsm_fwd, [('shift_out_file', 'shift_in_file')]), - (mask_mag_dil, vsm_fwd, [('out_file', 'mask_file')]), - (inputnode, vsm_fwd, [('fieldmap_mag', 'in_file')]), - (vsm_fwd, vsm_reg, [('warped_file', 'in_file')]), - (vsm_reg, msk_applyxfm, [('out_matrix_file', 'in_matrix_file')]), - (select_epi, msk_applyxfm, [('roi_file', 'reference')]), + (inputnode, select_epi, [('in_file', 'in_file'), ('ref_num', 't_min')]), + (select_epi, vsm_reg, [('roi_file', 'reference')]), + (vsm, vsm_fwd, [('shift_out_file', 'shift_in_file')]), + (mask_mag_dil, vsm_fwd, [('out_file', 'mask_file')]), + (inputnode, vsm_fwd, [('fieldmap_mag', 'in_file')]), + (vsm_fwd, vsm_reg, [('warped_file', 'in_file')]), + (vsm_reg, msk_applyxfm, [('out_matrix_file', 'in_matrix_file')]), + (select_epi, msk_applyxfm, [('roi_file', 'reference')]), (mask_mag_dil, msk_applyxfm, [('out_file', 'in_file')]), - (vsm_reg, vsm_applyxfm, [('out_matrix_file', 'in_matrix_file')]), - (select_epi, vsm_applyxfm, [('roi_file', 'reference')]), - (vsm_mean, vsm_applyxfm, [('out_file', 'in_file')]), + (vsm_reg, vsm_applyxfm, [('out_matrix_file', 'in_matrix_file')]), + (select_epi, vsm_applyxfm, [('roi_file', 'reference')]), + (vsm_mean, vsm_applyxfm, [('out_file', 'in_file')]), (msk_applyxfm, dwi_applyxfm, [('out_file', 'mask_file')]), (vsm_applyxfm, dwi_applyxfm, [('out_file', 'shift_in_file')]) ]) else: pipeline.connect([ (mask_mag_dil, dwi_applyxfm, [('out_file', 'mask_file')]), - (vsm_mean, dwi_applyxfm, [('out_file', 'shift_in_file')]) + (vsm_mean, dwi_applyxfm, [('out_file', 'shift_in_file')]) ]) return pipeline diff --git a/nipype/workflows/dmri/fsl/utils.py b/nipype/workflows/dmri/fsl/utils.py index e89696418f..c7cff21521 100644 --- a/nipype/workflows/dmri/fsl/utils.py +++ b/nipype/workflows/dmri/fsl/utils.py @@ -36,18 +36,18 @@ def cleanup_edge_pipeline(name='Cleanup'): wf = pe.Workflow(name=name) wf.connect([ - (inputnode, fugue, [('in_file', 'fmap_in_file'), - ('in_mask', 'mask_file')]), - (inputnode, erode, [('in_mask', 'in_file')]), - (inputnode, newmsk, [('in_mask', 'in_file')]), - (erode, newmsk, [('out_file', 'operand_files')]), - (fugue, applymsk, [('fmap_out_file', 'in_file')]), - (newmsk, applymsk, [('out_file', 'mask_file')]), - (erode, join, [('out_file', 'in1')]), - (applymsk, join, [('out_file', 'in2')]), - (inputnode, addedge, [('in_file', 'in_file')]), - (join, addedge, [('out', 'operand_files')]), - (addedge, outputnode, [('out_file', 'out_file')]) + (inputnode, fugue, [('in_file', 'fmap_in_file'), + ('in_mask', 'mask_file')]), + (inputnode, erode, [('in_mask', 'in_file')]), + (inputnode, newmsk, [('in_mask', 'in_file')]), + (erode, newmsk, [('out_file', 'operand_files')]), + (fugue, applymsk, [('fmap_out_file', 'in_file')]), + (newmsk, applymsk, [('out_file', 'mask_file')]), + (erode, join, [('out_file', 'in1')]), + (applymsk, join, [('out_file', 'in2')]), + (inputnode, addedge, [('in_file', 'in_file')]), + (join, addedge, [('out', 'operand_files')]), + (addedge, outputnode, [('out_file', 'out_file')]) ]) return wf @@ -69,14 +69,14 @@ def vsm2warp(name='Shiftmap2Warping'): wf = pe.Workflow(name=name) wf.connect([ - (inputnode, fixhdr, [('in_vsm', 'in_file'), - ('in_ref', 'in_file_hdr')]), - (inputnode, vsm, [('scaling', 'operand_value')]), - (fixhdr, vsm, [('out_file', 'in_file')]), - (vsm, vsm2dfm, [('out_file', 'shift_in_file')]), - (inputnode, vsm2dfm, [('in_ref', 'reference'), - ('enc_dir', 'shift_direction')]), - (vsm2dfm, outputnode, [('out_file', 'out_warp')]) + (inputnode, fixhdr, [('in_vsm', 'in_file'), + ('in_ref', 'in_file_hdr')]), + (inputnode, vsm, [('scaling', 'operand_value')]), + (fixhdr, vsm, [('out_file', 'in_file')]), + (vsm, vsm2dfm, [('out_file', 'shift_in_file')]), + (inputnode, vsm2dfm, [('in_ref', 'reference'), + ('enc_dir', 'shift_direction')]), + (vsm2dfm, outputnode, [('out_file', 'out_warp')]) ]) return wf @@ -115,25 +115,25 @@ def dwi_flirt(name='DWICoregistration', excl_nodiff=False, fields=['out_file', 'out_xfms']), name='outputnode') wf = pe.Workflow(name=name) wf.connect([ - (inputnode, split, [('in_file', 'in_file')]), - (inputnode, dilate, [('ref_mask', 'in_file')]), - (inputnode, enhb0, [('ref_mask', 'in_mask')]), - (inputnode, initmat, [('in_xfms', 'in_xfms'), - ('in_bval', 'in_bval')]), - (inputnode, n4, [('reference', 'input_image'), - ('ref_mask', 'mask_image')]), - (dilate, flirt, [('out_file', 'ref_weight'), - ('out_file', 'in_weight')]), - (n4, enhb0, [('output_image', 'in_file')]), - (split, enhdw, [('out_files', 'in_file')]), - (dilate, enhdw, [('out_file', 'in_mask')]), - (enhb0, flirt, [('out_file', 'reference')]), - (enhdw, flirt, [('out_file', 'in_file')]), - (initmat, flirt, [('init_xfms', 'in_matrix_file')]), - (flirt, thres, [('out_file', 'in_file')]), - (thres, merge, [('out_file', 'in_files')]), - (merge, outputnode, [('merged_file', 'out_file')]), - (flirt, outputnode, [('out_matrix_file', 'out_xfms')]) + (inputnode, split, [('in_file', 'in_file')]), + (inputnode, dilate, [('ref_mask', 'in_file')]), + (inputnode, enhb0, [('ref_mask', 'in_mask')]), + (inputnode, initmat, [('in_xfms', 'in_xfms'), + ('in_bval', 'in_bval')]), + (inputnode, n4, [('reference', 'input_image'), + ('ref_mask', 'mask_image')]), + (dilate, flirt, [('out_file', 'ref_weight'), + ('out_file', 'in_weight')]), + (n4, enhb0, [('output_image', 'in_file')]), + (split, enhdw, [('out_files', 'in_file')]), + (dilate, enhdw, [('out_file', 'in_mask')]), + (enhb0, flirt, [('out_file', 'reference')]), + (enhdw, flirt, [('out_file', 'in_file')]), + (initmat, flirt, [('init_xfms', 'in_matrix_file')]), + (flirt, thres, [('out_file', 'in_file')]), + (thres, merge, [('out_file', 'in_files')]), + (merge, outputnode, [('merged_file', 'out_file')]), + (flirt, outputnode, [('out_matrix_file', 'out_xfms')]) ]) return wf @@ -175,27 +175,27 @@ def apply_all_corrections(name='UnwarpArtifacts'): wf = pe.Workflow(name=name) wf.connect([ - (inputnode, warps, [('in_sdc', 'warp1'), - ('in_hmc', 'premat'), - ('in_ecc', 'postmat'), - ('in_dwi', 'reference')]), - (inputnode, split, [('in_dwi', 'in_file')]), - (split, selref, [('out_files', 'inlist')]), - (warps, unwarp, [('out_file', 'field_file')]), - (split, unwarp, [('out_files', 'in_file')]), - (selref, unwarp, [('out', 'ref_file')]), - (selref, coeffs, [('out', 'reference')]), - (warps, coeffs, [('out_file', 'in_file')]), - (selref, jacobian, [('out', 'reference')]), - (coeffs, jacobian, [('out_file', 'in_file')]), - (unwarp, jacmult, [('out_file', 'in_file')]), - (jacobian, jacmult, [('out_jacobian', 'operand_files')]), - (jacmult, thres, [('out_file', 'in_file')]), - (thres, merge, [('out_file', 'in_files')]), - (warps, outputnode, [('out_file', 'out_warp')]), - (coeffs, outputnode, [('out_file', 'out_coeff')]), - (jacobian, outputnode, [('out_jacobian', 'out_jacobian')]), - (merge, outputnode, [('merged_file', 'out_file')]) + (inputnode, warps, [('in_sdc', 'warp1'), + ('in_hmc', 'premat'), + ('in_ecc', 'postmat'), + ('in_dwi', 'reference')]), + (inputnode, split, [('in_dwi', 'in_file')]), + (split, selref, [('out_files', 'inlist')]), + (warps, unwarp, [('out_file', 'field_file')]), + (split, unwarp, [('out_files', 'in_file')]), + (selref, unwarp, [('out', 'ref_file')]), + (selref, coeffs, [('out', 'reference')]), + (warps, coeffs, [('out_file', 'in_file')]), + (selref, jacobian, [('out', 'reference')]), + (coeffs, jacobian, [('out_file', 'in_file')]), + (unwarp, jacmult, [('out_file', 'in_file')]), + (jacobian, jacmult, [('out_jacobian', 'operand_files')]), + (jacmult, thres, [('out_file', 'in_file')]), + (thres, merge, [('out_file', 'in_files')]), + (warps, outputnode, [('out_file', 'out_warp')]), + (coeffs, outputnode, [('out_file', 'out_coeff')]), + (jacobian, outputnode, [('out_jacobian', 'out_jacobian')]), + (merge, outputnode, [('merged_file', 'out_file')]) ]) return wf diff --git a/nipype/workflows/smri/ants/ANTSBuildTemplate.py b/nipype/workflows/smri/ants/ANTSBuildTemplate.py index fd92c18a1e..11bcbb9809 100644 --- a/nipype/workflows/smri/ants/ANTSBuildTemplate.py +++ b/nipype/workflows/smri/ants/ANTSBuildTemplate.py @@ -244,7 +244,7 @@ def ANTSTemplateBuildSingleIterationWF(iterationPhasePrefix=''): iterfield=['transformation_series', 'input_image'], name='wimtPassivedeformed') TemplateBuildSingleIterationWF.connect(AvgDeformedImages, 'output_average_image', wimtPassivedeformed, 'reference_image') - TemplateBuildSingleIterationWF.connect(FlattenTransformAndImagesListNode, 'flattened_images', wimtPassivedeformed, 'input_image') + TemplateBuildSingleIterationWF.connect(FlattenTransformAndImagesListNode, 'flattened_images', wimtPassivedeformed, 'input_image') TemplateBuildSingleIterationWF.connect(FlattenTransformAndImagesListNode, 'flattened_transforms', wimtPassivedeformed, 'transformation_series') RenestDeformedPassiveImagesNode = pe.Node(Function(function=RenestDeformedPassiveImages, diff --git a/nipype/workflows/smri/ants/antsRegistrationBuildTemplate.py b/nipype/workflows/smri/ants/antsRegistrationBuildTemplate.py index 54b61794d8..e58b62177d 100644 --- a/nipype/workflows/smri/ants/antsRegistrationBuildTemplate.py +++ b/nipype/workflows/smri/ants/antsRegistrationBuildTemplate.py @@ -197,16 +197,16 @@ def antsRegistrationTemplateBuildSingleIterationWF(iterationPhasePrefix=''): BeginANTS = pe.MapNode(interface=Registration(), name='BeginANTS', iterfield=['moving_image']) BeginANTS.inputs.dimension = 3 BeginANTS.inputs.output_transform_prefix = str(iterationPhasePrefix) + '_tfm' - BeginANTS.inputs.transforms = ["Affine", "SyN"] - BeginANTS.inputs.transform_parameters = [[0.9], [0.25, 3.0, 0.0]] - BeginANTS.inputs.metric = ['Mattes', 'CC'] - BeginANTS.inputs.metric_weight = [1.0, 1.0] - BeginANTS.inputs.radius_or_number_of_bins = [32, 5] + BeginANTS.inputs.transforms = ["Affine", "SyN"] + BeginANTS.inputs.transform_parameters = [[0.9], [0.25, 3.0, 0.0]] + BeginANTS.inputs.metric = ['Mattes', 'CC'] + BeginANTS.inputs.metric_weight = [1.0, 1.0] + BeginANTS.inputs.radius_or_number_of_bins = [32, 5] BeginANTS.inputs.number_of_iterations = [[1000, 1000, 1000], [50, 35, 15]] - BeginANTS.inputs.use_histogram_matching = [True, True] - BeginANTS.inputs.use_estimate_learning_rate_once = [False, False] - BeginANTS.inputs.shrink_factors = [[3, 2, 1], [3, 2, 1]] - BeginANTS.inputs.smoothing_sigmas = [[3, 2, 0], [3, 2, 0]] + BeginANTS.inputs.use_histogram_matching = [True, True] + BeginANTS.inputs.use_estimate_learning_rate_once = [False, False] + BeginANTS.inputs.shrink_factors = [[3, 2, 1], [3, 2, 1]] + BeginANTS.inputs.smoothing_sigmas = [[3, 2, 0], [3, 2, 0]] BeginANTS.inputs.sigma_units = ["vox"] * 2 GetMovingImagesNode = pe.Node(interface=util.Function(function=GetMovingImages, @@ -333,7 +333,7 @@ def antsRegistrationTemplateBuildSingleIterationWF(iterationPhasePrefix=''): wimtPassivedeformed.default_value = 0 TemplateBuildSingleIterationWF.connect(AvgDeformedImages, 'output_average_image', wimtPassivedeformed, 'reference_image') TemplateBuildSingleIterationWF.connect(FlattenTransformAndImagesListNode, 'flattened_interpolation_type', wimtPassivedeformed, 'interpolation') - TemplateBuildSingleIterationWF.connect(FlattenTransformAndImagesListNode, 'flattened_images', wimtPassivedeformed, 'input_image') + TemplateBuildSingleIterationWF.connect(FlattenTransformAndImagesListNode, 'flattened_images', wimtPassivedeformed, 'input_image') TemplateBuildSingleIterationWF.connect(FlattenTransformAndImagesListNode, 'flattened_transforms', wimtPassivedeformed, 'transforms') TemplateBuildSingleIterationWF.connect(FlattenTransformAndImagesListNode, 'flattened_invert_transform_flags', wimtPassivedeformed, 'invert_transform_flags') From 712ab695e09dfd80b7a7dfbef242b358f2b0fdf1 Mon Sep 17 00:00:00 2001 From: miykael Date: Sun, 1 Nov 2015 13:16:02 +0100 Subject: [PATCH 18/19] STY: PEP8 style correction in auto-generated test files. Those corrections were caused by changes in tools/checkspecs.py from the previous PR #1255 --- .../tests/test_auto_AddCSVColumn.py | 3 +- .../algorithms/tests/test_auto_AddCSVRow.py | 3 +- nipype/algorithms/tests/test_auto_AddNoise.py | 3 +- .../tests/test_auto_ArtifactDetect.py | 3 +- .../test_auto_CalculateNormalizedMoments.py | 3 +- .../tests/test_auto_ComputeMeshWarp.py | 3 +- .../algorithms/tests/test_auto_CreateNifti.py | 3 +- nipype/algorithms/tests/test_auto_Distance.py | 3 +- nipype/algorithms/tests/test_auto_ErrorMap.py | 35 ++++++++++++++ .../tests/test_auto_FuzzyOverlap.py | 3 +- nipype/algorithms/tests/test_auto_Gunzip.py | 3 +- nipype/algorithms/tests/test_auto_ICC.py | 3 +- .../algorithms/tests/test_auto_Matlab2CSV.py | 3 +- .../tests/test_auto_MergeCSVFiles.py | 3 +- .../algorithms/tests/test_auto_MergeROIs.py | 3 +- .../tests/test_auto_MeshWarpMaths.py | 3 +- .../tests/test_auto_ModifyAffine.py | 3 +- .../test_auto_NormalizeProbabilityMapSet.py | 3 +- nipype/algorithms/tests/test_auto_Overlap.py | 47 +++++++++++++++++++ .../algorithms/tests/test_auto_P2PDistance.py | 3 +- .../algorithms/tests/test_auto_PickAtlas.py | 3 +- .../algorithms/tests/test_auto_Similarity.py | 3 +- .../tests/test_auto_SimpleThreshold.py | 3 +- .../tests/test_auto_SpecifyModel.py | 3 +- .../tests/test_auto_SpecifySPMModel.py | 3 +- .../tests/test_auto_SpecifySparseModel.py | 3 +- .../algorithms/tests/test_auto_SplitROIs.py | 3 +- .../tests/test_auto_StimulusCorrelation.py | 3 +- nipype/algorithms/tests/test_auto_TSNR.py | 3 +- .../algorithms/tests/test_auto_WarpPoints.py | 3 +- .../afni/tests/test_auto_AFNICommand.py | 1 + .../afni/tests/test_auto_AFNItoNIFTI.py | 3 +- .../afni/tests/test_auto_Allineate.py | 3 +- .../afni/tests/test_auto_AutoTcorrelate.py | 3 +- .../afni/tests/test_auto_Autobox.py | 3 +- .../afni/tests/test_auto_Automask.py | 3 +- .../afni/tests/test_auto_Bandpass.py | 3 +- .../afni/tests/test_auto_BlurInMask.py | 3 +- .../afni/tests/test_auto_BrickStat.py | 3 +- .../interfaces/afni/tests/test_auto_Calc.py | 3 +- .../interfaces/afni/tests/test_auto_Copy.py | 3 +- .../afni/tests/test_auto_Despike.py | 3 +- .../afni/tests/test_auto_Detrend.py | 3 +- .../interfaces/afni/tests/test_auto_Eval.py | 3 +- nipype/interfaces/afni/tests/test_auto_Fim.py | 3 +- .../afni/tests/test_auto_Fourier.py | 3 +- .../afni/tests/test_auto_Maskave.py | 3 +- .../interfaces/afni/tests/test_auto_Means.py | 3 +- .../interfaces/afni/tests/test_auto_Merge.py | 3 +- .../afni/tests/test_auto_ROIStats.py | 3 +- .../interfaces/afni/tests/test_auto_Refit.py | 3 +- .../afni/tests/test_auto_Resample.py | 3 +- .../afni/tests/test_auto_Retroicor.py | 3 +- .../afni/tests/test_auto_SVMTest.py | 3 +- .../afni/tests/test_auto_SVMTrain.py | 3 +- .../afni/tests/test_auto_SkullStrip.py | 3 +- .../interfaces/afni/tests/test_auto_TCat.py | 3 +- .../afni/tests/test_auto_TCorr1D.py | 3 +- .../afni/tests/test_auto_TCorrMap.py | 3 +- .../afni/tests/test_auto_TCorrelate.py | 3 +- .../interfaces/afni/tests/test_auto_TShift.py | 3 +- .../interfaces/afni/tests/test_auto_TStat.py | 3 +- .../interfaces/afni/tests/test_auto_To3D.py | 3 +- .../interfaces/afni/tests/test_auto_Volreg.py | 3 +- .../interfaces/afni/tests/test_auto_Warp.py | 3 +- .../interfaces/afni/tests/test_auto_ZCutUp.py | 3 +- .../interfaces/ants/tests/test_auto_ANTS.py | 3 +- .../ants/tests/test_auto_ANTSCommand.py | 1 + .../ants/tests/test_auto_ApplyTransforms.py | 3 +- .../test_auto_ApplyTransformsToPoints.py | 3 +- .../ants/tests/test_auto_Atropos.py | 3 +- .../tests/test_auto_AverageAffineTransform.py | 3 +- .../ants/tests/test_auto_AverageImages.py | 3 +- .../test_auto_ConvertScalarImageToRGB.py | 3 +- .../ants/tests/test_auto_CreateTiledMosaic.py | 3 +- .../ants/tests/test_auto_GenWarpFields.py | 3 +- .../tests/test_auto_JacobianDeterminant.py | 3 +- .../ants/tests/test_auto_JointFusion.py | 3 +- .../tests/test_auto_LaplacianThickness.py | 3 +- .../ants/tests/test_auto_MultiplyImages.py | 3 +- .../tests/test_auto_N4BiasFieldCorrection.py | 3 +- .../ants/tests/test_auto_Registration.py | 3 +- .../test_auto_WarpImageMultiTransform.py | 3 +- ..._auto_WarpTimeSeriesImageMultiTransform.py | 3 +- .../tests/test_auto_antsCorticalThickness.py | 3 +- .../ants/tests/test_auto_antsIntroduction.py | 3 +- .../tests/test_auto_buildtemplateparallel.py | 3 +- .../camino/tests/test_auto_AnalyzeHeader.py | 3 +- .../tests/test_auto_ComputeEigensystem.py | 3 +- .../test_auto_ComputeFractionalAnisotropy.py | 3 +- .../tests/test_auto_ComputeMeanDiffusivity.py | 3 +- .../tests/test_auto_ComputeTensorTrace.py | 3 +- .../camino/tests/test_auto_Conmat.py | 3 +- .../camino/tests/test_auto_DT2NIfTI.py | 3 +- .../camino/tests/test_auto_DTIFit.py | 3 +- .../camino/tests/test_auto_DTLUTGen.py | 3 +- .../camino/tests/test_auto_DTMetric.py | 3 +- .../camino/tests/test_auto_FSL2Scheme.py | 3 +- .../camino/tests/test_auto_Image2Voxel.py | 3 +- .../camino/tests/test_auto_ImageStats.py | 3 +- .../camino/tests/test_auto_LinRecon.py | 3 +- .../interfaces/camino/tests/test_auto_MESD.py | 3 +- .../camino/tests/test_auto_ModelFit.py | 3 +- .../camino/tests/test_auto_NIfTIDT2Camino.py | 3 +- .../camino/tests/test_auto_PicoPDFs.py | 3 +- .../camino/tests/test_auto_ProcStreamlines.py | 3 +- .../camino/tests/test_auto_QBallMX.py | 3 +- .../camino/tests/test_auto_SFLUTGen.py | 3 +- .../camino/tests/test_auto_SFPICOCalibData.py | 3 +- .../camino/tests/test_auto_SFPeaks.py | 3 +- .../camino/tests/test_auto_Shredder.py | 3 +- .../camino/tests/test_auto_Track.py | 3 +- .../camino/tests/test_auto_TrackBallStick.py | 3 +- .../camino/tests/test_auto_TrackBayesDirac.py | 3 +- .../tests/test_auto_TrackBedpostxDeter.py | 3 +- .../tests/test_auto_TrackBedpostxProba.py | 3 +- .../camino/tests/test_auto_TrackBootstrap.py | 3 +- .../camino/tests/test_auto_TrackDT.py | 3 +- .../camino/tests/test_auto_TrackPICo.py | 3 +- .../camino/tests/test_auto_TractShredder.py | 3 +- .../camino/tests/test_auto_VtkStreamlines.py | 3 +- .../tests/test_auto_Camino2Trackvis.py | 3 +- .../tests/test_auto_Trackvis2Camino.py | 3 +- .../cmtk/tests/test_auto_AverageNetworks.py | 3 +- .../cmtk/tests/test_auto_CFFConverter.py | 3 +- .../cmtk/tests/test_auto_CreateMatrix.py | 3 +- .../cmtk/tests/test_auto_CreateNodes.py | 3 +- .../cmtk/tests/test_auto_MergeCNetworks.py | 3 +- .../tests/test_auto_NetworkBasedStatistic.py | 3 +- .../cmtk/tests/test_auto_NetworkXMetrics.py | 3 +- .../cmtk/tests/test_auto_Parcellate.py | 3 +- .../interfaces/cmtk/tests/test_auto_ROIGen.py | 3 +- .../tests/test_auto_DTIRecon.py | 3 +- .../tests/test_auto_DTITracker.py | 3 +- .../tests/test_auto_HARDIMat.py | 3 +- .../tests/test_auto_ODFRecon.py | 3 +- .../tests/test_auto_ODFTracker.py | 3 +- .../tests/test_auto_SplineFilter.py | 3 +- .../tests/test_auto_TrackMerge.py | 3 +- nipype/interfaces/dipy/tests/test_auto_DTI.py | 3 +- .../dipy/tests/test_auto_Denoise.py | 3 +- .../dipy/tests/test_auto_Resample.py | 3 +- .../tests/test_auto_SimulateMultiTensor.py | 3 +- .../dipy/tests/test_auto_TensorMode.py | 3 +- .../dipy/tests/test_auto_TrackDensityMap.py | 3 +- .../elastix/tests/test_auto_AnalyzeWarp.py | 3 +- .../elastix/tests/test_auto_ApplyWarp.py | 3 +- .../elastix/tests/test_auto_EditTransform.py | 3 +- .../elastix/tests/test_auto_PointsWarp.py | 3 +- .../elastix/tests/test_auto_Registration.py | 3 +- .../freesurfer/tests/test_auto_ApplyMask.py | 3 +- .../tests/test_auto_ApplyVolTransform.py | 3 +- .../freesurfer/tests/test_auto_BBRegister.py | 3 +- .../freesurfer/tests/test_auto_Binarize.py | 3 +- .../freesurfer/tests/test_auto_Concatenate.py | 3 +- .../tests/test_auto_DICOMConvert.py | 1 + .../tests/test_auto_ExtractMainComponent.py | 3 +- .../freesurfer/tests/test_auto_FSCommand.py | 1 + .../freesurfer/tests/test_auto_FitMSParams.py | 3 +- .../freesurfer/tests/test_auto_GLMFit.py | 3 +- .../freesurfer/tests/test_auto_ImageInfo.py | 3 +- .../freesurfer/tests/test_auto_Label2Vol.py | 3 +- .../freesurfer/tests/test_auto_MRIConvert.py | 3 +- .../tests/test_auto_MRIMarchingCubes.py | 3 +- .../freesurfer/tests/test_auto_MRIPretess.py | 3 +- .../freesurfer/tests/test_auto_MRISPreproc.py | 3 +- .../tests/test_auto_MRITessellate.py | 3 +- .../freesurfer/tests/test_auto_MRIsConvert.py | 3 +- .../freesurfer/tests/test_auto_MS_LDA.py | 3 +- .../tests/test_auto_MakeAverageSubject.py | 3 +- .../tests/test_auto_OneSampleTTest.py | 3 +- .../tests/test_auto_ParseDICOMDir.py | 3 +- .../freesurfer/tests/test_auto_ReconAll.py | 3 +- .../freesurfer/tests/test_auto_Resample.py | 3 +- .../tests/test_auto_RobustRegister.py | 3 +- .../tests/test_auto_SampleToSurface.py | 3 +- .../freesurfer/tests/test_auto_SegStats.py | 3 +- .../freesurfer/tests/test_auto_Smooth.py | 3 +- .../tests/test_auto_SmoothTessellation.py | 3 +- .../tests/test_auto_Surface2VolTransform.py | 3 +- .../tests/test_auto_SurfaceSmooth.py | 3 +- .../tests/test_auto_SurfaceSnapshots.py | 3 +- .../tests/test_auto_SurfaceTransform.py | 3 +- .../tests/test_auto_SynthesizeFLASH.py | 3 +- .../freesurfer/tests/test_auto_Tkregister2.py | 3 +- .../tests/test_auto_UnpackSDICOMDir.py | 1 + .../fsl/tests/test_auto_ApplyMask.py | 3 +- .../fsl/tests/test_auto_ApplyTOPUP.py | 3 +- .../fsl/tests/test_auto_ApplyWarp.py | 3 +- .../fsl/tests/test_auto_ApplyXfm.py | 3 +- .../interfaces/fsl/tests/test_auto_AvScale.py | 3 +- .../fsl/tests/test_auto_BEDPOSTX4.py | 3 +- .../fsl/tests/test_auto_BEDPOSTX5.py | 3 +- nipype/interfaces/fsl/tests/test_auto_BET.py | 3 +- .../fsl/tests/test_auto_BinaryMaths.py | 3 +- .../fsl/tests/test_auto_ChangeDataType.py | 3 +- .../interfaces/fsl/tests/test_auto_Cluster.py | 3 +- .../interfaces/fsl/tests/test_auto_Complex.py | 3 +- .../fsl/tests/test_auto_ContrastMgr.py | 3 +- .../fsl/tests/test_auto_ConvertWarp.py | 3 +- .../fsl/tests/test_auto_ConvertXFM.py | 3 +- .../fsl/tests/test_auto_CopyGeom.py | 3 +- .../interfaces/fsl/tests/test_auto_DTIFit.py | 3 +- .../fsl/tests/test_auto_DilateImage.py | 3 +- .../fsl/tests/test_auto_DistanceMap.py | 3 +- .../fsl/tests/test_auto_EPIDeWarp.py | 3 +- nipype/interfaces/fsl/tests/test_auto_Eddy.py | 3 +- .../fsl/tests/test_auto_EddyCorrect.py | 3 +- .../interfaces/fsl/tests/test_auto_EpiReg.py | 3 +- .../fsl/tests/test_auto_ErodeImage.py | 3 +- .../fsl/tests/test_auto_ExtractROI.py | 3 +- nipype/interfaces/fsl/tests/test_auto_FAST.py | 3 +- nipype/interfaces/fsl/tests/test_auto_FEAT.py | 3 +- .../fsl/tests/test_auto_FEATModel.py | 3 +- .../fsl/tests/test_auto_FEATRegister.py | 3 +- .../interfaces/fsl/tests/test_auto_FIRST.py | 3 +- .../interfaces/fsl/tests/test_auto_FLAMEO.py | 3 +- .../interfaces/fsl/tests/test_auto_FLIRT.py | 3 +- .../interfaces/fsl/tests/test_auto_FNIRT.py | 3 +- .../fsl/tests/test_auto_FSLCommand.py | 1 + .../fsl/tests/test_auto_FSLXCommand.py | 3 +- .../interfaces/fsl/tests/test_auto_FUGUE.py | 3 +- .../fsl/tests/test_auto_FilterRegressor.py | 3 +- .../fsl/tests/test_auto_FindTheBiggest.py | 3 +- nipype/interfaces/fsl/tests/test_auto_GLM.py | 3 +- .../fsl/tests/test_auto_ImageMaths.py | 3 +- .../fsl/tests/test_auto_ImageMeants.py | 3 +- .../fsl/tests/test_auto_ImageStats.py | 3 +- .../interfaces/fsl/tests/test_auto_InvWarp.py | 3 +- .../fsl/tests/test_auto_IsotropicSmooth.py | 3 +- .../interfaces/fsl/tests/test_auto_L2Model.py | 3 +- .../fsl/tests/test_auto_Level1Design.py | 3 +- .../interfaces/fsl/tests/test_auto_MCFLIRT.py | 3 +- .../interfaces/fsl/tests/test_auto_MELODIC.py | 3 +- .../fsl/tests/test_auto_MakeDyadicVectors.py | 3 +- .../fsl/tests/test_auto_MathsCommand.py | 3 +- .../fsl/tests/test_auto_MaxImage.py | 3 +- .../fsl/tests/test_auto_MeanImage.py | 3 +- .../interfaces/fsl/tests/test_auto_Merge.py | 3 +- .../fsl/tests/test_auto_MotionOutliers.py | 3 +- .../fsl/tests/test_auto_MultiImageMaths.py | 3 +- .../tests/test_auto_MultipleRegressDesign.py | 3 +- .../interfaces/fsl/tests/test_auto_Overlay.py | 3 +- .../interfaces/fsl/tests/test_auto_PRELUDE.py | 3 +- .../fsl/tests/test_auto_PlotMotionParams.py | 3 +- .../fsl/tests/test_auto_PlotTimeSeries.py | 3 +- .../fsl/tests/test_auto_PowerSpectrum.py | 3 +- .../fsl/tests/test_auto_PrepareFieldmap.py | 3 +- .../fsl/tests/test_auto_ProbTrackX.py | 3 +- .../fsl/tests/test_auto_ProbTrackX2.py | 3 +- .../fsl/tests/test_auto_ProjThresh.py | 3 +- .../fsl/tests/test_auto_Randomise.py | 3 +- .../fsl/tests/test_auto_Reorient2Std.py | 3 +- .../fsl/tests/test_auto_RobustFOV.py | 3 +- nipype/interfaces/fsl/tests/test_auto_SMM.py | 3 +- .../interfaces/fsl/tests/test_auto_SUSAN.py | 3 +- .../interfaces/fsl/tests/test_auto_SigLoss.py | 3 +- .../fsl/tests/test_auto_SliceTimer.py | 3 +- .../interfaces/fsl/tests/test_auto_Slicer.py | 3 +- .../interfaces/fsl/tests/test_auto_Smooth.py | 3 +- .../fsl/tests/test_auto_SmoothEstimate.py | 3 +- .../fsl/tests/test_auto_SpatialFilter.py | 3 +- .../interfaces/fsl/tests/test_auto_Split.py | 3 +- .../fsl/tests/test_auto_SwapDimensions.py | 3 +- .../interfaces/fsl/tests/test_auto_TOPUP.py | 3 +- .../fsl/tests/test_auto_TemporalFilter.py | 3 +- .../fsl/tests/test_auto_Threshold.py | 3 +- .../fsl/tests/test_auto_TractSkeleton.py | 3 +- .../fsl/tests/test_auto_UnaryMaths.py | 3 +- .../interfaces/fsl/tests/test_auto_VecReg.py | 3 +- .../fsl/tests/test_auto_WarpPoints.py | 3 +- .../fsl/tests/test_auto_WarpPointsToStd.py | 3 +- .../fsl/tests/test_auto_WarpUtils.py | 3 +- .../fsl/tests/test_auto_XFibres4.py | 3 +- .../fsl/tests/test_auto_XFibres5.py | 3 +- .../test_auto_JistBrainMgdmSegmentation.py | 3 +- ...est_auto_JistBrainMp2rageDuraEstimation.py | 3 +- ...est_auto_JistBrainMp2rageSkullStripping.py | 3 +- .../test_auto_JistBrainPartialVolumeFilter.py | 3 +- ...est_auto_JistCortexSurfaceMeshInflation.py | 3 +- .../test_auto_JistIntensityMp2rageMasking.py | 3 +- 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.../tests/test_auto_EstimateResponseForSH.py | 3 +- .../mrtrix/tests/test_auto_FSL2MRTrix.py | 3 +- .../mrtrix/tests/test_auto_FilterTracks.py | 3 +- .../mrtrix/tests/test_auto_FindShPeaks.py | 3 +- .../tests/test_auto_GenerateDirections.py | 3 +- .../test_auto_GenerateWhiteMatterMask.py | 3 +- .../mrtrix/tests/test_auto_MRConvert.py | 3 +- .../mrtrix/tests/test_auto_MRMultiply.py | 3 +- .../mrtrix/tests/test_auto_MRTransform.py | 3 +- .../mrtrix/tests/test_auto_MRTrix2TrackVis.py | 3 +- .../mrtrix/tests/test_auto_MRTrixInfo.py | 3 +- .../mrtrix/tests/test_auto_MRTrixViewer.py | 3 +- .../mrtrix/tests/test_auto_MedianFilter3D.py | 3 +- ...cSphericallyDeconvolutedStreamlineTrack.py | 3 +- ..._SphericallyDeconvolutedStreamlineTrack.py | 3 +- .../mrtrix/tests/test_auto_StreamlineTrack.py | 3 +- .../test_auto_Tensor2ApparentDiffusion.py | 3 +- .../test_auto_Tensor2FractionalAnisotropy.py | 3 +- .../mrtrix/tests/test_auto_Tensor2Vector.py | 3 +- .../mrtrix/tests/test_auto_Threshold.py | 3 +- 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3 +- .../test_auto_gtractCopyImageOrientation.py | 3 +- .../tests/test_auto_gtractCoregBvalues.py | 3 +- .../tests/test_auto_gtractCostFastMarching.py | 3 +- .../tests/test_auto_gtractCreateGuideFiber.py | 3 +- .../test_auto_gtractFastMarchingTracking.py | 3 +- .../tests/test_auto_gtractFiberTracking.py | 3 +- .../tests/test_auto_gtractImageConformity.py | 3 +- .../test_auto_gtractInvertBSplineTransform.py | 3 +- ...test_auto_gtractInvertDisplacementField.py | 3 +- .../test_auto_gtractInvertRigidTransform.py | 3 +- .../test_auto_gtractResampleAnisotropy.py | 3 +- .../tests/test_auto_gtractResampleB0.py | 3 +- .../test_auto_gtractResampleCodeImage.py | 3 +- .../test_auto_gtractResampleDWIInPlace.py | 3 +- .../tests/test_auto_gtractResampleFibers.py | 3 +- .../diffusion/tests/test_auto_gtractTensor.py | 3 +- ...auto_gtractTransformToDisplacementField.py | 3 +- .../diffusion/tests/test_auto_maxcurvature.py | 3 +- .../tests/test_auto_UKFTractography.py | 3 +- .../tests/test_auto_fiberprocess.py | 3 +- .../tests/test_auto_fiberstats.py | 3 +- .../tests/test_auto_fibertrack.py | 3 +- .../filtering/tests/test_auto_CannyEdge.py | 3 +- ...to_CannySegmentationLevelSetImageFilter.py | 3 +- .../filtering/tests/test_auto_DilateImage.py | 3 +- .../filtering/tests/test_auto_DilateMask.py | 3 +- .../filtering/tests/test_auto_DistanceMaps.py | 3 +- .../test_auto_DumpBinaryTrainingVectors.py | 3 +- .../filtering/tests/test_auto_ErodeImage.py | 3 +- .../tests/test_auto_FlippedDifference.py | 3 +- .../test_auto_GenerateBrainClippedImage.py | 3 +- .../test_auto_GenerateSummedGradientImage.py | 3 +- .../tests/test_auto_GenerateTestImage.py | 3 +- ...GradientAnisotropicDiffusionImageFilter.py | 3 +- .../tests/test_auto_HammerAttributeCreator.py | 3 +- .../tests/test_auto_NeighborhoodMean.py | 3 +- .../tests/test_auto_NeighborhoodMedian.py | 3 +- .../tests/test_auto_STAPLEAnalysis.py | 3 +- .../test_auto_TextureFromNoiseImageFilter.py | 3 +- .../tests/test_auto_TextureMeasureFilter.py | 3 +- .../tests/test_auto_UnbiasedNonLocalMeans.py | 3 +- .../legacy/tests/test_auto_scalartransform.py | 3 +- .../tests/test_auto_BRAINSDemonWarp.py | 3 +- .../registration/tests/test_auto_BRAINSFit.py | 3 +- .../tests/test_auto_BRAINSResample.py | 3 +- .../tests/test_auto_BRAINSResize.py | 3 +- .../test_auto_BRAINSTransformFromFiducials.py | 3 +- .../tests/test_auto_VBRAINSDemonWarp.py | 3 +- .../segmentation/tests/test_auto_BRAINSABC.py | 3 +- .../test_auto_BRAINSConstellationDetector.py | 3 +- ...BRAINSCreateLabelMapFromProbabilityMaps.py | 3 +- .../segmentation/tests/test_auto_BRAINSCut.py | 3 +- .../tests/test_auto_BRAINSMultiSTAPLE.py | 3 +- .../tests/test_auto_BRAINSROIAuto.py | 3 +- ...t_auto_BinaryMaskEditorBasedOnLandmarks.py | 3 +- .../segmentation/tests/test_auto_ESLR.py | 3 +- .../semtools/tests/test_auto_DWICompare.py | 3 +- .../tests/test_auto_DWISimpleCompare.py | 3 +- ...o_GenerateCsfClippedFromClassifiedImage.py | 3 +- .../tests/test_auto_BRAINSAlignMSP.py | 3 +- .../tests/test_auto_BRAINSClipInferior.py | 3 +- .../test_auto_BRAINSConstellationModeler.py | 3 +- .../tests/test_auto_BRAINSEyeDetector.py | 3 +- ...est_auto_BRAINSInitializedControlPoints.py | 3 +- .../test_auto_BRAINSLandmarkInitializer.py | 3 +- .../test_auto_BRAINSLinearModelerEPCA.py | 3 +- .../tests/test_auto_BRAINSLmkTransform.py | 3 +- .../utilities/tests/test_auto_BRAINSMush.py | 3 +- .../tests/test_auto_BRAINSSnapShotWriter.py | 3 +- .../tests/test_auto_BRAINSTransformConvert.py | 3 +- ...st_auto_BRAINSTrimForegroundInDirection.py | 3 +- .../tests/test_auto_CleanUpOverlapLabels.py | 3 +- .../tests/test_auto_FindCenterOfBrain.py | 3 +- ...auto_GenerateLabelMapFromProbabilityMap.py | 3 +- .../tests/test_auto_ImageRegionPlotter.py | 3 +- .../tests/test_auto_JointHistogram.py | 3 +- .../tests/test_auto_ShuffleVectorsModule.py | 3 +- .../utilities/tests/test_auto_fcsv_to_hdf5.py | 3 +- .../tests/test_auto_insertMidACPCpoint.py | 3 +- ...test_auto_landmarksConstellationAligner.py | 3 +- ...test_auto_landmarksConstellationWeights.py | 3 +- .../diffusion/tests/test_auto_DTIexport.py | 3 +- .../diffusion/tests/test_auto_DTIimport.py | 3 +- .../test_auto_DWIJointRicianLMMSEFilter.py | 3 +- .../tests/test_auto_DWIRicianLMMSEFilter.py | 3 +- .../tests/test_auto_DWIToDTIEstimation.py | 3 +- ..._auto_DiffusionTensorScalarMeasurements.py | 3 +- ...est_auto_DiffusionWeightedVolumeMasking.py | 3 +- .../tests/test_auto_ResampleDTIVolume.py | 3 +- .../test_auto_TractographyLabelMapSeeding.py | 3 +- .../tests/test_auto_AddScalarVolumes.py | 3 +- .../tests/test_auto_CastScalarVolume.py | 3 +- .../tests/test_auto_CheckerBoardFilter.py | 3 +- ...test_auto_CurvatureAnisotropicDiffusion.py | 3 +- .../tests/test_auto_ExtractSkeleton.py | 3 +- .../test_auto_GaussianBlurImageFilter.py | 3 +- .../test_auto_GradientAnisotropicDiffusion.py | 3 +- .../test_auto_GrayscaleFillHoleImageFilter.py | 3 +- ...test_auto_GrayscaleGrindPeakImageFilter.py | 3 +- .../tests/test_auto_HistogramMatching.py | 3 +- .../tests/test_auto_ImageLabelCombine.py | 3 +- .../tests/test_auto_MaskScalarVolume.py | 3 +- .../tests/test_auto_MedianImageFilter.py | 3 +- .../tests/test_auto_MultiplyScalarVolumes.py | 3 +- .../test_auto_N4ITKBiasFieldCorrection.py | 3 +- ...test_auto_ResampleScalarVectorDWIVolume.py | 3 +- .../tests/test_auto_SubtractScalarVolumes.py | 3 +- .../tests/test_auto_ThresholdScalarVolume.py | 3 +- ...auto_VotingBinaryHoleFillingImageFilter.py | 3 +- ...est_auto_DWIUnbiasedNonLocalMeansFilter.py | 3 +- .../tests/test_auto_AffineRegistration.py | 3 +- ...test_auto_BSplineDeformableRegistration.py | 3 +- .../test_auto_BSplineToDeformationField.py | 3 +- .../test_auto_ExpertAutomatedRegistration.py | 3 +- .../tests/test_auto_LinearRegistration.py | 3 +- ..._auto_MultiResolutionAffineRegistration.py | 3 +- .../test_auto_OtsuThresholdImageFilter.py | 3 +- .../test_auto_OtsuThresholdSegmentation.py | 3 +- .../tests/test_auto_ResampleScalarVolume.py | 3 +- .../tests/test_auto_RigidRegistration.py | 3 +- .../test_auto_IntensityDifferenceMetric.py | 3 +- ..._auto_PETStandardUptakeValueComputation.py | 3 +- .../tests/test_auto_ACPCTransform.py | 3 +- .../tests/test_auto_BRAINSDemonWarp.py | 3 +- .../registration/tests/test_auto_BRAINSFit.py | 3 +- .../tests/test_auto_BRAINSResample.py | 3 +- .../tests/test_auto_FiducialRegistration.py | 3 +- .../tests/test_auto_VBRAINSDemonWarp.py | 3 +- .../tests/test_auto_BRAINSROIAuto.py | 3 +- .../tests/test_auto_EMSegmentCommandLine.py | 3 +- .../test_auto_RobustStatisticsSegmenter.py | 3 +- ...st_auto_SimpleRegionGrowingSegmentation.py | 3 +- .../tests/test_auto_DicomToNrrdConverter.py | 3 +- ...test_auto_EMSegmentTransformToNewFormat.py | 3 +- .../tests/test_auto_GrayscaleModelMaker.py | 3 +- .../tests/test_auto_LabelMapSmoothing.py | 3 +- .../slicer/tests/test_auto_MergeModels.py | 3 +- .../slicer/tests/test_auto_ModelMaker.py | 3 +- .../slicer/tests/test_auto_ModelToLabelMap.py | 3 +- .../tests/test_auto_OrientScalarVolume.py | 3 +- .../tests/test_auto_ProbeVolumeWithModel.py | 3 +- .../tests/test_auto_SlicerCommandLine.py | 1 + .../spm/tests/test_auto_Analyze2nii.py | 3 +- .../spm/tests/test_auto_ApplyDeformations.py | 3 +- .../test_auto_ApplyInverseDeformation.py | 3 +- .../spm/tests/test_auto_ApplyTransform.py | 3 +- .../spm/tests/test_auto_CalcCoregAffine.py | 3 +- .../spm/tests/test_auto_Coregister.py | 3 +- .../spm/tests/test_auto_CreateWarped.py | 3 +- .../interfaces/spm/tests/test_auto_DARTEL.py | 3 +- .../spm/tests/test_auto_DARTELNorm2MNI.py | 3 +- .../spm/tests/test_auto_DicomImport.py | 3 +- .../spm/tests/test_auto_EstimateContrast.py | 3 +- .../spm/tests/test_auto_EstimateModel.py | 3 +- .../spm/tests/test_auto_FactorialDesign.py | 3 +- .../spm/tests/test_auto_Level1Design.py | 3 +- .../test_auto_MultipleRegressionDesign.py | 3 +- .../spm/tests/test_auto_NewSegment.py | 3 +- .../spm/tests/test_auto_Normalize.py | 3 +- .../spm/tests/test_auto_Normalize12.py | 3 +- .../tests/test_auto_OneSampleTTestDesign.py | 3 +- .../spm/tests/test_auto_PairedTTestDesign.py | 3 +- .../interfaces/spm/tests/test_auto_Realign.py | 3 +- .../interfaces/spm/tests/test_auto_Reslice.py | 3 +- .../spm/tests/test_auto_ResliceToReference.py | 3 +- .../spm/tests/test_auto_SPMCommand.py | 1 + .../interfaces/spm/tests/test_auto_Segment.py | 3 +- .../spm/tests/test_auto_SliceTiming.py | 3 +- .../interfaces/spm/tests/test_auto_Smooth.py | 3 +- .../spm/tests/test_auto_Threshold.py | 3 +- .../tests/test_auto_ThresholdStatistics.py | 3 +- .../tests/test_auto_TwoSampleTTestDesign.py | 3 +- .../spm/tests/test_auto_VBMSegment.py | 3 +- .../interfaces/tests/test_auto_AssertEqual.py | 1 + .../tests/test_auto_BaseInterface.py | 1 + .../tests/test_auto_C3dAffineTool.py | 3 +- .../interfaces/tests/test_auto_CSVReader.py | 3 +- .../interfaces/tests/test_auto_CommandLine.py | 1 + nipype/interfaces/tests/test_auto_CopyMeta.py | 3 +- .../interfaces/tests/test_auto_DataFinder.py | 3 +- .../interfaces/tests/test_auto_DataGrabber.py | 3 +- nipype/interfaces/tests/test_auto_DataSink.py | 3 +- nipype/interfaces/tests/test_auto_Dcm2nii.py | 3 +- nipype/interfaces/tests/test_auto_DcmStack.py | 3 +- .../tests/test_auto_FreeSurferSource.py | 3 +- nipype/interfaces/tests/test_auto_Function.py | 3 +- .../tests/test_auto_GroupAndStack.py | 3 +- nipype/interfaces/tests/test_auto_IOBase.py | 1 + .../tests/test_auto_IdentityInterface.py | 3 +- .../tests/test_auto_JSONFileGrabber.py | 3 +- .../tests/test_auto_JSONFileSink.py | 3 +- .../interfaces/tests/test_auto_LookupMeta.py | 3 +- .../tests/test_auto_MatlabCommand.py | 1 + nipype/interfaces/tests/test_auto_Merge.py | 3 +- .../interfaces/tests/test_auto_MergeNifti.py | 3 +- nipype/interfaces/tests/test_auto_MeshFix.py | 3 +- .../tests/test_auto_MpiCommandLine.py | 1 + .../interfaces/tests/test_auto_MySQLSink.py | 1 + .../tests/test_auto_NiftiGeneratorBase.py | 1 + nipype/interfaces/tests/test_auto_Rename.py | 3 +- .../tests/test_auto_S3DataGrabber.py | 3 +- .../interfaces/tests/test_auto_S3DataSink.py | 3 +- .../tests/test_auto_SEMLikeCommandLine.py | 1 + .../interfaces/tests/test_auto_SQLiteSink.py | 1 + .../tests/test_auto_SSHDataGrabber.py | 3 +- nipype/interfaces/tests/test_auto_Select.py | 3 +- .../interfaces/tests/test_auto_SelectFiles.py | 3 +- .../tests/test_auto_SlicerCommandLine.py | 3 +- nipype/interfaces/tests/test_auto_Split.py | 3 +- .../interfaces/tests/test_auto_SplitNifti.py | 3 +- .../tests/test_auto_StdOutCommandLine.py | 1 + nipype/interfaces/tests/test_auto_XNATSink.py | 1 + .../interfaces/tests/test_auto_XNATSource.py | 3 +- .../vista/tests/test_auto_Vnifti2Image.py | 3 +- .../vista/tests/test_auto_VtoMat.py | 3 +- 575 files changed, 1207 insertions(+), 552 deletions(-) create mode 100644 nipype/algorithms/tests/test_auto_ErrorMap.py create mode 100644 nipype/algorithms/tests/test_auto_Overlap.py diff --git a/nipype/algorithms/tests/test_auto_AddCSVColumn.py b/nipype/algorithms/tests/test_auto_AddCSVColumn.py index 14b6dfb452..89a52b8abe 100644 --- a/nipype/algorithms/tests/test_auto_AddCSVColumn.py +++ b/nipype/algorithms/tests/test_auto_AddCSVColumn.py @@ -2,6 +2,7 @@ from ...testing import assert_equal from ..misc import AddCSVColumn + def test_AddCSVColumn_inputs(): input_map = dict(extra_column_heading=dict(), extra_field=dict(), @@ -16,6 +17,7 @@ def test_AddCSVColumn_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_AddCSVColumn_outputs(): output_map = dict(csv_file=dict(), ) @@ -24,4 +26,3 @@ def test_AddCSVColumn_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/algorithms/tests/test_auto_AddCSVRow.py b/nipype/algorithms/tests/test_auto_AddCSVRow.py index 766665a816..eaac3370c9 100644 --- a/nipype/algorithms/tests/test_auto_AddCSVRow.py +++ b/nipype/algorithms/tests/test_auto_AddCSVRow.py @@ -2,6 +2,7 @@ from ...testing import assert_equal from ..misc import AddCSVRow + def test_AddCSVRow_inputs(): input_map = dict(_outputs=dict(usedefault=True, ), @@ -17,6 +18,7 @@ def test_AddCSVRow_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_AddCSVRow_outputs(): output_map = dict(csv_file=dict(), ) @@ -25,4 +27,3 @@ def test_AddCSVRow_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/algorithms/tests/test_auto_AddNoise.py b/nipype/algorithms/tests/test_auto_AddNoise.py index 747bf51a21..50aa563ce0 100644 --- a/nipype/algorithms/tests/test_auto_AddNoise.py +++ b/nipype/algorithms/tests/test_auto_AddNoise.py @@ -2,6 +2,7 @@ from ...testing import assert_equal from ..misc import AddNoise + def test_AddNoise_inputs(): input_map = dict(bg_dist=dict(mandatory=True, usedefault=True, @@ -22,6 +23,7 @@ def test_AddNoise_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_AddNoise_outputs(): output_map = dict(out_file=dict(), ) @@ -30,4 +32,3 @@ def test_AddNoise_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/algorithms/tests/test_auto_ArtifactDetect.py b/nipype/algorithms/tests/test_auto_ArtifactDetect.py index 4e1c5a1641..961b7dd2d0 100644 --- a/nipype/algorithms/tests/test_auto_ArtifactDetect.py +++ b/nipype/algorithms/tests/test_auto_ArtifactDetect.py @@ -2,6 +2,7 @@ from ...testing import assert_equal from ..rapidart import ArtifactDetect + def test_ArtifactDetect_inputs(): input_map = dict(bound_by_brainmask=dict(usedefault=True, ), @@ -50,6 +51,7 @@ def test_ArtifactDetect_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ArtifactDetect_outputs(): output_map = dict(displacement_files=dict(), intensity_files=dict(), @@ -64,4 +66,3 @@ def test_ArtifactDetect_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/algorithms/tests/test_auto_CalculateNormalizedMoments.py b/nipype/algorithms/tests/test_auto_CalculateNormalizedMoments.py index f779679928..62a7b67b0c 100644 --- a/nipype/algorithms/tests/test_auto_CalculateNormalizedMoments.py +++ b/nipype/algorithms/tests/test_auto_CalculateNormalizedMoments.py @@ -2,6 +2,7 @@ from ...testing import assert_equal from ..misc import CalculateNormalizedMoments + def test_CalculateNormalizedMoments_inputs(): input_map = dict(moment=dict(mandatory=True, ), @@ -14,6 +15,7 @@ def test_CalculateNormalizedMoments_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_CalculateNormalizedMoments_outputs(): output_map = dict(moments=dict(), ) @@ -22,4 +24,3 @@ def test_CalculateNormalizedMoments_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/algorithms/tests/test_auto_ComputeMeshWarp.py b/nipype/algorithms/tests/test_auto_ComputeMeshWarp.py index b1727ca477..e0a2d5f85c 100644 --- a/nipype/algorithms/tests/test_auto_ComputeMeshWarp.py +++ b/nipype/algorithms/tests/test_auto_ComputeMeshWarp.py @@ -2,6 +2,7 @@ from ...testing import assert_equal from ..mesh import ComputeMeshWarp + def test_ComputeMeshWarp_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, @@ -25,6 +26,7 @@ def test_ComputeMeshWarp_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ComputeMeshWarp_outputs(): output_map = dict(distance=dict(), out_file=dict(), @@ -35,4 +37,3 @@ def test_ComputeMeshWarp_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/algorithms/tests/test_auto_CreateNifti.py b/nipype/algorithms/tests/test_auto_CreateNifti.py index 62c0926bb9..0e12142783 100644 --- a/nipype/algorithms/tests/test_auto_CreateNifti.py +++ b/nipype/algorithms/tests/test_auto_CreateNifti.py @@ -2,6 +2,7 @@ from ...testing import assert_equal from ..misc import CreateNifti + def test_CreateNifti_inputs(): input_map = dict(affine=dict(), data_file=dict(mandatory=True, @@ -18,6 +19,7 @@ def test_CreateNifti_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_CreateNifti_outputs(): output_map = dict(nifti_file=dict(), ) @@ -26,4 +28,3 @@ def test_CreateNifti_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/algorithms/tests/test_auto_Distance.py b/nipype/algorithms/tests/test_auto_Distance.py index 9ae3e7f9b0..4e5da64ba9 100644 --- a/nipype/algorithms/tests/test_auto_Distance.py +++ b/nipype/algorithms/tests/test_auto_Distance.py @@ -2,6 +2,7 @@ from ...testing import assert_equal from ..misc import Distance + def test_Distance_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, @@ -20,6 +21,7 @@ def test_Distance_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Distance_outputs(): output_map = dict(distance=dict(), histogram=dict(), @@ -31,4 +33,3 @@ def test_Distance_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/algorithms/tests/test_auto_ErrorMap.py b/nipype/algorithms/tests/test_auto_ErrorMap.py new file mode 100644 index 0000000000..69484529dd --- /dev/null +++ b/nipype/algorithms/tests/test_auto_ErrorMap.py @@ -0,0 +1,35 @@ +# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT +from ...testing import assert_equal +from ..metrics import ErrorMap + + +def test_ErrorMap_inputs(): + input_map = dict(ignore_exception=dict(nohash=True, + usedefault=True, + ), + in_ref=dict(mandatory=True, + ), + in_tst=dict(mandatory=True, + ), + mask=dict(), + metric=dict(mandatory=True, + usedefault=True, + ), + out_map=dict(), + ) + inputs = ErrorMap.input_spec() + + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): + yield assert_equal, getattr(inputs.traits()[key], metakey), value + + +def test_ErrorMap_outputs(): + output_map = dict(distance=dict(), + out_map=dict(), + ) + outputs = ErrorMap.output_spec() + + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): + yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/algorithms/tests/test_auto_FuzzyOverlap.py b/nipype/algorithms/tests/test_auto_FuzzyOverlap.py index b303866349..dbc0c02474 100644 --- a/nipype/algorithms/tests/test_auto_FuzzyOverlap.py +++ b/nipype/algorithms/tests/test_auto_FuzzyOverlap.py @@ -2,6 +2,7 @@ from ...testing import assert_equal from ..misc import FuzzyOverlap + def test_FuzzyOverlap_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, @@ -21,6 +22,7 @@ def test_FuzzyOverlap_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_FuzzyOverlap_outputs(): output_map = dict(class_fdi=dict(), class_fji=dict(), @@ -33,4 +35,3 @@ def test_FuzzyOverlap_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/algorithms/tests/test_auto_Gunzip.py b/nipype/algorithms/tests/test_auto_Gunzip.py index ad48e0b405..b77e6dfbd5 100644 --- a/nipype/algorithms/tests/test_auto_Gunzip.py +++ b/nipype/algorithms/tests/test_auto_Gunzip.py @@ -2,6 +2,7 @@ from ...testing import assert_equal from ..misc import Gunzip + def test_Gunzip_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, @@ -15,6 +16,7 @@ def test_Gunzip_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Gunzip_outputs(): output_map = dict(out_file=dict(), ) @@ -23,4 +25,3 @@ def test_Gunzip_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/algorithms/tests/test_auto_ICC.py b/nipype/algorithms/tests/test_auto_ICC.py index 292e8ae7a8..76b70b3369 100644 --- a/nipype/algorithms/tests/test_auto_ICC.py +++ b/nipype/algorithms/tests/test_auto_ICC.py @@ -2,6 +2,7 @@ from ...testing import assert_equal from ..icc import ICC + def test_ICC_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, @@ -17,6 +18,7 @@ def test_ICC_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ICC_outputs(): output_map = dict(icc_map=dict(), session_var_map=dict(), @@ -27,4 +29,3 @@ def test_ICC_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/algorithms/tests/test_auto_Matlab2CSV.py b/nipype/algorithms/tests/test_auto_Matlab2CSV.py index 41f91baebd..1382385dc3 100644 --- a/nipype/algorithms/tests/test_auto_Matlab2CSV.py +++ b/nipype/algorithms/tests/test_auto_Matlab2CSV.py @@ -2,6 +2,7 @@ from ...testing import assert_equal from ..misc import Matlab2CSV + def test_Matlab2CSV_inputs(): input_map = dict(in_file=dict(mandatory=True, ), @@ -14,6 +15,7 @@ def test_Matlab2CSV_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Matlab2CSV_outputs(): output_map = dict(csv_files=dict(), ) @@ -22,4 +24,3 @@ def test_Matlab2CSV_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/algorithms/tests/test_auto_MergeCSVFiles.py b/nipype/algorithms/tests/test_auto_MergeCSVFiles.py index d63189e1ab..4d2d896db3 100644 --- a/nipype/algorithms/tests/test_auto_MergeCSVFiles.py +++ b/nipype/algorithms/tests/test_auto_MergeCSVFiles.py @@ -2,6 +2,7 @@ from ...testing import assert_equal from ..misc import MergeCSVFiles + def test_MergeCSVFiles_inputs(): input_map = dict(column_headings=dict(), extra_column_heading=dict(), @@ -20,6 +21,7 @@ def test_MergeCSVFiles_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MergeCSVFiles_outputs(): output_map = dict(csv_file=dict(), ) @@ -28,4 +30,3 @@ def test_MergeCSVFiles_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/algorithms/tests/test_auto_MergeROIs.py b/nipype/algorithms/tests/test_auto_MergeROIs.py index 6fc41742f8..83eed3a4d4 100644 --- a/nipype/algorithms/tests/test_auto_MergeROIs.py +++ b/nipype/algorithms/tests/test_auto_MergeROIs.py @@ -2,6 +2,7 @@ from ...testing import assert_equal from ..misc import MergeROIs + def test_MergeROIs_inputs(): input_map = dict(in_files=dict(), in_index=dict(), @@ -13,6 +14,7 @@ def test_MergeROIs_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MergeROIs_outputs(): output_map = dict(merged_file=dict(), ) @@ -21,4 +23,3 @@ def test_MergeROIs_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/algorithms/tests/test_auto_MeshWarpMaths.py b/nipype/algorithms/tests/test_auto_MeshWarpMaths.py index 21a34fb9b8..dfd4c5bd63 100644 --- a/nipype/algorithms/tests/test_auto_MeshWarpMaths.py +++ b/nipype/algorithms/tests/test_auto_MeshWarpMaths.py @@ -2,6 +2,7 @@ from ...testing import assert_equal from ..mesh import MeshWarpMaths + def test_MeshWarpMaths_inputs(): input_map = dict(float_trait=dict(), ignore_exception=dict(nohash=True, @@ -24,6 +25,7 @@ def test_MeshWarpMaths_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MeshWarpMaths_outputs(): output_map = dict(out_file=dict(), out_warp=dict(), @@ -33,4 +35,3 @@ def test_MeshWarpMaths_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/algorithms/tests/test_auto_ModifyAffine.py b/nipype/algorithms/tests/test_auto_ModifyAffine.py index 7817620e1b..fb8c5ca876 100644 --- a/nipype/algorithms/tests/test_auto_ModifyAffine.py +++ b/nipype/algorithms/tests/test_auto_ModifyAffine.py @@ -2,6 +2,7 @@ from ...testing import assert_equal from ..misc import ModifyAffine + def test_ModifyAffine_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, @@ -17,6 +18,7 @@ def test_ModifyAffine_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ModifyAffine_outputs(): output_map = dict(transformed_volumes=dict(), ) @@ -25,4 +27,3 @@ def test_ModifyAffine_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/algorithms/tests/test_auto_NormalizeProbabilityMapSet.py b/nipype/algorithms/tests/test_auto_NormalizeProbabilityMapSet.py index 49a7035037..c2595baa72 100644 --- a/nipype/algorithms/tests/test_auto_NormalizeProbabilityMapSet.py +++ b/nipype/algorithms/tests/test_auto_NormalizeProbabilityMapSet.py @@ -2,6 +2,7 @@ from ...testing import assert_equal from ..misc import NormalizeProbabilityMapSet + def test_NormalizeProbabilityMapSet_inputs(): input_map = dict(in_files=dict(), in_mask=dict(), @@ -12,6 +13,7 @@ def test_NormalizeProbabilityMapSet_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_NormalizeProbabilityMapSet_outputs(): output_map = dict(out_files=dict(), ) @@ -20,4 +22,3 @@ def test_NormalizeProbabilityMapSet_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/algorithms/tests/test_auto_Overlap.py b/nipype/algorithms/tests/test_auto_Overlap.py new file mode 100644 index 0000000000..a5a3874bd1 --- /dev/null +++ b/nipype/algorithms/tests/test_auto_Overlap.py @@ -0,0 +1,47 @@ +# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT +from ...testing import assert_equal +from ..misc import Overlap + + +def test_Overlap_inputs(): + input_map = dict(bg_overlap=dict(mandatory=True, + usedefault=True, + ), + ignore_exception=dict(nohash=True, + usedefault=True, + ), + mask_volume=dict(), + out_file=dict(usedefault=True, + ), + vol_units=dict(mandatory=True, + usedefault=True, + ), + volume1=dict(mandatory=True, + ), + volume2=dict(mandatory=True, + ), + weighting=dict(usedefault=True, + ), + ) + inputs = Overlap.input_spec() + + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): + yield assert_equal, getattr(inputs.traits()[key], metakey), value + + +def test_Overlap_outputs(): + output_map = dict(dice=dict(), + diff_file=dict(), + jaccard=dict(), + labels=dict(), + roi_di=dict(), + roi_ji=dict(), + roi_voldiff=dict(), + volume_difference=dict(), + ) + outputs = Overlap.output_spec() + + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): + yield assert_equal, getattr(outputs.traits()[key], metakey), value diff --git a/nipype/algorithms/tests/test_auto_P2PDistance.py b/nipype/algorithms/tests/test_auto_P2PDistance.py index fa8f582fd4..0a30a382c9 100644 --- a/nipype/algorithms/tests/test_auto_P2PDistance.py +++ b/nipype/algorithms/tests/test_auto_P2PDistance.py @@ -2,6 +2,7 @@ from ...testing import assert_equal from ..mesh import P2PDistance + def test_P2PDistance_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, @@ -25,6 +26,7 @@ def test_P2PDistance_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_P2PDistance_outputs(): output_map = dict(distance=dict(), out_file=dict(), @@ -35,4 +37,3 @@ def test_P2PDistance_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/algorithms/tests/test_auto_PickAtlas.py b/nipype/algorithms/tests/test_auto_PickAtlas.py index a60645a368..27aaac7d41 100644 --- a/nipype/algorithms/tests/test_auto_PickAtlas.py +++ b/nipype/algorithms/tests/test_auto_PickAtlas.py @@ -2,6 +2,7 @@ from ...testing import assert_equal from ..misc import PickAtlas + def test_PickAtlas_inputs(): input_map = dict(atlas=dict(mandatory=True, ), @@ -22,6 +23,7 @@ def test_PickAtlas_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_PickAtlas_outputs(): output_map = dict(mask_file=dict(), ) @@ -30,4 +32,3 @@ def test_PickAtlas_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/algorithms/tests/test_auto_Similarity.py b/nipype/algorithms/tests/test_auto_Similarity.py index a69dcb5f1b..109933677c 100644 --- a/nipype/algorithms/tests/test_auto_Similarity.py +++ b/nipype/algorithms/tests/test_auto_Similarity.py @@ -2,6 +2,7 @@ from ...testing import assert_equal from ..metrics import Similarity + def test_Similarity_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, @@ -21,6 +22,7 @@ def test_Similarity_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Similarity_outputs(): output_map = dict(similarity=dict(), ) @@ -29,4 +31,3 @@ def test_Similarity_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/algorithms/tests/test_auto_SimpleThreshold.py b/nipype/algorithms/tests/test_auto_SimpleThreshold.py index f0840a6fd9..ff46592c11 100644 --- a/nipype/algorithms/tests/test_auto_SimpleThreshold.py +++ b/nipype/algorithms/tests/test_auto_SimpleThreshold.py @@ -2,6 +2,7 @@ from ...testing import assert_equal from ..misc import SimpleThreshold + def test_SimpleThreshold_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, @@ -17,6 +18,7 @@ def test_SimpleThreshold_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_SimpleThreshold_outputs(): output_map = dict(thresholded_volumes=dict(), ) @@ -25,4 +27,3 @@ def test_SimpleThreshold_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/algorithms/tests/test_auto_SpecifyModel.py b/nipype/algorithms/tests/test_auto_SpecifyModel.py index ca3ccc69d3..69a528c3c2 100644 --- a/nipype/algorithms/tests/test_auto_SpecifyModel.py +++ b/nipype/algorithms/tests/test_auto_SpecifyModel.py @@ -2,6 +2,7 @@ from ...testing import assert_equal from ..modelgen import SpecifyModel + def test_SpecifyModel_inputs(): input_map = dict(event_files=dict(mandatory=True, xor=['subject_info', 'event_files'], @@ -32,6 +33,7 @@ def test_SpecifyModel_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_SpecifyModel_outputs(): output_map = dict(session_info=dict(), ) @@ -40,4 +42,3 @@ def test_SpecifyModel_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/algorithms/tests/test_auto_SpecifySPMModel.py b/nipype/algorithms/tests/test_auto_SpecifySPMModel.py index e0c300b621..19ccaa9ba5 100644 --- a/nipype/algorithms/tests/test_auto_SpecifySPMModel.py +++ b/nipype/algorithms/tests/test_auto_SpecifySPMModel.py @@ -2,6 +2,7 @@ from ...testing import assert_equal from ..modelgen import SpecifySPMModel + def test_SpecifySPMModel_inputs(): input_map = dict(concatenate_runs=dict(usedefault=True, ), @@ -36,6 +37,7 @@ def test_SpecifySPMModel_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_SpecifySPMModel_outputs(): output_map = dict(session_info=dict(), ) @@ -44,4 +46,3 @@ def test_SpecifySPMModel_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/algorithms/tests/test_auto_SpecifySparseModel.py b/nipype/algorithms/tests/test_auto_SpecifySparseModel.py index b8601014e1..aa641facf7 100644 --- a/nipype/algorithms/tests/test_auto_SpecifySparseModel.py +++ b/nipype/algorithms/tests/test_auto_SpecifySparseModel.py @@ -2,6 +2,7 @@ from ...testing import assert_equal from ..modelgen import SpecifySparseModel + def test_SpecifySparseModel_inputs(): input_map = dict(event_files=dict(mandatory=True, xor=['subject_info', 'event_files'], @@ -46,6 +47,7 @@ def test_SpecifySparseModel_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_SpecifySparseModel_outputs(): output_map = dict(session_info=dict(), sparse_png_file=dict(), @@ -56,4 +58,3 @@ def test_SpecifySparseModel_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/algorithms/tests/test_auto_SplitROIs.py b/nipype/algorithms/tests/test_auto_SplitROIs.py index 553f937a1c..cd23a51468 100644 --- a/nipype/algorithms/tests/test_auto_SplitROIs.py +++ b/nipype/algorithms/tests/test_auto_SplitROIs.py @@ -2,6 +2,7 @@ from ...testing import assert_equal from ..misc import SplitROIs + def test_SplitROIs_inputs(): input_map = dict(in_file=dict(mandatory=True, ), @@ -14,6 +15,7 @@ def test_SplitROIs_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_SplitROIs_outputs(): output_map = dict(out_files=dict(), out_index=dict(), @@ -24,4 +26,3 @@ def test_SplitROIs_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/algorithms/tests/test_auto_StimulusCorrelation.py b/nipype/algorithms/tests/test_auto_StimulusCorrelation.py index 3f7f9ed11b..f1b786aa8e 100644 --- a/nipype/algorithms/tests/test_auto_StimulusCorrelation.py +++ b/nipype/algorithms/tests/test_auto_StimulusCorrelation.py @@ -2,6 +2,7 @@ from ...testing import assert_equal from ..rapidart import StimulusCorrelation + def test_StimulusCorrelation_inputs(): input_map = dict(concatenated_design=dict(mandatory=True, ), @@ -21,6 +22,7 @@ def test_StimulusCorrelation_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_StimulusCorrelation_outputs(): output_map = dict(stimcorr_files=dict(), ) @@ -29,4 +31,3 @@ def test_StimulusCorrelation_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/algorithms/tests/test_auto_TSNR.py b/nipype/algorithms/tests/test_auto_TSNR.py index 1ea1bc6192..044712c362 100644 --- a/nipype/algorithms/tests/test_auto_TSNR.py +++ b/nipype/algorithms/tests/test_auto_TSNR.py @@ -2,6 +2,7 @@ from ...testing import assert_equal from ..misc import TSNR + def test_TSNR_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, @@ -16,6 +17,7 @@ def test_TSNR_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_TSNR_outputs(): output_map = dict(detrended_file=dict(), mean_file=dict(), @@ -27,4 +29,3 @@ def test_TSNR_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/algorithms/tests/test_auto_WarpPoints.py b/nipype/algorithms/tests/test_auto_WarpPoints.py index 918a8eeb96..741b9f0c60 100644 --- a/nipype/algorithms/tests/test_auto_WarpPoints.py +++ b/nipype/algorithms/tests/test_auto_WarpPoints.py @@ -2,6 +2,7 @@ from ...testing import assert_equal from ..mesh import WarpPoints + def test_WarpPoints_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, @@ -25,6 +26,7 @@ def test_WarpPoints_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_WarpPoints_outputs(): output_map = dict(out_points=dict(), ) @@ -33,4 +35,3 @@ def test_WarpPoints_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/afni/tests/test_auto_AFNICommand.py b/nipype/interfaces/afni/tests/test_auto_AFNICommand.py index 14769735dd..f822168eb8 100644 --- a/nipype/interfaces/afni/tests/test_auto_AFNICommand.py +++ b/nipype/interfaces/afni/tests/test_auto_AFNICommand.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..base import AFNICommand + def test_AFNICommand_inputs(): input_map = dict(args=dict(argstr='%s', ), diff --git a/nipype/interfaces/afni/tests/test_auto_AFNItoNIFTI.py b/nipype/interfaces/afni/tests/test_auto_AFNItoNIFTI.py index 96334c4a20..1e46cccd56 100644 --- a/nipype/interfaces/afni/tests/test_auto_AFNItoNIFTI.py +++ b/nipype/interfaces/afni/tests/test_auto_AFNItoNIFTI.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import AFNItoNIFTI + def test_AFNItoNIFTI_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -30,6 +31,7 @@ def test_AFNItoNIFTI_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_AFNItoNIFTI_outputs(): output_map = dict(out_file=dict(), ) @@ -38,4 +40,3 @@ def test_AFNItoNIFTI_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/afni/tests/test_auto_Allineate.py b/nipype/interfaces/afni/tests/test_auto_Allineate.py index 6f30731692..27a1cc5dae 100644 --- a/nipype/interfaces/afni/tests/test_auto_Allineate.py +++ b/nipype/interfaces/afni/tests/test_auto_Allineate.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import Allineate + def test_Allineate_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -110,6 +111,7 @@ def test_Allineate_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Allineate_outputs(): output_map = dict(matrix=dict(), out_file=dict(), @@ -119,4 +121,3 @@ def test_Allineate_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/afni/tests/test_auto_AutoTcorrelate.py b/nipype/interfaces/afni/tests/test_auto_AutoTcorrelate.py index 312ab7ef90..0591a7eb7f 100644 --- a/nipype/interfaces/afni/tests/test_auto_AutoTcorrelate.py +++ b/nipype/interfaces/afni/tests/test_auto_AutoTcorrelate.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import AutoTcorrelate + def test_AutoTcorrelate_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -42,6 +43,7 @@ def test_AutoTcorrelate_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_AutoTcorrelate_outputs(): output_map = dict(out_file=dict(), ) @@ -50,4 +52,3 @@ def test_AutoTcorrelate_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/afni/tests/test_auto_Autobox.py b/nipype/interfaces/afni/tests/test_auto_Autobox.py index 184956660c..3a23e751a3 100644 --- a/nipype/interfaces/afni/tests/test_auto_Autobox.py +++ b/nipype/interfaces/afni/tests/test_auto_Autobox.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import Autobox + def test_Autobox_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -32,6 +33,7 @@ def test_Autobox_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Autobox_outputs(): output_map = dict(out_file=dict(), x_max=dict(), @@ -46,4 +48,3 @@ def test_Autobox_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/afni/tests/test_auto_Automask.py b/nipype/interfaces/afni/tests/test_auto_Automask.py index 514559fad6..5ee4b08162 100644 --- a/nipype/interfaces/afni/tests/test_auto_Automask.py +++ b/nipype/interfaces/afni/tests/test_auto_Automask.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import Automask + def test_Automask_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -40,6 +41,7 @@ def test_Automask_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Automask_outputs(): output_map = dict(brain_file=dict(), out_file=dict(), @@ -49,4 +51,3 @@ def test_Automask_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/afni/tests/test_auto_Bandpass.py b/nipype/interfaces/afni/tests/test_auto_Bandpass.py index bf4e819284..519d8fd501 100644 --- a/nipype/interfaces/afni/tests/test_auto_Bandpass.py +++ b/nipype/interfaces/afni/tests/test_auto_Bandpass.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import Bandpass + def test_Bandpass_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -65,6 +66,7 @@ def test_Bandpass_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Bandpass_outputs(): output_map = dict(out_file=dict(), ) @@ -73,4 +75,3 @@ def test_Bandpass_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/afni/tests/test_auto_BlurInMask.py b/nipype/interfaces/afni/tests/test_auto_BlurInMask.py index a911469623..276cf8a81f 100644 --- a/nipype/interfaces/afni/tests/test_auto_BlurInMask.py +++ b/nipype/interfaces/afni/tests/test_auto_BlurInMask.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import BlurInMask + def test_BlurInMask_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -47,6 +48,7 @@ def test_BlurInMask_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_BlurInMask_outputs(): output_map = dict(out_file=dict(), ) @@ -55,4 +57,3 @@ def test_BlurInMask_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/afni/tests/test_auto_BrickStat.py b/nipype/interfaces/afni/tests/test_auto_BrickStat.py index 6c423a2232..0c47101656 100644 --- a/nipype/interfaces/afni/tests/test_auto_BrickStat.py +++ b/nipype/interfaces/afni/tests/test_auto_BrickStat.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import BrickStat + def test_BrickStat_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -35,6 +36,7 @@ def test_BrickStat_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_BrickStat_outputs(): output_map = dict(min_val=dict(), ) @@ -43,4 +45,3 @@ def test_BrickStat_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/afni/tests/test_auto_Calc.py b/nipype/interfaces/afni/tests/test_auto_Calc.py index b33fc3de88..c15431a5a8 100644 --- a/nipype/interfaces/afni/tests/test_auto_Calc.py +++ b/nipype/interfaces/afni/tests/test_auto_Calc.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import Calc + def test_Calc_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -46,6 +47,7 @@ def test_Calc_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Calc_outputs(): output_map = dict(out_file=dict(), ) @@ -54,4 +56,3 @@ def test_Calc_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/afni/tests/test_auto_Copy.py b/nipype/interfaces/afni/tests/test_auto_Copy.py index c82385085e..fffc9267d1 100644 --- a/nipype/interfaces/afni/tests/test_auto_Copy.py +++ b/nipype/interfaces/afni/tests/test_auto_Copy.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import Copy + def test_Copy_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -31,6 +32,7 @@ def test_Copy_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Copy_outputs(): output_map = dict(out_file=dict(), ) @@ -39,4 +41,3 @@ def test_Copy_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/afni/tests/test_auto_Despike.py b/nipype/interfaces/afni/tests/test_auto_Despike.py index 51590348de..0e8c5876f9 100644 --- a/nipype/interfaces/afni/tests/test_auto_Despike.py +++ b/nipype/interfaces/afni/tests/test_auto_Despike.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import Despike + def test_Despike_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -30,6 +31,7 @@ def test_Despike_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Despike_outputs(): output_map = dict(out_file=dict(), ) @@ -38,4 +40,3 @@ def test_Despike_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/afni/tests/test_auto_Detrend.py b/nipype/interfaces/afni/tests/test_auto_Detrend.py index b066a58b88..2fd8bf3d6f 100644 --- a/nipype/interfaces/afni/tests/test_auto_Detrend.py +++ b/nipype/interfaces/afni/tests/test_auto_Detrend.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import Detrend + def test_Detrend_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -30,6 +31,7 @@ def test_Detrend_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Detrend_outputs(): output_map = dict(out_file=dict(), ) @@ -38,4 +40,3 @@ def test_Detrend_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/afni/tests/test_auto_Eval.py b/nipype/interfaces/afni/tests/test_auto_Eval.py index 3f9ad93ec5..0ca8e85bc0 100644 --- a/nipype/interfaces/afni/tests/test_auto_Eval.py +++ b/nipype/interfaces/afni/tests/test_auto_Eval.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import Eval + def test_Eval_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -48,6 +49,7 @@ def test_Eval_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Eval_outputs(): output_map = dict(out_file=dict(), ) @@ -56,4 +58,3 @@ def test_Eval_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/afni/tests/test_auto_Fim.py b/nipype/interfaces/afni/tests/test_auto_Fim.py index a926568c3a..60aa963b28 100644 --- a/nipype/interfaces/afni/tests/test_auto_Fim.py +++ b/nipype/interfaces/afni/tests/test_auto_Fim.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import Fim + def test_Fim_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -40,6 +41,7 @@ def test_Fim_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Fim_outputs(): output_map = dict(out_file=dict(), ) @@ -48,4 +50,3 @@ def test_Fim_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/afni/tests/test_auto_Fourier.py b/nipype/interfaces/afni/tests/test_auto_Fourier.py index 0ae0aec8bf..0bc9e03b6c 100644 --- a/nipype/interfaces/afni/tests/test_auto_Fourier.py +++ b/nipype/interfaces/afni/tests/test_auto_Fourier.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import Fourier + def test_Fourier_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -38,6 +39,7 @@ def test_Fourier_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Fourier_outputs(): output_map = dict(out_file=dict(), ) @@ -46,4 +48,3 @@ def test_Fourier_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/afni/tests/test_auto_Maskave.py b/nipype/interfaces/afni/tests/test_auto_Maskave.py index d85d2ad213..dbff513cc8 100644 --- a/nipype/interfaces/afni/tests/test_auto_Maskave.py +++ b/nipype/interfaces/afni/tests/test_auto_Maskave.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import Maskave + def test_Maskave_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -38,6 +39,7 @@ def test_Maskave_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Maskave_outputs(): output_map = dict(out_file=dict(), ) @@ -46,4 +48,3 @@ def test_Maskave_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/afni/tests/test_auto_Means.py b/nipype/interfaces/afni/tests/test_auto_Means.py index 567f9d50d8..de764464b5 100644 --- a/nipype/interfaces/afni/tests/test_auto_Means.py +++ b/nipype/interfaces/afni/tests/test_auto_Means.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import Means + def test_Means_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -48,6 +49,7 @@ def test_Means_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Means_outputs(): output_map = dict(out_file=dict(), ) @@ -56,4 +58,3 @@ def test_Means_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/afni/tests/test_auto_Merge.py b/nipype/interfaces/afni/tests/test_auto_Merge.py index 2513765f4f..9851b90b9c 100644 --- a/nipype/interfaces/afni/tests/test_auto_Merge.py +++ b/nipype/interfaces/afni/tests/test_auto_Merge.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import Merge + def test_Merge_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -35,6 +36,7 @@ def test_Merge_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Merge_outputs(): output_map = dict(out_file=dict(), ) @@ -43,4 +45,3 @@ def test_Merge_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/afni/tests/test_auto_ROIStats.py b/nipype/interfaces/afni/tests/test_auto_ROIStats.py index 5a72acb63b..447b5000f6 100644 --- a/nipype/interfaces/afni/tests/test_auto_ROIStats.py +++ b/nipype/interfaces/afni/tests/test_auto_ROIStats.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import ROIStats + def test_ROIStats_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -35,6 +36,7 @@ def test_ROIStats_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ROIStats_outputs(): output_map = dict(stats=dict(), ) @@ -43,4 +45,3 @@ def test_ROIStats_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/afni/tests/test_auto_Refit.py b/nipype/interfaces/afni/tests/test_auto_Refit.py index abd12546b4..124655276a 100644 --- a/nipype/interfaces/afni/tests/test_auto_Refit.py +++ b/nipype/interfaces/afni/tests/test_auto_Refit.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import Refit + def test_Refit_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -41,6 +42,7 @@ def test_Refit_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Refit_outputs(): output_map = dict(out_file=dict(), ) @@ -49,4 +51,3 @@ def test_Refit_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/afni/tests/test_auto_Resample.py b/nipype/interfaces/afni/tests/test_auto_Resample.py index be5534f3de..8aa40f92ee 100644 --- a/nipype/interfaces/afni/tests/test_auto_Resample.py +++ b/nipype/interfaces/afni/tests/test_auto_Resample.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import Resample + def test_Resample_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -38,6 +39,7 @@ def test_Resample_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Resample_outputs(): output_map = dict(out_file=dict(), ) @@ -46,4 +48,3 @@ def test_Resample_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/afni/tests/test_auto_Retroicor.py b/nipype/interfaces/afni/tests/test_auto_Retroicor.py index 5c9729e83b..2d5fb74175 100644 --- a/nipype/interfaces/afni/tests/test_auto_Retroicor.py +++ b/nipype/interfaces/afni/tests/test_auto_Retroicor.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import Retroicor + def test_Retroicor_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -50,6 +51,7 @@ def test_Retroicor_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Retroicor_outputs(): output_map = dict(out_file=dict(), ) @@ -58,4 +60,3 @@ def test_Retroicor_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/afni/tests/test_auto_SVMTest.py b/nipype/interfaces/afni/tests/test_auto_SVMTest.py index 86cc47f6d7..a1566c59f7 100644 --- a/nipype/interfaces/afni/tests/test_auto_SVMTest.py +++ b/nipype/interfaces/afni/tests/test_auto_SVMTest.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..svm import SVMTest + def test_SVMTest_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -42,6 +43,7 @@ def test_SVMTest_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_SVMTest_outputs(): output_map = dict(out_file=dict(), ) @@ -50,4 +52,3 @@ def test_SVMTest_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/afni/tests/test_auto_SVMTrain.py b/nipype/interfaces/afni/tests/test_auto_SVMTrain.py index 9006b45fb5..eb13dcb531 100644 --- a/nipype/interfaces/afni/tests/test_auto_SVMTrain.py +++ b/nipype/interfaces/afni/tests/test_auto_SVMTrain.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..svm import SVMTrain + def test_SVMTrain_inputs(): input_map = dict(alphas=dict(argstr='-alpha %s', name_source='in_file', @@ -61,6 +62,7 @@ def test_SVMTrain_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_SVMTrain_outputs(): output_map = dict(alphas=dict(), model=dict(), @@ -71,4 +73,3 @@ def test_SVMTrain_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/afni/tests/test_auto_SkullStrip.py b/nipype/interfaces/afni/tests/test_auto_SkullStrip.py index 2bcdb7a6b5..12449c331f 100644 --- a/nipype/interfaces/afni/tests/test_auto_SkullStrip.py +++ b/nipype/interfaces/afni/tests/test_auto_SkullStrip.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import SkullStrip + def test_SkullStrip_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -30,6 +31,7 @@ def test_SkullStrip_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_SkullStrip_outputs(): output_map = dict(out_file=dict(), ) @@ -38,4 +40,3 @@ def test_SkullStrip_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/afni/tests/test_auto_TCat.py b/nipype/interfaces/afni/tests/test_auto_TCat.py index 47aac8af8a..ce1e8fbaac 100644 --- a/nipype/interfaces/afni/tests/test_auto_TCat.py +++ b/nipype/interfaces/afni/tests/test_auto_TCat.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import TCat + def test_TCat_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -33,6 +34,7 @@ def test_TCat_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_TCat_outputs(): output_map = dict(out_file=dict(), ) @@ -41,4 +43,3 @@ def test_TCat_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/afni/tests/test_auto_TCorr1D.py b/nipype/interfaces/afni/tests/test_auto_TCorr1D.py index 6de2ba4f07..96ebdbe3a6 100644 --- a/nipype/interfaces/afni/tests/test_auto_TCorr1D.py +++ b/nipype/interfaces/afni/tests/test_auto_TCorr1D.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import TCorr1D + def test_TCorr1D_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -51,6 +52,7 @@ def test_TCorr1D_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_TCorr1D_outputs(): output_map = dict(out_file=dict(), ) @@ -59,4 +61,3 @@ def test_TCorr1D_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/afni/tests/test_auto_TCorrMap.py b/nipype/interfaces/afni/tests/test_auto_TCorrMap.py index d2185e3641..15c98d2aac 100644 --- a/nipype/interfaces/afni/tests/test_auto_TCorrMap.py +++ b/nipype/interfaces/afni/tests/test_auto_TCorrMap.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import TCorrMap + def test_TCorrMap_inputs(): input_map = dict(absolute_threshold=dict(argstr='-Thresh %f %s', name_source='in_file', @@ -106,6 +107,7 @@ def test_TCorrMap_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_TCorrMap_outputs(): output_map = dict(absolute_threshold=dict(), average_expr=dict(), @@ -126,4 +128,3 @@ def test_TCorrMap_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/afni/tests/test_auto_TCorrelate.py b/nipype/interfaces/afni/tests/test_auto_TCorrelate.py index f0b9000213..4a5d68f9e9 100644 --- a/nipype/interfaces/afni/tests/test_auto_TCorrelate.py +++ b/nipype/interfaces/afni/tests/test_auto_TCorrelate.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import TCorrelate + def test_TCorrelate_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -41,6 +42,7 @@ def test_TCorrelate_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_TCorrelate_outputs(): output_map = dict(out_file=dict(), ) @@ -49,4 +51,3 @@ def test_TCorrelate_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/afni/tests/test_auto_TShift.py b/nipype/interfaces/afni/tests/test_auto_TShift.py index b7252feef8..a67893c811 100644 --- a/nipype/interfaces/afni/tests/test_auto_TShift.py +++ b/nipype/interfaces/afni/tests/test_auto_TShift.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import TShift + def test_TShift_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -48,6 +49,7 @@ def test_TShift_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_TShift_outputs(): output_map = dict(out_file=dict(), ) @@ -56,4 +58,3 @@ def test_TShift_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/afni/tests/test_auto_TStat.py b/nipype/interfaces/afni/tests/test_auto_TStat.py index 8a82a42cc6..f7a60ca78c 100644 --- a/nipype/interfaces/afni/tests/test_auto_TStat.py +++ b/nipype/interfaces/afni/tests/test_auto_TStat.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import TStat + def test_TStat_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -34,6 +35,7 @@ def test_TStat_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_TStat_outputs(): output_map = dict(out_file=dict(), ) @@ -42,4 +44,3 @@ def test_TStat_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/afni/tests/test_auto_To3D.py b/nipype/interfaces/afni/tests/test_auto_To3D.py index 7e47b9c9e4..4357ee96da 100644 --- a/nipype/interfaces/afni/tests/test_auto_To3D.py +++ b/nipype/interfaces/afni/tests/test_auto_To3D.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import To3D + def test_To3D_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -39,6 +40,7 @@ def test_To3D_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_To3D_outputs(): output_map = dict(out_file=dict(), ) @@ -47,4 +49,3 @@ def test_To3D_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/afni/tests/test_auto_Volreg.py b/nipype/interfaces/afni/tests/test_auto_Volreg.py index 784715dc32..f97afe6366 100644 --- a/nipype/interfaces/afni/tests/test_auto_Volreg.py +++ b/nipype/interfaces/afni/tests/test_auto_Volreg.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import Volreg + def test_Volreg_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -58,6 +59,7 @@ def test_Volreg_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Volreg_outputs(): output_map = dict(md1d_file=dict(), oned_file=dict(), @@ -69,4 +71,3 @@ def test_Volreg_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/afni/tests/test_auto_Warp.py b/nipype/interfaces/afni/tests/test_auto_Warp.py index 4d7ba9ec22..c749d7fade 100644 --- a/nipype/interfaces/afni/tests/test_auto_Warp.py +++ b/nipype/interfaces/afni/tests/test_auto_Warp.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import Warp + def test_Warp_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -46,6 +47,7 @@ def test_Warp_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Warp_outputs(): output_map = dict(out_file=dict(), ) @@ -54,4 +56,3 @@ def test_Warp_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/afni/tests/test_auto_ZCutUp.py b/nipype/interfaces/afni/tests/test_auto_ZCutUp.py index 998bfe3d97..f3ede54b3e 100644 --- a/nipype/interfaces/afni/tests/test_auto_ZCutUp.py +++ b/nipype/interfaces/afni/tests/test_auto_ZCutUp.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import ZCutUp + def test_ZCutUp_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -32,6 +33,7 @@ def test_ZCutUp_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ZCutUp_outputs(): output_map = dict(out_file=dict(), ) @@ -40,4 +42,3 @@ def test_ZCutUp_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/ants/tests/test_auto_ANTS.py b/nipype/interfaces/ants/tests/test_auto_ANTS.py index 955170b803..36f153c532 100644 --- a/nipype/interfaces/ants/tests/test_auto_ANTS.py +++ b/nipype/interfaces/ants/tests/test_auto_ANTS.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..registration import ANTS + def test_ANTS_inputs(): input_map = dict(affine_gradient_descent_option=dict(argstr='%s', ), @@ -79,6 +80,7 @@ def test_ANTS_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ANTS_outputs(): output_map = dict(affine_transform=dict(), inverse_warp_transform=dict(), @@ -91,4 +93,3 @@ def test_ANTS_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/ants/tests/test_auto_ANTSCommand.py b/nipype/interfaces/ants/tests/test_auto_ANTSCommand.py index 8db8ffd534..1c2a67f3bb 100644 --- a/nipype/interfaces/ants/tests/test_auto_ANTSCommand.py +++ b/nipype/interfaces/ants/tests/test_auto_ANTSCommand.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..base import ANTSCommand + def test_ANTSCommand_inputs(): input_map = dict(args=dict(argstr='%s', ), diff --git a/nipype/interfaces/ants/tests/test_auto_ApplyTransforms.py b/nipype/interfaces/ants/tests/test_auto_ApplyTransforms.py index a20be833ea..b8c71173fe 100644 --- a/nipype/interfaces/ants/tests/test_auto_ApplyTransforms.py +++ b/nipype/interfaces/ants/tests/test_auto_ApplyTransforms.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..resampling import ApplyTransforms + def test_ApplyTransforms_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -51,6 +52,7 @@ def test_ApplyTransforms_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ApplyTransforms_outputs(): output_map = dict(output_image=dict(), ) @@ -59,4 +61,3 @@ def test_ApplyTransforms_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/ants/tests/test_auto_ApplyTransformsToPoints.py b/nipype/interfaces/ants/tests/test_auto_ApplyTransformsToPoints.py index 42011a59e2..3c6be3669a 100644 --- a/nipype/interfaces/ants/tests/test_auto_ApplyTransformsToPoints.py +++ b/nipype/interfaces/ants/tests/test_auto_ApplyTransformsToPoints.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..resampling import ApplyTransformsToPoints + def test_ApplyTransformsToPoints_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -37,6 +38,7 @@ def test_ApplyTransformsToPoints_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ApplyTransformsToPoints_outputs(): output_map = dict(output_file=dict(), ) @@ -45,4 +47,3 @@ def test_ApplyTransformsToPoints_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/ants/tests/test_auto_Atropos.py b/nipype/interfaces/ants/tests/test_auto_Atropos.py index b4672972b1..102d91b911 100644 --- a/nipype/interfaces/ants/tests/test_auto_Atropos.py +++ b/nipype/interfaces/ants/tests/test_auto_Atropos.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..segmentation import Atropos + def test_Atropos_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -67,6 +68,7 @@ def test_Atropos_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Atropos_outputs(): output_map = dict(classified_image=dict(), posteriors=dict(), @@ -76,4 +78,3 @@ def test_Atropos_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/ants/tests/test_auto_AverageAffineTransform.py b/nipype/interfaces/ants/tests/test_auto_AverageAffineTransform.py index df53cfe25e..347b07ef6e 100644 --- a/nipype/interfaces/ants/tests/test_auto_AverageAffineTransform.py +++ b/nipype/interfaces/ants/tests/test_auto_AverageAffineTransform.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..utils import AverageAffineTransform + def test_AverageAffineTransform_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -36,6 +37,7 @@ def test_AverageAffineTransform_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_AverageAffineTransform_outputs(): output_map = dict(affine_transform=dict(), ) @@ -44,4 +46,3 @@ def test_AverageAffineTransform_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/ants/tests/test_auto_AverageImages.py b/nipype/interfaces/ants/tests/test_auto_AverageImages.py index 370b4967dc..2e25305f3a 100644 --- a/nipype/interfaces/ants/tests/test_auto_AverageImages.py +++ b/nipype/interfaces/ants/tests/test_auto_AverageImages.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..utils import AverageImages + def test_AverageImages_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -40,6 +41,7 @@ def test_AverageImages_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_AverageImages_outputs(): output_map = dict(output_average_image=dict(), ) @@ -48,4 +50,3 @@ def test_AverageImages_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/ants/tests/test_auto_ConvertScalarImageToRGB.py b/nipype/interfaces/ants/tests/test_auto_ConvertScalarImageToRGB.py index 82638eb74a..cc2dfada40 100644 --- a/nipype/interfaces/ants/tests/test_auto_ConvertScalarImageToRGB.py +++ b/nipype/interfaces/ants/tests/test_auto_ConvertScalarImageToRGB.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..visualization import ConvertScalarImageToRGB + def test_ConvertScalarImageToRGB_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -65,6 +66,7 @@ def test_ConvertScalarImageToRGB_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ConvertScalarImageToRGB_outputs(): output_map = dict(output_image=dict(), ) @@ -73,4 +75,3 @@ def test_ConvertScalarImageToRGB_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/ants/tests/test_auto_CreateTiledMosaic.py b/nipype/interfaces/ants/tests/test_auto_CreateTiledMosaic.py index 079043e4b3..a5222ef3de 100644 --- a/nipype/interfaces/ants/tests/test_auto_CreateTiledMosaic.py +++ b/nipype/interfaces/ants/tests/test_auto_CreateTiledMosaic.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..visualization import CreateTiledMosaic + def test_CreateTiledMosaic_inputs(): input_map = dict(alpha_value=dict(argstr='-a %.2f', ), @@ -48,6 +49,7 @@ def test_CreateTiledMosaic_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_CreateTiledMosaic_outputs(): output_map = dict(output_image=dict(), ) @@ -56,4 +58,3 @@ def test_CreateTiledMosaic_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/ants/tests/test_auto_GenWarpFields.py b/nipype/interfaces/ants/tests/test_auto_GenWarpFields.py index 6005f18db4..a6a3e5c6a7 100644 --- a/nipype/interfaces/ants/tests/test_auto_GenWarpFields.py +++ b/nipype/interfaces/ants/tests/test_auto_GenWarpFields.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..legacy import GenWarpFields + def test_GenWarpFields_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -54,6 +55,7 @@ def test_GenWarpFields_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_GenWarpFields_outputs(): output_map = dict(affine_transformation=dict(), input_file=dict(), @@ -66,4 +68,3 @@ def test_GenWarpFields_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/ants/tests/test_auto_JacobianDeterminant.py b/nipype/interfaces/ants/tests/test_auto_JacobianDeterminant.py index dbba4dd31f..c83a95a5f9 100644 --- a/nipype/interfaces/ants/tests/test_auto_JacobianDeterminant.py +++ b/nipype/interfaces/ants/tests/test_auto_JacobianDeterminant.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..utils import JacobianDeterminant + def test_JacobianDeterminant_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -50,6 +51,7 @@ def test_JacobianDeterminant_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_JacobianDeterminant_outputs(): output_map = dict(jacobian_image=dict(), ) @@ -58,4 +60,3 @@ def test_JacobianDeterminant_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/ants/tests/test_auto_JointFusion.py b/nipype/interfaces/ants/tests/test_auto_JointFusion.py index c354c3eefc..76d8d46969 100644 --- a/nipype/interfaces/ants/tests/test_auto_JointFusion.py +++ b/nipype/interfaces/ants/tests/test_auto_JointFusion.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..segmentation import JointFusion + def test_JointFusion_inputs(): input_map = dict(alpha=dict(requires=['method'], usedefault=True, @@ -70,6 +71,7 @@ def test_JointFusion_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_JointFusion_outputs(): output_map = dict(output_label_image=dict(), ) @@ -78,4 +80,3 @@ def test_JointFusion_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/ants/tests/test_auto_LaplacianThickness.py b/nipype/interfaces/ants/tests/test_auto_LaplacianThickness.py index fbfce8e0e6..60cfb494e3 100644 --- a/nipype/interfaces/ants/tests/test_auto_LaplacianThickness.py +++ b/nipype/interfaces/ants/tests/test_auto_LaplacianThickness.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..segmentation import LaplacianThickness + def test_LaplacianThickness_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -53,6 +54,7 @@ def test_LaplacianThickness_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_LaplacianThickness_outputs(): output_map = dict(output_image=dict(), ) @@ -61,4 +63,3 @@ def test_LaplacianThickness_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/ants/tests/test_auto_MultiplyImages.py b/nipype/interfaces/ants/tests/test_auto_MultiplyImages.py index 951a277deb..5a3d682551 100644 --- a/nipype/interfaces/ants/tests/test_auto_MultiplyImages.py +++ b/nipype/interfaces/ants/tests/test_auto_MultiplyImages.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..utils import MultiplyImages + def test_MultiplyImages_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -40,6 +41,7 @@ def test_MultiplyImages_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MultiplyImages_outputs(): output_map = dict(output_product_image=dict(), ) @@ -48,4 +50,3 @@ def test_MultiplyImages_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/ants/tests/test_auto_N4BiasFieldCorrection.py b/nipype/interfaces/ants/tests/test_auto_N4BiasFieldCorrection.py index 4c7ba99e02..18921d811c 100644 --- a/nipype/interfaces/ants/tests/test_auto_N4BiasFieldCorrection.py +++ b/nipype/interfaces/ants/tests/test_auto_N4BiasFieldCorrection.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..segmentation import N4BiasFieldCorrection + def test_N4BiasFieldCorrection_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -53,6 +54,7 @@ def test_N4BiasFieldCorrection_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_N4BiasFieldCorrection_outputs(): output_map = dict(bias_image=dict(), output_image=dict(), @@ -62,4 +64,3 @@ def test_N4BiasFieldCorrection_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/ants/tests/test_auto_Registration.py b/nipype/interfaces/ants/tests/test_auto_Registration.py index 6c3006e14f..4d1b68912a 100644 --- a/nipype/interfaces/ants/tests/test_auto_Registration.py +++ b/nipype/interfaces/ants/tests/test_auto_Registration.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..registration import Registration + def test_Registration_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -118,6 +119,7 @@ def test_Registration_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Registration_outputs(): output_map = dict(composite_transform=dict(), forward_invert_flags=dict(), @@ -134,4 +136,3 @@ def test_Registration_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/ants/tests/test_auto_WarpImageMultiTransform.py b/nipype/interfaces/ants/tests/test_auto_WarpImageMultiTransform.py index 0c04deea33..09770d9d0f 100644 --- a/nipype/interfaces/ants/tests/test_auto_WarpImageMultiTransform.py +++ b/nipype/interfaces/ants/tests/test_auto_WarpImageMultiTransform.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..resampling import WarpImageMultiTransform + def test_WarpImageMultiTransform_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -58,6 +59,7 @@ def test_WarpImageMultiTransform_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_WarpImageMultiTransform_outputs(): output_map = dict(output_image=dict(), ) @@ -66,4 +68,3 @@ def test_WarpImageMultiTransform_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/ants/tests/test_auto_WarpTimeSeriesImageMultiTransform.py b/nipype/interfaces/ants/tests/test_auto_WarpTimeSeriesImageMultiTransform.py index 7b741cd5c0..0e46ce34a5 100644 --- a/nipype/interfaces/ants/tests/test_auto_WarpTimeSeriesImageMultiTransform.py +++ b/nipype/interfaces/ants/tests/test_auto_WarpTimeSeriesImageMultiTransform.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..resampling import WarpTimeSeriesImageMultiTransform + def test_WarpTimeSeriesImageMultiTransform_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -51,6 +52,7 @@ def test_WarpTimeSeriesImageMultiTransform_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_WarpTimeSeriesImageMultiTransform_outputs(): output_map = dict(output_image=dict(), ) @@ -59,4 +61,3 @@ def test_WarpTimeSeriesImageMultiTransform_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/ants/tests/test_auto_antsCorticalThickness.py b/nipype/interfaces/ants/tests/test_auto_antsCorticalThickness.py index d51d52e011..0944ebf1b7 100644 --- a/nipype/interfaces/ants/tests/test_auto_antsCorticalThickness.py +++ b/nipype/interfaces/ants/tests/test_auto_antsCorticalThickness.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..segmentation import antsCorticalThickness + def test_antsCorticalThickness_inputs(): input_map = dict(anatomical_image=dict(argstr='-a %s', mandatory=True, @@ -73,6 +74,7 @@ def test_antsCorticalThickness_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_antsCorticalThickness_outputs(): output_map = dict(BrainExtractionMask=dict(), BrainSegmentation=dict(), @@ -92,4 +94,3 @@ def test_antsCorticalThickness_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/ants/tests/test_auto_antsIntroduction.py b/nipype/interfaces/ants/tests/test_auto_antsIntroduction.py index dcd08203b6..be61025e30 100644 --- a/nipype/interfaces/ants/tests/test_auto_antsIntroduction.py +++ b/nipype/interfaces/ants/tests/test_auto_antsIntroduction.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..legacy import antsIntroduction + def test_antsIntroduction_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -54,6 +55,7 @@ def test_antsIntroduction_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_antsIntroduction_outputs(): output_map = dict(affine_transformation=dict(), input_file=dict(), @@ -66,4 +68,3 @@ def test_antsIntroduction_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/ants/tests/test_auto_buildtemplateparallel.py b/nipype/interfaces/ants/tests/test_auto_buildtemplateparallel.py index c75c9ca133..6992ce5c11 100644 --- a/nipype/interfaces/ants/tests/test_auto_buildtemplateparallel.py +++ b/nipype/interfaces/ants/tests/test_auto_buildtemplateparallel.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..legacy import buildtemplateparallel + def test_buildtemplateparallel_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -58,6 +59,7 @@ def test_buildtemplateparallel_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_buildtemplateparallel_outputs(): output_map = dict(final_template_file=dict(), subject_outfiles=dict(), @@ -68,4 +70,3 @@ def test_buildtemplateparallel_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/camino/tests/test_auto_AnalyzeHeader.py b/nipype/interfaces/camino/tests/test_auto_AnalyzeHeader.py index bfe53e3624..324fe35d1b 100644 --- a/nipype/interfaces/camino/tests/test_auto_AnalyzeHeader.py +++ b/nipype/interfaces/camino/tests/test_auto_AnalyzeHeader.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..convert import AnalyzeHeader + def test_AnalyzeHeader_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -85,6 +86,7 @@ def test_AnalyzeHeader_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_AnalyzeHeader_outputs(): output_map = dict(header=dict(), ) @@ -93,4 +95,3 @@ def test_AnalyzeHeader_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/camino/tests/test_auto_ComputeEigensystem.py b/nipype/interfaces/camino/tests/test_auto_ComputeEigensystem.py index 37a744a05c..d62e37c212 100644 --- a/nipype/interfaces/camino/tests/test_auto_ComputeEigensystem.py +++ b/nipype/interfaces/camino/tests/test_auto_ComputeEigensystem.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..dti import ComputeEigensystem + def test_ComputeEigensystem_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -38,6 +39,7 @@ def test_ComputeEigensystem_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ComputeEigensystem_outputs(): output_map = dict(eigen=dict(), ) @@ -46,4 +48,3 @@ def test_ComputeEigensystem_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/camino/tests/test_auto_ComputeFractionalAnisotropy.py b/nipype/interfaces/camino/tests/test_auto_ComputeFractionalAnisotropy.py index 3727068e2b..0a022eb1c3 100644 --- a/nipype/interfaces/camino/tests/test_auto_ComputeFractionalAnisotropy.py +++ b/nipype/interfaces/camino/tests/test_auto_ComputeFractionalAnisotropy.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..dti import ComputeFractionalAnisotropy + def test_ComputeFractionalAnisotropy_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -37,6 +38,7 @@ def test_ComputeFractionalAnisotropy_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ComputeFractionalAnisotropy_outputs(): output_map = dict(fa=dict(), ) @@ -45,4 +47,3 @@ def test_ComputeFractionalAnisotropy_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/camino/tests/test_auto_ComputeMeanDiffusivity.py b/nipype/interfaces/camino/tests/test_auto_ComputeMeanDiffusivity.py index 690f014b99..213ff038fc 100644 --- a/nipype/interfaces/camino/tests/test_auto_ComputeMeanDiffusivity.py +++ b/nipype/interfaces/camino/tests/test_auto_ComputeMeanDiffusivity.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..dti import ComputeMeanDiffusivity + def test_ComputeMeanDiffusivity_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -37,6 +38,7 @@ def test_ComputeMeanDiffusivity_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ComputeMeanDiffusivity_outputs(): output_map = dict(md=dict(), ) @@ -45,4 +47,3 @@ def test_ComputeMeanDiffusivity_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/camino/tests/test_auto_ComputeTensorTrace.py b/nipype/interfaces/camino/tests/test_auto_ComputeTensorTrace.py index 58a1479d24..b7d7561cdb 100644 --- a/nipype/interfaces/camino/tests/test_auto_ComputeTensorTrace.py +++ b/nipype/interfaces/camino/tests/test_auto_ComputeTensorTrace.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..dti import ComputeTensorTrace + def test_ComputeTensorTrace_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -37,6 +38,7 @@ def test_ComputeTensorTrace_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ComputeTensorTrace_outputs(): output_map = dict(trace=dict(), ) @@ -45,4 +47,3 @@ def test_ComputeTensorTrace_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/camino/tests/test_auto_Conmat.py b/nipype/interfaces/camino/tests/test_auto_Conmat.py index 5839e02b76..c5aa705c6c 100644 --- a/nipype/interfaces/camino/tests/test_auto_Conmat.py +++ b/nipype/interfaces/camino/tests/test_auto_Conmat.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..connectivity import Conmat + def test_Conmat_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -43,6 +44,7 @@ def test_Conmat_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Conmat_outputs(): output_map = dict(conmat_sc=dict(), conmat_ts=dict(), @@ -52,4 +54,3 @@ def test_Conmat_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/camino/tests/test_auto_DT2NIfTI.py b/nipype/interfaces/camino/tests/test_auto_DT2NIfTI.py index 754201435f..9bc58fecdd 100644 --- a/nipype/interfaces/camino/tests/test_auto_DT2NIfTI.py +++ b/nipype/interfaces/camino/tests/test_auto_DT2NIfTI.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..convert import DT2NIfTI + def test_DT2NIfTI_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -32,6 +33,7 @@ def test_DT2NIfTI_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_DT2NIfTI_outputs(): output_map = dict(dt=dict(), exitcode=dict(), @@ -42,4 +44,3 @@ def test_DT2NIfTI_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/camino/tests/test_auto_DTIFit.py b/nipype/interfaces/camino/tests/test_auto_DTIFit.py index 4d4bb35174..8607d3d7ae 100644 --- a/nipype/interfaces/camino/tests/test_auto_DTIFit.py +++ b/nipype/interfaces/camino/tests/test_auto_DTIFit.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..dti import DTIFit + def test_DTIFit_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -37,6 +38,7 @@ def test_DTIFit_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_DTIFit_outputs(): output_map = dict(tensor_fitted=dict(), ) @@ -45,4 +47,3 @@ def test_DTIFit_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/camino/tests/test_auto_DTLUTGen.py b/nipype/interfaces/camino/tests/test_auto_DTLUTGen.py index 2774a6acab..6cae7fee81 100644 --- a/nipype/interfaces/camino/tests/test_auto_DTLUTGen.py +++ b/nipype/interfaces/camino/tests/test_auto_DTLUTGen.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..dti import DTLUTGen + def test_DTLUTGen_inputs(): input_map = dict(acg=dict(argstr='-acg', ), @@ -57,6 +58,7 @@ def test_DTLUTGen_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_DTLUTGen_outputs(): output_map = dict(dtLUT=dict(), ) @@ -65,4 +67,3 @@ def test_DTLUTGen_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/camino/tests/test_auto_DTMetric.py b/nipype/interfaces/camino/tests/test_auto_DTMetric.py index 45d1029dec..d4cec76afb 100644 --- a/nipype/interfaces/camino/tests/test_auto_DTMetric.py +++ b/nipype/interfaces/camino/tests/test_auto_DTMetric.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..dti import DTMetric + def test_DTMetric_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -37,6 +38,7 @@ def test_DTMetric_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_DTMetric_outputs(): output_map = dict(metric_stats=dict(), ) @@ -45,4 +47,3 @@ def test_DTMetric_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/camino/tests/test_auto_FSL2Scheme.py b/nipype/interfaces/camino/tests/test_auto_FSL2Scheme.py index 81d7e3861e..b182c5a862 100644 --- a/nipype/interfaces/camino/tests/test_auto_FSL2Scheme.py +++ b/nipype/interfaces/camino/tests/test_auto_FSL2Scheme.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..convert import FSL2Scheme + def test_FSL2Scheme_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -51,6 +52,7 @@ def test_FSL2Scheme_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_FSL2Scheme_outputs(): output_map = dict(scheme=dict(), ) @@ -59,4 +61,3 @@ def test_FSL2Scheme_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/camino/tests/test_auto_Image2Voxel.py b/nipype/interfaces/camino/tests/test_auto_Image2Voxel.py index ab862918ef..57da324d6c 100644 --- a/nipype/interfaces/camino/tests/test_auto_Image2Voxel.py +++ b/nipype/interfaces/camino/tests/test_auto_Image2Voxel.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..convert import Image2Voxel + def test_Image2Voxel_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -32,6 +33,7 @@ def test_Image2Voxel_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Image2Voxel_outputs(): output_map = dict(voxel_order=dict(), ) @@ -40,4 +42,3 @@ def test_Image2Voxel_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/camino/tests/test_auto_ImageStats.py b/nipype/interfaces/camino/tests/test_auto_ImageStats.py index 4c719e5fc2..2fd6293a24 100644 --- a/nipype/interfaces/camino/tests/test_auto_ImageStats.py +++ b/nipype/interfaces/camino/tests/test_auto_ImageStats.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..utils import ImageStats + def test_ImageStats_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -34,6 +35,7 @@ def test_ImageStats_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ImageStats_outputs(): output_map = dict(out_file=dict(), ) @@ -42,4 +44,3 @@ def test_ImageStats_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/camino/tests/test_auto_LinRecon.py b/nipype/interfaces/camino/tests/test_auto_LinRecon.py index 29835c88dd..311bd70fdf 100644 --- a/nipype/interfaces/camino/tests/test_auto_LinRecon.py +++ b/nipype/interfaces/camino/tests/test_auto_LinRecon.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..odf import LinRecon + def test_LinRecon_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -42,6 +43,7 @@ def test_LinRecon_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_LinRecon_outputs(): output_map = dict(recon_data=dict(), ) @@ -50,4 +52,3 @@ def test_LinRecon_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/camino/tests/test_auto_MESD.py b/nipype/interfaces/camino/tests/test_auto_MESD.py index 41f2468492..018d820a96 100644 --- a/nipype/interfaces/camino/tests/test_auto_MESD.py +++ b/nipype/interfaces/camino/tests/test_auto_MESD.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..odf import MESD + def test_MESD_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -50,6 +51,7 @@ def test_MESD_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MESD_outputs(): output_map = dict(mesd_data=dict(), ) @@ -58,4 +60,3 @@ def test_MESD_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/camino/tests/test_auto_ModelFit.py b/nipype/interfaces/camino/tests/test_auto_ModelFit.py index 201df1069d..f56a605962 100644 --- a/nipype/interfaces/camino/tests/test_auto_ModelFit.py +++ b/nipype/interfaces/camino/tests/test_auto_ModelFit.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..dti import ModelFit + def test_ModelFit_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -57,6 +58,7 @@ def test_ModelFit_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ModelFit_outputs(): output_map = dict(fitted_data=dict(), ) @@ -65,4 +67,3 @@ def test_ModelFit_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/camino/tests/test_auto_NIfTIDT2Camino.py b/nipype/interfaces/camino/tests/test_auto_NIfTIDT2Camino.py index 70ca86a7e9..dd710905b2 100644 --- a/nipype/interfaces/camino/tests/test_auto_NIfTIDT2Camino.py +++ b/nipype/interfaces/camino/tests/test_auto_NIfTIDT2Camino.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..convert import NIfTIDT2Camino + def test_NIfTIDT2Camino_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -40,6 +41,7 @@ def test_NIfTIDT2Camino_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_NIfTIDT2Camino_outputs(): output_map = dict(out_file=dict(), ) @@ -48,4 +50,3 @@ def test_NIfTIDT2Camino_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/camino/tests/test_auto_PicoPDFs.py b/nipype/interfaces/camino/tests/test_auto_PicoPDFs.py index 2a1bfb2dc2..4f4a0b75be 100644 --- a/nipype/interfaces/camino/tests/test_auto_PicoPDFs.py +++ b/nipype/interfaces/camino/tests/test_auto_PicoPDFs.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..dti import PicoPDFs + def test_PicoPDFs_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -47,6 +48,7 @@ def test_PicoPDFs_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_PicoPDFs_outputs(): output_map = dict(pdfs=dict(), ) @@ -55,4 +57,3 @@ def test_PicoPDFs_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/camino/tests/test_auto_ProcStreamlines.py b/nipype/interfaces/camino/tests/test_auto_ProcStreamlines.py index 9cc7627408..99ecff3624 100644 --- a/nipype/interfaces/camino/tests/test_auto_ProcStreamlines.py +++ b/nipype/interfaces/camino/tests/test_auto_ProcStreamlines.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..convert import ProcStreamlines + def test_ProcStreamlines_inputs(): input_map = dict(allowmultitargets=dict(argstr='-allowmultitargets', ), @@ -105,6 +106,7 @@ def test_ProcStreamlines_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ProcStreamlines_outputs(): output_map = dict(outputroot_files=dict(), proc=dict(), @@ -114,4 +116,3 @@ def test_ProcStreamlines_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/camino/tests/test_auto_QBallMX.py b/nipype/interfaces/camino/tests/test_auto_QBallMX.py index c6ed4ce435..9a4b2375c8 100644 --- a/nipype/interfaces/camino/tests/test_auto_QBallMX.py +++ b/nipype/interfaces/camino/tests/test_auto_QBallMX.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..odf import QBallMX + def test_QBallMX_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -42,6 +43,7 @@ def test_QBallMX_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_QBallMX_outputs(): output_map = dict(qmat=dict(), ) @@ -50,4 +52,3 @@ def test_QBallMX_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/camino/tests/test_auto_SFLUTGen.py b/nipype/interfaces/camino/tests/test_auto_SFLUTGen.py index 5bef04c474..6d59c40c3e 100644 --- a/nipype/interfaces/camino/tests/test_auto_SFLUTGen.py +++ b/nipype/interfaces/camino/tests/test_auto_SFLUTGen.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..calib import SFLUTGen + def test_SFLUTGen_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -47,6 +48,7 @@ def test_SFLUTGen_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_SFLUTGen_outputs(): output_map = dict(lut_one_fibre=dict(), lut_two_fibres=dict(), @@ -56,4 +58,3 @@ def test_SFLUTGen_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/camino/tests/test_auto_SFPICOCalibData.py b/nipype/interfaces/camino/tests/test_auto_SFPICOCalibData.py index 6988c53f4c..4adfe50709 100644 --- a/nipype/interfaces/camino/tests/test_auto_SFPICOCalibData.py +++ b/nipype/interfaces/camino/tests/test_auto_SFPICOCalibData.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..calib import SFPICOCalibData + def test_SFPICOCalibData_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -65,6 +66,7 @@ def test_SFPICOCalibData_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_SFPICOCalibData_outputs(): output_map = dict(PICOCalib=dict(), calib_info=dict(), @@ -74,4 +76,3 @@ def test_SFPICOCalibData_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/camino/tests/test_auto_SFPeaks.py b/nipype/interfaces/camino/tests/test_auto_SFPeaks.py index 4f767b3b54..69c85404c1 100644 --- a/nipype/interfaces/camino/tests/test_auto_SFPeaks.py +++ b/nipype/interfaces/camino/tests/test_auto_SFPeaks.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..odf import SFPeaks + def test_SFPeaks_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -61,6 +62,7 @@ def test_SFPeaks_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_SFPeaks_outputs(): output_map = dict(peaks=dict(), ) @@ -69,4 +71,3 @@ def test_SFPeaks_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/camino/tests/test_auto_Shredder.py b/nipype/interfaces/camino/tests/test_auto_Shredder.py index 58482b0795..7f36415c0c 100644 --- a/nipype/interfaces/camino/tests/test_auto_Shredder.py +++ b/nipype/interfaces/camino/tests/test_auto_Shredder.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..convert import Shredder + def test_Shredder_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -40,6 +41,7 @@ def test_Shredder_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Shredder_outputs(): output_map = dict(shredded=dict(), ) @@ -48,4 +50,3 @@ def test_Shredder_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/camino/tests/test_auto_Track.py b/nipype/interfaces/camino/tests/test_auto_Track.py index e3b14aa85e..a8fd980b79 100644 --- a/nipype/interfaces/camino/tests/test_auto_Track.py +++ b/nipype/interfaces/camino/tests/test_auto_Track.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..dti import Track + def test_Track_inputs(): input_map = dict(anisfile=dict(argstr='-anisfile %s', ), @@ -73,6 +74,7 @@ def test_Track_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Track_outputs(): output_map = dict(tracked=dict(), ) @@ -81,4 +83,3 @@ def test_Track_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/camino/tests/test_auto_TrackBallStick.py b/nipype/interfaces/camino/tests/test_auto_TrackBallStick.py index 57d7a3e098..1d563f873c 100644 --- a/nipype/interfaces/camino/tests/test_auto_TrackBallStick.py +++ b/nipype/interfaces/camino/tests/test_auto_TrackBallStick.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..dti import TrackBallStick + def test_TrackBallStick_inputs(): input_map = dict(anisfile=dict(argstr='-anisfile %s', ), @@ -73,6 +74,7 @@ def test_TrackBallStick_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_TrackBallStick_outputs(): output_map = dict(tracked=dict(), ) @@ -81,4 +83,3 @@ def test_TrackBallStick_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/camino/tests/test_auto_TrackBayesDirac.py b/nipype/interfaces/camino/tests/test_auto_TrackBayesDirac.py index 40a5418c35..f2c2aecede 100644 --- a/nipype/interfaces/camino/tests/test_auto_TrackBayesDirac.py +++ b/nipype/interfaces/camino/tests/test_auto_TrackBayesDirac.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..dti import TrackBayesDirac + def test_TrackBayesDirac_inputs(): input_map = dict(anisfile=dict(argstr='-anisfile %s', ), @@ -93,6 +94,7 @@ def test_TrackBayesDirac_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_TrackBayesDirac_outputs(): output_map = dict(tracked=dict(), ) @@ -101,4 +103,3 @@ def test_TrackBayesDirac_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/camino/tests/test_auto_TrackBedpostxDeter.py b/nipype/interfaces/camino/tests/test_auto_TrackBedpostxDeter.py index 0e44d68310..9f9e40d284 100644 --- a/nipype/interfaces/camino/tests/test_auto_TrackBedpostxDeter.py +++ b/nipype/interfaces/camino/tests/test_auto_TrackBedpostxDeter.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..dti import TrackBedpostxDeter + def test_TrackBedpostxDeter_inputs(): input_map = dict(anisfile=dict(argstr='-anisfile %s', ), @@ -79,6 +80,7 @@ def test_TrackBedpostxDeter_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_TrackBedpostxDeter_outputs(): output_map = dict(tracked=dict(), ) @@ -87,4 +89,3 @@ def test_TrackBedpostxDeter_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/camino/tests/test_auto_TrackBedpostxProba.py b/nipype/interfaces/camino/tests/test_auto_TrackBedpostxProba.py index 2fe581ec1e..40f01d1b37 100644 --- a/nipype/interfaces/camino/tests/test_auto_TrackBedpostxProba.py +++ b/nipype/interfaces/camino/tests/test_auto_TrackBedpostxProba.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..dti import TrackBedpostxProba + def test_TrackBedpostxProba_inputs(): input_map = dict(anisfile=dict(argstr='-anisfile %s', ), @@ -82,6 +83,7 @@ def test_TrackBedpostxProba_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_TrackBedpostxProba_outputs(): output_map = dict(tracked=dict(), ) @@ -90,4 +92,3 @@ def test_TrackBedpostxProba_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/camino/tests/test_auto_TrackBootstrap.py b/nipype/interfaces/camino/tests/test_auto_TrackBootstrap.py index aa0af20159..091fa6bd90 100644 --- a/nipype/interfaces/camino/tests/test_auto_TrackBootstrap.py +++ b/nipype/interfaces/camino/tests/test_auto_TrackBootstrap.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..dti import TrackBootstrap + def test_TrackBootstrap_inputs(): input_map = dict(anisfile=dict(argstr='-anisfile %s', ), @@ -86,6 +87,7 @@ def test_TrackBootstrap_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_TrackBootstrap_outputs(): output_map = dict(tracked=dict(), ) @@ -94,4 +96,3 @@ def test_TrackBootstrap_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/camino/tests/test_auto_TrackDT.py b/nipype/interfaces/camino/tests/test_auto_TrackDT.py index 4b04104ec6..0376ff7d55 100644 --- a/nipype/interfaces/camino/tests/test_auto_TrackDT.py +++ b/nipype/interfaces/camino/tests/test_auto_TrackDT.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..dti import TrackDT + def test_TrackDT_inputs(): input_map = dict(anisfile=dict(argstr='-anisfile %s', ), @@ -73,6 +74,7 @@ def test_TrackDT_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_TrackDT_outputs(): output_map = dict(tracked=dict(), ) @@ -81,4 +83,3 @@ def test_TrackDT_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/camino/tests/test_auto_TrackPICo.py b/nipype/interfaces/camino/tests/test_auto_TrackPICo.py index 374e04bb36..c95a7e8812 100644 --- a/nipype/interfaces/camino/tests/test_auto_TrackPICo.py +++ b/nipype/interfaces/camino/tests/test_auto_TrackPICo.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..dti import TrackPICo + def test_TrackPICo_inputs(): input_map = dict(anisfile=dict(argstr='-anisfile %s', ), @@ -78,6 +79,7 @@ def test_TrackPICo_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_TrackPICo_outputs(): output_map = dict(tracked=dict(), ) @@ -86,4 +88,3 @@ def test_TrackPICo_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/camino/tests/test_auto_TractShredder.py b/nipype/interfaces/camino/tests/test_auto_TractShredder.py index e129b51363..d18ec2e9ca 100644 --- a/nipype/interfaces/camino/tests/test_auto_TractShredder.py +++ b/nipype/interfaces/camino/tests/test_auto_TractShredder.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..convert import TractShredder + def test_TractShredder_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -40,6 +41,7 @@ def test_TractShredder_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_TractShredder_outputs(): output_map = dict(shredded=dict(), ) @@ -48,4 +50,3 @@ def test_TractShredder_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/camino/tests/test_auto_VtkStreamlines.py b/nipype/interfaces/camino/tests/test_auto_VtkStreamlines.py index 6ebcae1985..805f4709cb 100644 --- a/nipype/interfaces/camino/tests/test_auto_VtkStreamlines.py +++ b/nipype/interfaces/camino/tests/test_auto_VtkStreamlines.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..convert import VtkStreamlines + def test_VtkStreamlines_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -50,6 +51,7 @@ def test_VtkStreamlines_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_VtkStreamlines_outputs(): output_map = dict(vtk=dict(), ) @@ -58,4 +60,3 @@ def test_VtkStreamlines_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/camino2trackvis/tests/test_auto_Camino2Trackvis.py b/nipype/interfaces/camino2trackvis/tests/test_auto_Camino2Trackvis.py index 8a0e0590cf..4feaae6bf3 100644 --- a/nipype/interfaces/camino2trackvis/tests/test_auto_Camino2Trackvis.py +++ b/nipype/interfaces/camino2trackvis/tests/test_auto_Camino2Trackvis.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..convert import Camino2Trackvis + def test_Camino2Trackvis_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -49,6 +50,7 @@ def test_Camino2Trackvis_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Camino2Trackvis_outputs(): output_map = dict(trackvis=dict(), ) @@ -57,4 +59,3 @@ def test_Camino2Trackvis_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/camino2trackvis/tests/test_auto_Trackvis2Camino.py b/nipype/interfaces/camino2trackvis/tests/test_auto_Trackvis2Camino.py index 7ebf190c39..fe24f0f99b 100644 --- a/nipype/interfaces/camino2trackvis/tests/test_auto_Trackvis2Camino.py +++ b/nipype/interfaces/camino2trackvis/tests/test_auto_Trackvis2Camino.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..convert import Trackvis2Camino + def test_Trackvis2Camino_inputs(): input_map = dict(append_file=dict(argstr='-a %s', position=2, @@ -31,6 +32,7 @@ def test_Trackvis2Camino_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Trackvis2Camino_outputs(): output_map = dict(camino=dict(), ) @@ -39,4 +41,3 @@ def test_Trackvis2Camino_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/cmtk/tests/test_auto_AverageNetworks.py b/nipype/interfaces/cmtk/tests/test_auto_AverageNetworks.py index b150dff97c..e4d649585e 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_AverageNetworks.py +++ b/nipype/interfaces/cmtk/tests/test_auto_AverageNetworks.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..nx import AverageNetworks + def test_AverageNetworks_inputs(): input_map = dict(group_id=dict(usedefault=True, ), @@ -20,6 +21,7 @@ def test_AverageNetworks_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_AverageNetworks_outputs(): output_map = dict(gexf_groupavg=dict(), gpickled_groupavg=dict(), @@ -30,4 +32,3 @@ def test_AverageNetworks_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/cmtk/tests/test_auto_CFFConverter.py b/nipype/interfaces/cmtk/tests/test_auto_CFFConverter.py index 395c2ee38f..261a0babaa 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_CFFConverter.py +++ b/nipype/interfaces/cmtk/tests/test_auto_CFFConverter.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..convert import CFFConverter + def test_CFFConverter_inputs(): input_map = dict(creator=dict(), data_files=dict(), @@ -36,6 +37,7 @@ def test_CFFConverter_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_CFFConverter_outputs(): output_map = dict(connectome_file=dict(), ) @@ -44,4 +46,3 @@ def test_CFFConverter_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/cmtk/tests/test_auto_CreateMatrix.py b/nipype/interfaces/cmtk/tests/test_auto_CreateMatrix.py index 7da385220c..c986c02c7b 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_CreateMatrix.py +++ b/nipype/interfaces/cmtk/tests/test_auto_CreateMatrix.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..cmtk import CreateMatrix + def test_CreateMatrix_inputs(): input_map = dict(count_region_intersections=dict(usedefault=True, ), @@ -32,6 +33,7 @@ def test_CreateMatrix_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_CreateMatrix_outputs(): output_map = dict(endpoint_file=dict(), endpoint_file_mm=dict(), @@ -57,4 +59,3 @@ def test_CreateMatrix_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/cmtk/tests/test_auto_CreateNodes.py b/nipype/interfaces/cmtk/tests/test_auto_CreateNodes.py index 84f3e38ad3..c5d9fe4163 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_CreateNodes.py +++ b/nipype/interfaces/cmtk/tests/test_auto_CreateNodes.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..cmtk import CreateNodes + def test_CreateNodes_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, @@ -19,6 +20,7 @@ def test_CreateNodes_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_CreateNodes_outputs(): output_map = dict(node_network=dict(), ) @@ -27,4 +29,3 @@ def test_CreateNodes_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/cmtk/tests/test_auto_MergeCNetworks.py b/nipype/interfaces/cmtk/tests/test_auto_MergeCNetworks.py index a7e7fe169b..73654ced71 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_MergeCNetworks.py +++ b/nipype/interfaces/cmtk/tests/test_auto_MergeCNetworks.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..convert import MergeCNetworks + def test_MergeCNetworks_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, @@ -17,6 +18,7 @@ def test_MergeCNetworks_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MergeCNetworks_outputs(): output_map = dict(connectome_file=dict(), ) @@ -25,4 +27,3 @@ def test_MergeCNetworks_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/cmtk/tests/test_auto_NetworkBasedStatistic.py b/nipype/interfaces/cmtk/tests/test_auto_NetworkBasedStatistic.py index 3a038ae6c9..70857e1b98 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_NetworkBasedStatistic.py +++ b/nipype/interfaces/cmtk/tests/test_auto_NetworkBasedStatistic.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..nbs import NetworkBasedStatistic + def test_NetworkBasedStatistic_inputs(): input_map = dict(edge_key=dict(usedefault=True, ), @@ -28,6 +29,7 @@ def test_NetworkBasedStatistic_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_NetworkBasedStatistic_outputs(): output_map = dict(nbs_network=dict(), nbs_pval_network=dict(), @@ -38,4 +40,3 @@ def test_NetworkBasedStatistic_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/cmtk/tests/test_auto_NetworkXMetrics.py b/nipype/interfaces/cmtk/tests/test_auto_NetworkXMetrics.py index eb596fa650..e26c389974 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_NetworkXMetrics.py +++ b/nipype/interfaces/cmtk/tests/test_auto_NetworkXMetrics.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..nx import NetworkXMetrics + def test_NetworkXMetrics_inputs(): input_map = dict(compute_clique_related_measures=dict(usedefault=True, ), @@ -33,6 +34,7 @@ def test_NetworkXMetrics_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_NetworkXMetrics_outputs(): output_map = dict(edge_measure_networks=dict(), edge_measures_matlab=dict(), @@ -53,4 +55,3 @@ def test_NetworkXMetrics_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/cmtk/tests/test_auto_Parcellate.py b/nipype/interfaces/cmtk/tests/test_auto_Parcellate.py index d7cde3f392..eff984ea54 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_Parcellate.py +++ b/nipype/interfaces/cmtk/tests/test_auto_Parcellate.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..parcellation import Parcellate + def test_Parcellate_inputs(): input_map = dict(dilation=dict(usedefault=True, ), @@ -23,6 +24,7 @@ def test_Parcellate_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Parcellate_outputs(): output_map = dict(aseg_file=dict(), cc_unknown_file=dict(), @@ -38,4 +40,3 @@ def test_Parcellate_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/cmtk/tests/test_auto_ROIGen.py b/nipype/interfaces/cmtk/tests/test_auto_ROIGen.py index dde9200bd8..2869299324 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_ROIGen.py +++ b/nipype/interfaces/cmtk/tests/test_auto_ROIGen.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..cmtk import ROIGen + def test_ROIGen_inputs(): input_map = dict(LUT_file=dict(xor=['use_freesurfer_LUT'], ), @@ -25,6 +26,7 @@ def test_ROIGen_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ROIGen_outputs(): output_map = dict(dict_file=dict(), roi_file=dict(), @@ -34,4 +36,3 @@ def test_ROIGen_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTIRecon.py b/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTIRecon.py index 591ead36a9..907df7eb13 100644 --- a/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTIRecon.py +++ b/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTIRecon.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..dti import DTIRecon + def test_DTIRecon_inputs(): input_map = dict(DWI=dict(argstr='%s', mandatory=True, @@ -44,6 +45,7 @@ def test_DTIRecon_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_DTIRecon_outputs(): output_map = dict(ADC=dict(), B0=dict(), @@ -63,4 +65,3 @@ def test_DTIRecon_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTITracker.py b/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTITracker.py index 47f5b85b75..d21a6ecb34 100644 --- a/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTITracker.py +++ b/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTITracker.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..dti import DTITracker + def test_DTITracker_inputs(): input_map = dict(angle_threshold=dict(argstr='-at %f', ), @@ -68,6 +69,7 @@ def test_DTITracker_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_DTITracker_outputs(): output_map = dict(mask_file=dict(), track_file=dict(), @@ -77,4 +79,3 @@ def test_DTITracker_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/diffusion_toolkit/tests/test_auto_HARDIMat.py b/nipype/interfaces/diffusion_toolkit/tests/test_auto_HARDIMat.py index 449ccc0fb6..725bbef73a 100644 --- a/nipype/interfaces/diffusion_toolkit/tests/test_auto_HARDIMat.py +++ b/nipype/interfaces/diffusion_toolkit/tests/test_auto_HARDIMat.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..odf import HARDIMat + def test_HARDIMat_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -42,6 +43,7 @@ def test_HARDIMat_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_HARDIMat_outputs(): output_map = dict(out_file=dict(), ) @@ -50,4 +52,3 @@ def test_HARDIMat_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFRecon.py b/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFRecon.py index f255fe57b5..641fb1ad93 100644 --- a/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFRecon.py +++ b/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFRecon.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..odf import ODFRecon + def test_ODFRecon_inputs(): input_map = dict(DWI=dict(argstr='%s', mandatory=True, @@ -59,6 +60,7 @@ def test_ODFRecon_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ODFRecon_outputs(): output_map = dict(B0=dict(), DWI=dict(), @@ -71,4 +73,3 @@ def test_ODFRecon_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFTracker.py b/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFTracker.py index 172d3608a9..ba57c26e02 100644 --- a/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFTracker.py +++ b/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFTracker.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..odf import ODFTracker + def test_ODFTracker_inputs(): input_map = dict(ODF=dict(mandatory=True, ), @@ -78,6 +79,7 @@ def test_ODFTracker_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ODFTracker_outputs(): output_map = dict(track_file=dict(), ) @@ -86,4 +88,3 @@ def test_ODFTracker_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/diffusion_toolkit/tests/test_auto_SplineFilter.py b/nipype/interfaces/diffusion_toolkit/tests/test_auto_SplineFilter.py index e830e4e345..8079634c80 100644 --- a/nipype/interfaces/diffusion_toolkit/tests/test_auto_SplineFilter.py +++ b/nipype/interfaces/diffusion_toolkit/tests/test_auto_SplineFilter.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..postproc import SplineFilter + def test_SplineFilter_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -32,6 +33,7 @@ def test_SplineFilter_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_SplineFilter_outputs(): output_map = dict(smoothed_track_file=dict(), ) @@ -40,4 +42,3 @@ def test_SplineFilter_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/diffusion_toolkit/tests/test_auto_TrackMerge.py b/nipype/interfaces/diffusion_toolkit/tests/test_auto_TrackMerge.py index 290f7955b2..5eaa8f1224 100644 --- a/nipype/interfaces/diffusion_toolkit/tests/test_auto_TrackMerge.py +++ b/nipype/interfaces/diffusion_toolkit/tests/test_auto_TrackMerge.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..postproc import TrackMerge + def test_TrackMerge_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -28,6 +29,7 @@ def test_TrackMerge_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_TrackMerge_outputs(): output_map = dict(track_file=dict(), ) @@ -36,4 +38,3 @@ def test_TrackMerge_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/dipy/tests/test_auto_DTI.py b/nipype/interfaces/dipy/tests/test_auto_DTI.py index 9a979fa262..0abba84540 100644 --- a/nipype/interfaces/dipy/tests/test_auto_DTI.py +++ b/nipype/interfaces/dipy/tests/test_auto_DTI.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..tensors import DTI + def test_DTI_inputs(): input_map = dict(bvals=dict(mandatory=True, ), @@ -19,6 +20,7 @@ def test_DTI_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_DTI_outputs(): output_map = dict(out_file=dict(), ) @@ -27,4 +29,3 @@ def test_DTI_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/dipy/tests/test_auto_Denoise.py b/nipype/interfaces/dipy/tests/test_auto_Denoise.py index 4383e1029b..dad60ccb5f 100644 --- a/nipype/interfaces/dipy/tests/test_auto_Denoise.py +++ b/nipype/interfaces/dipy/tests/test_auto_Denoise.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import Denoise + def test_Denoise_inputs(): input_map = dict(block_radius=dict(), in_file=dict(mandatory=True, @@ -19,6 +20,7 @@ def test_Denoise_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Denoise_outputs(): output_map = dict(out_file=dict(), ) @@ -27,4 +29,3 @@ def test_Denoise_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/dipy/tests/test_auto_Resample.py b/nipype/interfaces/dipy/tests/test_auto_Resample.py index 9b5636ca80..06c462dd2d 100644 --- a/nipype/interfaces/dipy/tests/test_auto_Resample.py +++ b/nipype/interfaces/dipy/tests/test_auto_Resample.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import Resample + def test_Resample_inputs(): input_map = dict(in_file=dict(mandatory=True, ), @@ -16,6 +17,7 @@ def test_Resample_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Resample_outputs(): output_map = dict(out_file=dict(), ) @@ -24,4 +26,3 @@ def test_Resample_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/dipy/tests/test_auto_SimulateMultiTensor.py b/nipype/interfaces/dipy/tests/test_auto_SimulateMultiTensor.py index 88c3f20bcd..5bc7a2928f 100644 --- a/nipype/interfaces/dipy/tests/test_auto_SimulateMultiTensor.py +++ b/nipype/interfaces/dipy/tests/test_auto_SimulateMultiTensor.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..simulate import SimulateMultiTensor + def test_SimulateMultiTensor_inputs(): input_map = dict(baseline=dict(mandatory=True, ), @@ -45,6 +46,7 @@ def test_SimulateMultiTensor_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_SimulateMultiTensor_outputs(): output_map = dict(out_bval=dict(), out_bvec=dict(), @@ -56,4 +58,3 @@ def test_SimulateMultiTensor_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/dipy/tests/test_auto_TensorMode.py b/nipype/interfaces/dipy/tests/test_auto_TensorMode.py index aca8f63751..dc2f0a06ff 100644 --- a/nipype/interfaces/dipy/tests/test_auto_TensorMode.py +++ b/nipype/interfaces/dipy/tests/test_auto_TensorMode.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..tensors import TensorMode + def test_TensorMode_inputs(): input_map = dict(bvals=dict(mandatory=True, ), @@ -19,6 +20,7 @@ def test_TensorMode_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_TensorMode_outputs(): output_map = dict(out_file=dict(), ) @@ -27,4 +29,3 @@ def test_TensorMode_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/dipy/tests/test_auto_TrackDensityMap.py b/nipype/interfaces/dipy/tests/test_auto_TrackDensityMap.py index c4f926ac8a..5c2e2d0b8d 100644 --- a/nipype/interfaces/dipy/tests/test_auto_TrackDensityMap.py +++ b/nipype/interfaces/dipy/tests/test_auto_TrackDensityMap.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..tracks import TrackDensityMap + def test_TrackDensityMap_inputs(): input_map = dict(data_dims=dict(), in_file=dict(mandatory=True, @@ -19,6 +20,7 @@ def test_TrackDensityMap_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_TrackDensityMap_outputs(): output_map = dict(out_file=dict(), ) @@ -27,4 +29,3 @@ def test_TrackDensityMap_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/elastix/tests/test_auto_AnalyzeWarp.py b/nipype/interfaces/elastix/tests/test_auto_AnalyzeWarp.py index 0f992772cf..a298b4ade6 100644 --- a/nipype/interfaces/elastix/tests/test_auto_AnalyzeWarp.py +++ b/nipype/interfaces/elastix/tests/test_auto_AnalyzeWarp.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..registration import AnalyzeWarp + def test_AnalyzeWarp_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -30,6 +31,7 @@ def test_AnalyzeWarp_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_AnalyzeWarp_outputs(): output_map = dict(disp_field=dict(), jacdet_map=dict(), @@ -40,4 +42,3 @@ def test_AnalyzeWarp_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/elastix/tests/test_auto_ApplyWarp.py b/nipype/interfaces/elastix/tests/test_auto_ApplyWarp.py index a367c647e5..1d6addb92a 100644 --- a/nipype/interfaces/elastix/tests/test_auto_ApplyWarp.py +++ b/nipype/interfaces/elastix/tests/test_auto_ApplyWarp.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..registration import ApplyWarp + def test_ApplyWarp_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -33,6 +34,7 @@ def test_ApplyWarp_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ApplyWarp_outputs(): output_map = dict(warped_file=dict(), ) @@ -41,4 +43,3 @@ def test_ApplyWarp_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/elastix/tests/test_auto_EditTransform.py b/nipype/interfaces/elastix/tests/test_auto_EditTransform.py index 794977331c..9b5c082299 100644 --- a/nipype/interfaces/elastix/tests/test_auto_EditTransform.py +++ b/nipype/interfaces/elastix/tests/test_auto_EditTransform.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..utils import EditTransform + def test_EditTransform_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, @@ -24,6 +25,7 @@ def test_EditTransform_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_EditTransform_outputs(): output_map = dict(output_file=dict(), ) @@ -32,4 +34,3 @@ def test_EditTransform_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/elastix/tests/test_auto_PointsWarp.py b/nipype/interfaces/elastix/tests/test_auto_PointsWarp.py index 9084016d2e..de12ae5698 100644 --- a/nipype/interfaces/elastix/tests/test_auto_PointsWarp.py +++ b/nipype/interfaces/elastix/tests/test_auto_PointsWarp.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..registration import PointsWarp + def test_PointsWarp_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -33,6 +34,7 @@ def test_PointsWarp_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_PointsWarp_outputs(): output_map = dict(warped_file=dict(), ) @@ -41,4 +43,3 @@ def test_PointsWarp_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/elastix/tests/test_auto_Registration.py b/nipype/interfaces/elastix/tests/test_auto_Registration.py index 74450da13b..4bbe547488 100644 --- a/nipype/interfaces/elastix/tests/test_auto_Registration.py +++ b/nipype/interfaces/elastix/tests/test_auto_Registration.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..registration import Registration + def test_Registration_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -42,6 +43,7 @@ def test_Registration_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Registration_outputs(): output_map = dict(transform=dict(), warped_file=dict(), @@ -53,4 +55,3 @@ def test_Registration_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ApplyMask.py b/nipype/interfaces/freesurfer/tests/test_auto_ApplyMask.py index 76d3afa4f1..23bff662ce 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ApplyMask.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ApplyMask.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..utils import ApplyMask + def test_ApplyMask_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -45,6 +46,7 @@ def test_ApplyMask_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ApplyMask_outputs(): output_map = dict(out_file=dict(), ) @@ -53,4 +55,3 @@ def test_ApplyMask_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ApplyVolTransform.py b/nipype/interfaces/freesurfer/tests/test_auto_ApplyVolTransform.py index 414eab974f..0912bc80dd 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ApplyVolTransform.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ApplyVolTransform.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import ApplyVolTransform + def test_ApplyVolTransform_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -77,6 +78,7 @@ def test_ApplyVolTransform_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ApplyVolTransform_outputs(): output_map = dict(transformed_file=dict(), ) @@ -85,4 +87,3 @@ def test_ApplyVolTransform_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/freesurfer/tests/test_auto_BBRegister.py b/nipype/interfaces/freesurfer/tests/test_auto_BBRegister.py index 1336d122f2..cb3444c2f0 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_BBRegister.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_BBRegister.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import BBRegister + def test_BBRegister_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -58,6 +59,7 @@ def test_BBRegister_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_BBRegister_outputs(): output_map = dict(min_cost_file=dict(), out_fsl_file=dict(), @@ -69,4 +71,3 @@ def test_BBRegister_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Binarize.py b/nipype/interfaces/freesurfer/tests/test_auto_Binarize.py index a08eed564b..b22d6a98e6 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Binarize.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Binarize.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..model import Binarize + def test_Binarize_inputs(): input_map = dict(abs=dict(argstr='--abs', ), @@ -79,6 +80,7 @@ def test_Binarize_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Binarize_outputs(): output_map = dict(binary_file=dict(), count_file=dict(), @@ -88,4 +90,3 @@ def test_Binarize_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Concatenate.py b/nipype/interfaces/freesurfer/tests/test_auto_Concatenate.py index 38b5833527..1a5e51758e 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Concatenate.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Concatenate.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..model import Concatenate + def test_Concatenate_inputs(): input_map = dict(add_val=dict(argstr='--add %f', ), @@ -57,6 +58,7 @@ def test_Concatenate_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Concatenate_outputs(): output_map = dict(concatenated_file=dict(), ) @@ -65,4 +67,3 @@ def test_Concatenate_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/freesurfer/tests/test_auto_DICOMConvert.py b/nipype/interfaces/freesurfer/tests/test_auto_DICOMConvert.py index 88c63c2abb..1551f3e44c 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_DICOMConvert.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_DICOMConvert.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import DICOMConvert + def test_DICOMConvert_inputs(): input_map = dict(args=dict(argstr='%s', ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ExtractMainComponent.py b/nipype/interfaces/freesurfer/tests/test_auto_ExtractMainComponent.py index 9a73f060b3..617a696a2b 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ExtractMainComponent.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ExtractMainComponent.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..utils import ExtractMainComponent + def test_ExtractMainComponent_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -29,6 +30,7 @@ def test_ExtractMainComponent_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ExtractMainComponent_outputs(): output_map = dict(out_file=dict(), ) @@ -37,4 +39,3 @@ def test_ExtractMainComponent_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/freesurfer/tests/test_auto_FSCommand.py b/nipype/interfaces/freesurfer/tests/test_auto_FSCommand.py index 6e44fdbf17..f463310c33 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_FSCommand.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_FSCommand.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..base import FSCommand + def test_FSCommand_inputs(): input_map = dict(args=dict(argstr='%s', ), diff --git a/nipype/interfaces/freesurfer/tests/test_auto_FitMSParams.py b/nipype/interfaces/freesurfer/tests/test_auto_FitMSParams.py index 947f58ebcf..e54c0ddcc7 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_FitMSParams.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_FitMSParams.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import FitMSParams + def test_FitMSParams_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -33,6 +34,7 @@ def test_FitMSParams_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_FitMSParams_outputs(): output_map = dict(pd_image=dict(), t1_image=dict(), @@ -43,4 +45,3 @@ def test_FitMSParams_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/freesurfer/tests/test_auto_GLMFit.py b/nipype/interfaces/freesurfer/tests/test_auto_GLMFit.py index 323e425006..41f09cb1a8 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_GLMFit.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_GLMFit.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..model import GLMFit + def test_GLMFit_inputs(): input_map = dict(allow_ill_cond=dict(argstr='--illcond', ), @@ -142,6 +143,7 @@ def test_GLMFit_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_GLMFit_outputs(): output_map = dict(beta_file=dict(), dof_file=dict(), @@ -166,4 +168,3 @@ def test_GLMFit_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ImageInfo.py b/nipype/interfaces/freesurfer/tests/test_auto_ImageInfo.py index 1e37537505..5d409f2966 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ImageInfo.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ImageInfo.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..utils import ImageInfo + def test_ImageInfo_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -24,6 +25,7 @@ def test_ImageInfo_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ImageInfo_outputs(): output_map = dict(TE=dict(), TI=dict(), @@ -42,4 +44,3 @@ def test_ImageInfo_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Label2Vol.py b/nipype/interfaces/freesurfer/tests/test_auto_Label2Vol.py index 5e294b9457..4ed1bb441c 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Label2Vol.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Label2Vol.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..model import Label2Vol + def test_Label2Vol_inputs(): input_map = dict(annot_file=dict(argstr='--annot %s', copyfile=False, @@ -77,6 +78,7 @@ def test_Label2Vol_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Label2Vol_outputs(): output_map = dict(vol_label_file=dict(), ) @@ -85,4 +87,3 @@ def test_Label2Vol_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIConvert.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIConvert.py index 29ed1ad76c..ad6fd9e55c 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIConvert.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIConvert.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import MRIConvert + def test_MRIConvert_inputs(): input_map = dict(apply_inv_transform=dict(argstr='--apply_inverse_transform %s', ), @@ -188,6 +189,7 @@ def test_MRIConvert_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MRIConvert_outputs(): output_map = dict(out_file=dict(), ) @@ -196,4 +198,3 @@ def test_MRIConvert_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIMarchingCubes.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIMarchingCubes.py index d91c90ca53..44c4725e8e 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIMarchingCubes.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIMarchingCubes.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..utils import MRIMarchingCubes + def test_MRIMarchingCubes_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -37,6 +38,7 @@ def test_MRIMarchingCubes_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MRIMarchingCubes_outputs(): output_map = dict(surface=dict(), ) @@ -45,4 +47,3 @@ def test_MRIMarchingCubes_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIPretess.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIPretess.py index 07dbaf8b1c..ce3e7a244b 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIPretess.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIPretess.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..utils import MRIPretess + def test_MRIPretess_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -44,6 +45,7 @@ def test_MRIPretess_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MRIPretess_outputs(): output_map = dict(out_file=dict(), ) @@ -52,4 +54,3 @@ def test_MRIPretess_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRISPreproc.py b/nipype/interfaces/freesurfer/tests/test_auto_MRISPreproc.py index 97af2b2602..306ca4cd8e 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRISPreproc.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRISPreproc.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..model import MRISPreproc + def test_MRISPreproc_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -70,6 +71,7 @@ def test_MRISPreproc_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MRISPreproc_outputs(): output_map = dict(out_file=dict(), ) @@ -78,4 +80,3 @@ def test_MRISPreproc_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRITessellate.py b/nipype/interfaces/freesurfer/tests/test_auto_MRITessellate.py index 1b25dbe252..3aea6fb331 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRITessellate.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRITessellate.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..utils import MRITessellate + def test_MRITessellate_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -37,6 +38,7 @@ def test_MRITessellate_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MRITessellate_outputs(): output_map = dict(surface=dict(), ) @@ -45,4 +47,3 @@ def test_MRITessellate_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIsConvert.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIsConvert.py index 09a3a09dd3..ef99cd1f58 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIsConvert.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIsConvert.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..utils import MRIsConvert + def test_MRIsConvert_inputs(): input_map = dict(annot_file=dict(argstr='--annot %s', ), @@ -61,6 +62,7 @@ def test_MRIsConvert_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MRIsConvert_outputs(): output_map = dict(converted=dict(), ) @@ -69,4 +71,3 @@ def test_MRIsConvert_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MS_LDA.py b/nipype/interfaces/freesurfer/tests/test_auto_MS_LDA.py index 6be8c00ea6..30264881c8 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MS_LDA.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MS_LDA.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..model import MS_LDA + def test_MS_LDA_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -46,6 +47,7 @@ def test_MS_LDA_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MS_LDA_outputs(): output_map = dict(vol_synth_file=dict(), weight_file=dict(), @@ -55,4 +57,3 @@ def test_MS_LDA_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MakeAverageSubject.py b/nipype/interfaces/freesurfer/tests/test_auto_MakeAverageSubject.py index 18570afbd7..5dd694a707 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MakeAverageSubject.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MakeAverageSubject.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..utils import MakeAverageSubject + def test_MakeAverageSubject_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -28,6 +29,7 @@ def test_MakeAverageSubject_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MakeAverageSubject_outputs(): output_map = dict(average_subject_name=dict(), ) @@ -36,4 +38,3 @@ def test_MakeAverageSubject_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/freesurfer/tests/test_auto_OneSampleTTest.py b/nipype/interfaces/freesurfer/tests/test_auto_OneSampleTTest.py index e91215fcec..b33ecf5856 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_OneSampleTTest.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_OneSampleTTest.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..model import OneSampleTTest + def test_OneSampleTTest_inputs(): input_map = dict(allow_ill_cond=dict(argstr='--illcond', ), @@ -142,6 +143,7 @@ def test_OneSampleTTest_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_OneSampleTTest_outputs(): output_map = dict(beta_file=dict(), dof_file=dict(), @@ -166,4 +168,3 @@ def test_OneSampleTTest_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ParseDICOMDir.py b/nipype/interfaces/freesurfer/tests/test_auto_ParseDICOMDir.py index ff200ace85..a2afa891d9 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ParseDICOMDir.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ParseDICOMDir.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import ParseDICOMDir + def test_ParseDICOMDir_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -31,6 +32,7 @@ def test_ParseDICOMDir_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ParseDICOMDir_outputs(): output_map = dict(dicom_info_file=dict(), ) @@ -39,4 +41,3 @@ def test_ParseDICOMDir_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ReconAll.py b/nipype/interfaces/freesurfer/tests/test_auto_ReconAll.py index d12305bcb2..11ffc6786c 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ReconAll.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ReconAll.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import ReconAll + def test_ReconAll_inputs(): input_map = dict(T1_files=dict(argstr='-i %s...', ), @@ -42,6 +43,7 @@ def test_ReconAll_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ReconAll_outputs(): output_map = dict(BA_stats=dict(altkey='BA', loc='stats', @@ -127,4 +129,3 @@ def test_ReconAll_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Resample.py b/nipype/interfaces/freesurfer/tests/test_auto_Resample.py index 71c212d0f6..befb0b9d01 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Resample.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Resample.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import Resample + def test_Resample_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -32,6 +33,7 @@ def test_Resample_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Resample_outputs(): output_map = dict(resampled_file=dict(), ) @@ -40,4 +42,3 @@ def test_Resample_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/freesurfer/tests/test_auto_RobustRegister.py b/nipype/interfaces/freesurfer/tests/test_auto_RobustRegister.py index 88ad8be0c1..9c52782acc 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_RobustRegister.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_RobustRegister.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import RobustRegister + def test_RobustRegister_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -86,6 +87,7 @@ def test_RobustRegister_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_RobustRegister_outputs(): output_map = dict(half_source=dict(), half_source_xfm=dict(), @@ -101,4 +103,3 @@ def test_RobustRegister_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SampleToSurface.py b/nipype/interfaces/freesurfer/tests/test_auto_SampleToSurface.py index add9a45d9f..8a08a621f8 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SampleToSurface.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SampleToSurface.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..utils import SampleToSurface + def test_SampleToSurface_inputs(): input_map = dict(apply_rot=dict(argstr='--rot %.3f %.3f %.3f', ), @@ -109,6 +110,7 @@ def test_SampleToSurface_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_SampleToSurface_outputs(): output_map = dict(hits_file=dict(), out_file=dict(), @@ -119,4 +121,3 @@ def test_SampleToSurface_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SegStats.py b/nipype/interfaces/freesurfer/tests/test_auto_SegStats.py index 5c51c8726f..2a69e99de3 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SegStats.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SegStats.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..model import SegStats + def test_SegStats_inputs(): input_map = dict(annot=dict(argstr='--annot %s %s %s', mandatory=True, @@ -92,6 +93,7 @@ def test_SegStats_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_SegStats_outputs(): output_map = dict(avgwf_file=dict(), avgwf_txt_file=dict(), @@ -103,4 +105,3 @@ def test_SegStats_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Smooth.py b/nipype/interfaces/freesurfer/tests/test_auto_Smooth.py index 07ea5583db..16fefa2873 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Smooth.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Smooth.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import Smooth + def test_Smooth_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -47,6 +48,7 @@ def test_Smooth_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Smooth_outputs(): output_map = dict(smoothed_file=dict(), ) @@ -55,4 +57,3 @@ def test_Smooth_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SmoothTessellation.py b/nipype/interfaces/freesurfer/tests/test_auto_SmoothTessellation.py index 33c38965ba..2ba9b80134 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SmoothTessellation.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SmoothTessellation.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..utils import SmoothTessellation + def test_SmoothTessellation_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -58,6 +59,7 @@ def test_SmoothTessellation_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_SmoothTessellation_outputs(): output_map = dict(surface=dict(), ) @@ -66,4 +68,3 @@ def test_SmoothTessellation_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Surface2VolTransform.py b/nipype/interfaces/freesurfer/tests/test_auto_Surface2VolTransform.py index 65296762f6..42689a458b 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Surface2VolTransform.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Surface2VolTransform.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..utils import Surface2VolTransform + def test_Surface2VolTransform_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -54,6 +55,7 @@ def test_Surface2VolTransform_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Surface2VolTransform_outputs(): output_map = dict(transformed_file=dict(), vertexvol_file=dict(), @@ -63,4 +65,3 @@ def test_Surface2VolTransform_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSmooth.py b/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSmooth.py index d519f8d413..92d145cfc9 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSmooth.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSmooth.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..utils import SurfaceSmooth + def test_SurfaceSmooth_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -44,6 +45,7 @@ def test_SurfaceSmooth_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_SurfaceSmooth_outputs(): output_map = dict(out_file=dict(), ) @@ -52,4 +54,3 @@ def test_SurfaceSmooth_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSnapshots.py b/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSnapshots.py index 89907da712..46411c9fca 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSnapshots.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSnapshots.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..utils import SurfaceSnapshots + def test_SurfaceSnapshots_inputs(): input_map = dict(annot_file=dict(argstr='-annotation %s', xor=['annot_name'], @@ -98,6 +99,7 @@ def test_SurfaceSnapshots_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_SurfaceSnapshots_outputs(): output_map = dict(snapshots=dict(), ) @@ -106,4 +108,3 @@ def test_SurfaceSnapshots_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SurfaceTransform.py b/nipype/interfaces/freesurfer/tests/test_auto_SurfaceTransform.py index 1567b402c5..250f697402 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SurfaceTransform.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SurfaceTransform.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..utils import SurfaceTransform + def test_SurfaceTransform_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -52,6 +53,7 @@ def test_SurfaceTransform_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_SurfaceTransform_outputs(): output_map = dict(out_file=dict(), ) @@ -60,4 +62,3 @@ def test_SurfaceTransform_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SynthesizeFLASH.py b/nipype/interfaces/freesurfer/tests/test_auto_SynthesizeFLASH.py index c507b91e7c..fc213c7411 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SynthesizeFLASH.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SynthesizeFLASH.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import SynthesizeFLASH + def test_SynthesizeFLASH_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -47,6 +48,7 @@ def test_SynthesizeFLASH_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_SynthesizeFLASH_outputs(): output_map = dict(out_file=dict(), ) @@ -55,4 +57,3 @@ def test_SynthesizeFLASH_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Tkregister2.py b/nipype/interfaces/freesurfer/tests/test_auto_Tkregister2.py index 5e03c1fc26..150bfac675 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Tkregister2.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Tkregister2.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..utils import Tkregister2 + def test_Tkregister2_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -52,6 +53,7 @@ def test_Tkregister2_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Tkregister2_outputs(): output_map = dict(fsl_file=dict(), reg_file=dict(), @@ -61,4 +63,3 @@ def test_Tkregister2_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/freesurfer/tests/test_auto_UnpackSDICOMDir.py b/nipype/interfaces/freesurfer/tests/test_auto_UnpackSDICOMDir.py index fc9cdca56b..40e1c65378 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_UnpackSDICOMDir.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_UnpackSDICOMDir.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import UnpackSDICOMDir + def test_UnpackSDICOMDir_inputs(): input_map = dict(args=dict(argstr='%s', ), diff --git a/nipype/interfaces/fsl/tests/test_auto_ApplyMask.py b/nipype/interfaces/fsl/tests/test_auto_ApplyMask.py index a771f914e1..d374567662 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ApplyMask.py +++ b/nipype/interfaces/fsl/tests/test_auto_ApplyMask.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..maths import ApplyMask + def test_ApplyMask_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -43,6 +44,7 @@ def test_ApplyMask_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ApplyMask_outputs(): output_map = dict(out_file=dict(), ) @@ -51,4 +53,3 @@ def test_ApplyMask_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_ApplyTOPUP.py b/nipype/interfaces/fsl/tests/test_auto_ApplyTOPUP.py index b6f0d00fcc..77a11e3232 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ApplyTOPUP.py +++ b/nipype/interfaces/fsl/tests/test_auto_ApplyTOPUP.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..epi import ApplyTOPUP + def test_ApplyTOPUP_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -49,6 +50,7 @@ def test_ApplyTOPUP_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ApplyTOPUP_outputs(): output_map = dict(out_corrected=dict(), ) @@ -57,4 +59,3 @@ def test_ApplyTOPUP_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_ApplyWarp.py b/nipype/interfaces/fsl/tests/test_auto_ApplyWarp.py index 8cb17890dd..47e2703cb6 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ApplyWarp.py +++ b/nipype/interfaces/fsl/tests/test_auto_ApplyWarp.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import ApplyWarp + def test_ApplyWarp_inputs(): input_map = dict(abswarp=dict(argstr='--abs', xor=['relwarp'], @@ -58,6 +59,7 @@ def test_ApplyWarp_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ApplyWarp_outputs(): output_map = dict(out_file=dict(), ) @@ -66,4 +68,3 @@ def test_ApplyWarp_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_ApplyXfm.py b/nipype/interfaces/fsl/tests/test_auto_ApplyXfm.py index ed830ba059..897d6478ed 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ApplyXfm.py +++ b/nipype/interfaces/fsl/tests/test_auto_ApplyXfm.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import ApplyXfm + def test_ApplyXfm_inputs(): input_map = dict(angle_rep=dict(argstr='-anglerep %s', ), @@ -150,6 +151,7 @@ def test_ApplyXfm_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ApplyXfm_outputs(): output_map = dict(out_file=dict(), out_log=dict(), @@ -160,4 +162,3 @@ def test_ApplyXfm_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_AvScale.py b/nipype/interfaces/fsl/tests/test_auto_AvScale.py index 5d62437360..0d750ddbc0 100644 --- a/nipype/interfaces/fsl/tests/test_auto_AvScale.py +++ b/nipype/interfaces/fsl/tests/test_auto_AvScale.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..utils import AvScale + def test_AvScale_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -24,6 +25,7 @@ def test_AvScale_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_AvScale_outputs(): output_map = dict(average_scaling=dict(), backward_half_transform=dict(), @@ -39,4 +41,3 @@ def test_AvScale_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_BEDPOSTX4.py b/nipype/interfaces/fsl/tests/test_auto_BEDPOSTX4.py index 677cc8c089..ca71395c20 100644 --- a/nipype/interfaces/fsl/tests/test_auto_BEDPOSTX4.py +++ b/nipype/interfaces/fsl/tests/test_auto_BEDPOSTX4.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..dti import BEDPOSTX4 + def test_BEDPOSTX4_inputs(): input_map = dict(all_ard=dict(argstr='--allard', xor=('no_ard', 'all_ard'), @@ -84,6 +85,7 @@ def test_BEDPOSTX4_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_BEDPOSTX4_outputs(): output_map = dict(bpx_out_directory=dict(), dyads=dict(), @@ -100,4 +102,3 @@ def test_BEDPOSTX4_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_BEDPOSTX5.py b/nipype/interfaces/fsl/tests/test_auto_BEDPOSTX5.py index 1d7fc047a8..48f229eabd 100644 --- a/nipype/interfaces/fsl/tests/test_auto_BEDPOSTX5.py +++ b/nipype/interfaces/fsl/tests/test_auto_BEDPOSTX5.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..dti import BEDPOSTX5 + def test_BEDPOSTX5_inputs(): input_map = dict(all_ard=dict(argstr='--allard', xor=('no_ard', 'all_ard'), @@ -85,6 +86,7 @@ def test_BEDPOSTX5_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_BEDPOSTX5_outputs(): output_map = dict(dyads=dict(), dyads_dispersion=dict(), @@ -102,4 +104,3 @@ def test_BEDPOSTX5_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_BET.py b/nipype/interfaces/fsl/tests/test_auto_BET.py index 242f27753a..9f91d76d2f 100644 --- a/nipype/interfaces/fsl/tests/test_auto_BET.py +++ b/nipype/interfaces/fsl/tests/test_auto_BET.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import BET + def test_BET_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -73,6 +74,7 @@ def test_BET_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_BET_outputs(): output_map = dict(inskull_mask_file=dict(), inskull_mesh_file=dict(), @@ -91,4 +93,3 @@ def test_BET_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_BinaryMaths.py b/nipype/interfaces/fsl/tests/test_auto_BinaryMaths.py index 34db882f71..dfc8dcec09 100644 --- a/nipype/interfaces/fsl/tests/test_auto_BinaryMaths.py +++ b/nipype/interfaces/fsl/tests/test_auto_BinaryMaths.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..maths import BinaryMaths + def test_BinaryMaths_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -53,6 +54,7 @@ def test_BinaryMaths_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_BinaryMaths_outputs(): output_map = dict(out_file=dict(), ) @@ -61,4 +63,3 @@ def test_BinaryMaths_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_ChangeDataType.py b/nipype/interfaces/fsl/tests/test_auto_ChangeDataType.py index 5ce774f9de..4de7103895 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ChangeDataType.py +++ b/nipype/interfaces/fsl/tests/test_auto_ChangeDataType.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..maths import ChangeDataType + def test_ChangeDataType_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -40,6 +41,7 @@ def test_ChangeDataType_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ChangeDataType_outputs(): output_map = dict(out_file=dict(), ) @@ -48,4 +50,3 @@ def test_ChangeDataType_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_Cluster.py b/nipype/interfaces/fsl/tests/test_auto_Cluster.py index f96db2b872..7b460a5fd6 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Cluster.py +++ b/nipype/interfaces/fsl/tests/test_auto_Cluster.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..model import Cluster + def test_Cluster_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -78,6 +79,7 @@ def test_Cluster_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Cluster_outputs(): output_map = dict(index_file=dict(), localmax_txt_file=dict(), @@ -93,4 +95,3 @@ def test_Cluster_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_Complex.py b/nipype/interfaces/fsl/tests/test_auto_Complex.py index dc0e3e7edd..eae95be846 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Complex.py +++ b/nipype/interfaces/fsl/tests/test_auto_Complex.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..utils import Complex + def test_Complex_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -94,6 +95,7 @@ def test_Complex_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Complex_outputs(): output_map = dict(complex_out_file=dict(), imaginary_out_file=dict(), @@ -106,4 +108,3 @@ def test_Complex_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_ContrastMgr.py b/nipype/interfaces/fsl/tests/test_auto_ContrastMgr.py index 4bf7c7a78d..361f9cd086 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ContrastMgr.py +++ b/nipype/interfaces/fsl/tests/test_auto_ContrastMgr.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..model import ContrastMgr + def test_ContrastMgr_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -47,6 +48,7 @@ def test_ContrastMgr_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ContrastMgr_outputs(): output_map = dict(copes=dict(), fstats=dict(), @@ -61,4 +63,3 @@ def test_ContrastMgr_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_ConvertWarp.py b/nipype/interfaces/fsl/tests/test_auto_ConvertWarp.py index d87cc28a93..d140396548 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ConvertWarp.py +++ b/nipype/interfaces/fsl/tests/test_auto_ConvertWarp.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..utils import ConvertWarp + def test_ConvertWarp_inputs(): input_map = dict(abswarp=dict(argstr='--abs', xor=['relwarp'], @@ -64,6 +65,7 @@ def test_ConvertWarp_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ConvertWarp_outputs(): output_map = dict(out_file=dict(), ) @@ -72,4 +74,3 @@ def test_ConvertWarp_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_ConvertXFM.py b/nipype/interfaces/fsl/tests/test_auto_ConvertXFM.py index 43ca0d63c9..21bfe5ff1c 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ConvertXFM.py +++ b/nipype/interfaces/fsl/tests/test_auto_ConvertXFM.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..utils import ConvertXFM + def test_ConvertXFM_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -47,6 +48,7 @@ def test_ConvertXFM_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ConvertXFM_outputs(): output_map = dict(out_file=dict(), ) @@ -55,4 +57,3 @@ def test_ConvertXFM_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_CopyGeom.py b/nipype/interfaces/fsl/tests/test_auto_CopyGeom.py index 9c0a9104fe..75e58ee331 100644 --- a/nipype/interfaces/fsl/tests/test_auto_CopyGeom.py +++ b/nipype/interfaces/fsl/tests/test_auto_CopyGeom.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..utils import CopyGeom + def test_CopyGeom_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -36,6 +37,7 @@ def test_CopyGeom_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_CopyGeom_outputs(): output_map = dict(out_file=dict(), ) @@ -44,4 +46,3 @@ def test_CopyGeom_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_DTIFit.py b/nipype/interfaces/fsl/tests/test_auto_DTIFit.py index 53fedc778e..803a78b930 100644 --- a/nipype/interfaces/fsl/tests/test_auto_DTIFit.py +++ b/nipype/interfaces/fsl/tests/test_auto_DTIFit.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..dti import DTIFit + def test_DTIFit_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -63,6 +64,7 @@ def test_DTIFit_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_DTIFit_outputs(): output_map = dict(FA=dict(), L1=dict(), @@ -81,4 +83,3 @@ def test_DTIFit_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_DilateImage.py b/nipype/interfaces/fsl/tests/test_auto_DilateImage.py index 93c4ea8faa..7c0f3e9823 100644 --- a/nipype/interfaces/fsl/tests/test_auto_DilateImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_DilateImage.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..maths import DilateImage + def test_DilateImage_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -54,6 +55,7 @@ def test_DilateImage_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_DilateImage_outputs(): output_map = dict(out_file=dict(), ) @@ -62,4 +64,3 @@ def test_DilateImage_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_DistanceMap.py b/nipype/interfaces/fsl/tests/test_auto_DistanceMap.py index 1a217d6127..083590ed5d 100644 --- a/nipype/interfaces/fsl/tests/test_auto_DistanceMap.py +++ b/nipype/interfaces/fsl/tests/test_auto_DistanceMap.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..dti import DistanceMap + def test_DistanceMap_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -35,6 +36,7 @@ def test_DistanceMap_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_DistanceMap_outputs(): output_map = dict(distance_map=dict(), local_max_file=dict(), @@ -44,4 +46,3 @@ def test_DistanceMap_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_EPIDeWarp.py b/nipype/interfaces/fsl/tests/test_auto_EPIDeWarp.py index cd92a2d776..2f1eaf2522 100644 --- a/nipype/interfaces/fsl/tests/test_auto_EPIDeWarp.py +++ b/nipype/interfaces/fsl/tests/test_auto_EPIDeWarp.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..epi import EPIDeWarp + def test_EPIDeWarp_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -58,6 +59,7 @@ def test_EPIDeWarp_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_EPIDeWarp_outputs(): output_map = dict(exf_mask=dict(), exfdw=dict(), @@ -69,4 +71,3 @@ def test_EPIDeWarp_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_Eddy.py b/nipype/interfaces/fsl/tests/test_auto_Eddy.py index 8b5298cbca..07b17244c9 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Eddy.py +++ b/nipype/interfaces/fsl/tests/test_auto_Eddy.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..epi import Eddy + def test_Eddy_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -62,6 +63,7 @@ def test_Eddy_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Eddy_outputs(): output_map = dict(out_corrected=dict(), out_parameter=dict(), @@ -71,4 +73,3 @@ def test_Eddy_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_EddyCorrect.py b/nipype/interfaces/fsl/tests/test_auto_EddyCorrect.py index 68fbf8f798..b7f93f0b52 100644 --- a/nipype/interfaces/fsl/tests/test_auto_EddyCorrect.py +++ b/nipype/interfaces/fsl/tests/test_auto_EddyCorrect.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..epi import EddyCorrect + def test_EddyCorrect_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -36,6 +37,7 @@ def test_EddyCorrect_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_EddyCorrect_outputs(): output_map = dict(eddy_corrected=dict(), ) @@ -44,4 +46,3 @@ def test_EddyCorrect_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_EpiReg.py b/nipype/interfaces/fsl/tests/test_auto_EpiReg.py index 9be961c33b..8cde315c16 100644 --- a/nipype/interfaces/fsl/tests/test_auto_EpiReg.py +++ b/nipype/interfaces/fsl/tests/test_auto_EpiReg.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..epi import EpiReg + def test_EpiReg_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -55,6 +56,7 @@ def test_EpiReg_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_EpiReg_outputs(): output_map = dict(epi2str_inv=dict(), epi2str_mat=dict(), @@ -75,4 +77,3 @@ def test_EpiReg_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_ErodeImage.py b/nipype/interfaces/fsl/tests/test_auto_ErodeImage.py index 7c27b20f6d..3981afc1a5 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ErodeImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_ErodeImage.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..maths import ErodeImage + def test_ErodeImage_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -54,6 +55,7 @@ def test_ErodeImage_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ErodeImage_outputs(): output_map = dict(out_file=dict(), ) @@ -62,4 +64,3 @@ def test_ErodeImage_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_ExtractROI.py b/nipype/interfaces/fsl/tests/test_auto_ExtractROI.py index 23708a2df3..4368a41256 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ExtractROI.py +++ b/nipype/interfaces/fsl/tests/test_auto_ExtractROI.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..utils import ExtractROI + def test_ExtractROI_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -58,6 +59,7 @@ def test_ExtractROI_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ExtractROI_outputs(): output_map = dict(roi_file=dict(), ) @@ -66,4 +68,3 @@ def test_ExtractROI_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_FAST.py b/nipype/interfaces/fsl/tests/test_auto_FAST.py index e50fb80951..3dc8ca73f2 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FAST.py +++ b/nipype/interfaces/fsl/tests/test_auto_FAST.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import FAST + def test_FAST_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -69,6 +70,7 @@ def test_FAST_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_FAST_outputs(): output_map = dict(bias_field=dict(), mixeltype=dict(), @@ -84,4 +86,3 @@ def test_FAST_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_FEAT.py b/nipype/interfaces/fsl/tests/test_auto_FEAT.py index 66a8e88419..8500302502 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FEAT.py +++ b/nipype/interfaces/fsl/tests/test_auto_FEAT.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..model import FEAT + def test_FEAT_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -25,6 +26,7 @@ def test_FEAT_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_FEAT_outputs(): output_map = dict(feat_dir=dict(), ) @@ -33,4 +35,3 @@ def test_FEAT_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_FEATModel.py b/nipype/interfaces/fsl/tests/test_auto_FEATModel.py index 0db2b6dd46..06cbe57d84 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FEATModel.py +++ b/nipype/interfaces/fsl/tests/test_auto_FEATModel.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..model import FEATModel + def test_FEATModel_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -31,6 +32,7 @@ def test_FEATModel_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_FEATModel_outputs(): output_map = dict(con_file=dict(), design_cov=dict(), @@ -43,4 +45,3 @@ def test_FEATModel_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_FEATRegister.py b/nipype/interfaces/fsl/tests/test_auto_FEATRegister.py index b3b1ebac68..3af3b4695d 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FEATRegister.py +++ b/nipype/interfaces/fsl/tests/test_auto_FEATRegister.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..model import FEATRegister + def test_FEATRegister_inputs(): input_map = dict(feat_dirs=dict(mandatory=True, ), @@ -19,6 +20,7 @@ def test_FEATRegister_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_FEATRegister_outputs(): output_map = dict(fsf_file=dict(), ) @@ -27,4 +29,3 @@ def test_FEATRegister_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_FIRST.py b/nipype/interfaces/fsl/tests/test_auto_FIRST.py index ac94aa5873..876f89f5b6 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FIRST.py +++ b/nipype/interfaces/fsl/tests/test_auto_FIRST.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import FIRST + def test_FIRST_inputs(): input_map = dict(affine_file=dict(argstr='-a %s', position=6, @@ -56,6 +57,7 @@ def test_FIRST_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_FIRST_outputs(): output_map = dict(bvars=dict(), original_segmentations=dict(), @@ -67,4 +69,3 @@ def test_FIRST_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_FLAMEO.py b/nipype/interfaces/fsl/tests/test_auto_FLAMEO.py index 496b9fc85b..bd4d938ffb 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FLAMEO.py +++ b/nipype/interfaces/fsl/tests/test_auto_FLAMEO.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..model import FLAMEO + def test_FLAMEO_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -64,6 +65,7 @@ def test_FLAMEO_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_FLAMEO_outputs(): output_map = dict(copes=dict(), fstats=dict(), @@ -83,4 +85,3 @@ def test_FLAMEO_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_FLIRT.py b/nipype/interfaces/fsl/tests/test_auto_FLIRT.py index 17bf945b48..8bba532da8 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FLIRT.py +++ b/nipype/interfaces/fsl/tests/test_auto_FLIRT.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import FLIRT + def test_FLIRT_inputs(): input_map = dict(angle_rep=dict(argstr='-anglerep %s', ), @@ -149,6 +150,7 @@ def test_FLIRT_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_FLIRT_outputs(): output_map = dict(out_file=dict(), out_log=dict(), @@ -159,4 +161,3 @@ def test_FLIRT_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_FNIRT.py b/nipype/interfaces/fsl/tests/test_auto_FNIRT.py index 696d2044a4..f37e3b7eb2 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FNIRT.py +++ b/nipype/interfaces/fsl/tests/test_auto_FNIRT.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import FNIRT + def test_FNIRT_inputs(): input_map = dict(affine_file=dict(argstr='--aff=%s', ), @@ -127,6 +128,7 @@ def test_FNIRT_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_FNIRT_outputs(): output_map = dict(field_file=dict(), fieldcoeff_file=dict(), @@ -141,4 +143,3 @@ def test_FNIRT_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_FSLCommand.py b/nipype/interfaces/fsl/tests/test_auto_FSLCommand.py index 07fe34c5f2..c5b0bb63a2 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FSLCommand.py +++ b/nipype/interfaces/fsl/tests/test_auto_FSLCommand.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..base import FSLCommand + def test_FSLCommand_inputs(): input_map = dict(args=dict(argstr='%s', ), diff --git a/nipype/interfaces/fsl/tests/test_auto_FSLXCommand.py b/nipype/interfaces/fsl/tests/test_auto_FSLXCommand.py index b0e9a35d18..57b06760d5 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FSLXCommand.py +++ b/nipype/interfaces/fsl/tests/test_auto_FSLXCommand.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..dti import FSLXCommand + def test_FSLXCommand_inputs(): input_map = dict(all_ard=dict(argstr='--allard', xor=('no_ard', 'all_ard'), @@ -82,6 +83,7 @@ def test_FSLXCommand_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_FSLXCommand_outputs(): output_map = dict(dyads=dict(), fsamples=dict(), @@ -97,4 +99,3 @@ def test_FSLXCommand_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_FUGUE.py b/nipype/interfaces/fsl/tests/test_auto_FUGUE.py index 69f21693a0..84de7126df 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FUGUE.py +++ b/nipype/interfaces/fsl/tests/test_auto_FUGUE.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import FUGUE + def test_FUGUE_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -93,6 +94,7 @@ def test_FUGUE_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_FUGUE_outputs(): output_map = dict(fmap_out_file=dict(), shift_out_file=dict(), @@ -104,4 +106,3 @@ def test_FUGUE_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_FilterRegressor.py b/nipype/interfaces/fsl/tests/test_auto_FilterRegressor.py index 913a8feb27..2904b70798 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FilterRegressor.py +++ b/nipype/interfaces/fsl/tests/test_auto_FilterRegressor.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..utils import FilterRegressor + def test_FilterRegressor_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -50,6 +51,7 @@ def test_FilterRegressor_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_FilterRegressor_outputs(): output_map = dict(out_file=dict(), ) @@ -58,4 +60,3 @@ def test_FilterRegressor_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_FindTheBiggest.py b/nipype/interfaces/fsl/tests/test_auto_FindTheBiggest.py index 015928d443..0fd902dbf0 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FindTheBiggest.py +++ b/nipype/interfaces/fsl/tests/test_auto_FindTheBiggest.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..dti import FindTheBiggest + def test_FindTheBiggest_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -30,6 +31,7 @@ def test_FindTheBiggest_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_FindTheBiggest_outputs(): output_map = dict(out_file=dict(argstr='%s', ), @@ -39,4 +41,3 @@ def test_FindTheBiggest_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_GLM.py b/nipype/interfaces/fsl/tests/test_auto_GLM.py index 09a15af967..3aeef972c0 100644 --- a/nipype/interfaces/fsl/tests/test_auto_GLM.py +++ b/nipype/interfaces/fsl/tests/test_auto_GLM.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..model import GLM + def test_GLM_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -71,6 +72,7 @@ def test_GLM_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_GLM_outputs(): output_map = dict(out_cope=dict(), out_data=dict(), @@ -90,4 +92,3 @@ def test_GLM_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_ImageMaths.py b/nipype/interfaces/fsl/tests/test_auto_ImageMaths.py index 671a9a8f7a..008516f571 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ImageMaths.py +++ b/nipype/interfaces/fsl/tests/test_auto_ImageMaths.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..utils import ImageMaths + def test_ImageMaths_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -40,6 +41,7 @@ def test_ImageMaths_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ImageMaths_outputs(): output_map = dict(out_file=dict(), ) @@ -48,4 +50,3 @@ def test_ImageMaths_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_ImageMeants.py b/nipype/interfaces/fsl/tests/test_auto_ImageMeants.py index e726e775c8..2a07ee64f0 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ImageMeants.py +++ b/nipype/interfaces/fsl/tests/test_auto_ImageMeants.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..utils import ImageMeants + def test_ImageMeants_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -46,6 +47,7 @@ def test_ImageMeants_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ImageMeants_outputs(): output_map = dict(out_file=dict(), ) @@ -54,4 +56,3 @@ def test_ImageMeants_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_ImageStats.py b/nipype/interfaces/fsl/tests/test_auto_ImageStats.py index 72e4e0b5b3..86be9772c4 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ImageStats.py +++ b/nipype/interfaces/fsl/tests/test_auto_ImageStats.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..utils import ImageStats + def test_ImageStats_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -34,6 +35,7 @@ def test_ImageStats_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ImageStats_outputs(): output_map = dict(out_stat=dict(), ) @@ -42,4 +44,3 @@ def test_ImageStats_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_InvWarp.py b/nipype/interfaces/fsl/tests/test_auto_InvWarp.py index c0910b5cb0..ad367bf904 100644 --- a/nipype/interfaces/fsl/tests/test_auto_InvWarp.py +++ b/nipype/interfaces/fsl/tests/test_auto_InvWarp.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..utils import InvWarp + def test_InvWarp_inputs(): input_map = dict(absolute=dict(argstr='--abs', xor=['relative'], @@ -48,6 +49,7 @@ def test_InvWarp_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_InvWarp_outputs(): output_map = dict(inverse_warp=dict(), ) @@ -56,4 +58,3 @@ def test_InvWarp_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_IsotropicSmooth.py b/nipype/interfaces/fsl/tests/test_auto_IsotropicSmooth.py index 89ab3ebeab..2d1023d674 100644 --- a/nipype/interfaces/fsl/tests/test_auto_IsotropicSmooth.py +++ b/nipype/interfaces/fsl/tests/test_auto_IsotropicSmooth.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..maths import IsotropicSmooth + def test_IsotropicSmooth_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -49,6 +50,7 @@ def test_IsotropicSmooth_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_IsotropicSmooth_outputs(): output_map = dict(out_file=dict(), ) @@ -57,4 +59,3 @@ def test_IsotropicSmooth_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_L2Model.py b/nipype/interfaces/fsl/tests/test_auto_L2Model.py index 996410a5ec..bcf3737fdd 100644 --- a/nipype/interfaces/fsl/tests/test_auto_L2Model.py +++ b/nipype/interfaces/fsl/tests/test_auto_L2Model.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..model import L2Model + def test_L2Model_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, @@ -15,6 +16,7 @@ def test_L2Model_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_L2Model_outputs(): output_map = dict(design_con=dict(), design_grp=dict(), @@ -25,4 +27,3 @@ def test_L2Model_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_Level1Design.py b/nipype/interfaces/fsl/tests/test_auto_Level1Design.py index 8b9a245cea..f1500d42be 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Level1Design.py +++ b/nipype/interfaces/fsl/tests/test_auto_Level1Design.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..model import Level1Design + def test_Level1Design_inputs(): input_map = dict(bases=dict(mandatory=True, ), @@ -22,6 +23,7 @@ def test_Level1Design_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Level1Design_outputs(): output_map = dict(ev_files=dict(), fsf_files=dict(), @@ -31,4 +33,3 @@ def test_Level1Design_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_MCFLIRT.py b/nipype/interfaces/fsl/tests/test_auto_MCFLIRT.py index 1afc30885a..355c9ab527 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MCFLIRT.py +++ b/nipype/interfaces/fsl/tests/test_auto_MCFLIRT.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import MCFLIRT + def test_MCFLIRT_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -65,6 +66,7 @@ def test_MCFLIRT_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MCFLIRT_outputs(): output_map = dict(mat_file=dict(), mean_img=dict(), @@ -79,4 +81,3 @@ def test_MCFLIRT_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_MELODIC.py b/nipype/interfaces/fsl/tests/test_auto_MELODIC.py index 6baf56e764..3f4c0047ca 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MELODIC.py +++ b/nipype/interfaces/fsl/tests/test_auto_MELODIC.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..model import MELODIC + def test_MELODIC_inputs(): input_map = dict(ICs=dict(argstr='--ICs=%s', ), @@ -113,6 +114,7 @@ def test_MELODIC_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MELODIC_outputs(): output_map = dict(out_dir=dict(), report_dir=dict(), @@ -122,4 +124,3 @@ def test_MELODIC_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_MakeDyadicVectors.py b/nipype/interfaces/fsl/tests/test_auto_MakeDyadicVectors.py index b1b1c5bdaf..cbc35e34c9 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MakeDyadicVectors.py +++ b/nipype/interfaces/fsl/tests/test_auto_MakeDyadicVectors.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..dti import MakeDyadicVectors + def test_MakeDyadicVectors_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -40,6 +41,7 @@ def test_MakeDyadicVectors_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MakeDyadicVectors_outputs(): output_map = dict(dispersion=dict(), dyads=dict(), @@ -49,4 +51,3 @@ def test_MakeDyadicVectors_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_MathsCommand.py b/nipype/interfaces/fsl/tests/test_auto_MathsCommand.py index c931261962..3c3eee3d14 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MathsCommand.py +++ b/nipype/interfaces/fsl/tests/test_auto_MathsCommand.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..maths import MathsCommand + def test_MathsCommand_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -39,6 +40,7 @@ def test_MathsCommand_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MathsCommand_outputs(): output_map = dict(out_file=dict(), ) @@ -47,4 +49,3 @@ def test_MathsCommand_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_MaxImage.py b/nipype/interfaces/fsl/tests/test_auto_MaxImage.py index 86732a6af2..4edd2cfb13 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MaxImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_MaxImage.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..maths import MaxImage + def test_MaxImage_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -43,6 +44,7 @@ def test_MaxImage_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MaxImage_outputs(): output_map = dict(out_file=dict(), ) @@ -51,4 +53,3 @@ def test_MaxImage_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_MeanImage.py b/nipype/interfaces/fsl/tests/test_auto_MeanImage.py index fba966582b..f6792d368d 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MeanImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_MeanImage.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..maths import MeanImage + def test_MeanImage_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -43,6 +44,7 @@ def test_MeanImage_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MeanImage_outputs(): output_map = dict(out_file=dict(), ) @@ -51,4 +53,3 @@ def test_MeanImage_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_Merge.py b/nipype/interfaces/fsl/tests/test_auto_Merge.py index 9a882c9a18..621d43dd65 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Merge.py +++ b/nipype/interfaces/fsl/tests/test_auto_Merge.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..utils import Merge + def test_Merge_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -38,6 +39,7 @@ def test_Merge_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Merge_outputs(): output_map = dict(merged_file=dict(), ) @@ -46,4 +48,3 @@ def test_Merge_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_MotionOutliers.py b/nipype/interfaces/fsl/tests/test_auto_MotionOutliers.py index d0ffbb9d34..d8d88d809e 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MotionOutliers.py +++ b/nipype/interfaces/fsl/tests/test_auto_MotionOutliers.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..utils import MotionOutliers + def test_MotionOutliers_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -52,6 +53,7 @@ def test_MotionOutliers_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MotionOutliers_outputs(): output_map = dict(out_file=dict(), out_metric_plot=dict(), @@ -62,4 +64,3 @@ def test_MotionOutliers_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_MultiImageMaths.py b/nipype/interfaces/fsl/tests/test_auto_MultiImageMaths.py index 04a8c10c23..91b5f03657 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MultiImageMaths.py +++ b/nipype/interfaces/fsl/tests/test_auto_MultiImageMaths.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..maths import MultiImageMaths + def test_MultiImageMaths_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -45,6 +46,7 @@ def test_MultiImageMaths_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MultiImageMaths_outputs(): output_map = dict(out_file=dict(), ) @@ -53,4 +55,3 @@ def test_MultiImageMaths_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_MultipleRegressDesign.py b/nipype/interfaces/fsl/tests/test_auto_MultipleRegressDesign.py index 688a5bf29e..5e4a88cf79 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MultipleRegressDesign.py +++ b/nipype/interfaces/fsl/tests/test_auto_MultipleRegressDesign.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..model import MultipleRegressDesign + def test_MultipleRegressDesign_inputs(): input_map = dict(contrasts=dict(mandatory=True, ), @@ -18,6 +19,7 @@ def test_MultipleRegressDesign_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MultipleRegressDesign_outputs(): output_map = dict(design_con=dict(), design_fts=dict(), @@ -29,4 +31,3 @@ def test_MultipleRegressDesign_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_Overlay.py b/nipype/interfaces/fsl/tests/test_auto_Overlay.py index 091657fd1e..14257803be 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Overlay.py +++ b/nipype/interfaces/fsl/tests/test_auto_Overlay.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..utils import Overlay + def test_Overlay_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -75,6 +76,7 @@ def test_Overlay_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Overlay_outputs(): output_map = dict(out_file=dict(), ) @@ -83,4 +85,3 @@ def test_Overlay_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_PRELUDE.py b/nipype/interfaces/fsl/tests/test_auto_PRELUDE.py index 08dd904b26..434322da60 100644 --- a/nipype/interfaces/fsl/tests/test_auto_PRELUDE.py +++ b/nipype/interfaces/fsl/tests/test_auto_PRELUDE.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import PRELUDE + def test_PRELUDE_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -66,6 +67,7 @@ def test_PRELUDE_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_PRELUDE_outputs(): output_map = dict(unwrapped_phase_file=dict(), ) @@ -74,4 +76,3 @@ def test_PRELUDE_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_PlotMotionParams.py b/nipype/interfaces/fsl/tests/test_auto_PlotMotionParams.py index 583394d138..75d376e32e 100644 --- a/nipype/interfaces/fsl/tests/test_auto_PlotMotionParams.py +++ b/nipype/interfaces/fsl/tests/test_auto_PlotMotionParams.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..utils import PlotMotionParams + def test_PlotMotionParams_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -36,6 +37,7 @@ def test_PlotMotionParams_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_PlotMotionParams_outputs(): output_map = dict(out_file=dict(), ) @@ -44,4 +46,3 @@ def test_PlotMotionParams_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_PlotTimeSeries.py b/nipype/interfaces/fsl/tests/test_auto_PlotTimeSeries.py index bfb76d8043..e8c28c68de 100644 --- a/nipype/interfaces/fsl/tests/test_auto_PlotTimeSeries.py +++ b/nipype/interfaces/fsl/tests/test_auto_PlotTimeSeries.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..utils import PlotTimeSeries + def test_PlotTimeSeries_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -62,6 +63,7 @@ def test_PlotTimeSeries_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_PlotTimeSeries_outputs(): output_map = dict(out_file=dict(), ) @@ -70,4 +72,3 @@ def test_PlotTimeSeries_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_PowerSpectrum.py b/nipype/interfaces/fsl/tests/test_auto_PowerSpectrum.py index 1f495918ce..bacda34c21 100644 --- a/nipype/interfaces/fsl/tests/test_auto_PowerSpectrum.py +++ b/nipype/interfaces/fsl/tests/test_auto_PowerSpectrum.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..utils import PowerSpectrum + def test_PowerSpectrum_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -30,6 +31,7 @@ def test_PowerSpectrum_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_PowerSpectrum_outputs(): output_map = dict(out_file=dict(), ) @@ -38,4 +40,3 @@ def test_PowerSpectrum_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_PrepareFieldmap.py b/nipype/interfaces/fsl/tests/test_auto_PrepareFieldmap.py index e164bda3ac..01aea929dc 100644 --- a/nipype/interfaces/fsl/tests/test_auto_PrepareFieldmap.py +++ b/nipype/interfaces/fsl/tests/test_auto_PrepareFieldmap.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..epi import PrepareFieldmap + def test_PrepareFieldmap_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -45,6 +46,7 @@ def test_PrepareFieldmap_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_PrepareFieldmap_outputs(): output_map = dict(out_fieldmap=dict(), ) @@ -53,4 +55,3 @@ def test_PrepareFieldmap_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_ProbTrackX.py b/nipype/interfaces/fsl/tests/test_auto_ProbTrackX.py index 4793039e07..a4b60ff6f6 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ProbTrackX.py +++ b/nipype/interfaces/fsl/tests/test_auto_ProbTrackX.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..dti import ProbTrackX + def test_ProbTrackX_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -101,6 +102,7 @@ def test_ProbTrackX_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ProbTrackX_outputs(): output_map = dict(fdt_paths=dict(), log=dict(), @@ -113,4 +115,3 @@ def test_ProbTrackX_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_ProbTrackX2.py b/nipype/interfaces/fsl/tests/test_auto_ProbTrackX2.py index b6946401c3..df69f76670 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ProbTrackX2.py +++ b/nipype/interfaces/fsl/tests/test_auto_ProbTrackX2.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..dti import ProbTrackX2 + def test_ProbTrackX2_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -131,6 +132,7 @@ def test_ProbTrackX2_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ProbTrackX2_outputs(): output_map = dict(fdt_paths=dict(), log=dict(), @@ -148,4 +150,3 @@ def test_ProbTrackX2_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_ProjThresh.py b/nipype/interfaces/fsl/tests/test_auto_ProjThresh.py index f9403de75c..a8fbd352a9 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ProjThresh.py +++ b/nipype/interfaces/fsl/tests/test_auto_ProjThresh.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..dti import ProjThresh + def test_ProjThresh_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -29,6 +30,7 @@ def test_ProjThresh_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ProjThresh_outputs(): output_map = dict(out_files=dict(), ) @@ -37,4 +39,3 @@ def test_ProjThresh_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_Randomise.py b/nipype/interfaces/fsl/tests/test_auto_Randomise.py index 97d2ff6352..72a38393fd 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Randomise.py +++ b/nipype/interfaces/fsl/tests/test_auto_Randomise.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..model import Randomise + def test_Randomise_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -81,6 +82,7 @@ def test_Randomise_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Randomise_outputs(): output_map = dict(f_corrected_p_files=dict(), f_p_files=dict(), @@ -94,4 +96,3 @@ def test_Randomise_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_Reorient2Std.py b/nipype/interfaces/fsl/tests/test_auto_Reorient2Std.py index b064dd1e51..0f252d5d61 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Reorient2Std.py +++ b/nipype/interfaces/fsl/tests/test_auto_Reorient2Std.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..utils import Reorient2Std + def test_Reorient2Std_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -28,6 +29,7 @@ def test_Reorient2Std_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Reorient2Std_outputs(): output_map = dict(out_file=dict(), ) @@ -36,4 +38,3 @@ def test_Reorient2Std_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_RobustFOV.py b/nipype/interfaces/fsl/tests/test_auto_RobustFOV.py index 4b75cef50c..d28c8845dd 100644 --- a/nipype/interfaces/fsl/tests/test_auto_RobustFOV.py +++ b/nipype/interfaces/fsl/tests/test_auto_RobustFOV.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..utils import RobustFOV + def test_RobustFOV_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -30,6 +31,7 @@ def test_RobustFOV_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_RobustFOV_outputs(): output_map = dict(out_roi=dict(), ) @@ -38,4 +40,3 @@ def test_RobustFOV_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_SMM.py b/nipype/interfaces/fsl/tests/test_auto_SMM.py index 071d9c2960..b2440eaa7e 100644 --- a/nipype/interfaces/fsl/tests/test_auto_SMM.py +++ b/nipype/interfaces/fsl/tests/test_auto_SMM.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..model import SMM + def test_SMM_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -34,6 +35,7 @@ def test_SMM_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_SMM_outputs(): output_map = dict(activation_p_map=dict(), deactivation_p_map=dict(), @@ -44,4 +46,3 @@ def test_SMM_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_SUSAN.py b/nipype/interfaces/fsl/tests/test_auto_SUSAN.py index e577e1299c..0b813fc31e 100644 --- a/nipype/interfaces/fsl/tests/test_auto_SUSAN.py +++ b/nipype/interfaces/fsl/tests/test_auto_SUSAN.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import SUSAN + def test_SUSAN_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -50,6 +51,7 @@ def test_SUSAN_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_SUSAN_outputs(): output_map = dict(smoothed_file=dict(), ) @@ -58,4 +60,3 @@ def test_SUSAN_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_SigLoss.py b/nipype/interfaces/fsl/tests/test_auto_SigLoss.py index 6588a4cfb2..e42dc4ba88 100644 --- a/nipype/interfaces/fsl/tests/test_auto_SigLoss.py +++ b/nipype/interfaces/fsl/tests/test_auto_SigLoss.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..utils import SigLoss + def test_SigLoss_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -33,6 +34,7 @@ def test_SigLoss_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_SigLoss_outputs(): output_map = dict(out_file=dict(), ) @@ -41,4 +43,3 @@ def test_SigLoss_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_SliceTimer.py b/nipype/interfaces/fsl/tests/test_auto_SliceTimer.py index 5e4b75cf82..c02b80cf3b 100644 --- a/nipype/interfaces/fsl/tests/test_auto_SliceTimer.py +++ b/nipype/interfaces/fsl/tests/test_auto_SliceTimer.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import SliceTimer + def test_SliceTimer_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -43,6 +44,7 @@ def test_SliceTimer_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_SliceTimer_outputs(): output_map = dict(slice_time_corrected_file=dict(), ) @@ -51,4 +53,3 @@ def test_SliceTimer_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_Slicer.py b/nipype/interfaces/fsl/tests/test_auto_Slicer.py index a74470e555..edcaafaa30 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Slicer.py +++ b/nipype/interfaces/fsl/tests/test_auto_Slicer.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..utils import Slicer + def test_Slicer_inputs(): input_map = dict(all_axial=dict(argstr='-A', position=10, @@ -84,6 +85,7 @@ def test_Slicer_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Slicer_outputs(): output_map = dict(out_file=dict(), ) @@ -92,4 +94,3 @@ def test_Slicer_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_Smooth.py b/nipype/interfaces/fsl/tests/test_auto_Smooth.py index 6738ae4382..535e31b5dc 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Smooth.py +++ b/nipype/interfaces/fsl/tests/test_auto_Smooth.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..utils import Smooth + def test_Smooth_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -34,6 +35,7 @@ def test_Smooth_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Smooth_outputs(): output_map = dict(smoothed_file=dict(), ) @@ -42,4 +44,3 @@ def test_Smooth_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_SmoothEstimate.py b/nipype/interfaces/fsl/tests/test_auto_SmoothEstimate.py index 9e9195bf6b..5c3f8c46b0 100644 --- a/nipype/interfaces/fsl/tests/test_auto_SmoothEstimate.py +++ b/nipype/interfaces/fsl/tests/test_auto_SmoothEstimate.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..model import SmoothEstimate + def test_SmoothEstimate_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -34,6 +35,7 @@ def test_SmoothEstimate_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_SmoothEstimate_outputs(): output_map = dict(dlh=dict(), resels=dict(), @@ -44,4 +46,3 @@ def test_SmoothEstimate_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_SpatialFilter.py b/nipype/interfaces/fsl/tests/test_auto_SpatialFilter.py index 511072850f..ab605fed0b 100644 --- a/nipype/interfaces/fsl/tests/test_auto_SpatialFilter.py +++ b/nipype/interfaces/fsl/tests/test_auto_SpatialFilter.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..maths import SpatialFilter + def test_SpatialFilter_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -54,6 +55,7 @@ def test_SpatialFilter_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_SpatialFilter_outputs(): output_map = dict(out_file=dict(), ) @@ -62,4 +64,3 @@ def test_SpatialFilter_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_Split.py b/nipype/interfaces/fsl/tests/test_auto_Split.py index a910fef77e..a7469eca48 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Split.py +++ b/nipype/interfaces/fsl/tests/test_auto_Split.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..utils import Split + def test_Split_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -32,6 +33,7 @@ def test_Split_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Split_outputs(): output_map = dict(out_files=dict(), ) @@ -40,4 +42,3 @@ def test_Split_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_SwapDimensions.py b/nipype/interfaces/fsl/tests/test_auto_SwapDimensions.py index 65c93c5be6..60dd31a304 100644 --- a/nipype/interfaces/fsl/tests/test_auto_SwapDimensions.py +++ b/nipype/interfaces/fsl/tests/test_auto_SwapDimensions.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..utils import SwapDimensions + def test_SwapDimensions_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -32,6 +33,7 @@ def test_SwapDimensions_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_SwapDimensions_outputs(): output_map = dict(out_file=dict(), ) @@ -40,4 +42,3 @@ def test_SwapDimensions_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_TOPUP.py b/nipype/interfaces/fsl/tests/test_auto_TOPUP.py index 2edb5ff1db..3e097b26ab 100644 --- a/nipype/interfaces/fsl/tests/test_auto_TOPUP.py +++ b/nipype/interfaces/fsl/tests/test_auto_TOPUP.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..epi import TOPUP + def test_TOPUP_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -89,6 +90,7 @@ def test_TOPUP_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_TOPUP_outputs(): output_map = dict(out_corrected=dict(), out_enc_file=dict(), @@ -102,4 +104,3 @@ def test_TOPUP_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_TemporalFilter.py b/nipype/interfaces/fsl/tests/test_auto_TemporalFilter.py index d30e31801f..049af8bd52 100644 --- a/nipype/interfaces/fsl/tests/test_auto_TemporalFilter.py +++ b/nipype/interfaces/fsl/tests/test_auto_TemporalFilter.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..maths import TemporalFilter + def test_TemporalFilter_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -47,6 +48,7 @@ def test_TemporalFilter_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_TemporalFilter_outputs(): output_map = dict(out_file=dict(), ) @@ -55,4 +57,3 @@ def test_TemporalFilter_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_Threshold.py b/nipype/interfaces/fsl/tests/test_auto_Threshold.py index f2424ca25c..dfaa3594bb 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Threshold.py +++ b/nipype/interfaces/fsl/tests/test_auto_Threshold.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..maths import Threshold + def test_Threshold_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -48,6 +49,7 @@ def test_Threshold_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Threshold_outputs(): output_map = dict(out_file=dict(), ) @@ -56,4 +58,3 @@ def test_Threshold_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_TractSkeleton.py b/nipype/interfaces/fsl/tests/test_auto_TractSkeleton.py index f6dc2991a6..3808504b9d 100644 --- a/nipype/interfaces/fsl/tests/test_auto_TractSkeleton.py +++ b/nipype/interfaces/fsl/tests/test_auto_TractSkeleton.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..dti import TractSkeleton + def test_TractSkeleton_inputs(): input_map = dict(alt_data_file=dict(argstr='-a %s', ), @@ -42,6 +43,7 @@ def test_TractSkeleton_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_TractSkeleton_outputs(): output_map = dict(projected_data=dict(), skeleton_file=dict(), @@ -51,4 +53,3 @@ def test_TractSkeleton_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_UnaryMaths.py b/nipype/interfaces/fsl/tests/test_auto_UnaryMaths.py index d35f8e4738..9bc209e532 100644 --- a/nipype/interfaces/fsl/tests/test_auto_UnaryMaths.py +++ b/nipype/interfaces/fsl/tests/test_auto_UnaryMaths.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..maths import UnaryMaths + def test_UnaryMaths_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -43,6 +44,7 @@ def test_UnaryMaths_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_UnaryMaths_outputs(): output_map = dict(out_file=dict(), ) @@ -51,4 +53,3 @@ def test_UnaryMaths_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_VecReg.py b/nipype/interfaces/fsl/tests/test_auto_VecReg.py index 2e129bef92..55c84c1164 100644 --- a/nipype/interfaces/fsl/tests/test_auto_VecReg.py +++ b/nipype/interfaces/fsl/tests/test_auto_VecReg.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..dti import VecReg + def test_VecReg_inputs(): input_map = dict(affine_mat=dict(argstr='-t %s', ), @@ -45,6 +46,7 @@ def test_VecReg_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_VecReg_outputs(): output_map = dict(out_file=dict(), ) @@ -53,4 +55,3 @@ def test_VecReg_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_WarpPoints.py b/nipype/interfaces/fsl/tests/test_auto_WarpPoints.py index 553c63665b..984b3f77a1 100644 --- a/nipype/interfaces/fsl/tests/test_auto_WarpPoints.py +++ b/nipype/interfaces/fsl/tests/test_auto_WarpPoints.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..utils import WarpPoints + def test_WarpPoints_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -46,6 +47,7 @@ def test_WarpPoints_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_WarpPoints_outputs(): output_map = dict(out_file=dict(), ) @@ -54,4 +56,3 @@ def test_WarpPoints_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_WarpPointsToStd.py b/nipype/interfaces/fsl/tests/test_auto_WarpPointsToStd.py index f8f7941081..f6ecd09f2e 100644 --- a/nipype/interfaces/fsl/tests/test_auto_WarpPointsToStd.py +++ b/nipype/interfaces/fsl/tests/test_auto_WarpPointsToStd.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..utils import WarpPointsToStd + def test_WarpPointsToStd_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -48,6 +49,7 @@ def test_WarpPointsToStd_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_WarpPointsToStd_outputs(): output_map = dict(out_file=dict(), ) @@ -56,4 +58,3 @@ def test_WarpPointsToStd_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_WarpUtils.py b/nipype/interfaces/fsl/tests/test_auto_WarpUtils.py index eea3ada6aa..065e2b455b 100644 --- a/nipype/interfaces/fsl/tests/test_auto_WarpUtils.py +++ b/nipype/interfaces/fsl/tests/test_auto_WarpUtils.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..utils import WarpUtils + def test_WarpUtils_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -45,6 +46,7 @@ def test_WarpUtils_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_WarpUtils_outputs(): output_map = dict(out_file=dict(), out_jacobian=dict(), @@ -54,4 +56,3 @@ def test_WarpUtils_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_XFibres4.py b/nipype/interfaces/fsl/tests/test_auto_XFibres4.py index a5733fd892..5fa46bb954 100644 --- a/nipype/interfaces/fsl/tests/test_auto_XFibres4.py +++ b/nipype/interfaces/fsl/tests/test_auto_XFibres4.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..dti import XFibres4 + def test_XFibres4_inputs(): input_map = dict(all_ard=dict(argstr='--allard', xor=('no_ard', 'all_ard'), @@ -71,6 +72,7 @@ def test_XFibres4_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_XFibres4_outputs(): output_map = dict(dyads=dict(), fsamples=dict(), @@ -85,4 +87,3 @@ def test_XFibres4_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/fsl/tests/test_auto_XFibres5.py b/nipype/interfaces/fsl/tests/test_auto_XFibres5.py index 0e2b34d39d..f877d894e5 100644 --- a/nipype/interfaces/fsl/tests/test_auto_XFibres5.py +++ b/nipype/interfaces/fsl/tests/test_auto_XFibres5.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..dti import XFibres5 + def test_XFibres5_inputs(): input_map = dict(all_ard=dict(argstr='--allard', xor=('no_ard', 'all_ard'), @@ -84,6 +85,7 @@ def test_XFibres5_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_XFibres5_outputs(): output_map = dict(dyads=dict(), fsamples=dict(), @@ -99,4 +101,3 @@ def test_XFibres5_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/mipav/tests/test_auto_JistBrainMgdmSegmentation.py b/nipype/interfaces/mipav/tests/test_auto_JistBrainMgdmSegmentation.py index c4a08fa091..e326a579a2 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistBrainMgdmSegmentation.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistBrainMgdmSegmentation.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..developer import JistBrainMgdmSegmentation + def test_JistBrainMgdmSegmentation_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -73,6 +74,7 @@ def test_JistBrainMgdmSegmentation_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_JistBrainMgdmSegmentation_outputs(): output_map = dict(outLevelset=dict(), outPosterior2=dict(), @@ -84,4 +86,3 @@ def test_JistBrainMgdmSegmentation_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageDuraEstimation.py b/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageDuraEstimation.py index 13a3154a57..d8fab93f50 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageDuraEstimation.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageDuraEstimation.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..developer import JistBrainMp2rageDuraEstimation + def test_JistBrainMp2rageDuraEstimation_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -40,6 +41,7 @@ def test_JistBrainMp2rageDuraEstimation_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_JistBrainMp2rageDuraEstimation_outputs(): output_map = dict(outDura=dict(), ) @@ -48,4 +50,3 @@ def test_JistBrainMp2rageDuraEstimation_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageSkullStripping.py b/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageSkullStripping.py index 9535b7d171..12b3232fa7 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageSkullStripping.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistBrainMp2rageSkullStripping.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..developer import JistBrainMp2rageSkullStripping + def test_JistBrainMp2rageSkullStripping_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -51,6 +52,7 @@ def test_JistBrainMp2rageSkullStripping_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_JistBrainMp2rageSkullStripping_outputs(): output_map = dict(outBrain=dict(), outMasked=dict(), @@ -62,4 +64,3 @@ def test_JistBrainMp2rageSkullStripping_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/mipav/tests/test_auto_JistBrainPartialVolumeFilter.py b/nipype/interfaces/mipav/tests/test_auto_JistBrainPartialVolumeFilter.py index 487bb25bfb..659b4672b0 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistBrainPartialVolumeFilter.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistBrainPartialVolumeFilter.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..developer import JistBrainPartialVolumeFilter + def test_JistBrainPartialVolumeFilter_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -38,6 +39,7 @@ def test_JistBrainPartialVolumeFilter_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_JistBrainPartialVolumeFilter_outputs(): output_map = dict(outPartial=dict(), ) @@ -46,4 +48,3 @@ def test_JistBrainPartialVolumeFilter_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/mipav/tests/test_auto_JistCortexSurfaceMeshInflation.py b/nipype/interfaces/mipav/tests/test_auto_JistCortexSurfaceMeshInflation.py index caec86fbf4..c4bf2b4c64 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistCortexSurfaceMeshInflation.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistCortexSurfaceMeshInflation.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..developer import JistCortexSurfaceMeshInflation + def test_JistCortexSurfaceMeshInflation_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -49,6 +50,7 @@ def test_JistCortexSurfaceMeshInflation_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_JistCortexSurfaceMeshInflation_outputs(): output_map = dict(outInflated=dict(), outOriginal=dict(), @@ -58,4 +60,3 @@ def test_JistCortexSurfaceMeshInflation_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/mipav/tests/test_auto_JistIntensityMp2rageMasking.py b/nipype/interfaces/mipav/tests/test_auto_JistIntensityMp2rageMasking.py index 9ad0e07868..e5eb472c0f 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistIntensityMp2rageMasking.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistIntensityMp2rageMasking.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..developer import JistIntensityMp2rageMasking + def test_JistIntensityMp2rageMasking_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -53,6 +54,7 @@ def test_JistIntensityMp2rageMasking_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_JistIntensityMp2rageMasking_outputs(): output_map = dict(outMasked=dict(), outMasked2=dict(), @@ -64,4 +66,3 @@ def test_JistIntensityMp2rageMasking_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileCalculator.py b/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileCalculator.py index 360bc1cb9a..c00adac81c 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileCalculator.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileCalculator.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..developer import JistLaminarProfileCalculator + def test_JistLaminarProfileCalculator_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -38,6 +39,7 @@ def test_JistLaminarProfileCalculator_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_JistLaminarProfileCalculator_outputs(): output_map = dict(outResult=dict(), ) @@ -46,4 +48,3 @@ def test_JistLaminarProfileCalculator_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileGeometry.py b/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileGeometry.py index 91612a6106..b251f594db 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileGeometry.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileGeometry.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..developer import JistLaminarProfileGeometry + def test_JistLaminarProfileGeometry_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -42,6 +43,7 @@ def test_JistLaminarProfileGeometry_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_JistLaminarProfileGeometry_outputs(): output_map = dict(outResult=dict(), ) @@ -50,4 +52,3 @@ def test_JistLaminarProfileGeometry_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileSampling.py b/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileSampling.py index b33903f1e8..b9d5a067ec 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileSampling.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistLaminarProfileSampling.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..developer import JistLaminarProfileSampling + def test_JistLaminarProfileSampling_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -41,6 +42,7 @@ def test_JistLaminarProfileSampling_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_JistLaminarProfileSampling_outputs(): output_map = dict(outProfile2=dict(), outProfilemapped=dict(), @@ -50,4 +52,3 @@ def test_JistLaminarProfileSampling_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/mipav/tests/test_auto_JistLaminarROIAveraging.py b/nipype/interfaces/mipav/tests/test_auto_JistLaminarROIAveraging.py index a2f684e95d..2c22ad0e70 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistLaminarROIAveraging.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistLaminarROIAveraging.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..developer import JistLaminarROIAveraging + def test_JistLaminarROIAveraging_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -40,6 +41,7 @@ def test_JistLaminarROIAveraging_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_JistLaminarROIAveraging_outputs(): output_map = dict(outROI3=dict(), ) @@ -48,4 +50,3 @@ def test_JistLaminarROIAveraging_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/mipav/tests/test_auto_JistLaminarVolumetricLayering.py b/nipype/interfaces/mipav/tests/test_auto_JistLaminarVolumetricLayering.py index 4ad3f30476..40ff811855 100644 --- a/nipype/interfaces/mipav/tests/test_auto_JistLaminarVolumetricLayering.py +++ b/nipype/interfaces/mipav/tests/test_auto_JistLaminarVolumetricLayering.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..developer import JistLaminarVolumetricLayering + def test_JistLaminarVolumetricLayering_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -60,6 +61,7 @@ def test_JistLaminarVolumetricLayering_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_JistLaminarVolumetricLayering_outputs(): output_map = dict(outContinuous=dict(), outDiscrete=dict(), @@ -70,4 +72,3 @@ def test_JistLaminarVolumetricLayering_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmImageCalculator.py b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmImageCalculator.py index 6252555653..802669247f 100644 --- a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmImageCalculator.py +++ b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmImageCalculator.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..developer import MedicAlgorithmImageCalculator + def test_MedicAlgorithmImageCalculator_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -38,6 +39,7 @@ def test_MedicAlgorithmImageCalculator_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MedicAlgorithmImageCalculator_outputs(): output_map = dict(outResult=dict(), ) @@ -46,4 +48,3 @@ def test_MedicAlgorithmImageCalculator_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmLesionToads.py b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmLesionToads.py index 7b03410be4..232d6a1362 100644 --- a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmLesionToads.py +++ b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmLesionToads.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..developer import MedicAlgorithmLesionToads + def test_MedicAlgorithmLesionToads_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -98,6 +99,7 @@ def test_MedicAlgorithmLesionToads_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MedicAlgorithmLesionToads_outputs(): output_map = dict(outCortical=dict(), outFilled=dict(), @@ -114,4 +116,3 @@ def test_MedicAlgorithmLesionToads_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmMipavReorient.py b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmMipavReorient.py index b288aabc2f..a9e43b3b04 100644 --- a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmMipavReorient.py +++ b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmMipavReorient.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..developer import MedicAlgorithmMipavReorient + def test_MedicAlgorithmMipavReorient_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -51,6 +52,7 @@ def test_MedicAlgorithmMipavReorient_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MedicAlgorithmMipavReorient_outputs(): output_map = dict() outputs = MedicAlgorithmMipavReorient.output_spec() @@ -58,4 +60,3 @@ def test_MedicAlgorithmMipavReorient_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmN3.py b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmN3.py index 344e6924bb..58b3daa96f 100644 --- a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmN3.py +++ b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmN3.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..developer import MedicAlgorithmN3 + def test_MedicAlgorithmN3_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -53,6 +54,7 @@ def test_MedicAlgorithmN3_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MedicAlgorithmN3_outputs(): output_map = dict(outInhomogeneity=dict(), outInhomogeneity2=dict(), @@ -62,4 +64,3 @@ def test_MedicAlgorithmN3_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmSPECTRE2010.py b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmSPECTRE2010.py index f3edf74136..c8e005123b 100644 --- a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmSPECTRE2010.py +++ b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmSPECTRE2010.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..developer import MedicAlgorithmSPECTRE2010 + def test_MedicAlgorithmSPECTRE2010_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -124,6 +125,7 @@ def test_MedicAlgorithmSPECTRE2010_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MedicAlgorithmSPECTRE2010_outputs(): output_map = dict(outFANTASM=dict(), outMask=dict(), @@ -140,4 +142,3 @@ def test_MedicAlgorithmSPECTRE2010_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmThresholdToBinaryMask.py b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmThresholdToBinaryMask.py index 95db54b4c6..f472c7043f 100644 --- a/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmThresholdToBinaryMask.py +++ b/nipype/interfaces/mipav/tests/test_auto_MedicAlgorithmThresholdToBinaryMask.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..developer import MedicAlgorithmThresholdToBinaryMask + def test_MedicAlgorithmThresholdToBinaryMask_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -41,6 +42,7 @@ def test_MedicAlgorithmThresholdToBinaryMask_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MedicAlgorithmThresholdToBinaryMask_outputs(): output_map = dict() outputs = MedicAlgorithmThresholdToBinaryMask.output_spec() @@ -48,4 +50,3 @@ def test_MedicAlgorithmThresholdToBinaryMask_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/mipav/tests/test_auto_RandomVol.py b/nipype/interfaces/mipav/tests/test_auto_RandomVol.py index 0fd32c6296..be6839e209 100644 --- a/nipype/interfaces/mipav/tests/test_auto_RandomVol.py +++ b/nipype/interfaces/mipav/tests/test_auto_RandomVol.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..developer import RandomVol + def test_RandomVol_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -50,6 +51,7 @@ def test_RandomVol_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_RandomVol_outputs(): output_map = dict(outRand1=dict(), ) @@ -58,4 +60,3 @@ def test_RandomVol_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/mne/tests/test_auto_WatershedBEM.py b/nipype/interfaces/mne/tests/test_auto_WatershedBEM.py index 745cc8b99a..28c42e1c6d 100644 --- a/nipype/interfaces/mne/tests/test_auto_WatershedBEM.py +++ b/nipype/interfaces/mne/tests/test_auto_WatershedBEM.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..base import WatershedBEM + def test_WatershedBEM_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -34,6 +35,7 @@ def test_WatershedBEM_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_WatershedBEM_outputs(): output_map = dict(brain_surface=dict(loc='bem/watershed', ), @@ -56,4 +58,3 @@ def test_WatershedBEM_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/mrtrix/tests/test_auto_ConstrainedSphericalDeconvolution.py b/nipype/interfaces/mrtrix/tests/test_auto_ConstrainedSphericalDeconvolution.py index 2261a9c887..4bf97e42f7 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_ConstrainedSphericalDeconvolution.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_ConstrainedSphericalDeconvolution.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..tensors import ConstrainedSphericalDeconvolution + def test_ConstrainedSphericalDeconvolution_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -57,6 +58,7 @@ def test_ConstrainedSphericalDeconvolution_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ConstrainedSphericalDeconvolution_outputs(): output_map = dict(spherical_harmonics_image=dict(), ) @@ -65,4 +67,3 @@ def test_ConstrainedSphericalDeconvolution_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/mrtrix/tests/test_auto_DWI2SphericalHarmonicsImage.py b/nipype/interfaces/mrtrix/tests/test_auto_DWI2SphericalHarmonicsImage.py index 86d9d6259d..28d3c97831 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_DWI2SphericalHarmonicsImage.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_DWI2SphericalHarmonicsImage.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..tensors import DWI2SphericalHarmonicsImage + def test_DWI2SphericalHarmonicsImage_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -37,6 +38,7 @@ def test_DWI2SphericalHarmonicsImage_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_DWI2SphericalHarmonicsImage_outputs(): output_map = dict(spherical_harmonics_image=dict(), ) @@ -45,4 +47,3 @@ def test_DWI2SphericalHarmonicsImage_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/mrtrix/tests/test_auto_DWI2Tensor.py b/nipype/interfaces/mrtrix/tests/test_auto_DWI2Tensor.py index a8e0e1f3d8..1062277c13 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_DWI2Tensor.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_DWI2Tensor.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import DWI2Tensor + def test_DWI2Tensor_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -47,6 +48,7 @@ def test_DWI2Tensor_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_DWI2Tensor_outputs(): output_map = dict(tensor=dict(), ) @@ -55,4 +57,3 @@ def test_DWI2Tensor_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/mrtrix/tests/test_auto_DiffusionTensorStreamlineTrack.py b/nipype/interfaces/mrtrix/tests/test_auto_DiffusionTensorStreamlineTrack.py index 3cb6d42bc1..42cb14de9f 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_DiffusionTensorStreamlineTrack.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_DiffusionTensorStreamlineTrack.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..tracking import DiffusionTensorStreamlineTrack + def test_DiffusionTensorStreamlineTrack_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -107,6 +108,7 @@ def test_DiffusionTensorStreamlineTrack_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_DiffusionTensorStreamlineTrack_outputs(): output_map = dict(tracked=dict(), ) @@ -115,4 +117,3 @@ def test_DiffusionTensorStreamlineTrack_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/mrtrix/tests/test_auto_Directions2Amplitude.py b/nipype/interfaces/mrtrix/tests/test_auto_Directions2Amplitude.py index 5fedacb20b..1fb1d8d764 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_Directions2Amplitude.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_Directions2Amplitude.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..tensors import Directions2Amplitude + def test_Directions2Amplitude_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -44,6 +45,7 @@ def test_Directions2Amplitude_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Directions2Amplitude_outputs(): output_map = dict(out_file=dict(), ) @@ -52,4 +54,3 @@ def test_Directions2Amplitude_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/mrtrix/tests/test_auto_Erode.py b/nipype/interfaces/mrtrix/tests/test_auto_Erode.py index 3a159ae5e6..3161e6e0fd 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_Erode.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_Erode.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import Erode + def test_Erode_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -39,6 +40,7 @@ def test_Erode_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Erode_outputs(): output_map = dict(out_file=dict(), ) @@ -47,4 +49,3 @@ def test_Erode_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/mrtrix/tests/test_auto_EstimateResponseForSH.py b/nipype/interfaces/mrtrix/tests/test_auto_EstimateResponseForSH.py index 5b595183bc..ff6a638f14 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_EstimateResponseForSH.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_EstimateResponseForSH.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..tensors import EstimateResponseForSH + def test_EstimateResponseForSH_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -44,6 +45,7 @@ def test_EstimateResponseForSH_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_EstimateResponseForSH_outputs(): output_map = dict(response=dict(), ) @@ -52,4 +54,3 @@ def test_EstimateResponseForSH_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/mrtrix/tests/test_auto_FSL2MRTrix.py b/nipype/interfaces/mrtrix/tests/test_auto_FSL2MRTrix.py index 46a63b32c8..03cc06b2ed 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_FSL2MRTrix.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_FSL2MRTrix.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..tensors import FSL2MRTrix + def test_FSL2MRTrix_inputs(): input_map = dict(bval_file=dict(mandatory=True, ), @@ -22,6 +23,7 @@ def test_FSL2MRTrix_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_FSL2MRTrix_outputs(): output_map = dict(encoding_file=dict(), ) @@ -30,4 +32,3 @@ def test_FSL2MRTrix_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/mrtrix/tests/test_auto_FilterTracks.py b/nipype/interfaces/mrtrix/tests/test_auto_FilterTracks.py index 1947787160..099d08c2de 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_FilterTracks.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_FilterTracks.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..tracking import FilterTracks + def test_FilterTracks_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -61,6 +62,7 @@ def test_FilterTracks_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_FilterTracks_outputs(): output_map = dict(out_file=dict(), ) @@ -69,4 +71,3 @@ def test_FilterTracks_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/mrtrix/tests/test_auto_FindShPeaks.py b/nipype/interfaces/mrtrix/tests/test_auto_FindShPeaks.py index 37a82e7433..d4776cb4b3 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_FindShPeaks.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_FindShPeaks.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..tensors import FindShPeaks + def test_FindShPeaks_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -50,6 +51,7 @@ def test_FindShPeaks_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_FindShPeaks_outputs(): output_map = dict(out_file=dict(), ) @@ -58,4 +60,3 @@ def test_FindShPeaks_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/mrtrix/tests/test_auto_GenerateDirections.py b/nipype/interfaces/mrtrix/tests/test_auto_GenerateDirections.py index ccd0fdf3f3..bd54f78fb3 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_GenerateDirections.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_GenerateDirections.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..tensors import GenerateDirections + def test_GenerateDirections_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -40,6 +41,7 @@ def test_GenerateDirections_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_GenerateDirections_outputs(): output_map = dict(out_file=dict(), ) @@ -48,4 +50,3 @@ def test_GenerateDirections_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/mrtrix/tests/test_auto_GenerateWhiteMatterMask.py b/nipype/interfaces/mrtrix/tests/test_auto_GenerateWhiteMatterMask.py index b4c2b7fdda..909015a608 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_GenerateWhiteMatterMask.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_GenerateWhiteMatterMask.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import GenerateWhiteMatterMask + def test_GenerateWhiteMatterMask_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -38,6 +39,7 @@ def test_GenerateWhiteMatterMask_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_GenerateWhiteMatterMask_outputs(): output_map = dict(WMprobabilitymap=dict(), ) @@ -46,4 +48,3 @@ def test_GenerateWhiteMatterMask_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/mrtrix/tests/test_auto_MRConvert.py b/nipype/interfaces/mrtrix/tests/test_auto_MRConvert.py index 87304f7e64..75cb4ff985 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_MRConvert.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_MRConvert.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import MRConvert + def test_MRConvert_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -62,6 +63,7 @@ def test_MRConvert_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MRConvert_outputs(): output_map = dict(converted=dict(), ) @@ -70,4 +72,3 @@ def test_MRConvert_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/mrtrix/tests/test_auto_MRMultiply.py b/nipype/interfaces/mrtrix/tests/test_auto_MRMultiply.py index edd6fd187e..4c76a6f96c 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_MRMultiply.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_MRMultiply.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import MRMultiply + def test_MRMultiply_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -34,6 +35,7 @@ def test_MRMultiply_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MRMultiply_outputs(): output_map = dict(out_file=dict(), ) @@ -42,4 +44,3 @@ def test_MRMultiply_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/mrtrix/tests/test_auto_MRTransform.py b/nipype/interfaces/mrtrix/tests/test_auto_MRTransform.py index 1786a3c305..0376e9b4e1 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_MRTransform.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_MRTransform.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import MRTransform + def test_MRTransform_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -52,6 +53,7 @@ def test_MRTransform_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MRTransform_outputs(): output_map = dict(out_file=dict(), ) @@ -60,4 +62,3 @@ def test_MRTransform_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/mrtrix/tests/test_auto_MRTrix2TrackVis.py b/nipype/interfaces/mrtrix/tests/test_auto_MRTrix2TrackVis.py index 57318ad01b..d7da413c92 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_MRTrix2TrackVis.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_MRTrix2TrackVis.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..convert import MRTrix2TrackVis + def test_MRTrix2TrackVis_inputs(): input_map = dict(image_file=dict(), in_file=dict(mandatory=True, @@ -18,6 +19,7 @@ def test_MRTrix2TrackVis_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MRTrix2TrackVis_outputs(): output_map = dict(out_file=dict(), ) @@ -26,4 +28,3 @@ def test_MRTrix2TrackVis_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/mrtrix/tests/test_auto_MRTrixInfo.py b/nipype/interfaces/mrtrix/tests/test_auto_MRTrixInfo.py index 321c5bac12..73671df40c 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_MRTrixInfo.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_MRTrixInfo.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import MRTrixInfo + def test_MRTrixInfo_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -24,6 +25,7 @@ def test_MRTrixInfo_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MRTrixInfo_outputs(): output_map = dict() outputs = MRTrixInfo.output_spec() @@ -31,4 +33,3 @@ def test_MRTrixInfo_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/mrtrix/tests/test_auto_MRTrixViewer.py b/nipype/interfaces/mrtrix/tests/test_auto_MRTrixViewer.py index 783dc90bcb..d0e99f2348 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_MRTrixViewer.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_MRTrixViewer.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import MRTrixViewer + def test_MRTrixViewer_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -30,6 +31,7 @@ def test_MRTrixViewer_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MRTrixViewer_outputs(): output_map = dict() outputs = MRTrixViewer.output_spec() @@ -37,4 +39,3 @@ def test_MRTrixViewer_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/mrtrix/tests/test_auto_MedianFilter3D.py b/nipype/interfaces/mrtrix/tests/test_auto_MedianFilter3D.py index 670a88c038..7010acfda5 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_MedianFilter3D.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_MedianFilter3D.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import MedianFilter3D + def test_MedianFilter3D_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -34,6 +35,7 @@ def test_MedianFilter3D_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MedianFilter3D_outputs(): output_map = dict(out_file=dict(), ) @@ -42,4 +44,3 @@ def test_MedianFilter3D_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/mrtrix/tests/test_auto_ProbabilisticSphericallyDeconvolutedStreamlineTrack.py b/nipype/interfaces/mrtrix/tests/test_auto_ProbabilisticSphericallyDeconvolutedStreamlineTrack.py index 9bb78f5ff2..dfb1b57ddc 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_ProbabilisticSphericallyDeconvolutedStreamlineTrack.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_ProbabilisticSphericallyDeconvolutedStreamlineTrack.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..tracking import ProbabilisticSphericallyDeconvolutedStreamlineTrack + def test_ProbabilisticSphericallyDeconvolutedStreamlineTrack_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -105,6 +106,7 @@ def test_ProbabilisticSphericallyDeconvolutedStreamlineTrack_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ProbabilisticSphericallyDeconvolutedStreamlineTrack_outputs(): output_map = dict(tracked=dict(), ) @@ -113,4 +115,3 @@ def test_ProbabilisticSphericallyDeconvolutedStreamlineTrack_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/mrtrix/tests/test_auto_SphericallyDeconvolutedStreamlineTrack.py b/nipype/interfaces/mrtrix/tests/test_auto_SphericallyDeconvolutedStreamlineTrack.py index 74085472c5..2180af33eb 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_SphericallyDeconvolutedStreamlineTrack.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_SphericallyDeconvolutedStreamlineTrack.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..tracking import SphericallyDeconvolutedStreamlineTrack + def test_SphericallyDeconvolutedStreamlineTrack_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -103,6 +104,7 @@ def test_SphericallyDeconvolutedStreamlineTrack_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_SphericallyDeconvolutedStreamlineTrack_outputs(): output_map = dict(tracked=dict(), ) @@ -111,4 +113,3 @@ def test_SphericallyDeconvolutedStreamlineTrack_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/mrtrix/tests/test_auto_StreamlineTrack.py b/nipype/interfaces/mrtrix/tests/test_auto_StreamlineTrack.py index 9c4e24c857..86f3607f34 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_StreamlineTrack.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_StreamlineTrack.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..tracking import StreamlineTrack + def test_StreamlineTrack_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -103,6 +104,7 @@ def test_StreamlineTrack_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_StreamlineTrack_outputs(): output_map = dict(tracked=dict(), ) @@ -111,4 +113,3 @@ def test_StreamlineTrack_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/mrtrix/tests/test_auto_Tensor2ApparentDiffusion.py b/nipype/interfaces/mrtrix/tests/test_auto_Tensor2ApparentDiffusion.py index 7c23f3234a..c7bd91a610 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_Tensor2ApparentDiffusion.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_Tensor2ApparentDiffusion.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import Tensor2ApparentDiffusion + def test_Tensor2ApparentDiffusion_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -34,6 +35,7 @@ def test_Tensor2ApparentDiffusion_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Tensor2ApparentDiffusion_outputs(): output_map = dict(ADC=dict(), ) @@ -42,4 +44,3 @@ def test_Tensor2ApparentDiffusion_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/mrtrix/tests/test_auto_Tensor2FractionalAnisotropy.py b/nipype/interfaces/mrtrix/tests/test_auto_Tensor2FractionalAnisotropy.py index 64b71e3f3c..07a9fadc2f 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_Tensor2FractionalAnisotropy.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_Tensor2FractionalAnisotropy.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import Tensor2FractionalAnisotropy + def test_Tensor2FractionalAnisotropy_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -34,6 +35,7 @@ def test_Tensor2FractionalAnisotropy_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Tensor2FractionalAnisotropy_outputs(): output_map = dict(FA=dict(), ) @@ -42,4 +44,3 @@ def test_Tensor2FractionalAnisotropy_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/mrtrix/tests/test_auto_Tensor2Vector.py b/nipype/interfaces/mrtrix/tests/test_auto_Tensor2Vector.py index 06dec919ca..cc84f35f3a 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_Tensor2Vector.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_Tensor2Vector.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import Tensor2Vector + def test_Tensor2Vector_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -34,6 +35,7 @@ def test_Tensor2Vector_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Tensor2Vector_outputs(): output_map = dict(vector=dict(), ) @@ -42,4 +44,3 @@ def test_Tensor2Vector_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/mrtrix/tests/test_auto_Threshold.py b/nipype/interfaces/mrtrix/tests/test_auto_Threshold.py index daebdfbadf..c45e38f714 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_Threshold.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_Threshold.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import Threshold + def test_Threshold_inputs(): input_map = dict(absolute_threshold_value=dict(argstr='-abs %s', ), @@ -44,6 +45,7 @@ def test_Threshold_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Threshold_outputs(): output_map = dict(out_file=dict(), ) @@ -52,4 +54,3 @@ def test_Threshold_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/mrtrix/tests/test_auto_Tracks2Prob.py b/nipype/interfaces/mrtrix/tests/test_auto_Tracks2Prob.py index 2c91ba9052..5460b7b18e 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_Tracks2Prob.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_Tracks2Prob.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..tracking import Tracks2Prob + def test_Tracks2Prob_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -48,6 +49,7 @@ def test_Tracks2Prob_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Tracks2Prob_outputs(): output_map = dict(tract_image=dict(), ) @@ -56,4 +58,3 @@ def test_Tracks2Prob_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_ACTPrepareFSL.py b/nipype/interfaces/mrtrix3/tests/test_auto_ACTPrepareFSL.py index 9661a59842..45a1a9fef0 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_ACTPrepareFSL.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_ACTPrepareFSL.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import ACTPrepareFSL + def test_ACTPrepareFSL_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -29,6 +30,7 @@ def test_ACTPrepareFSL_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ACTPrepareFSL_outputs(): output_map = dict(out_file=dict(), ) @@ -37,4 +39,3 @@ def test_ACTPrepareFSL_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_BrainMask.py b/nipype/interfaces/mrtrix3/tests/test_auto_BrainMask.py index 5e6713290d..7581fe6059 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_BrainMask.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_BrainMask.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..utils import BrainMask + def test_BrainMask_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -41,6 +42,7 @@ def test_BrainMask_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_BrainMask_outputs(): output_map = dict(out_file=dict(), ) @@ -49,4 +51,3 @@ def test_BrainMask_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_BuildConnectome.py b/nipype/interfaces/mrtrix3/tests/test_auto_BuildConnectome.py index 24dd8d2d62..e4b97f4381 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_BuildConnectome.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_BuildConnectome.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..connectivity import BuildConnectome + def test_BuildConnectome_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -53,6 +54,7 @@ def test_BuildConnectome_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_BuildConnectome_outputs(): output_map = dict(out_file=dict(), ) @@ -61,4 +63,3 @@ def test_BuildConnectome_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_ComputeTDI.py b/nipype/interfaces/mrtrix3/tests/test_auto_ComputeTDI.py index 9112ece997..ef2fec18a5 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_ComputeTDI.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_ComputeTDI.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..utils import ComputeTDI + def test_ComputeTDI_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -64,6 +65,7 @@ def test_ComputeTDI_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ComputeTDI_outputs(): output_map = dict(out_file=dict(), ) @@ -72,4 +74,3 @@ def test_ComputeTDI_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_EstimateFOD.py b/nipype/interfaces/mrtrix3/tests/test_auto_EstimateFOD.py index 142283a10f..1f8b434843 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_EstimateFOD.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_EstimateFOD.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..reconst import EstimateFOD + def test_EstimateFOD_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -62,6 +63,7 @@ def test_EstimateFOD_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_EstimateFOD_outputs(): output_map = dict(out_file=dict(), ) @@ -70,4 +72,3 @@ def test_EstimateFOD_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_FitTensor.py b/nipype/interfaces/mrtrix3/tests/test_auto_FitTensor.py index 7102d75fbf..3d926e3bd3 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_FitTensor.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_FitTensor.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..reconst import FitTensor + def test_FitTensor_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -47,6 +48,7 @@ def test_FitTensor_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_FitTensor_outputs(): output_map = dict(out_file=dict(), ) @@ -55,4 +57,3 @@ def test_FitTensor_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_Generate5tt.py b/nipype/interfaces/mrtrix3/tests/test_auto_Generate5tt.py index 417a0b487f..b06b6362ab 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_Generate5tt.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_Generate5tt.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..utils import Generate5tt + def test_Generate5tt_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -32,6 +33,7 @@ def test_Generate5tt_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Generate5tt_outputs(): output_map = dict(out_file=dict(), ) @@ -40,4 +42,3 @@ def test_Generate5tt_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_LabelConfig.py b/nipype/interfaces/mrtrix3/tests/test_auto_LabelConfig.py index 895da00071..4f57c6246d 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_LabelConfig.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_LabelConfig.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..connectivity import LabelConfig + def test_LabelConfig_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -45,6 +46,7 @@ def test_LabelConfig_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_LabelConfig_outputs(): output_map = dict(out_file=dict(), ) @@ -53,4 +55,3 @@ def test_LabelConfig_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_MRTrix3Base.py b/nipype/interfaces/mrtrix3/tests/test_auto_MRTrix3Base.py index 7a82b5f98d..c03da343e2 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_MRTrix3Base.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_MRTrix3Base.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..base import MRTrix3Base + def test_MRTrix3Base_inputs(): input_map = dict(args=dict(argstr='%s', ), diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_Mesh2PVE.py b/nipype/interfaces/mrtrix3/tests/test_auto_Mesh2PVE.py index 5c4ef045aa..781d8b2e98 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_Mesh2PVE.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_Mesh2PVE.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..utils import Mesh2PVE + def test_Mesh2PVE_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -35,6 +36,7 @@ def test_Mesh2PVE_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Mesh2PVE_outputs(): output_map = dict(out_file=dict(), ) @@ -43,4 +45,3 @@ def test_Mesh2PVE_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_ReplaceFSwithFIRST.py b/nipype/interfaces/mrtrix3/tests/test_auto_ReplaceFSwithFIRST.py index a32cc65902..cb33fda95b 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_ReplaceFSwithFIRST.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_ReplaceFSwithFIRST.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import ReplaceFSwithFIRST + def test_ReplaceFSwithFIRST_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -36,6 +37,7 @@ def test_ReplaceFSwithFIRST_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ReplaceFSwithFIRST_outputs(): output_map = dict(out_file=dict(), ) @@ -44,4 +46,3 @@ def test_ReplaceFSwithFIRST_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_ResponseSD.py b/nipype/interfaces/mrtrix3/tests/test_auto_ResponseSD.py index 628981abb3..cb78159156 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_ResponseSD.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_ResponseSD.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import ResponseSD + def test_ResponseSD_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -62,6 +63,7 @@ def test_ResponseSD_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ResponseSD_outputs(): output_map = dict(out_file=dict(), out_sf=dict(), @@ -71,4 +73,3 @@ def test_ResponseSD_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_TCK2VTK.py b/nipype/interfaces/mrtrix3/tests/test_auto_TCK2VTK.py index aa3b05036c..d80b749fee 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_TCK2VTK.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_TCK2VTK.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..utils import TCK2VTK + def test_TCK2VTK_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -35,6 +36,7 @@ def test_TCK2VTK_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_TCK2VTK_outputs(): output_map = dict(out_file=dict(), ) @@ -43,4 +45,3 @@ def test_TCK2VTK_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_TensorMetrics.py b/nipype/interfaces/mrtrix3/tests/test_auto_TensorMetrics.py index 1dd22ef0aa..6be2bccab0 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_TensorMetrics.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_TensorMetrics.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..utils import TensorMetrics + def test_TensorMetrics_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -39,6 +40,7 @@ def test_TensorMetrics_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_TensorMetrics_outputs(): output_map = dict(out_adc=dict(), out_eval=dict(), @@ -50,4 +52,3 @@ def test_TensorMetrics_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/mrtrix3/tests/test_auto_Tractography.py b/nipype/interfaces/mrtrix3/tests/test_auto_Tractography.py index 60fae0c3d7..aeaff9b599 100644 --- a/nipype/interfaces/mrtrix3/tests/test_auto_Tractography.py +++ b/nipype/interfaces/mrtrix3/tests/test_auto_Tractography.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..tracking import Tractography + def test_Tractography_inputs(): input_map = dict(act_file=dict(argstr='-act %s', ), @@ -113,6 +114,7 @@ def test_Tractography_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Tractography_outputs(): output_map = dict(out_file=dict(), out_seeds=dict(), @@ -122,4 +124,3 @@ def test_Tractography_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/nipy/tests/test_auto_ComputeMask.py b/nipype/interfaces/nipy/tests/test_auto_ComputeMask.py index 057c1d46f0..607c2b1f9d 100644 --- a/nipype/interfaces/nipy/tests/test_auto_ComputeMask.py +++ b/nipype/interfaces/nipy/tests/test_auto_ComputeMask.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import ComputeMask + def test_ComputeMask_inputs(): input_map = dict(M=dict(), cc=dict(), @@ -19,6 +20,7 @@ def test_ComputeMask_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ComputeMask_outputs(): output_map = dict(brain_mask=dict(), ) @@ -27,4 +29,3 @@ def test_ComputeMask_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/nipy/tests/test_auto_EstimateContrast.py b/nipype/interfaces/nipy/tests/test_auto_EstimateContrast.py index f2ed249b8b..61e6d42146 100644 --- a/nipype/interfaces/nipy/tests/test_auto_EstimateContrast.py +++ b/nipype/interfaces/nipy/tests/test_auto_EstimateContrast.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..model import EstimateContrast + def test_EstimateContrast_inputs(): input_map = dict(axis=dict(mandatory=True, ), @@ -30,6 +31,7 @@ def test_EstimateContrast_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_EstimateContrast_outputs(): output_map = dict(p_maps=dict(), stat_maps=dict(), @@ -40,4 +42,3 @@ def test_EstimateContrast_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/nipy/tests/test_auto_FitGLM.py b/nipype/interfaces/nipy/tests/test_auto_FitGLM.py index 7524597ecd..0f15facdb1 100644 --- a/nipype/interfaces/nipy/tests/test_auto_FitGLM.py +++ b/nipype/interfaces/nipy/tests/test_auto_FitGLM.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..model import FitGLM + def test_FitGLM_inputs(): input_map = dict(TR=dict(mandatory=True, ), @@ -32,6 +33,7 @@ def test_FitGLM_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_FitGLM_outputs(): output_map = dict(a=dict(), axis=dict(), @@ -48,4 +50,3 @@ def test_FitGLM_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/nipy/tests/test_auto_FmriRealign4d.py b/nipype/interfaces/nipy/tests/test_auto_FmriRealign4d.py index 605dfc839a..917c1bbe9c 100644 --- a/nipype/interfaces/nipy/tests/test_auto_FmriRealign4d.py +++ b/nipype/interfaces/nipy/tests/test_auto_FmriRealign4d.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import FmriRealign4d + def test_FmriRealign4d_inputs(): input_map = dict(between_loops=dict(usedefault=True, ), @@ -31,6 +32,7 @@ def test_FmriRealign4d_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_FmriRealign4d_outputs(): output_map = dict(out_file=dict(), par_file=dict(), @@ -40,4 +42,3 @@ def test_FmriRealign4d_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/nipy/tests/test_auto_Similarity.py b/nipype/interfaces/nipy/tests/test_auto_Similarity.py index 7f39019026..ef370639ce 100644 --- a/nipype/interfaces/nipy/tests/test_auto_Similarity.py +++ b/nipype/interfaces/nipy/tests/test_auto_Similarity.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..utils import Similarity + def test_Similarity_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, @@ -21,6 +22,7 @@ def test_Similarity_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Similarity_outputs(): output_map = dict(similarity=dict(), ) @@ -29,4 +31,3 @@ def test_Similarity_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/nipy/tests/test_auto_SpaceTimeRealigner.py b/nipype/interfaces/nipy/tests/test_auto_SpaceTimeRealigner.py index e04a9d1b0b..1dc0a5e6df 100644 --- a/nipype/interfaces/nipy/tests/test_auto_SpaceTimeRealigner.py +++ b/nipype/interfaces/nipy/tests/test_auto_SpaceTimeRealigner.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import SpaceTimeRealigner + def test_SpaceTimeRealigner_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, @@ -21,6 +22,7 @@ def test_SpaceTimeRealigner_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_SpaceTimeRealigner_outputs(): output_map = dict(out_file=dict(), par_file=dict(), @@ -30,4 +32,3 @@ def test_SpaceTimeRealigner_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/nipy/tests/test_auto_Trim.py b/nipype/interfaces/nipy/tests/test_auto_Trim.py index 843774e686..98c8d0dea1 100644 --- a/nipype/interfaces/nipy/tests/test_auto_Trim.py +++ b/nipype/interfaces/nipy/tests/test_auto_Trim.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import Trim + def test_Trim_inputs(): input_map = dict(begin_index=dict(usedefault=True, ), @@ -22,6 +23,7 @@ def test_Trim_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Trim_outputs(): output_map = dict(out_file=dict(), ) @@ -30,4 +32,3 @@ def test_Trim_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/nitime/tests/test_auto_CoherenceAnalyzer.py b/nipype/interfaces/nitime/tests/test_auto_CoherenceAnalyzer.py index bda6746b44..2303b647c0 100644 --- a/nipype/interfaces/nitime/tests/test_auto_CoherenceAnalyzer.py +++ b/nipype/interfaces/nitime/tests/test_auto_CoherenceAnalyzer.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..analysis import CoherenceAnalyzer + def test_CoherenceAnalyzer_inputs(): input_map = dict(NFFT=dict(usedefault=True, ), @@ -27,6 +28,7 @@ def test_CoherenceAnalyzer_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_CoherenceAnalyzer_outputs(): output_map = dict(coherence_array=dict(), coherence_csv=dict(), @@ -40,4 +42,3 @@ def test_CoherenceAnalyzer_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSPosteriorToContinuousClass.py b/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSPosteriorToContinuousClass.py index 6d989a9493..7fa7c6db0b 100644 --- a/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSPosteriorToContinuousClass.py +++ b/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSPosteriorToContinuousClass.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..classify import BRAINSPosteriorToContinuousClass + def test_BRAINSPosteriorToContinuousClass_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -37,6 +38,7 @@ def test_BRAINSPosteriorToContinuousClass_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_BRAINSPosteriorToContinuousClass_outputs(): output_map = dict(outputVolume=dict(), ) @@ -45,4 +47,3 @@ def test_BRAINSPosteriorToContinuousClass_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairach.py b/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairach.py index 53363df141..51a08d06e2 100644 --- a/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairach.py +++ b/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairach.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..segmentation import BRAINSTalairach + def test_BRAINSTalairach_inputs(): input_map = dict(AC=dict(argstr='--AC %s', sep=',', @@ -48,6 +49,7 @@ def test_BRAINSTalairach_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_BRAINSTalairach_outputs(): output_map = dict(outputBox=dict(), outputGrid=dict(), @@ -57,4 +59,3 @@ def test_BRAINSTalairach_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairachMask.py b/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairachMask.py index 6b94a9535e..e4eaa93073 100644 --- a/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairachMask.py +++ b/nipype/interfaces/semtools/brains/tests/test_auto_BRAINSTalairachMask.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..segmentation import BRAINSTalairachMask + def test_BRAINSTalairachMask_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -33,6 +34,7 @@ def test_BRAINSTalairachMask_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_BRAINSTalairachMask_outputs(): output_map = dict(outputVolume=dict(), ) @@ -41,4 +43,3 @@ def test_BRAINSTalairachMask_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/brains/tests/test_auto_HistogramMatchingFilter.py b/nipype/interfaces/semtools/brains/tests/test_auto_HistogramMatchingFilter.py index 8d360f2e58..41c4fb832f 100644 --- a/nipype/interfaces/semtools/brains/tests/test_auto_HistogramMatchingFilter.py +++ b/nipype/interfaces/semtools/brains/tests/test_auto_HistogramMatchingFilter.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..utilities import HistogramMatchingFilter + def test_HistogramMatchingFilter_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -41,6 +42,7 @@ def test_HistogramMatchingFilter_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_HistogramMatchingFilter_outputs(): output_map = dict(outputVolume=dict(), ) @@ -49,4 +51,3 @@ def test_HistogramMatchingFilter_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/brains/tests/test_auto_SimilarityIndex.py b/nipype/interfaces/semtools/brains/tests/test_auto_SimilarityIndex.py index 2b8f058872..3fbbbace73 100644 --- a/nipype/interfaces/semtools/brains/tests/test_auto_SimilarityIndex.py +++ b/nipype/interfaces/semtools/brains/tests/test_auto_SimilarityIndex.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..segmentation import SimilarityIndex + def test_SimilarityIndex_inputs(): input_map = dict(ANNContinuousVolume=dict(argstr='--ANNContinuousVolume %s', ), @@ -28,6 +29,7 @@ def test_SimilarityIndex_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_SimilarityIndex_outputs(): output_map = dict() outputs = SimilarityIndex.output_spec() @@ -35,4 +37,3 @@ def test_SimilarityIndex_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_DWIConvert.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_DWIConvert.py index 4b4d692385..15e293f3aa 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_DWIConvert.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_DWIConvert.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..diffusion import DWIConvert + def test_DWIConvert_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -57,6 +58,7 @@ def test_DWIConvert_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_DWIConvert_outputs(): output_map = dict(gradientVectorFile=dict(), outputBValues=dict(), @@ -69,4 +71,3 @@ def test_DWIConvert_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_compareTractInclusion.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_compareTractInclusion.py index 1b8a841b75..1a46be411a 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_compareTractInclusion.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_compareTractInclusion.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..gtract import compareTractInclusion + def test_compareTractInclusion_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -36,6 +37,7 @@ def test_compareTractInclusion_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_compareTractInclusion_outputs(): output_map = dict() outputs = compareTractInclusion.output_spec() @@ -43,4 +45,3 @@ def test_compareTractInclusion_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiaverage.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiaverage.py index 4306c604b8..7988994224 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiaverage.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiaverage.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..diffusion import dtiaverage + def test_dtiaverage_inputs(): input_map = dict(DTI_double=dict(argstr='--DTI_double ', ), @@ -29,6 +30,7 @@ def test_dtiaverage_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_dtiaverage_outputs(): output_map = dict(tensor_output=dict(), ) @@ -37,4 +39,3 @@ def test_dtiaverage_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiestim.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiestim.py index 220d80ba9c..1b488807b9 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiestim.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiestim.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..diffusion import dtiestim + def test_dtiestim_inputs(): input_map = dict(B0=dict(argstr='--B0 %s', hash_files=False, @@ -61,6 +62,7 @@ def test_dtiestim_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_dtiestim_outputs(): output_map = dict(B0=dict(), B0_mask_output=dict(), @@ -72,4 +74,3 @@ def test_dtiestim_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiprocess.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiprocess.py index 7d77c6d799..94bd061f75 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiprocess.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_dtiprocess.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..diffusion import dtiprocess + def test_dtiprocess_inputs(): input_map = dict(DTI_double=dict(argstr='--DTI_double ', ), @@ -93,6 +94,7 @@ def test_dtiprocess_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_dtiprocess_outputs(): output_map = dict(RD_output=dict(), color_fa_output=dict(), @@ -115,4 +117,3 @@ def test_dtiprocess_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_extractNrrdVectorIndex.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_extractNrrdVectorIndex.py index 081858b122..79400fea82 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_extractNrrdVectorIndex.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_extractNrrdVectorIndex.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..gtract import extractNrrdVectorIndex + def test_extractNrrdVectorIndex_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -31,6 +32,7 @@ def test_extractNrrdVectorIndex_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_extractNrrdVectorIndex_outputs(): output_map = dict(outputVolume=dict(), ) @@ -39,4 +41,3 @@ def test_extractNrrdVectorIndex_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAnisotropyMap.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAnisotropyMap.py index 779a9f4155..eccf216089 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAnisotropyMap.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAnisotropyMap.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..gtract import gtractAnisotropyMap + def test_gtractAnisotropyMap_inputs(): input_map = dict(anisotropyType=dict(argstr='--anisotropyType %s', ), @@ -29,6 +30,7 @@ def test_gtractAnisotropyMap_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_gtractAnisotropyMap_outputs(): output_map = dict(outputVolume=dict(), ) @@ -37,4 +39,3 @@ def test_gtractAnisotropyMap_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAverageBvalues.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAverageBvalues.py index 25dfb3e1f7..3c00c388cf 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAverageBvalues.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractAverageBvalues.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..gtract import gtractAverageBvalues + def test_gtractAverageBvalues_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -31,6 +32,7 @@ def test_gtractAverageBvalues_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_gtractAverageBvalues_outputs(): output_map = dict(outputVolume=dict(), ) @@ -39,4 +41,3 @@ def test_gtractAverageBvalues_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractClipAnisotropy.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractClipAnisotropy.py index 66827b5129..95970529ef 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractClipAnisotropy.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractClipAnisotropy.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..gtract import gtractClipAnisotropy + def test_gtractClipAnisotropy_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -31,6 +32,7 @@ def test_gtractClipAnisotropy_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_gtractClipAnisotropy_outputs(): output_map = dict(outputVolume=dict(), ) @@ -39,4 +41,3 @@ def test_gtractClipAnisotropy_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoRegAnatomy.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoRegAnatomy.py index b08543b760..60ce5e72a4 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoRegAnatomy.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoRegAnatomy.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..gtract import gtractCoRegAnatomy + def test_gtractCoRegAnatomy_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -70,6 +71,7 @@ def test_gtractCoRegAnatomy_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_gtractCoRegAnatomy_outputs(): output_map = dict(outputTransformName=dict(), ) @@ -78,4 +80,3 @@ def test_gtractCoRegAnatomy_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractConcatDwi.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractConcatDwi.py index a553336672..0cfe65e61d 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractConcatDwi.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractConcatDwi.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..gtract import gtractConcatDwi + def test_gtractConcatDwi_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -29,6 +30,7 @@ def test_gtractConcatDwi_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_gtractConcatDwi_outputs(): output_map = dict(outputVolume=dict(), ) @@ -37,4 +39,3 @@ def test_gtractConcatDwi_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCopyImageOrientation.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCopyImageOrientation.py index ef8dacf00f..e16d80814d 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCopyImageOrientation.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCopyImageOrientation.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..gtract import gtractCopyImageOrientation + def test_gtractCopyImageOrientation_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -29,6 +30,7 @@ def test_gtractCopyImageOrientation_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_gtractCopyImageOrientation_outputs(): output_map = dict(outputVolume=dict(), ) @@ -37,4 +39,3 @@ def test_gtractCopyImageOrientation_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoregBvalues.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoregBvalues.py index c210e61cbd..c6b69bc116 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoregBvalues.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCoregBvalues.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..gtract import gtractCoregBvalues + def test_gtractCoregBvalues_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -54,6 +55,7 @@ def test_gtractCoregBvalues_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_gtractCoregBvalues_outputs(): output_map = dict(outputTransform=dict(), outputVolume=dict(), @@ -63,4 +65,3 @@ def test_gtractCoregBvalues_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCostFastMarching.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCostFastMarching.py index 7faf8558f3..84b91e79dc 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCostFastMarching.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCostFastMarching.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..gtract import gtractCostFastMarching + def test_gtractCostFastMarching_inputs(): input_map = dict(anisotropyWeight=dict(argstr='--anisotropyWeight %f', ), @@ -42,6 +43,7 @@ def test_gtractCostFastMarching_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_gtractCostFastMarching_outputs(): output_map = dict(outputCostVolume=dict(), outputSpeedVolume=dict(), @@ -51,4 +53,3 @@ def test_gtractCostFastMarching_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCreateGuideFiber.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCreateGuideFiber.py index 1ff8663d6c..ed4c3a7891 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCreateGuideFiber.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractCreateGuideFiber.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..gtract import gtractCreateGuideFiber + def test_gtractCreateGuideFiber_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -31,6 +32,7 @@ def test_gtractCreateGuideFiber_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_gtractCreateGuideFiber_outputs(): output_map = dict(outputFiber=dict(), ) @@ -39,4 +41,3 @@ def test_gtractCreateGuideFiber_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFastMarchingTracking.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFastMarchingTracking.py index d7ab24874b..80b431b91d 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFastMarchingTracking.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFastMarchingTracking.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..gtract import gtractFastMarchingTracking + def test_gtractFastMarchingTracking_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -49,6 +50,7 @@ def test_gtractFastMarchingTracking_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_gtractFastMarchingTracking_outputs(): output_map = dict(outputTract=dict(), ) @@ -57,4 +59,3 @@ def test_gtractFastMarchingTracking_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFiberTracking.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFiberTracking.py index a634895777..e9aa021e41 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFiberTracking.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractFiberTracking.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..gtract import gtractFiberTracking + def test_gtractFiberTracking_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -77,6 +78,7 @@ def test_gtractFiberTracking_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_gtractFiberTracking_outputs(): output_map = dict(outputTract=dict(), ) @@ -85,4 +87,3 @@ def test_gtractFiberTracking_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractImageConformity.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractImageConformity.py index 1f555d1afd..f14f17359a 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractImageConformity.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractImageConformity.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..gtract import gtractImageConformity + def test_gtractImageConformity_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -29,6 +30,7 @@ def test_gtractImageConformity_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_gtractImageConformity_outputs(): output_map = dict(outputVolume=dict(), ) @@ -37,4 +39,3 @@ def test_gtractImageConformity_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertBSplineTransform.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertBSplineTransform.py index 84a5b8c6d0..476a05e6ec 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertBSplineTransform.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertBSplineTransform.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..gtract import gtractInvertBSplineTransform + def test_gtractInvertBSplineTransform_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -32,6 +33,7 @@ def test_gtractInvertBSplineTransform_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_gtractInvertBSplineTransform_outputs(): output_map = dict(outputTransform=dict(), ) @@ -40,4 +42,3 @@ def test_gtractInvertBSplineTransform_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertDisplacementField.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertDisplacementField.py index d1cf84126c..db5b1e8b7a 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertDisplacementField.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertDisplacementField.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..gtract import gtractInvertDisplacementField + def test_gtractInvertDisplacementField_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -31,6 +32,7 @@ def test_gtractInvertDisplacementField_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_gtractInvertDisplacementField_outputs(): output_map = dict(outputVolume=dict(), ) @@ -39,4 +41,3 @@ def test_gtractInvertDisplacementField_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertRigidTransform.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertRigidTransform.py index c76a097da9..4286c0769e 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertRigidTransform.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractInvertRigidTransform.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..gtract import gtractInvertRigidTransform + def test_gtractInvertRigidTransform_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -27,6 +28,7 @@ def test_gtractInvertRigidTransform_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_gtractInvertRigidTransform_outputs(): output_map = dict(outputTransform=dict(), ) @@ -35,4 +37,3 @@ def test_gtractInvertRigidTransform_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleAnisotropy.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleAnisotropy.py index a373d9802b..1887a216b9 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleAnisotropy.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleAnisotropy.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..gtract import gtractResampleAnisotropy + def test_gtractResampleAnisotropy_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -33,6 +34,7 @@ def test_gtractResampleAnisotropy_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_gtractResampleAnisotropy_outputs(): output_map = dict(outputVolume=dict(), ) @@ -41,4 +43,3 @@ def test_gtractResampleAnisotropy_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleB0.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleB0.py index 1eaf64701f..1623574a96 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleB0.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleB0.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..gtract import gtractResampleB0 + def test_gtractResampleB0_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -35,6 +36,7 @@ def test_gtractResampleB0_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_gtractResampleB0_outputs(): output_map = dict(outputVolume=dict(), ) @@ -43,4 +45,3 @@ def test_gtractResampleB0_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleCodeImage.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleCodeImage.py index e66f094f90..78fc493bb0 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleCodeImage.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleCodeImage.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..gtract import gtractResampleCodeImage + def test_gtractResampleCodeImage_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -33,6 +34,7 @@ def test_gtractResampleCodeImage_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_gtractResampleCodeImage_outputs(): output_map = dict(outputVolume=dict(), ) @@ -41,4 +43,3 @@ def test_gtractResampleCodeImage_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleDWIInPlace.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleDWIInPlace.py index 3e1d5011e1..da647cf1f0 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleDWIInPlace.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleDWIInPlace.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..gtract import gtractResampleDWIInPlace + def test_gtractResampleDWIInPlace_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -41,6 +42,7 @@ def test_gtractResampleDWIInPlace_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_gtractResampleDWIInPlace_outputs(): output_map = dict(outputResampledB0=dict(), outputVolume=dict(), @@ -50,4 +52,3 @@ def test_gtractResampleDWIInPlace_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleFibers.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleFibers.py index 483d52d89c..f8954b20fb 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleFibers.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractResampleFibers.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..gtract import gtractResampleFibers + def test_gtractResampleFibers_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -33,6 +34,7 @@ def test_gtractResampleFibers_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_gtractResampleFibers_outputs(): output_map = dict(outputTract=dict(), ) @@ -41,4 +43,3 @@ def test_gtractResampleFibers_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTensor.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTensor.py index 890b1dc9af..9b35d8ffd5 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTensor.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTensor.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..gtract import gtractTensor + def test_gtractTensor_inputs(): input_map = dict(applyMeasurementFrame=dict(argstr='--applyMeasurementFrame ', ), @@ -47,6 +48,7 @@ def test_gtractTensor_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_gtractTensor_outputs(): output_map = dict(outputVolume=dict(), ) @@ -55,4 +57,3 @@ def test_gtractTensor_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTransformToDisplacementField.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTransformToDisplacementField.py index 75f4671bdc..1e74ff01ee 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTransformToDisplacementField.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_gtractTransformToDisplacementField.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..gtract import gtractTransformToDisplacementField + def test_gtractTransformToDisplacementField_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -29,6 +30,7 @@ def test_gtractTransformToDisplacementField_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_gtractTransformToDisplacementField_outputs(): output_map = dict(outputDeformationFieldVolume=dict(), ) @@ -37,4 +39,3 @@ def test_gtractTransformToDisplacementField_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/diffusion/tests/test_auto_maxcurvature.py b/nipype/interfaces/semtools/diffusion/tests/test_auto_maxcurvature.py index 84f476b1a7..12958f9a32 100644 --- a/nipype/interfaces/semtools/diffusion/tests/test_auto_maxcurvature.py +++ b/nipype/interfaces/semtools/diffusion/tests/test_auto_maxcurvature.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..maxcurvature import maxcurvature + def test_maxcurvature_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -29,6 +30,7 @@ def test_maxcurvature_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_maxcurvature_outputs(): output_map = dict(output=dict(), ) @@ -37,4 +39,3 @@ def test_maxcurvature_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_UKFTractography.py b/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_UKFTractography.py index 98c9a05add..5550a1e903 100644 --- a/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_UKFTractography.py +++ b/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_UKFTractography.py @@ -2,6 +2,7 @@ from ......testing import assert_equal from ..ukftractography import UKFTractography + def test_UKFTractography_inputs(): input_map = dict(Ql=dict(argstr='--Ql %f', ), @@ -89,6 +90,7 @@ def test_UKFTractography_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_UKFTractography_outputs(): output_map = dict(tracts=dict(), tractsWithSecondTensor=dict(), @@ -98,4 +100,3 @@ def test_UKFTractography_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fiberprocess.py b/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fiberprocess.py index a1ba70176c..b607a189d7 100644 --- a/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fiberprocess.py +++ b/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fiberprocess.py @@ -2,6 +2,7 @@ from ......testing import assert_equal from ..fiberprocess import fiberprocess + def test_fiberprocess_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -50,6 +51,7 @@ def test_fiberprocess_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_fiberprocess_outputs(): output_map = dict(fiber_output=dict(), voxelize=dict(), @@ -59,4 +61,3 @@ def test_fiberprocess_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fiberstats.py b/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fiberstats.py index f2c5af669d..8521e59239 100644 --- a/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fiberstats.py +++ b/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fiberstats.py @@ -2,6 +2,7 @@ from ......testing import assert_equal from ..commandlineonly import fiberstats + def test_fiberstats_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -24,6 +25,7 @@ def test_fiberstats_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_fiberstats_outputs(): output_map = dict() outputs = fiberstats.output_spec() @@ -31,4 +33,3 @@ def test_fiberstats_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fibertrack.py b/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fibertrack.py index a903b0fa7d..d12c437f1c 100644 --- a/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fibertrack.py +++ b/nipype/interfaces/semtools/diffusion/tractography/tests/test_auto_fibertrack.py @@ -2,6 +2,7 @@ from ......testing import assert_equal from ..fibertrack import fibertrack + def test_fibertrack_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -47,6 +48,7 @@ def test_fibertrack_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_fibertrack_outputs(): output_map = dict(output_fiber_file=dict(), ) @@ -55,4 +57,3 @@ def test_fibertrack_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_CannyEdge.py b/nipype/interfaces/semtools/filtering/tests/test_auto_CannyEdge.py index 49f6caeaa7..f09e7e139a 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_CannyEdge.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_CannyEdge.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..featuredetection import CannyEdge + def test_CannyEdge_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -31,6 +32,7 @@ def test_CannyEdge_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_CannyEdge_outputs(): output_map = dict(outputVolume=dict(), ) @@ -39,4 +41,3 @@ def test_CannyEdge_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_CannySegmentationLevelSetImageFilter.py b/nipype/interfaces/semtools/filtering/tests/test_auto_CannySegmentationLevelSetImageFilter.py index d8d4af7c35..5dd69484aa 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_CannySegmentationLevelSetImageFilter.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_CannySegmentationLevelSetImageFilter.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..featuredetection import CannySegmentationLevelSetImageFilter + def test_CannySegmentationLevelSetImageFilter_inputs(): input_map = dict(advectionWeight=dict(argstr='--advectionWeight %f', ), @@ -40,6 +41,7 @@ def test_CannySegmentationLevelSetImageFilter_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_CannySegmentationLevelSetImageFilter_outputs(): output_map = dict(outputSpeedVolume=dict(), outputVolume=dict(), @@ -49,4 +51,3 @@ def test_CannySegmentationLevelSetImageFilter_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_DilateImage.py b/nipype/interfaces/semtools/filtering/tests/test_auto_DilateImage.py index f419053ea4..353924d80f 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_DilateImage.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_DilateImage.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..featuredetection import DilateImage + def test_DilateImage_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -29,6 +30,7 @@ def test_DilateImage_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_DilateImage_outputs(): output_map = dict(outputVolume=dict(), ) @@ -37,4 +39,3 @@ def test_DilateImage_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_DilateMask.py b/nipype/interfaces/semtools/filtering/tests/test_auto_DilateMask.py index 40e1e30a33..91fb032420 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_DilateMask.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_DilateMask.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..featuredetection import DilateMask + def test_DilateMask_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -31,6 +32,7 @@ def test_DilateMask_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_DilateMask_outputs(): output_map = dict(outputVolume=dict(), ) @@ -39,4 +41,3 @@ def test_DilateMask_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_DistanceMaps.py b/nipype/interfaces/semtools/filtering/tests/test_auto_DistanceMaps.py index 866b57d539..6e43ad16ee 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_DistanceMaps.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_DistanceMaps.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..featuredetection import DistanceMaps + def test_DistanceMaps_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -29,6 +30,7 @@ def test_DistanceMaps_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_DistanceMaps_outputs(): output_map = dict(outputVolume=dict(), ) @@ -37,4 +39,3 @@ def test_DistanceMaps_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_DumpBinaryTrainingVectors.py b/nipype/interfaces/semtools/filtering/tests/test_auto_DumpBinaryTrainingVectors.py index a00278d312..b588e4bcf6 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_DumpBinaryTrainingVectors.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_DumpBinaryTrainingVectors.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..featuredetection import DumpBinaryTrainingVectors + def test_DumpBinaryTrainingVectors_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -24,6 +25,7 @@ def test_DumpBinaryTrainingVectors_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_DumpBinaryTrainingVectors_outputs(): output_map = dict() outputs = DumpBinaryTrainingVectors.output_spec() @@ -31,4 +33,3 @@ def test_DumpBinaryTrainingVectors_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_ErodeImage.py b/nipype/interfaces/semtools/filtering/tests/test_auto_ErodeImage.py index f041f1857e..81c8429e13 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_ErodeImage.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_ErodeImage.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..featuredetection import ErodeImage + def test_ErodeImage_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -29,6 +30,7 @@ def test_ErodeImage_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ErodeImage_outputs(): output_map = dict(outputVolume=dict(), ) @@ -37,4 +39,3 @@ def test_ErodeImage_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_FlippedDifference.py b/nipype/interfaces/semtools/filtering/tests/test_auto_FlippedDifference.py index bde8e2d405..3c86f288fa 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_FlippedDifference.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_FlippedDifference.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..featuredetection import FlippedDifference + def test_FlippedDifference_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -27,6 +28,7 @@ def test_FlippedDifference_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_FlippedDifference_outputs(): output_map = dict(outputVolume=dict(), ) @@ -35,4 +37,3 @@ def test_FlippedDifference_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateBrainClippedImage.py b/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateBrainClippedImage.py index b85e616ff8..c605f8deea 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateBrainClippedImage.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateBrainClippedImage.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..featuredetection import GenerateBrainClippedImage + def test_GenerateBrainClippedImage_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -29,6 +30,7 @@ def test_GenerateBrainClippedImage_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_GenerateBrainClippedImage_outputs(): output_map = dict(outputFileName=dict(), ) @@ -37,4 +39,3 @@ def test_GenerateBrainClippedImage_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateSummedGradientImage.py b/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateSummedGradientImage.py index 5873f1e8a7..fe720a4850 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateSummedGradientImage.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateSummedGradientImage.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..featuredetection import GenerateSummedGradientImage + def test_GenerateSummedGradientImage_inputs(): input_map = dict(MaximumGradient=dict(argstr='--MaximumGradient ', ), @@ -31,6 +32,7 @@ def test_GenerateSummedGradientImage_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_GenerateSummedGradientImage_outputs(): output_map = dict(outputFileName=dict(), ) @@ -39,4 +41,3 @@ def test_GenerateSummedGradientImage_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateTestImage.py b/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateTestImage.py index cd786d6097..869788f527 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateTestImage.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_GenerateTestImage.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..featuredetection import GenerateTestImage + def test_GenerateTestImage_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -31,6 +32,7 @@ def test_GenerateTestImage_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_GenerateTestImage_outputs(): output_map = dict(outputVolume=dict(), ) @@ -39,4 +41,3 @@ def test_GenerateTestImage_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_GradientAnisotropicDiffusionImageFilter.py b/nipype/interfaces/semtools/filtering/tests/test_auto_GradientAnisotropicDiffusionImageFilter.py index cf0f3ccca1..d31e178ccb 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_GradientAnisotropicDiffusionImageFilter.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_GradientAnisotropicDiffusionImageFilter.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..featuredetection import GradientAnisotropicDiffusionImageFilter + def test_GradientAnisotropicDiffusionImageFilter_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -31,6 +32,7 @@ def test_GradientAnisotropicDiffusionImageFilter_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_GradientAnisotropicDiffusionImageFilter_outputs(): output_map = dict(outputVolume=dict(), ) @@ -39,4 +41,3 @@ def test_GradientAnisotropicDiffusionImageFilter_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_HammerAttributeCreator.py b/nipype/interfaces/semtools/filtering/tests/test_auto_HammerAttributeCreator.py index 4c8813a1c4..2d7cfa38a8 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_HammerAttributeCreator.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_HammerAttributeCreator.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..featuredetection import HammerAttributeCreator + def test_HammerAttributeCreator_inputs(): input_map = dict(Scale=dict(argstr='--Scale %d', ), @@ -32,6 +33,7 @@ def test_HammerAttributeCreator_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_HammerAttributeCreator_outputs(): output_map = dict() outputs = HammerAttributeCreator.output_spec() @@ -39,4 +41,3 @@ def test_HammerAttributeCreator_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMean.py b/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMean.py index 5d9cfae916..82b34513f5 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMean.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMean.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..featuredetection import NeighborhoodMean + def test_NeighborhoodMean_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -29,6 +30,7 @@ def test_NeighborhoodMean_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_NeighborhoodMean_outputs(): output_map = dict(outputVolume=dict(), ) @@ -37,4 +39,3 @@ def test_NeighborhoodMean_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMedian.py b/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMedian.py index 1f59a35b07..3c22450067 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMedian.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_NeighborhoodMedian.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..featuredetection import NeighborhoodMedian + def test_NeighborhoodMedian_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -29,6 +30,7 @@ def test_NeighborhoodMedian_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_NeighborhoodMedian_outputs(): output_map = dict(outputVolume=dict(), ) @@ -37,4 +39,3 @@ def test_NeighborhoodMedian_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_STAPLEAnalysis.py b/nipype/interfaces/semtools/filtering/tests/test_auto_STAPLEAnalysis.py index 2cc852cefe..410cfc40b7 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_STAPLEAnalysis.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_STAPLEAnalysis.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..featuredetection import STAPLEAnalysis + def test_STAPLEAnalysis_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -27,6 +28,7 @@ def test_STAPLEAnalysis_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_STAPLEAnalysis_outputs(): output_map = dict(outputVolume=dict(), ) @@ -35,4 +37,3 @@ def test_STAPLEAnalysis_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_TextureFromNoiseImageFilter.py b/nipype/interfaces/semtools/filtering/tests/test_auto_TextureFromNoiseImageFilter.py index 1c29c32681..2b20435355 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_TextureFromNoiseImageFilter.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_TextureFromNoiseImageFilter.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..featuredetection import TextureFromNoiseImageFilter + def test_TextureFromNoiseImageFilter_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -27,6 +28,7 @@ def test_TextureFromNoiseImageFilter_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_TextureFromNoiseImageFilter_outputs(): output_map = dict(outputVolume=dict(), ) @@ -35,4 +37,3 @@ def test_TextureFromNoiseImageFilter_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_TextureMeasureFilter.py b/nipype/interfaces/semtools/filtering/tests/test_auto_TextureMeasureFilter.py index 74f3adfe9f..77c1f8220d 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_TextureMeasureFilter.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_TextureMeasureFilter.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..featuredetection import TextureMeasureFilter + def test_TextureMeasureFilter_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -31,6 +32,7 @@ def test_TextureMeasureFilter_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_TextureMeasureFilter_outputs(): output_map = dict(outputFilename=dict(), ) @@ -39,4 +41,3 @@ def test_TextureMeasureFilter_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/filtering/tests/test_auto_UnbiasedNonLocalMeans.py b/nipype/interfaces/semtools/filtering/tests/test_auto_UnbiasedNonLocalMeans.py index 9d1ec355c4..9d4de6b37b 100644 --- a/nipype/interfaces/semtools/filtering/tests/test_auto_UnbiasedNonLocalMeans.py +++ b/nipype/interfaces/semtools/filtering/tests/test_auto_UnbiasedNonLocalMeans.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..denoising import UnbiasedNonLocalMeans + def test_UnbiasedNonLocalMeans_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -39,6 +40,7 @@ def test_UnbiasedNonLocalMeans_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_UnbiasedNonLocalMeans_outputs(): output_map = dict(outputVolume=dict(position=-1, ), @@ -48,4 +50,3 @@ def test_UnbiasedNonLocalMeans_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/legacy/tests/test_auto_scalartransform.py b/nipype/interfaces/semtools/legacy/tests/test_auto_scalartransform.py index 1d49041ea6..5885b351e0 100644 --- a/nipype/interfaces/semtools/legacy/tests/test_auto_scalartransform.py +++ b/nipype/interfaces/semtools/legacy/tests/test_auto_scalartransform.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..registration import scalartransform + def test_scalartransform_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -36,6 +37,7 @@ def test_scalartransform_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_scalartransform_outputs(): output_map = dict(output_image=dict(), transformation=dict(), @@ -45,4 +47,3 @@ def test_scalartransform_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSDemonWarp.py b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSDemonWarp.py index 6bb0b716cc..fa3caa8d79 100644 --- a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSDemonWarp.py +++ b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSDemonWarp.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..specialized import BRAINSDemonWarp + def test_BRAINSDemonWarp_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -110,6 +111,7 @@ def test_BRAINSDemonWarp_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_BRAINSDemonWarp_outputs(): output_map = dict(outputCheckerboardVolume=dict(), outputDisplacementFieldVolume=dict(), @@ -120,4 +122,3 @@ def test_BRAINSDemonWarp_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSFit.py b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSFit.py index 8a3c229d99..feb165f1e2 100644 --- a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSFit.py +++ b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSFit.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..brainsfit import BRAINSFit + def test_BRAINSFit_inputs(): input_map = dict(ROIAutoClosingSize=dict(argstr='--ROIAutoClosingSize %f', ), @@ -163,6 +164,7 @@ def test_BRAINSFit_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_BRAINSFit_outputs(): output_map = dict(bsplineTransform=dict(), linearTransform=dict(), @@ -178,4 +180,3 @@ def test_BRAINSFit_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResample.py b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResample.py index 9dd1c3c00a..e6d8c39ae8 100644 --- a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResample.py +++ b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResample.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..brainsresample import BRAINSResample + def test_BRAINSResample_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -44,6 +45,7 @@ def test_BRAINSResample_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_BRAINSResample_outputs(): output_map = dict(outputVolume=dict(), ) @@ -52,4 +54,3 @@ def test_BRAINSResample_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResize.py b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResize.py index e1180bd075..8ea205c2c6 100644 --- a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResize.py +++ b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSResize.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..brainsresize import BRAINSResize + def test_BRAINSResize_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -29,6 +30,7 @@ def test_BRAINSResize_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_BRAINSResize_outputs(): output_map = dict(outputVolume=dict(), ) @@ -37,4 +39,3 @@ def test_BRAINSResize_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSTransformFromFiducials.py b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSTransformFromFiducials.py index 69abf621d3..f7e228e28d 100644 --- a/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSTransformFromFiducials.py +++ b/nipype/interfaces/semtools/registration/tests/test_auto_BRAINSTransformFromFiducials.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..specialized import BRAINSTransformFromFiducials + def test_BRAINSTransformFromFiducials_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -35,6 +36,7 @@ def test_BRAINSTransformFromFiducials_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_BRAINSTransformFromFiducials_outputs(): output_map = dict(saveTransform=dict(), ) @@ -43,4 +45,3 @@ def test_BRAINSTransformFromFiducials_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/registration/tests/test_auto_VBRAINSDemonWarp.py b/nipype/interfaces/semtools/registration/tests/test_auto_VBRAINSDemonWarp.py index b0445a4380..50df05872a 100644 --- a/nipype/interfaces/semtools/registration/tests/test_auto_VBRAINSDemonWarp.py +++ b/nipype/interfaces/semtools/registration/tests/test_auto_VBRAINSDemonWarp.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..specialized import VBRAINSDemonWarp + def test_VBRAINSDemonWarp_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -113,6 +114,7 @@ def test_VBRAINSDemonWarp_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_VBRAINSDemonWarp_outputs(): output_map = dict(outputCheckerboardVolume=dict(), outputDisplacementFieldVolume=dict(), @@ -123,4 +125,3 @@ def test_VBRAINSDemonWarp_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSABC.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSABC.py index 30d070119d..2d0ea9442f 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSABC.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSABC.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..specialized import BRAINSABC + def test_BRAINSABC_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -91,6 +92,7 @@ def test_BRAINSABC_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_BRAINSABC_outputs(): output_map = dict(atlasToSubjectInitialTransform=dict(), atlasToSubjectTransform=dict(), @@ -106,4 +108,3 @@ def test_BRAINSABC_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSConstellationDetector.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSConstellationDetector.py index 208f6ceba9..39556f42d0 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSConstellationDetector.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSConstellationDetector.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..specialized import BRAINSConstellationDetector + def test_BRAINSConstellationDetector_inputs(): input_map = dict(BackgroundFillValue=dict(argstr='--BackgroundFillValue %s', ), @@ -115,6 +116,7 @@ def test_BRAINSConstellationDetector_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_BRAINSConstellationDetector_outputs(): output_map = dict(outputLandmarksInACPCAlignedSpace=dict(), outputLandmarksInInputSpace=dict(), @@ -132,4 +134,3 @@ def test_BRAINSConstellationDetector_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCreateLabelMapFromProbabilityMaps.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCreateLabelMapFromProbabilityMaps.py index d583f7458c..88ce476209 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCreateLabelMapFromProbabilityMaps.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCreateLabelMapFromProbabilityMaps.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..specialized import BRAINSCreateLabelMapFromProbabilityMaps + def test_BRAINSCreateLabelMapFromProbabilityMaps_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -38,6 +39,7 @@ def test_BRAINSCreateLabelMapFromProbabilityMaps_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_BRAINSCreateLabelMapFromProbabilityMaps_outputs(): output_map = dict(cleanLabelVolume=dict(), dirtyLabelVolume=dict(), @@ -47,4 +49,3 @@ def test_BRAINSCreateLabelMapFromProbabilityMaps_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCut.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCut.py index ce6273d108..7efdf9a1cc 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCut.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSCut.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..specialized import BRAINSCut + def test_BRAINSCut_inputs(): input_map = dict(NoTrainingVectorShuffling=dict(argstr='--NoTrainingVectorShuffling ', ), @@ -54,6 +55,7 @@ def test_BRAINSCut_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_BRAINSCut_outputs(): output_map = dict() outputs = BRAINSCut.output_spec() @@ -61,4 +63,3 @@ def test_BRAINSCut_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSMultiSTAPLE.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSMultiSTAPLE.py index ad12b7a00d..86daa0bb17 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSMultiSTAPLE.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSMultiSTAPLE.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..specialized import BRAINSMultiSTAPLE + def test_BRAINSMultiSTAPLE_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -38,6 +39,7 @@ def test_BRAINSMultiSTAPLE_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_BRAINSMultiSTAPLE_outputs(): output_map = dict(outputConfusionMatrix=dict(), outputMultiSTAPLE=dict(), @@ -47,4 +49,3 @@ def test_BRAINSMultiSTAPLE_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSROIAuto.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSROIAuto.py index 10b4df6a6a..eaffbf7909 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSROIAuto.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_BRAINSROIAuto.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..specialized import BRAINSROIAuto + def test_BRAINSROIAuto_inputs(): input_map = dict(ROIAutoDilateSize=dict(argstr='--ROIAutoDilateSize %f', ), @@ -44,6 +45,7 @@ def test_BRAINSROIAuto_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_BRAINSROIAuto_outputs(): output_map = dict(outputROIMaskVolume=dict(), outputVolume=dict(), @@ -53,4 +55,3 @@ def test_BRAINSROIAuto_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_BinaryMaskEditorBasedOnLandmarks.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_BinaryMaskEditorBasedOnLandmarks.py index d6dcaee899..85ae45ffa7 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_BinaryMaskEditorBasedOnLandmarks.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_BinaryMaskEditorBasedOnLandmarks.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..specialized import BinaryMaskEditorBasedOnLandmarks + def test_BinaryMaskEditorBasedOnLandmarks_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -39,6 +40,7 @@ def test_BinaryMaskEditorBasedOnLandmarks_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_BinaryMaskEditorBasedOnLandmarks_outputs(): output_map = dict(outputBinaryVolume=dict(), ) @@ -47,4 +49,3 @@ def test_BinaryMaskEditorBasedOnLandmarks_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/segmentation/tests/test_auto_ESLR.py b/nipype/interfaces/semtools/segmentation/tests/test_auto_ESLR.py index 8903cb7a29..943e609b99 100644 --- a/nipype/interfaces/semtools/segmentation/tests/test_auto_ESLR.py +++ b/nipype/interfaces/semtools/segmentation/tests/test_auto_ESLR.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..specialized import ESLR + def test_ESLR_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -39,6 +40,7 @@ def test_ESLR_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ESLR_outputs(): output_map = dict(outputVolume=dict(), ) @@ -47,4 +49,3 @@ def test_ESLR_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/tests/test_auto_DWICompare.py b/nipype/interfaces/semtools/tests/test_auto_DWICompare.py index 107767e57e..264ebfbd86 100644 --- a/nipype/interfaces/semtools/tests/test_auto_DWICompare.py +++ b/nipype/interfaces/semtools/tests/test_auto_DWICompare.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..converters import DWICompare + def test_DWICompare_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -24,6 +25,7 @@ def test_DWICompare_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_DWICompare_outputs(): output_map = dict() outputs = DWICompare.output_spec() @@ -31,4 +33,3 @@ def test_DWICompare_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/tests/test_auto_DWISimpleCompare.py b/nipype/interfaces/semtools/tests/test_auto_DWISimpleCompare.py index 6160e9f642..017abf83af 100644 --- a/nipype/interfaces/semtools/tests/test_auto_DWISimpleCompare.py +++ b/nipype/interfaces/semtools/tests/test_auto_DWISimpleCompare.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..converters import DWISimpleCompare + def test_DWISimpleCompare_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -26,6 +27,7 @@ def test_DWISimpleCompare_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_DWISimpleCompare_outputs(): output_map = dict() outputs = DWISimpleCompare.output_spec() @@ -33,4 +35,3 @@ def test_DWISimpleCompare_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/tests/test_auto_GenerateCsfClippedFromClassifiedImage.py b/nipype/interfaces/semtools/tests/test_auto_GenerateCsfClippedFromClassifiedImage.py index 48a7310d00..ccb2e8abd6 100644 --- a/nipype/interfaces/semtools/tests/test_auto_GenerateCsfClippedFromClassifiedImage.py +++ b/nipype/interfaces/semtools/tests/test_auto_GenerateCsfClippedFromClassifiedImage.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..featurecreator import GenerateCsfClippedFromClassifiedImage + def test_GenerateCsfClippedFromClassifiedImage_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -25,6 +26,7 @@ def test_GenerateCsfClippedFromClassifiedImage_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_GenerateCsfClippedFromClassifiedImage_outputs(): output_map = dict(outputVolume=dict(), ) @@ -33,4 +35,3 @@ def test_GenerateCsfClippedFromClassifiedImage_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSAlignMSP.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSAlignMSP.py index 2d04886661..98837c75a7 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSAlignMSP.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSAlignMSP.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..brains import BRAINSAlignMSP + def test_BRAINSAlignMSP_inputs(): input_map = dict(BackgroundFillValue=dict(argstr='--BackgroundFillValue %s', ), @@ -47,6 +48,7 @@ def test_BRAINSAlignMSP_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_BRAINSAlignMSP_outputs(): output_map = dict(OutputresampleMSP=dict(), resultsDir=dict(), @@ -56,4 +58,3 @@ def test_BRAINSAlignMSP_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSClipInferior.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSClipInferior.py index 9952b24563..f7636c95d1 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSClipInferior.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSClipInferior.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..brains import BRAINSClipInferior + def test_BRAINSClipInferior_inputs(): input_map = dict(BackgroundFillValue=dict(argstr='--BackgroundFillValue %s', ), @@ -31,6 +32,7 @@ def test_BRAINSClipInferior_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_BRAINSClipInferior_outputs(): output_map = dict(outputVolume=dict(), ) @@ -39,4 +41,3 @@ def test_BRAINSClipInferior_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSConstellationModeler.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSConstellationModeler.py index f18173e992..ee8b7bb018 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSConstellationModeler.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSConstellationModeler.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..brains import BRAINSConstellationModeler + def test_BRAINSConstellationModeler_inputs(): input_map = dict(BackgroundFillValue=dict(argstr='--BackgroundFillValue %s', ), @@ -49,6 +50,7 @@ def test_BRAINSConstellationModeler_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_BRAINSConstellationModeler_outputs(): output_map = dict(outputModel=dict(), resultsDir=dict(), @@ -58,4 +60,3 @@ def test_BRAINSConstellationModeler_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSEyeDetector.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSEyeDetector.py index 83a26253c6..20072ed902 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSEyeDetector.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSEyeDetector.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..brains import BRAINSEyeDetector + def test_BRAINSEyeDetector_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -29,6 +30,7 @@ def test_BRAINSEyeDetector_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_BRAINSEyeDetector_outputs(): output_map = dict(outputVolume=dict(), ) @@ -37,4 +39,3 @@ def test_BRAINSEyeDetector_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSInitializedControlPoints.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSInitializedControlPoints.py index 70672b58a6..fb5d164f9b 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSInitializedControlPoints.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSInitializedControlPoints.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..brains import BRAINSInitializedControlPoints + def test_BRAINSInitializedControlPoints_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -35,6 +36,7 @@ def test_BRAINSInitializedControlPoints_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_BRAINSInitializedControlPoints_outputs(): output_map = dict(outputVolume=dict(), ) @@ -43,4 +45,3 @@ def test_BRAINSInitializedControlPoints_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLandmarkInitializer.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLandmarkInitializer.py index e006d86724..def6a40242 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLandmarkInitializer.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLandmarkInitializer.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..brains import BRAINSLandmarkInitializer + def test_BRAINSLandmarkInitializer_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -29,6 +30,7 @@ def test_BRAINSLandmarkInitializer_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_BRAINSLandmarkInitializer_outputs(): output_map = dict(outputTransformFilename=dict(), ) @@ -37,4 +39,3 @@ def test_BRAINSLandmarkInitializer_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLinearModelerEPCA.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLinearModelerEPCA.py index 8738c68876..f15061c8b4 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLinearModelerEPCA.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLinearModelerEPCA.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..brains import BRAINSLinearModelerEPCA + def test_BRAINSLinearModelerEPCA_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -24,6 +25,7 @@ def test_BRAINSLinearModelerEPCA_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_BRAINSLinearModelerEPCA_outputs(): output_map = dict() outputs = BRAINSLinearModelerEPCA.output_spec() @@ -31,4 +33,3 @@ def test_BRAINSLinearModelerEPCA_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLmkTransform.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLmkTransform.py index 71643b90d3..7bda89c361 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLmkTransform.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSLmkTransform.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..brains import BRAINSLmkTransform + def test_BRAINSLmkTransform_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -36,6 +37,7 @@ def test_BRAINSLmkTransform_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_BRAINSLmkTransform_outputs(): output_map = dict(outputAffineTransform=dict(), outputResampledVolume=dict(), @@ -45,4 +47,3 @@ def test_BRAINSLmkTransform_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSMush.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSMush.py index 1137807abc..4a351563d1 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSMush.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSMush.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..brains import BRAINSMush + def test_BRAINSMush_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -58,6 +59,7 @@ def test_BRAINSMush_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_BRAINSMush_outputs(): output_map = dict(outputMask=dict(), outputVolume=dict(), @@ -68,4 +70,3 @@ def test_BRAINSMush_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSSnapShotWriter.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSSnapShotWriter.py index c3dc623af4..5ebceb6933 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSSnapShotWriter.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSSnapShotWriter.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..brains import BRAINSSnapShotWriter + def test_BRAINSSnapShotWriter_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -39,6 +40,7 @@ def test_BRAINSSnapShotWriter_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_BRAINSSnapShotWriter_outputs(): output_map = dict(outputFilename=dict(), ) @@ -47,4 +49,3 @@ def test_BRAINSSnapShotWriter_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTransformConvert.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTransformConvert.py index 262c752e4b..dd909677cc 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTransformConvert.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTransformConvert.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..brains import BRAINSTransformConvert + def test_BRAINSTransformConvert_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -34,6 +35,7 @@ def test_BRAINSTransformConvert_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_BRAINSTransformConvert_outputs(): output_map = dict(displacementVolume=dict(), outputTransform=dict(), @@ -43,4 +45,3 @@ def test_BRAINSTransformConvert_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTrimForegroundInDirection.py b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTrimForegroundInDirection.py index e9da3f550d..a63835efc8 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTrimForegroundInDirection.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_BRAINSTrimForegroundInDirection.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..brains import BRAINSTrimForegroundInDirection + def test_BRAINSTrimForegroundInDirection_inputs(): input_map = dict(BackgroundFillValue=dict(argstr='--BackgroundFillValue %s', ), @@ -37,6 +38,7 @@ def test_BRAINSTrimForegroundInDirection_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_BRAINSTrimForegroundInDirection_outputs(): output_map = dict(outputVolume=dict(), ) @@ -45,4 +47,3 @@ def test_BRAINSTrimForegroundInDirection_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_CleanUpOverlapLabels.py b/nipype/interfaces/semtools/utilities/tests/test_auto_CleanUpOverlapLabels.py index d946909659..16e64f7910 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_CleanUpOverlapLabels.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_CleanUpOverlapLabels.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..brains import CleanUpOverlapLabels + def test_CleanUpOverlapLabels_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -25,6 +26,7 @@ def test_CleanUpOverlapLabels_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_CleanUpOverlapLabels_outputs(): output_map = dict(outputBinaryVolumes=dict(), ) @@ -33,4 +35,3 @@ def test_CleanUpOverlapLabels_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_FindCenterOfBrain.py b/nipype/interfaces/semtools/utilities/tests/test_auto_FindCenterOfBrain.py index 4000b9b184..51cd6c5b70 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_FindCenterOfBrain.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_FindCenterOfBrain.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..brains import FindCenterOfBrain + def test_FindCenterOfBrain_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -58,6 +59,7 @@ def test_FindCenterOfBrain_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_FindCenterOfBrain_outputs(): output_map = dict(clippedImageMask=dict(), debugAfterGridComputationsForegroundImage=dict(), @@ -71,4 +73,3 @@ def test_FindCenterOfBrain_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_GenerateLabelMapFromProbabilityMap.py b/nipype/interfaces/semtools/utilities/tests/test_auto_GenerateLabelMapFromProbabilityMap.py index 92fe22f2aa..28d2675275 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_GenerateLabelMapFromProbabilityMap.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_GenerateLabelMapFromProbabilityMap.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..brains import GenerateLabelMapFromProbabilityMap + def test_GenerateLabelMapFromProbabilityMap_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -27,6 +28,7 @@ def test_GenerateLabelMapFromProbabilityMap_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_GenerateLabelMapFromProbabilityMap_outputs(): output_map = dict(outputLabelVolume=dict(), ) @@ -35,4 +37,3 @@ def test_GenerateLabelMapFromProbabilityMap_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_ImageRegionPlotter.py b/nipype/interfaces/semtools/utilities/tests/test_auto_ImageRegionPlotter.py index 290476cc71..6c7f5215f8 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_ImageRegionPlotter.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_ImageRegionPlotter.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..brains import ImageRegionPlotter + def test_ImageRegionPlotter_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -38,6 +39,7 @@ def test_ImageRegionPlotter_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ImageRegionPlotter_outputs(): output_map = dict() outputs = ImageRegionPlotter.output_spec() @@ -45,4 +47,3 @@ def test_ImageRegionPlotter_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_JointHistogram.py b/nipype/interfaces/semtools/utilities/tests/test_auto_JointHistogram.py index f78ebbb4ec..5f1ddedcb8 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_JointHistogram.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_JointHistogram.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..brains import JointHistogram + def test_JointHistogram_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -32,6 +33,7 @@ def test_JointHistogram_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_JointHistogram_outputs(): output_map = dict() outputs = JointHistogram.output_spec() @@ -39,4 +41,3 @@ def test_JointHistogram_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_ShuffleVectorsModule.py b/nipype/interfaces/semtools/utilities/tests/test_auto_ShuffleVectorsModule.py index 9fce96a5e1..8d84a541b8 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_ShuffleVectorsModule.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_ShuffleVectorsModule.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..brains import ShuffleVectorsModule + def test_ShuffleVectorsModule_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -27,6 +28,7 @@ def test_ShuffleVectorsModule_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ShuffleVectorsModule_outputs(): output_map = dict(outputVectorFileBaseName=dict(), ) @@ -35,4 +37,3 @@ def test_ShuffleVectorsModule_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_fcsv_to_hdf5.py b/nipype/interfaces/semtools/utilities/tests/test_auto_fcsv_to_hdf5.py index 274ed3460d..9bee62f991 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_fcsv_to_hdf5.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_fcsv_to_hdf5.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..brains import fcsv_to_hdf5 + def test_fcsv_to_hdf5_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -34,6 +35,7 @@ def test_fcsv_to_hdf5_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_fcsv_to_hdf5_outputs(): output_map = dict(landmarksInformationFile=dict(), modelFile=dict(), @@ -43,4 +45,3 @@ def test_fcsv_to_hdf5_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_insertMidACPCpoint.py b/nipype/interfaces/semtools/utilities/tests/test_auto_insertMidACPCpoint.py index 27be5441f5..8803f8263b 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_insertMidACPCpoint.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_insertMidACPCpoint.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..brains import insertMidACPCpoint + def test_insertMidACPCpoint_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -25,6 +26,7 @@ def test_insertMidACPCpoint_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_insertMidACPCpoint_outputs(): output_map = dict(outputLandmarkFile=dict(), ) @@ -33,4 +35,3 @@ def test_insertMidACPCpoint_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationAligner.py b/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationAligner.py index c8246f482c..d5b97d17b2 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationAligner.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationAligner.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..brains import landmarksConstellationAligner + def test_landmarksConstellationAligner_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -25,6 +26,7 @@ def test_landmarksConstellationAligner_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_landmarksConstellationAligner_outputs(): output_map = dict(outputLandmarksPaired=dict(), ) @@ -33,4 +35,3 @@ def test_landmarksConstellationAligner_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationWeights.py b/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationWeights.py index e4db760aab..154d17665d 100644 --- a/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationWeights.py +++ b/nipype/interfaces/semtools/utilities/tests/test_auto_landmarksConstellationWeights.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..brains import landmarksConstellationWeights + def test_landmarksConstellationWeights_inputs(): input_map = dict(LLSModel=dict(argstr='--LLSModel %s', ), @@ -29,6 +30,7 @@ def test_landmarksConstellationWeights_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_landmarksConstellationWeights_outputs(): output_map = dict(outputWeightsList=dict(), ) @@ -37,4 +39,3 @@ def test_landmarksConstellationWeights_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIexport.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIexport.py index 31635cae6c..1704c064f6 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIexport.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIexport.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..diffusion import DTIexport + def test_DTIexport_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -27,6 +28,7 @@ def test_DTIexport_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_DTIexport_outputs(): output_map = dict(outputFile=dict(position=-1, ), @@ -36,4 +38,3 @@ def test_DTIexport_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIimport.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIimport.py index 5b5fd34acc..dab8788688 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIimport.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIimport.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..diffusion import DTIimport + def test_DTIimport_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -29,6 +30,7 @@ def test_DTIimport_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_DTIimport_outputs(): output_map = dict(outputTensor=dict(position=-1, ), @@ -38,4 +40,3 @@ def test_DTIimport_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIJointRicianLMMSEFilter.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIJointRicianLMMSEFilter.py index c37d94420e..a5215c65b5 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIJointRicianLMMSEFilter.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIJointRicianLMMSEFilter.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..diffusion import DWIJointRicianLMMSEFilter + def test_DWIJointRicianLMMSEFilter_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -37,6 +38,7 @@ def test_DWIJointRicianLMMSEFilter_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_DWIJointRicianLMMSEFilter_outputs(): output_map = dict(outputVolume=dict(position=-1, ), @@ -46,4 +48,3 @@ def test_DWIJointRicianLMMSEFilter_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIRicianLMMSEFilter.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIRicianLMMSEFilter.py index a608997e0c..da2e1d4d07 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIRicianLMMSEFilter.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIRicianLMMSEFilter.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..diffusion import DWIRicianLMMSEFilter + def test_DWIRicianLMMSEFilter_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -49,6 +50,7 @@ def test_DWIRicianLMMSEFilter_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_DWIRicianLMMSEFilter_outputs(): output_map = dict(outputVolume=dict(position=-1, ), @@ -58,4 +60,3 @@ def test_DWIRicianLMMSEFilter_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIToDTIEstimation.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIToDTIEstimation.py index ce150df698..be0f92c092 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIToDTIEstimation.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIToDTIEstimation.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..diffusion import DWIToDTIEstimation + def test_DWIToDTIEstimation_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -37,6 +38,7 @@ def test_DWIToDTIEstimation_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_DWIToDTIEstimation_outputs(): output_map = dict(outputBaseline=dict(position=-1, ), @@ -48,4 +50,3 @@ def test_DWIToDTIEstimation_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionTensorScalarMeasurements.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionTensorScalarMeasurements.py index c7598a94ee..425800bd41 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionTensorScalarMeasurements.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionTensorScalarMeasurements.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..diffusion import DiffusionTensorScalarMeasurements + def test_DiffusionTensorScalarMeasurements_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -29,6 +30,7 @@ def test_DiffusionTensorScalarMeasurements_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_DiffusionTensorScalarMeasurements_outputs(): output_map = dict(outputScalar=dict(position=-1, ), @@ -38,4 +40,3 @@ def test_DiffusionTensorScalarMeasurements_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionWeightedVolumeMasking.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionWeightedVolumeMasking.py index b6f8e07d8a..d325afaf71 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionWeightedVolumeMasking.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionWeightedVolumeMasking.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..diffusion import DiffusionWeightedVolumeMasking + def test_DiffusionWeightedVolumeMasking_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -35,6 +36,7 @@ def test_DiffusionWeightedVolumeMasking_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_DiffusionWeightedVolumeMasking_outputs(): output_map = dict(outputBaseline=dict(position=-2, ), @@ -46,4 +48,3 @@ def test_DiffusionWeightedVolumeMasking_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_ResampleDTIVolume.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_ResampleDTIVolume.py index 976409cd75..9f7ded5f1c 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_ResampleDTIVolume.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_ResampleDTIVolume.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..diffusion import ResampleDTIVolume + def test_ResampleDTIVolume_inputs(): input_map = dict(Inverse_ITK_Transformation=dict(argstr='--Inverse_ITK_Transformation ', ), @@ -79,6 +80,7 @@ def test_ResampleDTIVolume_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ResampleDTIVolume_outputs(): output_map = dict(outputVolume=dict(position=-1, ), @@ -88,4 +90,3 @@ def test_ResampleDTIVolume_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_TractographyLabelMapSeeding.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_TractographyLabelMapSeeding.py index b9ec5ec713..f368cc2275 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_TractographyLabelMapSeeding.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_TractographyLabelMapSeeding.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..diffusion import TractographyLabelMapSeeding + def test_TractographyLabelMapSeeding_inputs(): input_map = dict(InputVolume=dict(argstr='%s', position=-2, @@ -58,6 +59,7 @@ def test_TractographyLabelMapSeeding_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_TractographyLabelMapSeeding_outputs(): output_map = dict(OutputFibers=dict(position=-1, ), @@ -68,4 +70,3 @@ def test_TractographyLabelMapSeeding_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_AddScalarVolumes.py b/nipype/interfaces/slicer/filtering/tests/test_auto_AddScalarVolumes.py index b251028a8f..1b196c557a 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_AddScalarVolumes.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_AddScalarVolumes.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..arithmetic import AddScalarVolumes + def test_AddScalarVolumes_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -32,6 +33,7 @@ def test_AddScalarVolumes_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_AddScalarVolumes_outputs(): output_map = dict(outputVolume=dict(position=-1, ), @@ -41,4 +43,3 @@ def test_AddScalarVolumes_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_CastScalarVolume.py b/nipype/interfaces/slicer/filtering/tests/test_auto_CastScalarVolume.py index e3785f9724..b24be436f8 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_CastScalarVolume.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_CastScalarVolume.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..arithmetic import CastScalarVolume + def test_CastScalarVolume_inputs(): input_map = dict(InputVolume=dict(argstr='%s', position=-2, @@ -29,6 +30,7 @@ def test_CastScalarVolume_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_CastScalarVolume_outputs(): output_map = dict(OutputVolume=dict(position=-1, ), @@ -38,4 +40,3 @@ def test_CastScalarVolume_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_CheckerBoardFilter.py b/nipype/interfaces/slicer/filtering/tests/test_auto_CheckerBoardFilter.py index 4852564e6d..2ddf46c861 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_CheckerBoardFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_CheckerBoardFilter.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..checkerboardfilter import CheckerBoardFilter + def test_CheckerBoardFilter_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -33,6 +34,7 @@ def test_CheckerBoardFilter_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_CheckerBoardFilter_outputs(): output_map = dict(outputVolume=dict(position=-1, ), @@ -42,4 +44,3 @@ def test_CheckerBoardFilter_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_CurvatureAnisotropicDiffusion.py b/nipype/interfaces/slicer/filtering/tests/test_auto_CurvatureAnisotropicDiffusion.py index d0e36b88cd..c31af700d5 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_CurvatureAnisotropicDiffusion.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_CurvatureAnisotropicDiffusion.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..denoising import CurvatureAnisotropicDiffusion + def test_CurvatureAnisotropicDiffusion_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -33,6 +34,7 @@ def test_CurvatureAnisotropicDiffusion_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_CurvatureAnisotropicDiffusion_outputs(): output_map = dict(outputVolume=dict(position=-1, ), @@ -42,4 +44,3 @@ def test_CurvatureAnisotropicDiffusion_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_ExtractSkeleton.py b/nipype/interfaces/slicer/filtering/tests/test_auto_ExtractSkeleton.py index 453bea8ff9..05b71f76ec 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_ExtractSkeleton.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_ExtractSkeleton.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..extractskeleton import ExtractSkeleton + def test_ExtractSkeleton_inputs(): input_map = dict(InputImageFileName=dict(argstr='%s', position=-2, @@ -35,6 +36,7 @@ def test_ExtractSkeleton_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ExtractSkeleton_outputs(): output_map = dict(OutputImageFileName=dict(position=-1, ), @@ -44,4 +46,3 @@ def test_ExtractSkeleton_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_GaussianBlurImageFilter.py b/nipype/interfaces/slicer/filtering/tests/test_auto_GaussianBlurImageFilter.py index efdfea9eea..d5b2d21589 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_GaussianBlurImageFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_GaussianBlurImageFilter.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..denoising import GaussianBlurImageFilter + def test_GaussianBlurImageFilter_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -29,6 +30,7 @@ def test_GaussianBlurImageFilter_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_GaussianBlurImageFilter_outputs(): output_map = dict(outputVolume=dict(position=-1, ), @@ -38,4 +40,3 @@ def test_GaussianBlurImageFilter_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_GradientAnisotropicDiffusion.py b/nipype/interfaces/slicer/filtering/tests/test_auto_GradientAnisotropicDiffusion.py index 58b51833ee..c5874901c8 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_GradientAnisotropicDiffusion.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_GradientAnisotropicDiffusion.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..denoising import GradientAnisotropicDiffusion + def test_GradientAnisotropicDiffusion_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -33,6 +34,7 @@ def test_GradientAnisotropicDiffusion_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_GradientAnisotropicDiffusion_outputs(): output_map = dict(outputVolume=dict(position=-1, ), @@ -42,4 +44,3 @@ def test_GradientAnisotropicDiffusion_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleFillHoleImageFilter.py b/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleFillHoleImageFilter.py index 81bf49025e..794f2833ee 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleFillHoleImageFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleFillHoleImageFilter.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..morphology import GrayscaleFillHoleImageFilter + def test_GrayscaleFillHoleImageFilter_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -27,6 +28,7 @@ def test_GrayscaleFillHoleImageFilter_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_GrayscaleFillHoleImageFilter_outputs(): output_map = dict(outputVolume=dict(position=-1, ), @@ -36,4 +38,3 @@ def test_GrayscaleFillHoleImageFilter_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleGrindPeakImageFilter.py b/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleGrindPeakImageFilter.py index 6b940e03f3..3bcfd4145c 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleGrindPeakImageFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleGrindPeakImageFilter.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..morphology import GrayscaleGrindPeakImageFilter + def test_GrayscaleGrindPeakImageFilter_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -27,6 +28,7 @@ def test_GrayscaleGrindPeakImageFilter_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_GrayscaleGrindPeakImageFilter_outputs(): output_map = dict(outputVolume=dict(position=-1, ), @@ -36,4 +38,3 @@ def test_GrayscaleGrindPeakImageFilter_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_HistogramMatching.py b/nipype/interfaces/slicer/filtering/tests/test_auto_HistogramMatching.py index bdf83e33e0..2d4e23c33e 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_HistogramMatching.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_HistogramMatching.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..histogrammatching import HistogramMatching + def test_HistogramMatching_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -36,6 +37,7 @@ def test_HistogramMatching_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_HistogramMatching_outputs(): output_map = dict(outputVolume=dict(position=-1, ), @@ -45,4 +47,3 @@ def test_HistogramMatching_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_ImageLabelCombine.py b/nipype/interfaces/slicer/filtering/tests/test_auto_ImageLabelCombine.py index 1841c77696..a02b922e86 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_ImageLabelCombine.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_ImageLabelCombine.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..imagelabelcombine import ImageLabelCombine + def test_ImageLabelCombine_inputs(): input_map = dict(InputLabelMap_A=dict(argstr='%s', position=-3, @@ -32,6 +33,7 @@ def test_ImageLabelCombine_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ImageLabelCombine_outputs(): output_map = dict(OutputLabelMap=dict(position=-1, ), @@ -41,4 +43,3 @@ def test_ImageLabelCombine_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_MaskScalarVolume.py b/nipype/interfaces/slicer/filtering/tests/test_auto_MaskScalarVolume.py index abbd67bf79..a627bae20e 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_MaskScalarVolume.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_MaskScalarVolume.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..arithmetic import MaskScalarVolume + def test_MaskScalarVolume_inputs(): input_map = dict(InputVolume=dict(argstr='%s', position=-3, @@ -34,6 +35,7 @@ def test_MaskScalarVolume_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MaskScalarVolume_outputs(): output_map = dict(OutputVolume=dict(position=-1, ), @@ -43,4 +45,3 @@ def test_MaskScalarVolume_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_MedianImageFilter.py b/nipype/interfaces/slicer/filtering/tests/test_auto_MedianImageFilter.py index feb020d09b..d8f3489fcd 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_MedianImageFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_MedianImageFilter.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..denoising import MedianImageFilter + def test_MedianImageFilter_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -30,6 +31,7 @@ def test_MedianImageFilter_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MedianImageFilter_outputs(): output_map = dict(outputVolume=dict(position=-1, ), @@ -39,4 +41,3 @@ def test_MedianImageFilter_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_MultiplyScalarVolumes.py b/nipype/interfaces/slicer/filtering/tests/test_auto_MultiplyScalarVolumes.py index 619af34f5e..d1038d8001 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_MultiplyScalarVolumes.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_MultiplyScalarVolumes.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..arithmetic import MultiplyScalarVolumes + def test_MultiplyScalarVolumes_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -32,6 +33,7 @@ def test_MultiplyScalarVolumes_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MultiplyScalarVolumes_outputs(): output_map = dict(outputVolume=dict(position=-1, ), @@ -41,4 +43,3 @@ def test_MultiplyScalarVolumes_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_N4ITKBiasFieldCorrection.py b/nipype/interfaces/slicer/filtering/tests/test_auto_N4ITKBiasFieldCorrection.py index fe815b8c4e..9e1b7df801 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_N4ITKBiasFieldCorrection.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_N4ITKBiasFieldCorrection.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..n4itkbiasfieldcorrection import N4ITKBiasFieldCorrection + def test_N4ITKBiasFieldCorrection_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -49,6 +50,7 @@ def test_N4ITKBiasFieldCorrection_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_N4ITKBiasFieldCorrection_outputs(): output_map = dict(outputbiasfield=dict(), outputimage=dict(), @@ -58,4 +60,3 @@ def test_N4ITKBiasFieldCorrection_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_ResampleScalarVectorDWIVolume.py b/nipype/interfaces/slicer/filtering/tests/test_auto_ResampleScalarVectorDWIVolume.py index b8fe840c58..363dfe4747 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_ResampleScalarVectorDWIVolume.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_ResampleScalarVectorDWIVolume.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..resamplescalarvectordwivolume import ResampleScalarVectorDWIVolume + def test_ResampleScalarVectorDWIVolume_inputs(): input_map = dict(Inverse_ITK_Transformation=dict(argstr='--Inverse_ITK_Transformation ', ), @@ -75,6 +76,7 @@ def test_ResampleScalarVectorDWIVolume_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ResampleScalarVectorDWIVolume_outputs(): output_map = dict(outputVolume=dict(position=-1, ), @@ -84,4 +86,3 @@ def test_ResampleScalarVectorDWIVolume_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_SubtractScalarVolumes.py b/nipype/interfaces/slicer/filtering/tests/test_auto_SubtractScalarVolumes.py index 74d7d15497..c95b4de042 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_SubtractScalarVolumes.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_SubtractScalarVolumes.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..arithmetic import SubtractScalarVolumes + def test_SubtractScalarVolumes_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -32,6 +33,7 @@ def test_SubtractScalarVolumes_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_SubtractScalarVolumes_outputs(): output_map = dict(outputVolume=dict(position=-1, ), @@ -41,4 +43,3 @@ def test_SubtractScalarVolumes_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_ThresholdScalarVolume.py b/nipype/interfaces/slicer/filtering/tests/test_auto_ThresholdScalarVolume.py index fcbd6ceb2d..a4f6d0f64a 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_ThresholdScalarVolume.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_ThresholdScalarVolume.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..thresholdscalarvolume import ThresholdScalarVolume + def test_ThresholdScalarVolume_inputs(): input_map = dict(InputVolume=dict(argstr='%s', position=-2, @@ -37,6 +38,7 @@ def test_ThresholdScalarVolume_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ThresholdScalarVolume_outputs(): output_map = dict(OutputVolume=dict(position=-1, ), @@ -46,4 +48,3 @@ def test_ThresholdScalarVolume_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_VotingBinaryHoleFillingImageFilter.py b/nipype/interfaces/slicer/filtering/tests/test_auto_VotingBinaryHoleFillingImageFilter.py index 314873e5e3..5c213925e0 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_VotingBinaryHoleFillingImageFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_VotingBinaryHoleFillingImageFilter.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..votingbinaryholefillingimagefilter import VotingBinaryHoleFillingImageFilter + def test_VotingBinaryHoleFillingImageFilter_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -36,6 +37,7 @@ def test_VotingBinaryHoleFillingImageFilter_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_VotingBinaryHoleFillingImageFilter_outputs(): output_map = dict(outputVolume=dict(position=-1, ), @@ -45,4 +47,3 @@ def test_VotingBinaryHoleFillingImageFilter_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/slicer/legacy/diffusion/tests/test_auto_DWIUnbiasedNonLocalMeansFilter.py b/nipype/interfaces/slicer/legacy/diffusion/tests/test_auto_DWIUnbiasedNonLocalMeansFilter.py index 331399e3f2..3f9c41c416 100644 --- a/nipype/interfaces/slicer/legacy/diffusion/tests/test_auto_DWIUnbiasedNonLocalMeansFilter.py +++ b/nipype/interfaces/slicer/legacy/diffusion/tests/test_auto_DWIUnbiasedNonLocalMeansFilter.py @@ -2,6 +2,7 @@ from ......testing import assert_equal from ..denoising import DWIUnbiasedNonLocalMeansFilter + def test_DWIUnbiasedNonLocalMeansFilter_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -40,6 +41,7 @@ def test_DWIUnbiasedNonLocalMeansFilter_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_DWIUnbiasedNonLocalMeansFilter_outputs(): output_map = dict(outputVolume=dict(position=-1, ), @@ -49,4 +51,3 @@ def test_DWIUnbiasedNonLocalMeansFilter_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_AffineRegistration.py b/nipype/interfaces/slicer/legacy/tests/test_auto_AffineRegistration.py index 89be9520be..bb46ea5f58 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_AffineRegistration.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_AffineRegistration.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..registration import AffineRegistration + def test_AffineRegistration_inputs(): input_map = dict(FixedImageFileName=dict(argstr='%s', position=-2, @@ -46,6 +47,7 @@ def test_AffineRegistration_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_AffineRegistration_outputs(): output_map = dict(outputtransform=dict(), resampledmovingfilename=dict(), @@ -55,4 +57,3 @@ def test_AffineRegistration_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineDeformableRegistration.py b/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineDeformableRegistration.py index 9210e0238c..761a605c75 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineDeformableRegistration.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineDeformableRegistration.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..registration import BSplineDeformableRegistration + def test_BSplineDeformableRegistration_inputs(): input_map = dict(FixedImageFileName=dict(argstr='%s', position=-2, @@ -51,6 +52,7 @@ def test_BSplineDeformableRegistration_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_BSplineDeformableRegistration_outputs(): output_map = dict(outputtransform=dict(), outputwarp=dict(), @@ -61,4 +63,3 @@ def test_BSplineDeformableRegistration_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineToDeformationField.py b/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineToDeformationField.py index d955a87e03..84173d2341 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineToDeformationField.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineToDeformationField.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..converters import BSplineToDeformationField + def test_BSplineToDeformationField_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -27,6 +28,7 @@ def test_BSplineToDeformationField_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_BSplineToDeformationField_outputs(): output_map = dict(defImage=dict(), ) @@ -35,4 +37,3 @@ def test_BSplineToDeformationField_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_ExpertAutomatedRegistration.py b/nipype/interfaces/slicer/legacy/tests/test_auto_ExpertAutomatedRegistration.py index 194c9889ae..e0e4c5d7eb 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_ExpertAutomatedRegistration.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_ExpertAutomatedRegistration.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..registration import ExpertAutomatedRegistration + def test_ExpertAutomatedRegistration_inputs(): input_map = dict(affineMaxIterations=dict(argstr='--affineMaxIterations %d', ), @@ -80,6 +81,7 @@ def test_ExpertAutomatedRegistration_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ExpertAutomatedRegistration_outputs(): output_map = dict(resampledImage=dict(), saveTransform=dict(), @@ -89,4 +91,3 @@ def test_ExpertAutomatedRegistration_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_LinearRegistration.py b/nipype/interfaces/slicer/legacy/tests/test_auto_LinearRegistration.py index 4a305cf83f..2945019abe 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_LinearRegistration.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_LinearRegistration.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..registration import LinearRegistration + def test_LinearRegistration_inputs(): input_map = dict(FixedImageFileName=dict(argstr='%s', position=-2, @@ -50,6 +51,7 @@ def test_LinearRegistration_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_LinearRegistration_outputs(): output_map = dict(outputtransform=dict(), resampledmovingfilename=dict(), @@ -59,4 +61,3 @@ def test_LinearRegistration_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_MultiResolutionAffineRegistration.py b/nipype/interfaces/slicer/legacy/tests/test_auto_MultiResolutionAffineRegistration.py index ad5d7a1c6d..b8ea765938 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_MultiResolutionAffineRegistration.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_MultiResolutionAffineRegistration.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..registration import MultiResolutionAffineRegistration + def test_MultiResolutionAffineRegistration_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -46,6 +47,7 @@ def test_MultiResolutionAffineRegistration_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MultiResolutionAffineRegistration_outputs(): output_map = dict(resampledImage=dict(), saveTransform=dict(), @@ -55,4 +57,3 @@ def test_MultiResolutionAffineRegistration_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdImageFilter.py b/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdImageFilter.py index 35be781ab1..0f4c9e3050 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdImageFilter.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdImageFilter.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..filtering import OtsuThresholdImageFilter + def test_OtsuThresholdImageFilter_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -33,6 +34,7 @@ def test_OtsuThresholdImageFilter_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_OtsuThresholdImageFilter_outputs(): output_map = dict(outputVolume=dict(position=-1, ), @@ -42,4 +44,3 @@ def test_OtsuThresholdImageFilter_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdSegmentation.py b/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdSegmentation.py index 98a54e95c9..29f00b8e5f 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdSegmentation.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdSegmentation.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..segmentation import OtsuThresholdSegmentation + def test_OtsuThresholdSegmentation_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -35,6 +36,7 @@ def test_OtsuThresholdSegmentation_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_OtsuThresholdSegmentation_outputs(): output_map = dict(outputVolume=dict(position=-1, ), @@ -44,4 +46,3 @@ def test_OtsuThresholdSegmentation_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_ResampleScalarVolume.py b/nipype/interfaces/slicer/legacy/tests/test_auto_ResampleScalarVolume.py index ccaaed954d..617ea6a3df 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_ResampleScalarVolume.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_ResampleScalarVolume.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..filtering import ResampleScalarVolume + def test_ResampleScalarVolume_inputs(): input_map = dict(InputVolume=dict(argstr='%s', position=-2, @@ -32,6 +33,7 @@ def test_ResampleScalarVolume_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ResampleScalarVolume_outputs(): output_map = dict(OutputVolume=dict(position=-1, ), @@ -41,4 +43,3 @@ def test_ResampleScalarVolume_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_RigidRegistration.py b/nipype/interfaces/slicer/legacy/tests/test_auto_RigidRegistration.py index 17a3e41a43..a721fd9401 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_RigidRegistration.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_RigidRegistration.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..registration import RigidRegistration + def test_RigidRegistration_inputs(): input_map = dict(FixedImageFileName=dict(argstr='%s', position=-2, @@ -52,6 +53,7 @@ def test_RigidRegistration_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_RigidRegistration_outputs(): output_map = dict(outputtransform=dict(), resampledmovingfilename=dict(), @@ -61,4 +63,3 @@ def test_RigidRegistration_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/slicer/quantification/tests/test_auto_IntensityDifferenceMetric.py b/nipype/interfaces/slicer/quantification/tests/test_auto_IntensityDifferenceMetric.py index a0211daff0..bcc651a10c 100644 --- a/nipype/interfaces/slicer/quantification/tests/test_auto_IntensityDifferenceMetric.py +++ b/nipype/interfaces/slicer/quantification/tests/test_auto_IntensityDifferenceMetric.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..changequantification import IntensityDifferenceMetric + def test_IntensityDifferenceMetric_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -40,6 +41,7 @@ def test_IntensityDifferenceMetric_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_IntensityDifferenceMetric_outputs(): output_map = dict(outputVolume=dict(position=-1, ), @@ -50,4 +52,3 @@ def test_IntensityDifferenceMetric_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/slicer/quantification/tests/test_auto_PETStandardUptakeValueComputation.py b/nipype/interfaces/slicer/quantification/tests/test_auto_PETStandardUptakeValueComputation.py index 75f63d3e47..9794302982 100644 --- a/nipype/interfaces/slicer/quantification/tests/test_auto_PETStandardUptakeValueComputation.py +++ b/nipype/interfaces/slicer/quantification/tests/test_auto_PETStandardUptakeValueComputation.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..petstandarduptakevaluecomputation import PETStandardUptakeValueComputation + def test_PETStandardUptakeValueComputation_inputs(): input_map = dict(OutputLabel=dict(argstr='--OutputLabel %s', ), @@ -41,6 +42,7 @@ def test_PETStandardUptakeValueComputation_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_PETStandardUptakeValueComputation_outputs(): output_map = dict(csvFile=dict(), ) @@ -49,4 +51,3 @@ def test_PETStandardUptakeValueComputation_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/slicer/registration/tests/test_auto_ACPCTransform.py b/nipype/interfaces/slicer/registration/tests/test_auto_ACPCTransform.py index 972f70b17c..a118de15c1 100644 --- a/nipype/interfaces/slicer/registration/tests/test_auto_ACPCTransform.py +++ b/nipype/interfaces/slicer/registration/tests/test_auto_ACPCTransform.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..specialized import ACPCTransform + def test_ACPCTransform_inputs(): input_map = dict(acpc=dict(argstr='--acpc %s...', ), @@ -29,6 +30,7 @@ def test_ACPCTransform_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ACPCTransform_outputs(): output_map = dict(outputTransform=dict(), ) @@ -37,4 +39,3 @@ def test_ACPCTransform_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSDemonWarp.py b/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSDemonWarp.py index 6bb0b716cc..fa3caa8d79 100644 --- a/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSDemonWarp.py +++ b/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSDemonWarp.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..specialized import BRAINSDemonWarp + def test_BRAINSDemonWarp_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -110,6 +111,7 @@ def test_BRAINSDemonWarp_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_BRAINSDemonWarp_outputs(): output_map = dict(outputCheckerboardVolume=dict(), outputDisplacementFieldVolume=dict(), @@ -120,4 +122,3 @@ def test_BRAINSDemonWarp_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSFit.py b/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSFit.py index 6aa9e0762e..b28da552ed 100644 --- a/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSFit.py +++ b/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSFit.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..brainsfit import BRAINSFit + def test_BRAINSFit_inputs(): input_map = dict(NEVER_USE_THIS_FLAG_IT_IS_OUTDATED_00=dict(argstr='--NEVER_USE_THIS_FLAG_IT_IS_OUTDATED_00 ', ), @@ -155,6 +156,7 @@ def test_BRAINSFit_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_BRAINSFit_outputs(): output_map = dict(bsplineTransform=dict(), linearTransform=dict(), @@ -169,4 +171,3 @@ def test_BRAINSFit_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSResample.py b/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSResample.py index 9dd1c3c00a..e6d8c39ae8 100644 --- a/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSResample.py +++ b/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSResample.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..brainsresample import BRAINSResample + def test_BRAINSResample_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -44,6 +45,7 @@ def test_BRAINSResample_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_BRAINSResample_outputs(): output_map = dict(outputVolume=dict(), ) @@ -52,4 +54,3 @@ def test_BRAINSResample_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/slicer/registration/tests/test_auto_FiducialRegistration.py b/nipype/interfaces/slicer/registration/tests/test_auto_FiducialRegistration.py index 24be6492df..de4cdaae40 100644 --- a/nipype/interfaces/slicer/registration/tests/test_auto_FiducialRegistration.py +++ b/nipype/interfaces/slicer/registration/tests/test_auto_FiducialRegistration.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..specialized import FiducialRegistration + def test_FiducialRegistration_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -33,6 +34,7 @@ def test_FiducialRegistration_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_FiducialRegistration_outputs(): output_map = dict(saveTransform=dict(), ) @@ -41,4 +43,3 @@ def test_FiducialRegistration_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/slicer/registration/tests/test_auto_VBRAINSDemonWarp.py b/nipype/interfaces/slicer/registration/tests/test_auto_VBRAINSDemonWarp.py index b0445a4380..50df05872a 100644 --- a/nipype/interfaces/slicer/registration/tests/test_auto_VBRAINSDemonWarp.py +++ b/nipype/interfaces/slicer/registration/tests/test_auto_VBRAINSDemonWarp.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..specialized import VBRAINSDemonWarp + def test_VBRAINSDemonWarp_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -113,6 +114,7 @@ def test_VBRAINSDemonWarp_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_VBRAINSDemonWarp_outputs(): output_map = dict(outputCheckerboardVolume=dict(), outputDisplacementFieldVolume=dict(), @@ -123,4 +125,3 @@ def test_VBRAINSDemonWarp_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/slicer/segmentation/tests/test_auto_BRAINSROIAuto.py b/nipype/interfaces/slicer/segmentation/tests/test_auto_BRAINSROIAuto.py index 478804d4b3..17d9993671 100644 --- a/nipype/interfaces/slicer/segmentation/tests/test_auto_BRAINSROIAuto.py +++ b/nipype/interfaces/slicer/segmentation/tests/test_auto_BRAINSROIAuto.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..specialized import BRAINSROIAuto + def test_BRAINSROIAuto_inputs(): input_map = dict(ROIAutoDilateSize=dict(argstr='--ROIAutoDilateSize %f', ), @@ -40,6 +41,7 @@ def test_BRAINSROIAuto_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_BRAINSROIAuto_outputs(): output_map = dict(outputClippedVolumeROI=dict(), outputROIMaskVolume=dict(), @@ -49,4 +51,3 @@ def test_BRAINSROIAuto_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/slicer/segmentation/tests/test_auto_EMSegmentCommandLine.py b/nipype/interfaces/slicer/segmentation/tests/test_auto_EMSegmentCommandLine.py index defce68ae1..3a98a84d41 100644 --- a/nipype/interfaces/slicer/segmentation/tests/test_auto_EMSegmentCommandLine.py +++ b/nipype/interfaces/slicer/segmentation/tests/test_auto_EMSegmentCommandLine.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..specialized import EMSegmentCommandLine + def test_EMSegmentCommandLine_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -65,6 +66,7 @@ def test_EMSegmentCommandLine_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_EMSegmentCommandLine_outputs(): output_map = dict(generateEmptyMRMLSceneAndQuit=dict(), resultMRMLSceneFileName=dict(), @@ -75,4 +77,3 @@ def test_EMSegmentCommandLine_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/slicer/segmentation/tests/test_auto_RobustStatisticsSegmenter.py b/nipype/interfaces/slicer/segmentation/tests/test_auto_RobustStatisticsSegmenter.py index 4754fafbab..8c8c954c68 100644 --- a/nipype/interfaces/slicer/segmentation/tests/test_auto_RobustStatisticsSegmenter.py +++ b/nipype/interfaces/slicer/segmentation/tests/test_auto_RobustStatisticsSegmenter.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..specialized import RobustStatisticsSegmenter + def test_RobustStatisticsSegmenter_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -40,6 +41,7 @@ def test_RobustStatisticsSegmenter_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_RobustStatisticsSegmenter_outputs(): output_map = dict(segmentedImageFileName=dict(position=-1, ), @@ -49,4 +51,3 @@ def test_RobustStatisticsSegmenter_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/slicer/segmentation/tests/test_auto_SimpleRegionGrowingSegmentation.py b/nipype/interfaces/slicer/segmentation/tests/test_auto_SimpleRegionGrowingSegmentation.py index 2d8329724c..a06926156e 100644 --- a/nipype/interfaces/slicer/segmentation/tests/test_auto_SimpleRegionGrowingSegmentation.py +++ b/nipype/interfaces/slicer/segmentation/tests/test_auto_SimpleRegionGrowingSegmentation.py @@ -2,6 +2,7 @@ from .....testing import assert_equal from ..simpleregiongrowingsegmentation import SimpleRegionGrowingSegmentation + def test_SimpleRegionGrowingSegmentation_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -41,6 +42,7 @@ def test_SimpleRegionGrowingSegmentation_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_SimpleRegionGrowingSegmentation_outputs(): output_map = dict(outputVolume=dict(position=-1, ), @@ -50,4 +52,3 @@ def test_SimpleRegionGrowingSegmentation_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/slicer/tests/test_auto_DicomToNrrdConverter.py b/nipype/interfaces/slicer/tests/test_auto_DicomToNrrdConverter.py index a559ed194c..e758a394f2 100644 --- a/nipype/interfaces/slicer/tests/test_auto_DicomToNrrdConverter.py +++ b/nipype/interfaces/slicer/tests/test_auto_DicomToNrrdConverter.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..converters import DicomToNrrdConverter + def test_DicomToNrrdConverter_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -35,6 +36,7 @@ def test_DicomToNrrdConverter_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_DicomToNrrdConverter_outputs(): output_map = dict(outputDirectory=dict(), ) @@ -43,4 +45,3 @@ def test_DicomToNrrdConverter_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/slicer/tests/test_auto_EMSegmentTransformToNewFormat.py b/nipype/interfaces/slicer/tests/test_auto_EMSegmentTransformToNewFormat.py index 96b8a229dd..3ef48595c8 100644 --- a/nipype/interfaces/slicer/tests/test_auto_EMSegmentTransformToNewFormat.py +++ b/nipype/interfaces/slicer/tests/test_auto_EMSegmentTransformToNewFormat.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..utilities import EMSegmentTransformToNewFormat + def test_EMSegmentTransformToNewFormat_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -27,6 +28,7 @@ def test_EMSegmentTransformToNewFormat_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_EMSegmentTransformToNewFormat_outputs(): output_map = dict(outputMRMLFileName=dict(), ) @@ -35,4 +37,3 @@ def test_EMSegmentTransformToNewFormat_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/slicer/tests/test_auto_GrayscaleModelMaker.py b/nipype/interfaces/slicer/tests/test_auto_GrayscaleModelMaker.py index 6e724e0d1a..5d871640f5 100644 --- a/nipype/interfaces/slicer/tests/test_auto_GrayscaleModelMaker.py +++ b/nipype/interfaces/slicer/tests/test_auto_GrayscaleModelMaker.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..surface import GrayscaleModelMaker + def test_GrayscaleModelMaker_inputs(): input_map = dict(InputVolume=dict(argstr='%s', position=-2, @@ -39,6 +40,7 @@ def test_GrayscaleModelMaker_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_GrayscaleModelMaker_outputs(): output_map = dict(OutputGeometry=dict(position=-1, ), @@ -48,4 +50,3 @@ def test_GrayscaleModelMaker_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/slicer/tests/test_auto_LabelMapSmoothing.py b/nipype/interfaces/slicer/tests/test_auto_LabelMapSmoothing.py index 00dfbb55c7..44bbf0179a 100644 --- a/nipype/interfaces/slicer/tests/test_auto_LabelMapSmoothing.py +++ b/nipype/interfaces/slicer/tests/test_auto_LabelMapSmoothing.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..surface import LabelMapSmoothing + def test_LabelMapSmoothing_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -35,6 +36,7 @@ def test_LabelMapSmoothing_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_LabelMapSmoothing_outputs(): output_map = dict(outputVolume=dict(position=-1, ), @@ -44,4 +46,3 @@ def test_LabelMapSmoothing_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/slicer/tests/test_auto_MergeModels.py b/nipype/interfaces/slicer/tests/test_auto_MergeModels.py index 3d76bb87a1..7dfcefb5be 100644 --- a/nipype/interfaces/slicer/tests/test_auto_MergeModels.py +++ b/nipype/interfaces/slicer/tests/test_auto_MergeModels.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..surface import MergeModels + def test_MergeModels_inputs(): input_map = dict(Model1=dict(argstr='%s', position=-3, @@ -30,6 +31,7 @@ def test_MergeModels_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MergeModels_outputs(): output_map = dict(ModelOutput=dict(position=-1, ), @@ -39,4 +41,3 @@ def test_MergeModels_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/slicer/tests/test_auto_ModelMaker.py b/nipype/interfaces/slicer/tests/test_auto_ModelMaker.py index a3cfc53d86..1137fe4898 100644 --- a/nipype/interfaces/slicer/tests/test_auto_ModelMaker.py +++ b/nipype/interfaces/slicer/tests/test_auto_ModelMaker.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..surface import ModelMaker + def test_ModelMaker_inputs(): input_map = dict(InputVolume=dict(argstr='%s', position=-1, @@ -59,6 +60,7 @@ def test_ModelMaker_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ModelMaker_outputs(): output_map = dict(modelSceneFile=dict(), ) @@ -67,4 +69,3 @@ def test_ModelMaker_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/slicer/tests/test_auto_ModelToLabelMap.py b/nipype/interfaces/slicer/tests/test_auto_ModelToLabelMap.py index 021ecb0738..2756e03782 100644 --- a/nipype/interfaces/slicer/tests/test_auto_ModelToLabelMap.py +++ b/nipype/interfaces/slicer/tests/test_auto_ModelToLabelMap.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..surface import ModelToLabelMap + def test_ModelToLabelMap_inputs(): input_map = dict(InputVolume=dict(argstr='%s', position=-3, @@ -32,6 +33,7 @@ def test_ModelToLabelMap_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ModelToLabelMap_outputs(): output_map = dict(OutputVolume=dict(position=-1, ), @@ -41,4 +43,3 @@ def test_ModelToLabelMap_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/slicer/tests/test_auto_OrientScalarVolume.py b/nipype/interfaces/slicer/tests/test_auto_OrientScalarVolume.py index cb44b3685d..4477681f60 100644 --- a/nipype/interfaces/slicer/tests/test_auto_OrientScalarVolume.py +++ b/nipype/interfaces/slicer/tests/test_auto_OrientScalarVolume.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..converters import OrientScalarVolume + def test_OrientScalarVolume_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -29,6 +30,7 @@ def test_OrientScalarVolume_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_OrientScalarVolume_outputs(): output_map = dict(outputVolume=dict(position=-1, ), @@ -38,4 +40,3 @@ def test_OrientScalarVolume_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/slicer/tests/test_auto_ProbeVolumeWithModel.py b/nipype/interfaces/slicer/tests/test_auto_ProbeVolumeWithModel.py index 6a50d3364b..842768fd27 100644 --- a/nipype/interfaces/slicer/tests/test_auto_ProbeVolumeWithModel.py +++ b/nipype/interfaces/slicer/tests/test_auto_ProbeVolumeWithModel.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..surface import ProbeVolumeWithModel + def test_ProbeVolumeWithModel_inputs(): input_map = dict(InputModel=dict(argstr='%s', position=-2, @@ -30,6 +31,7 @@ def test_ProbeVolumeWithModel_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ProbeVolumeWithModel_outputs(): output_map = dict(OutputModel=dict(position=-1, ), @@ -39,4 +41,3 @@ def test_ProbeVolumeWithModel_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/slicer/tests/test_auto_SlicerCommandLine.py b/nipype/interfaces/slicer/tests/test_auto_SlicerCommandLine.py index 9002270b19..e480e76324 100644 --- a/nipype/interfaces/slicer/tests/test_auto_SlicerCommandLine.py +++ b/nipype/interfaces/slicer/tests/test_auto_SlicerCommandLine.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..base import SlicerCommandLine + def test_SlicerCommandLine_inputs(): input_map = dict(args=dict(argstr='%s', ), diff --git a/nipype/interfaces/spm/tests/test_auto_Analyze2nii.py b/nipype/interfaces/spm/tests/test_auto_Analyze2nii.py index 9444246881..2f175f80f6 100644 --- a/nipype/interfaces/spm/tests/test_auto_Analyze2nii.py +++ b/nipype/interfaces/spm/tests/test_auto_Analyze2nii.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..utils import Analyze2nii + def test_Analyze2nii_inputs(): input_map = dict(analyze_file=dict(mandatory=True, ), @@ -23,6 +24,7 @@ def test_Analyze2nii_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Analyze2nii_outputs(): output_map = dict(ignore_exception=dict(nohash=True, usedefault=True, @@ -42,4 +44,3 @@ def test_Analyze2nii_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/spm/tests/test_auto_ApplyDeformations.py b/nipype/interfaces/spm/tests/test_auto_ApplyDeformations.py index c67359d5fc..a84d6e8246 100644 --- a/nipype/interfaces/spm/tests/test_auto_ApplyDeformations.py +++ b/nipype/interfaces/spm/tests/test_auto_ApplyDeformations.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import ApplyDeformations + def test_ApplyDeformations_inputs(): input_map = dict(deformation_field=dict(field='comp{1}.def', mandatory=True, @@ -32,6 +33,7 @@ def test_ApplyDeformations_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ApplyDeformations_outputs(): output_map = dict(out_files=dict(), ) @@ -40,4 +42,3 @@ def test_ApplyDeformations_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/spm/tests/test_auto_ApplyInverseDeformation.py b/nipype/interfaces/spm/tests/test_auto_ApplyInverseDeformation.py index 36117f1136..8eca900dd9 100644 --- a/nipype/interfaces/spm/tests/test_auto_ApplyInverseDeformation.py +++ b/nipype/interfaces/spm/tests/test_auto_ApplyInverseDeformation.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..utils import ApplyInverseDeformation + def test_ApplyInverseDeformation_inputs(): input_map = dict(bounding_box=dict(field='comp{1}.inv.comp{1}.sn2def.bb', ), @@ -38,6 +39,7 @@ def test_ApplyInverseDeformation_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ApplyInverseDeformation_outputs(): output_map = dict(out_files=dict(), ) @@ -46,4 +48,3 @@ def test_ApplyInverseDeformation_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/spm/tests/test_auto_ApplyTransform.py b/nipype/interfaces/spm/tests/test_auto_ApplyTransform.py index 3b1c3ea7e5..090ae3e200 100644 --- a/nipype/interfaces/spm/tests/test_auto_ApplyTransform.py +++ b/nipype/interfaces/spm/tests/test_auto_ApplyTransform.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..utils import ApplyTransform + def test_ApplyTransform_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, @@ -28,6 +29,7 @@ def test_ApplyTransform_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ApplyTransform_outputs(): output_map = dict(out_file=dict(), ) @@ -36,4 +38,3 @@ def test_ApplyTransform_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/spm/tests/test_auto_CalcCoregAffine.py b/nipype/interfaces/spm/tests/test_auto_CalcCoregAffine.py index 0fda6df16d..a058f57767 100644 --- a/nipype/interfaces/spm/tests/test_auto_CalcCoregAffine.py +++ b/nipype/interfaces/spm/tests/test_auto_CalcCoregAffine.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..utils import CalcCoregAffine + def test_CalcCoregAffine_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, @@ -28,6 +29,7 @@ def test_CalcCoregAffine_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_CalcCoregAffine_outputs(): output_map = dict(invmat=dict(), mat=dict(), @@ -37,4 +39,3 @@ def test_CalcCoregAffine_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/spm/tests/test_auto_Coregister.py b/nipype/interfaces/spm/tests/test_auto_Coregister.py index 27147d8996..5b8eb8f51f 100644 --- a/nipype/interfaces/spm/tests/test_auto_Coregister.py +++ b/nipype/interfaces/spm/tests/test_auto_Coregister.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import Coregister + def test_Coregister_inputs(): input_map = dict(apply_to_files=dict(copyfile=True, field='other', @@ -51,6 +52,7 @@ def test_Coregister_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Coregister_outputs(): output_map = dict(coregistered_files=dict(), coregistered_source=dict(), @@ -60,4 +62,3 @@ def test_Coregister_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/spm/tests/test_auto_CreateWarped.py b/nipype/interfaces/spm/tests/test_auto_CreateWarped.py index dff0490643..043847d15e 100644 --- a/nipype/interfaces/spm/tests/test_auto_CreateWarped.py +++ b/nipype/interfaces/spm/tests/test_auto_CreateWarped.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import CreateWarped + def test_CreateWarped_inputs(): input_map = dict(flowfield_files=dict(copyfile=False, field='crt_warped.flowfields', @@ -35,6 +36,7 @@ def test_CreateWarped_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_CreateWarped_outputs(): output_map = dict(warped_files=dict(), ) @@ -43,4 +45,3 @@ def test_CreateWarped_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/spm/tests/test_auto_DARTEL.py b/nipype/interfaces/spm/tests/test_auto_DARTEL.py index 30b0146191..0e3bb00668 100644 --- a/nipype/interfaces/spm/tests/test_auto_DARTEL.py +++ b/nipype/interfaces/spm/tests/test_auto_DARTEL.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import DARTEL + def test_DARTEL_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, @@ -34,6 +35,7 @@ def test_DARTEL_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_DARTEL_outputs(): output_map = dict(dartel_flow_fields=dict(), final_template_file=dict(), @@ -44,4 +46,3 @@ def test_DARTEL_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/spm/tests/test_auto_DARTELNorm2MNI.py b/nipype/interfaces/spm/tests/test_auto_DARTELNorm2MNI.py index 037d50eead..8af7fc0285 100644 --- a/nipype/interfaces/spm/tests/test_auto_DARTELNorm2MNI.py +++ b/nipype/interfaces/spm/tests/test_auto_DARTELNorm2MNI.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import DARTELNorm2MNI + def test_DARTELNorm2MNI_inputs(): input_map = dict(apply_to_files=dict(copyfile=False, field='mni_norm.data.subjs.images', @@ -40,6 +41,7 @@ def test_DARTELNorm2MNI_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_DARTELNorm2MNI_outputs(): output_map = dict(normalization_parameter_file=dict(), normalized_files=dict(), @@ -49,4 +51,3 @@ def test_DARTELNorm2MNI_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/spm/tests/test_auto_DicomImport.py b/nipype/interfaces/spm/tests/test_auto_DicomImport.py index 8b5c3f9107..9bc1c2762e 100644 --- a/nipype/interfaces/spm/tests/test_auto_DicomImport.py +++ b/nipype/interfaces/spm/tests/test_auto_DicomImport.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..utils import DicomImport + def test_DicomImport_inputs(): input_map = dict(format=dict(field='convopts.format', usedefault=True, @@ -36,6 +37,7 @@ def test_DicomImport_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_DicomImport_outputs(): output_map = dict(out_files=dict(), ) @@ -44,4 +46,3 @@ def test_DicomImport_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/spm/tests/test_auto_EstimateContrast.py b/nipype/interfaces/spm/tests/test_auto_EstimateContrast.py index 09dc2740b3..558790c20e 100644 --- a/nipype/interfaces/spm/tests/test_auto_EstimateContrast.py +++ b/nipype/interfaces/spm/tests/test_auto_EstimateContrast.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..model import EstimateContrast + def test_EstimateContrast_inputs(): input_map = dict(beta_images=dict(copyfile=False, mandatory=True, @@ -37,6 +38,7 @@ def test_EstimateContrast_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_EstimateContrast_outputs(): output_map = dict(con_images=dict(), ess_images=dict(), @@ -49,4 +51,3 @@ def test_EstimateContrast_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/spm/tests/test_auto_EstimateModel.py b/nipype/interfaces/spm/tests/test_auto_EstimateModel.py index aa1d2ce320..44d269e89c 100644 --- a/nipype/interfaces/spm/tests/test_auto_EstimateModel.py +++ b/nipype/interfaces/spm/tests/test_auto_EstimateModel.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..model import EstimateModel + def test_EstimateModel_inputs(): input_map = dict(estimation_method=dict(field='method', mandatory=True, @@ -29,6 +30,7 @@ def test_EstimateModel_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_EstimateModel_outputs(): output_map = dict(RPVimage=dict(), beta_images=dict(), @@ -41,4 +43,3 @@ def test_EstimateModel_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/spm/tests/test_auto_FactorialDesign.py b/nipype/interfaces/spm/tests/test_auto_FactorialDesign.py index 9c56e98132..c382ed3c8d 100644 --- a/nipype/interfaces/spm/tests/test_auto_FactorialDesign.py +++ b/nipype/interfaces/spm/tests/test_auto_FactorialDesign.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..model import FactorialDesign + def test_FactorialDesign_inputs(): input_map = dict(covariates=dict(field='cov', ), @@ -51,6 +52,7 @@ def test_FactorialDesign_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_FactorialDesign_outputs(): output_map = dict(spm_mat_file=dict(), ) @@ -59,4 +61,3 @@ def test_FactorialDesign_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/spm/tests/test_auto_Level1Design.py b/nipype/interfaces/spm/tests/test_auto_Level1Design.py index 7172a87736..de50c577c0 100644 --- a/nipype/interfaces/spm/tests/test_auto_Level1Design.py +++ b/nipype/interfaces/spm/tests/test_auto_Level1Design.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..model import Level1Design + def test_Level1Design_inputs(): input_map = dict(bases=dict(field='bases', mandatory=True, @@ -51,6 +52,7 @@ def test_Level1Design_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Level1Design_outputs(): output_map = dict(spm_mat_file=dict(), ) @@ -59,4 +61,3 @@ def test_Level1Design_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/spm/tests/test_auto_MultipleRegressionDesign.py b/nipype/interfaces/spm/tests/test_auto_MultipleRegressionDesign.py index 0bdb5ccb97..5fa47fadf2 100644 --- a/nipype/interfaces/spm/tests/test_auto_MultipleRegressionDesign.py +++ b/nipype/interfaces/spm/tests/test_auto_MultipleRegressionDesign.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..model import MultipleRegressionDesign + def test_MultipleRegressionDesign_inputs(): input_map = dict(covariates=dict(field='cov', ), @@ -59,6 +60,7 @@ def test_MultipleRegressionDesign_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MultipleRegressionDesign_outputs(): output_map = dict(spm_mat_file=dict(), ) @@ -67,4 +69,3 @@ def test_MultipleRegressionDesign_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/spm/tests/test_auto_NewSegment.py b/nipype/interfaces/spm/tests/test_auto_NewSegment.py index 9ca6703a97..89f6a5c18c 100644 --- a/nipype/interfaces/spm/tests/test_auto_NewSegment.py +++ b/nipype/interfaces/spm/tests/test_auto_NewSegment.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import NewSegment + def test_NewSegment_inputs(): input_map = dict(affine_regularization=dict(field='warp.affreg', ), @@ -37,6 +38,7 @@ def test_NewSegment_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_NewSegment_outputs(): output_map = dict(bias_corrected_images=dict(), bias_field_images=dict(), @@ -53,4 +55,3 @@ def test_NewSegment_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/spm/tests/test_auto_Normalize.py b/nipype/interfaces/spm/tests/test_auto_Normalize.py index 91e9af91ea..96ce55975e 100644 --- a/nipype/interfaces/spm/tests/test_auto_Normalize.py +++ b/nipype/interfaces/spm/tests/test_auto_Normalize.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import Normalize + def test_Normalize_inputs(): input_map = dict(DCT_period_cutoff=dict(field='eoptions.cutoff', ), @@ -72,6 +73,7 @@ def test_Normalize_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Normalize_outputs(): output_map = dict(normalization_parameters=dict(), normalized_files=dict(), @@ -82,4 +84,3 @@ def test_Normalize_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/spm/tests/test_auto_Normalize12.py b/nipype/interfaces/spm/tests/test_auto_Normalize12.py index e9f3e2c80d..7fedba9d86 100644 --- a/nipype/interfaces/spm/tests/test_auto_Normalize12.py +++ b/nipype/interfaces/spm/tests/test_auto_Normalize12.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import Normalize12 + def test_Normalize12_inputs(): input_map = dict(affine_regularization_type=dict(field='eoptions.affreg', ), @@ -58,6 +59,7 @@ def test_Normalize12_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Normalize12_outputs(): output_map = dict(deformation_field=dict(), normalized_files=dict(), @@ -68,4 +70,3 @@ def test_Normalize12_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/spm/tests/test_auto_OneSampleTTestDesign.py b/nipype/interfaces/spm/tests/test_auto_OneSampleTTestDesign.py index 5153531b84..51f4e9d4e2 100644 --- a/nipype/interfaces/spm/tests/test_auto_OneSampleTTestDesign.py +++ b/nipype/interfaces/spm/tests/test_auto_OneSampleTTestDesign.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..model import OneSampleTTestDesign + def test_OneSampleTTestDesign_inputs(): input_map = dict(covariates=dict(field='cov', ), @@ -54,6 +55,7 @@ def test_OneSampleTTestDesign_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_OneSampleTTestDesign_outputs(): output_map = dict(spm_mat_file=dict(), ) @@ -62,4 +64,3 @@ def test_OneSampleTTestDesign_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/spm/tests/test_auto_PairedTTestDesign.py b/nipype/interfaces/spm/tests/test_auto_PairedTTestDesign.py index 840b0ea963..b053cb58d1 100644 --- a/nipype/interfaces/spm/tests/test_auto_PairedTTestDesign.py +++ b/nipype/interfaces/spm/tests/test_auto_PairedTTestDesign.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..model import PairedTTestDesign + def test_PairedTTestDesign_inputs(): input_map = dict(ancova=dict(field='des.pt.ancova', ), @@ -58,6 +59,7 @@ def test_PairedTTestDesign_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_PairedTTestDesign_outputs(): output_map = dict(spm_mat_file=dict(), ) @@ -66,4 +68,3 @@ def test_PairedTTestDesign_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/spm/tests/test_auto_Realign.py b/nipype/interfaces/spm/tests/test_auto_Realign.py index 277ada55c1..6ee1c7a110 100644 --- a/nipype/interfaces/spm/tests/test_auto_Realign.py +++ b/nipype/interfaces/spm/tests/test_auto_Realign.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import Realign + def test_Realign_inputs(): input_map = dict(fwhm=dict(field='eoptions.fwhm', ), @@ -55,6 +56,7 @@ def test_Realign_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Realign_outputs(): output_map = dict(mean_image=dict(), modified_in_files=dict(), @@ -66,4 +68,3 @@ def test_Realign_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/spm/tests/test_auto_Reslice.py b/nipype/interfaces/spm/tests/test_auto_Reslice.py index 75fc35c8d4..1687309bd7 100644 --- a/nipype/interfaces/spm/tests/test_auto_Reslice.py +++ b/nipype/interfaces/spm/tests/test_auto_Reslice.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..utils import Reslice + def test_Reslice_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, @@ -28,6 +29,7 @@ def test_Reslice_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Reslice_outputs(): output_map = dict(out_file=dict(), ) @@ -36,4 +38,3 @@ def test_Reslice_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/spm/tests/test_auto_ResliceToReference.py b/nipype/interfaces/spm/tests/test_auto_ResliceToReference.py index 6eba2f6aee..d791b5965a 100644 --- a/nipype/interfaces/spm/tests/test_auto_ResliceToReference.py +++ b/nipype/interfaces/spm/tests/test_auto_ResliceToReference.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..utils import ResliceToReference + def test_ResliceToReference_inputs(): input_map = dict(bounding_box=dict(field='comp{2}.idbbvox.bb', ), @@ -32,6 +33,7 @@ def test_ResliceToReference_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ResliceToReference_outputs(): output_map = dict(out_files=dict(), ) @@ -40,4 +42,3 @@ def test_ResliceToReference_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/spm/tests/test_auto_SPMCommand.py b/nipype/interfaces/spm/tests/test_auto_SPMCommand.py index 3408497e0b..76676dd1ab 100644 --- a/nipype/interfaces/spm/tests/test_auto_SPMCommand.py +++ b/nipype/interfaces/spm/tests/test_auto_SPMCommand.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..base import SPMCommand + def test_SPMCommand_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, diff --git a/nipype/interfaces/spm/tests/test_auto_Segment.py b/nipype/interfaces/spm/tests/test_auto_Segment.py index bd8e7a0f4e..c32284105c 100644 --- a/nipype/interfaces/spm/tests/test_auto_Segment.py +++ b/nipype/interfaces/spm/tests/test_auto_Segment.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import Segment + def test_Segment_inputs(): input_map = dict(affine_regularization=dict(field='opts.regtype', ), @@ -53,6 +54,7 @@ def test_Segment_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Segment_outputs(): output_map = dict(bias_corrected_image=dict(), inverse_transformation_mat=dict(), @@ -75,4 +77,3 @@ def test_Segment_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/spm/tests/test_auto_SliceTiming.py b/nipype/interfaces/spm/tests/test_auto_SliceTiming.py index 18ee3dc537..c230c2909c 100644 --- a/nipype/interfaces/spm/tests/test_auto_SliceTiming.py +++ b/nipype/interfaces/spm/tests/test_auto_SliceTiming.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import SliceTiming + def test_SliceTiming_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, @@ -43,6 +44,7 @@ def test_SliceTiming_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_SliceTiming_outputs(): output_map = dict(timecorrected_files=dict(), ) @@ -51,4 +53,3 @@ def test_SliceTiming_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/spm/tests/test_auto_Smooth.py b/nipype/interfaces/spm/tests/test_auto_Smooth.py index b4fce66cd9..aa5708ba5f 100644 --- a/nipype/interfaces/spm/tests/test_auto_Smooth.py +++ b/nipype/interfaces/spm/tests/test_auto_Smooth.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import Smooth + def test_Smooth_inputs(): input_map = dict(data_type=dict(field='dtype', ), @@ -34,6 +35,7 @@ def test_Smooth_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Smooth_outputs(): output_map = dict(smoothed_files=dict(), ) @@ -42,4 +44,3 @@ def test_Smooth_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/spm/tests/test_auto_Threshold.py b/nipype/interfaces/spm/tests/test_auto_Threshold.py index e9afc7fa94..e79460f980 100644 --- a/nipype/interfaces/spm/tests/test_auto_Threshold.py +++ b/nipype/interfaces/spm/tests/test_auto_Threshold.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..model import Threshold + def test_Threshold_inputs(): input_map = dict(contrast_index=dict(mandatory=True, ), @@ -43,6 +44,7 @@ def test_Threshold_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Threshold_outputs(): output_map = dict(activation_forced=dict(), cluster_forming_thr=dict(), @@ -56,4 +58,3 @@ def test_Threshold_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/spm/tests/test_auto_ThresholdStatistics.py b/nipype/interfaces/spm/tests/test_auto_ThresholdStatistics.py index 04560e6178..a5363ebccd 100644 --- a/nipype/interfaces/spm/tests/test_auto_ThresholdStatistics.py +++ b/nipype/interfaces/spm/tests/test_auto_ThresholdStatistics.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..model import ThresholdStatistics + def test_ThresholdStatistics_inputs(): input_map = dict(contrast_index=dict(mandatory=True, ), @@ -33,6 +34,7 @@ def test_ThresholdStatistics_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ThresholdStatistics_outputs(): output_map = dict(clusterwise_P_FDR=dict(), clusterwise_P_RF=dict(), @@ -46,4 +48,3 @@ def test_ThresholdStatistics_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/spm/tests/test_auto_TwoSampleTTestDesign.py b/nipype/interfaces/spm/tests/test_auto_TwoSampleTTestDesign.py index 0bd2c399b3..c27ae684dc 100644 --- a/nipype/interfaces/spm/tests/test_auto_TwoSampleTTestDesign.py +++ b/nipype/interfaces/spm/tests/test_auto_TwoSampleTTestDesign.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..model import TwoSampleTTestDesign + def test_TwoSampleTTestDesign_inputs(): input_map = dict(covariates=dict(field='cov', ), @@ -61,6 +62,7 @@ def test_TwoSampleTTestDesign_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_TwoSampleTTestDesign_outputs(): output_map = dict(spm_mat_file=dict(), ) @@ -69,4 +71,3 @@ def test_TwoSampleTTestDesign_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/spm/tests/test_auto_VBMSegment.py b/nipype/interfaces/spm/tests/test_auto_VBMSegment.py index b4f9de6761..1b330af007 100644 --- a/nipype/interfaces/spm/tests/test_auto_VBMSegment.py +++ b/nipype/interfaces/spm/tests/test_auto_VBMSegment.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..preprocess import VBMSegment + def test_VBMSegment_inputs(): input_map = dict(bias_corrected_affine=dict(field='estwrite.output.bias.affine', usedefault=True, @@ -117,6 +118,7 @@ def test_VBMSegment_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_VBMSegment_outputs(): output_map = dict(bias_corrected_images=dict(), dartel_input_images=dict(), @@ -137,4 +139,3 @@ def test_VBMSegment_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/tests/test_auto_AssertEqual.py b/nipype/interfaces/tests/test_auto_AssertEqual.py index ebe528ff2f..4a1d763e43 100644 --- a/nipype/interfaces/tests/test_auto_AssertEqual.py +++ b/nipype/interfaces/tests/test_auto_AssertEqual.py @@ -2,6 +2,7 @@ from ...testing import assert_equal from ..utility import AssertEqual + def test_AssertEqual_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, diff --git a/nipype/interfaces/tests/test_auto_BaseInterface.py b/nipype/interfaces/tests/test_auto_BaseInterface.py index e47c27a9aa..5851add1da 100644 --- a/nipype/interfaces/tests/test_auto_BaseInterface.py +++ b/nipype/interfaces/tests/test_auto_BaseInterface.py @@ -2,6 +2,7 @@ from ...testing import assert_equal from ..base import BaseInterface + def test_BaseInterface_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, diff --git a/nipype/interfaces/tests/test_auto_C3dAffineTool.py b/nipype/interfaces/tests/test_auto_C3dAffineTool.py index efd5cb6d73..dc8cc37b8c 100644 --- a/nipype/interfaces/tests/test_auto_C3dAffineTool.py +++ b/nipype/interfaces/tests/test_auto_C3dAffineTool.py @@ -2,6 +2,7 @@ from ...testing import assert_equal from ..c3 import C3dAffineTool + def test_C3dAffineTool_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -36,6 +37,7 @@ def test_C3dAffineTool_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_C3dAffineTool_outputs(): output_map = dict(itk_transform=dict(), ) @@ -44,4 +46,3 @@ def test_C3dAffineTool_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/tests/test_auto_CSVReader.py b/nipype/interfaces/tests/test_auto_CSVReader.py index 2d950112f8..a6f42de676 100644 --- a/nipype/interfaces/tests/test_auto_CSVReader.py +++ b/nipype/interfaces/tests/test_auto_CSVReader.py @@ -2,6 +2,7 @@ from ...testing import assert_equal from ..utility import CSVReader + def test_CSVReader_inputs(): input_map = dict(header=dict(usedefault=True, ), @@ -14,6 +15,7 @@ def test_CSVReader_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_CSVReader_outputs(): output_map = dict() outputs = CSVReader.output_spec() @@ -21,4 +23,3 @@ def test_CSVReader_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/tests/test_auto_CommandLine.py b/nipype/interfaces/tests/test_auto_CommandLine.py index 48e2716557..9ea4f08937 100644 --- a/nipype/interfaces/tests/test_auto_CommandLine.py +++ b/nipype/interfaces/tests/test_auto_CommandLine.py @@ -2,6 +2,7 @@ from ...testing import assert_equal from ..base import CommandLine + def test_CommandLine_inputs(): input_map = dict(args=dict(argstr='%s', ), diff --git a/nipype/interfaces/tests/test_auto_CopyMeta.py b/nipype/interfaces/tests/test_auto_CopyMeta.py index e71481a5af..8b456d4e09 100644 --- a/nipype/interfaces/tests/test_auto_CopyMeta.py +++ b/nipype/interfaces/tests/test_auto_CopyMeta.py @@ -2,6 +2,7 @@ from ...testing import assert_equal from ..dcmstack import CopyMeta + def test_CopyMeta_inputs(): input_map = dict(dest_file=dict(mandatory=True, ), @@ -16,6 +17,7 @@ def test_CopyMeta_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_CopyMeta_outputs(): output_map = dict(dest_file=dict(), ) @@ -24,4 +26,3 @@ def test_CopyMeta_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/tests/test_auto_DataFinder.py b/nipype/interfaces/tests/test_auto_DataFinder.py index 946a7497d4..8eb5faa9ea 100644 --- a/nipype/interfaces/tests/test_auto_DataFinder.py +++ b/nipype/interfaces/tests/test_auto_DataFinder.py @@ -2,6 +2,7 @@ from ...testing import assert_equal from ..io import DataFinder + def test_DataFinder_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, @@ -22,6 +23,7 @@ def test_DataFinder_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_DataFinder_outputs(): output_map = dict() outputs = DataFinder.output_spec() @@ -29,4 +31,3 @@ def test_DataFinder_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/tests/test_auto_DataGrabber.py b/nipype/interfaces/tests/test_auto_DataGrabber.py index 4af03c2ddf..f72eb2bdfe 100644 --- a/nipype/interfaces/tests/test_auto_DataGrabber.py +++ b/nipype/interfaces/tests/test_auto_DataGrabber.py @@ -2,6 +2,7 @@ from ...testing import assert_equal from ..io import DataGrabber + def test_DataGrabber_inputs(): input_map = dict(base_directory=dict(), ignore_exception=dict(nohash=True, @@ -21,6 +22,7 @@ def test_DataGrabber_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_DataGrabber_outputs(): output_map = dict() outputs = DataGrabber.output_spec() @@ -28,4 +30,3 @@ def test_DataGrabber_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/tests/test_auto_DataSink.py b/nipype/interfaces/tests/test_auto_DataSink.py index 0e43c7727e..c49647f889 100644 --- a/nipype/interfaces/tests/test_auto_DataSink.py +++ b/nipype/interfaces/tests/test_auto_DataSink.py @@ -2,6 +2,7 @@ from ...testing import assert_equal from ..io import DataSink + def test_DataSink_inputs(): input_map = dict(_outputs=dict(usedefault=True, ), @@ -24,6 +25,7 @@ def test_DataSink_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_DataSink_outputs(): output_map = dict(out_file=dict(), ) @@ -32,4 +34,3 @@ def test_DataSink_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/tests/test_auto_Dcm2nii.py b/nipype/interfaces/tests/test_auto_Dcm2nii.py index ae556e8bdc..c322f76149 100644 --- a/nipype/interfaces/tests/test_auto_Dcm2nii.py +++ b/nipype/interfaces/tests/test_auto_Dcm2nii.py @@ -2,6 +2,7 @@ from ...testing import assert_equal from ..dcm2nii import Dcm2nii + def test_Dcm2nii_inputs(): input_map = dict(anonymize=dict(argstr='-a', usedefault=True, @@ -75,6 +76,7 @@ def test_Dcm2nii_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Dcm2nii_outputs(): output_map = dict(bvals=dict(), bvecs=dict(), @@ -87,4 +89,3 @@ def test_Dcm2nii_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/tests/test_auto_DcmStack.py b/nipype/interfaces/tests/test_auto_DcmStack.py index ef364f6696..c91379caa6 100644 --- a/nipype/interfaces/tests/test_auto_DcmStack.py +++ b/nipype/interfaces/tests/test_auto_DcmStack.py @@ -2,6 +2,7 @@ from ...testing import assert_equal from ..dcmstack import DcmStack + def test_DcmStack_inputs(): input_map = dict(dicom_files=dict(mandatory=True, ), @@ -21,6 +22,7 @@ def test_DcmStack_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_DcmStack_outputs(): output_map = dict(out_file=dict(), ) @@ -29,4 +31,3 @@ def test_DcmStack_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/tests/test_auto_FreeSurferSource.py b/nipype/interfaces/tests/test_auto_FreeSurferSource.py index c9e71c3886..8b393bf0c4 100644 --- a/nipype/interfaces/tests/test_auto_FreeSurferSource.py +++ b/nipype/interfaces/tests/test_auto_FreeSurferSource.py @@ -2,6 +2,7 @@ from ...testing import assert_equal from ..io import FreeSurferSource + def test_FreeSurferSource_inputs(): input_map = dict(hemi=dict(usedefault=True, ), @@ -19,6 +20,7 @@ def test_FreeSurferSource_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_FreeSurferSource_outputs(): output_map = dict(BA_stats=dict(altkey='BA', loc='stats', @@ -102,4 +104,3 @@ def test_FreeSurferSource_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/tests/test_auto_Function.py b/nipype/interfaces/tests/test_auto_Function.py index 7454cdec84..65afafbe47 100644 --- a/nipype/interfaces/tests/test_auto_Function.py +++ b/nipype/interfaces/tests/test_auto_Function.py @@ -2,6 +2,7 @@ from ...testing import assert_equal from ..utility import Function + def test_Function_inputs(): input_map = dict(function_str=dict(mandatory=True, ), @@ -15,6 +16,7 @@ def test_Function_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Function_outputs(): output_map = dict() outputs = Function.output_spec() @@ -22,4 +24,3 @@ def test_Function_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/tests/test_auto_GroupAndStack.py b/nipype/interfaces/tests/test_auto_GroupAndStack.py index cab06d673b..8523f76c32 100644 --- a/nipype/interfaces/tests/test_auto_GroupAndStack.py +++ b/nipype/interfaces/tests/test_auto_GroupAndStack.py @@ -2,6 +2,7 @@ from ...testing import assert_equal from ..dcmstack import GroupAndStack + def test_GroupAndStack_inputs(): input_map = dict(dicom_files=dict(mandatory=True, ), @@ -21,6 +22,7 @@ def test_GroupAndStack_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_GroupAndStack_outputs(): output_map = dict(out_list=dict(), ) @@ -29,4 +31,3 @@ def test_GroupAndStack_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/tests/test_auto_IOBase.py b/nipype/interfaces/tests/test_auto_IOBase.py index 1bcd8a8c0e..548b613986 100644 --- a/nipype/interfaces/tests/test_auto_IOBase.py +++ b/nipype/interfaces/tests/test_auto_IOBase.py @@ -2,6 +2,7 @@ from ...testing import assert_equal from ..io import IOBase + def test_IOBase_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, diff --git a/nipype/interfaces/tests/test_auto_IdentityInterface.py b/nipype/interfaces/tests/test_auto_IdentityInterface.py index 8a4ce3f464..f5787df81c 100644 --- a/nipype/interfaces/tests/test_auto_IdentityInterface.py +++ b/nipype/interfaces/tests/test_auto_IdentityInterface.py @@ -2,6 +2,7 @@ from ...testing import assert_equal from ..utility import IdentityInterface + def test_IdentityInterface_inputs(): input_map = dict() inputs = IdentityInterface.input_spec() @@ -10,6 +11,7 @@ def test_IdentityInterface_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_IdentityInterface_outputs(): output_map = dict() outputs = IdentityInterface.output_spec() @@ -17,4 +19,3 @@ def test_IdentityInterface_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/tests/test_auto_JSONFileGrabber.py b/nipype/interfaces/tests/test_auto_JSONFileGrabber.py index d7a7684f4d..a99c4c6ba2 100644 --- a/nipype/interfaces/tests/test_auto_JSONFileGrabber.py +++ b/nipype/interfaces/tests/test_auto_JSONFileGrabber.py @@ -2,6 +2,7 @@ from ...testing import assert_equal from ..io import JSONFileGrabber + def test_JSONFileGrabber_inputs(): input_map = dict(defaults=dict(), ignore_exception=dict(nohash=True, @@ -15,6 +16,7 @@ def test_JSONFileGrabber_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_JSONFileGrabber_outputs(): output_map = dict() outputs = JSONFileGrabber.output_spec() @@ -22,4 +24,3 @@ def test_JSONFileGrabber_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/tests/test_auto_JSONFileSink.py b/nipype/interfaces/tests/test_auto_JSONFileSink.py index 9632906e97..738166527f 100644 --- a/nipype/interfaces/tests/test_auto_JSONFileSink.py +++ b/nipype/interfaces/tests/test_auto_JSONFileSink.py @@ -2,6 +2,7 @@ from ...testing import assert_equal from ..io import JSONFileSink + def test_JSONFileSink_inputs(): input_map = dict(_outputs=dict(usedefault=True, ), @@ -18,6 +19,7 @@ def test_JSONFileSink_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_JSONFileSink_outputs(): output_map = dict(out_file=dict(), ) @@ -26,4 +28,3 @@ def test_JSONFileSink_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/tests/test_auto_LookupMeta.py b/nipype/interfaces/tests/test_auto_LookupMeta.py index 276362520c..7e89973931 100644 --- a/nipype/interfaces/tests/test_auto_LookupMeta.py +++ b/nipype/interfaces/tests/test_auto_LookupMeta.py @@ -2,6 +2,7 @@ from ...testing import assert_equal from ..dcmstack import LookupMeta + def test_LookupMeta_inputs(): input_map = dict(in_file=dict(mandatory=True, ), @@ -14,6 +15,7 @@ def test_LookupMeta_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_LookupMeta_outputs(): output_map = dict() outputs = LookupMeta.output_spec() @@ -21,4 +23,3 @@ def test_LookupMeta_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/tests/test_auto_MatlabCommand.py b/nipype/interfaces/tests/test_auto_MatlabCommand.py index e82fc2d665..bfc24cb064 100644 --- a/nipype/interfaces/tests/test_auto_MatlabCommand.py +++ b/nipype/interfaces/tests/test_auto_MatlabCommand.py @@ -2,6 +2,7 @@ from ...testing import assert_equal from ..matlab import MatlabCommand + def test_MatlabCommand_inputs(): input_map = dict(args=dict(argstr='%s', ), diff --git a/nipype/interfaces/tests/test_auto_Merge.py b/nipype/interfaces/tests/test_auto_Merge.py index 3a68555612..adddcdebd2 100644 --- a/nipype/interfaces/tests/test_auto_Merge.py +++ b/nipype/interfaces/tests/test_auto_Merge.py @@ -2,6 +2,7 @@ from ...testing import assert_equal from ..utility import Merge + def test_Merge_inputs(): input_map = dict(axis=dict(usedefault=True, ), @@ -17,6 +18,7 @@ def test_Merge_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Merge_outputs(): output_map = dict(out=dict(), ) @@ -25,4 +27,3 @@ def test_Merge_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/tests/test_auto_MergeNifti.py b/nipype/interfaces/tests/test_auto_MergeNifti.py index efa8dfdae9..3a6e0fc5a1 100644 --- a/nipype/interfaces/tests/test_auto_MergeNifti.py +++ b/nipype/interfaces/tests/test_auto_MergeNifti.py @@ -2,6 +2,7 @@ from ...testing import assert_equal from ..dcmstack import MergeNifti + def test_MergeNifti_inputs(): input_map = dict(in_files=dict(mandatory=True, ), @@ -18,6 +19,7 @@ def test_MergeNifti_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MergeNifti_outputs(): output_map = dict(out_file=dict(), ) @@ -26,4 +28,3 @@ def test_MergeNifti_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/tests/test_auto_MeshFix.py b/nipype/interfaces/tests/test_auto_MeshFix.py index f1452ef49c..4c0fd67596 100644 --- a/nipype/interfaces/tests/test_auto_MeshFix.py +++ b/nipype/interfaces/tests/test_auto_MeshFix.py @@ -2,6 +2,7 @@ from ...testing import assert_equal from ..meshfix import MeshFix + def test_MeshFix_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -94,6 +95,7 @@ def test_MeshFix_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MeshFix_outputs(): output_map = dict(mesh_file=dict(), ) @@ -102,4 +104,3 @@ def test_MeshFix_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/tests/test_auto_MpiCommandLine.py b/nipype/interfaces/tests/test_auto_MpiCommandLine.py index cd715de2e2..57d1611f4d 100644 --- a/nipype/interfaces/tests/test_auto_MpiCommandLine.py +++ b/nipype/interfaces/tests/test_auto_MpiCommandLine.py @@ -2,6 +2,7 @@ from ...testing import assert_equal from ..base import MpiCommandLine + def test_MpiCommandLine_inputs(): input_map = dict(args=dict(argstr='%s', ), diff --git a/nipype/interfaces/tests/test_auto_MySQLSink.py b/nipype/interfaces/tests/test_auto_MySQLSink.py index c731c08151..7b4ff10c0c 100644 --- a/nipype/interfaces/tests/test_auto_MySQLSink.py +++ b/nipype/interfaces/tests/test_auto_MySQLSink.py @@ -2,6 +2,7 @@ from ...testing import assert_equal from ..io import MySQLSink + def test_MySQLSink_inputs(): input_map = dict(config=dict(mandatory=True, xor=['host'], diff --git a/nipype/interfaces/tests/test_auto_NiftiGeneratorBase.py b/nipype/interfaces/tests/test_auto_NiftiGeneratorBase.py index 2fa8d50ffe..762c862ed8 100644 --- a/nipype/interfaces/tests/test_auto_NiftiGeneratorBase.py +++ b/nipype/interfaces/tests/test_auto_NiftiGeneratorBase.py @@ -2,6 +2,7 @@ from ...testing import assert_equal from ..dcmstack import NiftiGeneratorBase + def test_NiftiGeneratorBase_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, diff --git a/nipype/interfaces/tests/test_auto_Rename.py b/nipype/interfaces/tests/test_auto_Rename.py index 4df470a6ed..1cace232fe 100644 --- a/nipype/interfaces/tests/test_auto_Rename.py +++ b/nipype/interfaces/tests/test_auto_Rename.py @@ -2,6 +2,7 @@ from ...testing import assert_equal from ..utility import Rename + def test_Rename_inputs(): input_map = dict(format_string=dict(mandatory=True, ), @@ -18,6 +19,7 @@ def test_Rename_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Rename_outputs(): output_map = dict(out_file=dict(), ) @@ -26,4 +28,3 @@ def test_Rename_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/tests/test_auto_S3DataGrabber.py b/nipype/interfaces/tests/test_auto_S3DataGrabber.py index d675d60cae..584134ca8f 100644 --- a/nipype/interfaces/tests/test_auto_S3DataGrabber.py +++ b/nipype/interfaces/tests/test_auto_S3DataGrabber.py @@ -2,6 +2,7 @@ from ...testing import assert_equal from ..io import S3DataGrabber + def test_S3DataGrabber_inputs(): input_map = dict(anon=dict(usedefault=True, ), @@ -29,6 +30,7 @@ def test_S3DataGrabber_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_S3DataGrabber_outputs(): output_map = dict() outputs = S3DataGrabber.output_spec() @@ -36,4 +38,3 @@ def test_S3DataGrabber_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/tests/test_auto_S3DataSink.py b/nipype/interfaces/tests/test_auto_S3DataSink.py index add9ddb5c2..9ef342defb 100644 --- a/nipype/interfaces/tests/test_auto_S3DataSink.py +++ b/nipype/interfaces/tests/test_auto_S3DataSink.py @@ -2,6 +2,7 @@ from ...testing import assert_equal from ..io import S3DataSink + def test_S3DataSink_inputs(): input_map = dict(_outputs=dict(usedefault=True, ), @@ -32,6 +33,7 @@ def test_S3DataSink_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_S3DataSink_outputs(): output_map = dict(out_file=dict(), ) @@ -40,4 +42,3 @@ def test_S3DataSink_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/tests/test_auto_SEMLikeCommandLine.py b/nipype/interfaces/tests/test_auto_SEMLikeCommandLine.py index 5c42df7910..8afc2cdec2 100644 --- a/nipype/interfaces/tests/test_auto_SEMLikeCommandLine.py +++ b/nipype/interfaces/tests/test_auto_SEMLikeCommandLine.py @@ -2,6 +2,7 @@ from ...testing import assert_equal from ..base import SEMLikeCommandLine + def test_SEMLikeCommandLine_inputs(): input_map = dict(args=dict(argstr='%s', ), diff --git a/nipype/interfaces/tests/test_auto_SQLiteSink.py b/nipype/interfaces/tests/test_auto_SQLiteSink.py index 5017acac00..f215e3e424 100644 --- a/nipype/interfaces/tests/test_auto_SQLiteSink.py +++ b/nipype/interfaces/tests/test_auto_SQLiteSink.py @@ -2,6 +2,7 @@ from ...testing import assert_equal from ..io import SQLiteSink + def test_SQLiteSink_inputs(): input_map = dict(database_file=dict(mandatory=True, ), diff --git a/nipype/interfaces/tests/test_auto_SSHDataGrabber.py b/nipype/interfaces/tests/test_auto_SSHDataGrabber.py index 0ab83b764b..cbec846af1 100644 --- a/nipype/interfaces/tests/test_auto_SSHDataGrabber.py +++ b/nipype/interfaces/tests/test_auto_SSHDataGrabber.py @@ -2,6 +2,7 @@ from ...testing import assert_equal from ..io import SSHDataGrabber + def test_SSHDataGrabber_inputs(): input_map = dict(base_directory=dict(mandatory=True, ), @@ -32,6 +33,7 @@ def test_SSHDataGrabber_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_SSHDataGrabber_outputs(): output_map = dict() outputs = SSHDataGrabber.output_spec() @@ -39,4 +41,3 @@ def test_SSHDataGrabber_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/tests/test_auto_Select.py b/nipype/interfaces/tests/test_auto_Select.py index 6509148edf..26d629da4c 100644 --- a/nipype/interfaces/tests/test_auto_Select.py +++ b/nipype/interfaces/tests/test_auto_Select.py @@ -2,6 +2,7 @@ from ...testing import assert_equal from ..utility import Select + def test_Select_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, @@ -17,6 +18,7 @@ def test_Select_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Select_outputs(): output_map = dict(out=dict(), ) @@ -25,4 +27,3 @@ def test_Select_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/tests/test_auto_SelectFiles.py b/nipype/interfaces/tests/test_auto_SelectFiles.py index b30a53d899..49cb40dcf6 100644 --- a/nipype/interfaces/tests/test_auto_SelectFiles.py +++ b/nipype/interfaces/tests/test_auto_SelectFiles.py @@ -2,6 +2,7 @@ from ...testing import assert_equal from ..io import SelectFiles + def test_SelectFiles_inputs(): input_map = dict(base_directory=dict(), force_lists=dict(usedefault=True, @@ -20,6 +21,7 @@ def test_SelectFiles_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_SelectFiles_outputs(): output_map = dict() outputs = SelectFiles.output_spec() @@ -27,4 +29,3 @@ def test_SelectFiles_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/tests/test_auto_SlicerCommandLine.py b/nipype/interfaces/tests/test_auto_SlicerCommandLine.py index f2a8e4b717..131c8f851c 100644 --- a/nipype/interfaces/tests/test_auto_SlicerCommandLine.py +++ b/nipype/interfaces/tests/test_auto_SlicerCommandLine.py @@ -2,6 +2,7 @@ from ...testing import assert_equal from ..dynamic_slicer import SlicerCommandLine + def test_SlicerCommandLine_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -21,6 +22,7 @@ def test_SlicerCommandLine_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_SlicerCommandLine_outputs(): output_map = dict() outputs = SlicerCommandLine.output_spec() @@ -28,4 +30,3 @@ def test_SlicerCommandLine_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/tests/test_auto_Split.py b/nipype/interfaces/tests/test_auto_Split.py index 596d6a51da..03da66dec6 100644 --- a/nipype/interfaces/tests/test_auto_Split.py +++ b/nipype/interfaces/tests/test_auto_Split.py @@ -2,6 +2,7 @@ from ...testing import assert_equal from ..utility import Split + def test_Split_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, @@ -19,6 +20,7 @@ def test_Split_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Split_outputs(): output_map = dict() outputs = Split.output_spec() @@ -26,4 +28,3 @@ def test_Split_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/tests/test_auto_SplitNifti.py b/nipype/interfaces/tests/test_auto_SplitNifti.py index bcd389a0ca..1a0ad4aa15 100644 --- a/nipype/interfaces/tests/test_auto_SplitNifti.py +++ b/nipype/interfaces/tests/test_auto_SplitNifti.py @@ -2,6 +2,7 @@ from ...testing import assert_equal from ..dcmstack import SplitNifti + def test_SplitNifti_inputs(): input_map = dict(in_file=dict(mandatory=True, ), @@ -17,6 +18,7 @@ def test_SplitNifti_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_SplitNifti_outputs(): output_map = dict(out_list=dict(), ) @@ -25,4 +27,3 @@ def test_SplitNifti_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/tests/test_auto_StdOutCommandLine.py b/nipype/interfaces/tests/test_auto_StdOutCommandLine.py index e7a3089553..6c91c5de40 100644 --- a/nipype/interfaces/tests/test_auto_StdOutCommandLine.py +++ b/nipype/interfaces/tests/test_auto_StdOutCommandLine.py @@ -2,6 +2,7 @@ from ...testing import assert_equal from ..base import StdOutCommandLine + def test_StdOutCommandLine_inputs(): input_map = dict(args=dict(argstr='%s', ), diff --git a/nipype/interfaces/tests/test_auto_XNATSink.py b/nipype/interfaces/tests/test_auto_XNATSink.py index ee35b059ca..dd681af29f 100644 --- a/nipype/interfaces/tests/test_auto_XNATSink.py +++ b/nipype/interfaces/tests/test_auto_XNATSink.py @@ -2,6 +2,7 @@ from ...testing import assert_equal from ..io import XNATSink + def test_XNATSink_inputs(): input_map = dict(_outputs=dict(usedefault=True, ), diff --git a/nipype/interfaces/tests/test_auto_XNATSource.py b/nipype/interfaces/tests/test_auto_XNATSource.py index 1744ce7eb5..297c050a22 100644 --- a/nipype/interfaces/tests/test_auto_XNATSource.py +++ b/nipype/interfaces/tests/test_auto_XNATSource.py @@ -2,6 +2,7 @@ from ...testing import assert_equal from ..io import XNATSource + def test_XNATSource_inputs(): input_map = dict(cache_dir=dict(), config=dict(mandatory=True, @@ -27,6 +28,7 @@ def test_XNATSource_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_XNATSource_outputs(): output_map = dict() outputs = XNATSource.output_spec() @@ -34,4 +36,3 @@ def test_XNATSource_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/vista/tests/test_auto_Vnifti2Image.py b/nipype/interfaces/vista/tests/test_auto_Vnifti2Image.py index 4996b2b8de..16abe83a0e 100644 --- a/nipype/interfaces/vista/tests/test_auto_Vnifti2Image.py +++ b/nipype/interfaces/vista/tests/test_auto_Vnifti2Image.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..vista import Vnifti2Image + def test_Vnifti2Image_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -34,6 +35,7 @@ def test_Vnifti2Image_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Vnifti2Image_outputs(): output_map = dict(out_file=dict(), ) @@ -42,4 +44,3 @@ def test_Vnifti2Image_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - diff --git a/nipype/interfaces/vista/tests/test_auto_VtoMat.py b/nipype/interfaces/vista/tests/test_auto_VtoMat.py index 713dd9dbc6..77c814dab5 100644 --- a/nipype/interfaces/vista/tests/test_auto_VtoMat.py +++ b/nipype/interfaces/vista/tests/test_auto_VtoMat.py @@ -2,6 +2,7 @@ from ....testing import assert_equal from ..vista import VtoMat + def test_VtoMat_inputs(): input_map = dict(args=dict(argstr='%s', ), @@ -31,6 +32,7 @@ def test_VtoMat_inputs(): for metakey, value in list(metadata.items()): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_VtoMat_outputs(): output_map = dict(out_file=dict(), ) @@ -39,4 +41,3 @@ def test_VtoMat_outputs(): for key, metadata in list(output_map.items()): for metakey, value in list(metadata.items()): yield assert_equal, getattr(outputs.traits()[key], metakey), value - From 0d00610d27a11484b859a87ff7ad89063a36b70c Mon Sep 17 00:00:00 2001 From: miykael Date: Sun, 1 Nov 2015 17:51:19 +0100 Subject: [PATCH 19/19] FIX: correction for docparse test that changed because of PEP8 W291 style correction --- nipype/utils/docparse.py | 3 +-- 1 file changed, 1 insertion(+), 2 deletions(-) diff --git a/nipype/utils/docparse.py b/nipype/utils/docparse.py index d95adb40bf..a445262a15 100644 --- a/nipype/utils/docparse.py +++ b/nipype/utils/docparse.py @@ -216,9 +216,8 @@ def build_doc(doc, opts): if attr is not None: # newline = line.replace(flag, attr) # Replace the flag with our attribute name - linelist[0] = '%s :' % str(attr) + linelist[0] = '%s :\n ' % str(attr) # Add some line formatting - linelist.insert(1, '\n ') newline = ' '.join(linelist) newdoc.append(newline) else: