Merge branch 'master' into master

Author: jdkent

nipype/algorithms/icc.py

@@ -8,7 +8,7 @@
 from scipy.linalg import pinv
 from ..interfaces.base import BaseInterfaceInputSpec, TraitedSpec, \
     BaseInterface, traits, File
-from nipype.utils import NUMPY_MMAP
+from ..utils import NUMPY_MMAP
 
 
 class ICCInputSpec(BaseInterfaceInputSpec):

nipype/algorithms/metrics.py

@@ -30,7 +30,7 @@
 from ..interfaces.base import (BaseInterface, traits, TraitedSpec, File,
                                InputMultiPath,
                                BaseInterfaceInputSpec, isdefined)
-from nipype.utils import NUMPY_MMAP
+from ..utils import NUMPY_MMAP
 
 iflogger = logging.getLogger('interface')
 

nipype/algorithms/misc.py

@@ -34,7 +34,7 @@
                                BaseInterfaceInputSpec, isdefined,
                                DynamicTraitedSpec, Undefined)
 from ..utils.filemanip import fname_presuffix, split_filename
-from nipype.utils import NUMPY_MMAP
+from ..utils import NUMPY_MMAP
 
 from . import confounds
 

nipype/interfaces/afni/__init__.py

@@ -20,4 +20,4 @@
 from .utils import (AFNItoNIFTI, Autobox, BrickStat, Calc, Copy,
                     Eval, FWHMx,
                     MaskTool, Merge, Notes, Refit, Resample, TCat, TStat, To3D,
-                    Unifize, ZCutUp,)
+                    Unifize, ZCutUp, GCOR,)

nipype/interfaces/afni/tests/test_auto_GCOR.py

@@ -0,0 +1,44 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
+from ..utils import GCOR
+
+
+def test_GCOR_inputs():
+    input_map = dict(args=dict(argstr='%s',
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    in_file=dict(argstr='-input %s',
+    copyfile=False,
+    mandatory=True,
+    position=-1,
+    ),
+    mask=dict(argstr='-mask %s',
+    copyfile=False,
+    ),
+    nfirst=dict(argstr='-nfirst %d',
+    ),
+    no_demean=dict(argstr='-no_demean',
+    ),
+    terminal_output=dict(nohash=True,
+    ),
+    )
+    inputs = GCOR.input_spec()
+
+    for key, metadata in list(input_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(inputs.traits()[key], metakey) == value
+
+
+def test_GCOR_outputs():
+    output_map = dict(out=dict(),
+    )
+    outputs = GCOR.output_spec()
+
+    for key, metadata in list(output_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(outputs.traits()[key], metakey) == value

nipype/interfaces/afni/utils.py

@@ -1378,3 +1378,66 @@ class ZCutUp(AFNICommand):
     _cmd = '3dZcutup'
     input_spec = ZCutUpInputSpec
     output_spec = AFNICommandOutputSpec
+
+
+class GCORInputSpec(CommandLineInputSpec):
+    in_file = File(
+        desc='input dataset to compute the GCOR over',
+        argstr='-input %s',
+        position=-1,
+        mandatory=True,
+        exists=True,
+        copyfile=False)
+
+    mask = File(
+        desc='mask dataset, for restricting the computation',
+        argstr='-mask %s',
+        exists=True,
+        copyfile=False)
+
+    nfirst = traits.Int(0, argstr='-nfirst %d',
+                        desc='specify number of initial TRs to ignore')
+    no_demean = traits.Bool(False, argstr='-no_demean',
+                            desc='do not (need to) demean as first step')
+
+
+class GCOROutputSpec(TraitedSpec):
+    out = traits.Float(desc='global correlation value')
+
+
+class GCOR(CommandLine):
+    """
+    Computes the average correlation between every voxel
+    and ever other voxel, over any give mask.
+
+
+    For complete details, see the `@compute_gcor Documentation.
+    <https://afni.nimh.nih.gov/pub/dist/doc/program_help/@compute_gcor.html>`_
+
+    Examples
+    ========
+
+    >>> from nipype.interfaces import afni
+    >>> gcor = afni.GCOR()
+    >>> gcor.inputs.in_file = 'structural.nii'
+    >>> gcor.inputs.nfirst = 4
+    >>> gcor.cmdline  # doctest: +ALLOW_UNICODE
+    '@compute_gcor -nfirst 4 -input structural.nii'
+    >>> res = gcor.run()  # doctest: +SKIP
+
+    """
+
+    _cmd = '@compute_gcor'
+    input_spec = GCORInputSpec
+    output_spec = GCOROutputSpec
+
+    def _run_interface(self, runtime):
+        runtime = super(GCOR, self)._run_interface(runtime)
+
+        gcor_line = [line.strip() for line in runtime.stdout.split('\n')
+                     if line.strip().startswith('GCOR = ')][-1]
+        setattr(self, '_gcor', float(gcor_line[len('GCOR = '):]))
+        return runtime
+
+    def _list_outputs(self):
+        return {'out': getattr(self, '_gcor')}

nipype/interfaces/ants/registration.py

@@ -354,6 +354,16 @@ class RegistrationInputSpec(ANTSCommandInputSpec):
                                                                   ),
                                                      )
                                        )
+    restrict_deformation = traits.List(
+        traits.List(traits.Enum(0, 1)),
+        desc=("This option allows the user to restrict the optimization of "
+              "the displacement field, translation, rigid or affine transform "
+              "on a per-component basis. For example, if one wants to limit "
+              "the deformation or rotation of 3-D volume to the  first two "
+              "dimensions, this is possible by specifying a weight vector of "
+              "'1x1x0' for a deformation field or '1x1x0x1x1x0' for a rigid "
+              "transformation.  Low-dimensional restriction only works if "
+              "there are no preceding transformations."))
     # Convergence flags
     number_of_iterations = traits.List(traits.List(traits.Int()))
     smoothing_sigmas = traits.List(traits.List(traits.Float()), mandatory=True)
@@ -770,6 +780,9 @@ def _format_registration(self):
                 else:
                     histval = self.inputs.use_histogram_matching[ii]
                 retval.append('--use-histogram-matching %d' % histval)
+            if isdefined(self.inputs.restrict_deformation):
+                retval.append('--restrict-deformation %s' %
+                              self._format_xarray(self.inputs.restrict_deformation[ii]))
         return " ".join(retval)
 
     def _get_outputfilenames(self, inverse=False):

nipype/interfaces/ants/tests/test_auto_Registration.py

@@ -79,6 +79,7 @@ def test_Registration_inputs():
     ),
     restore_state=dict(argstr='--restore-state %s',
     ),
+    restrict_deformation=dict(),
     sampling_percentage=dict(requires=['sampling_strategy'],
     ),
     sampling_percentage_item_trait=dict(),

nipype/interfaces/dipy/preprocess.py

@@ -13,6 +13,8 @@
 import nibabel as nb
 import numpy as np
 
+from ...utils import NUMPY_MMAP
+
 from ... import logging
 from ..base import (traits, TraitedSpec, File, isdefined)
 from .base import DipyBaseInterface
@@ -179,7 +181,6 @@ def resample_proxy(in_file, order=3, new_zooms=None, out_file=None):
     Performs regridding of an image to set isotropic voxel sizes using dipy.
     """
     from dipy.align.reslice import reslice
-    from nipype.utils import NUMPY_MMAP
 
     if out_file is None:
         fname, fext = op.splitext(op.basename(in_file))
@@ -223,7 +224,6 @@ def nlmeans_proxy(in_file, settings,
     from dipy.denoise.nlmeans import nlmeans
     from scipy.ndimage.morphology import binary_erosion
     from scipy import ndimage
-    from nipype.utils import NUMPY_MMAP
 
     if out_file is None:
         fname, fext = op.splitext(op.basename(in_file))

nipype/interfaces/fsl/ICA_AROMA.py

@@ -10,18 +10,13 @@
     ...                            '../../testing/data'))
     >>> os.chdir(datadir)
 """
-from nipype.interfaces.base import (
-    TraitedSpec,
-    CommandLineInputSpec,
-    CommandLine,
-    File,
-    Directory,
-    traits,
-    OutputMultiPath,
-    isdefined
-)
+
+from __future__ import print_function, division, unicode_literals, absolute_import
+from ..base import (TraitedSpec, CommandLineInputSpec, CommandLine,
+                    File, Directory, traits)
 import os
 
+
 class ICA_AROMAInputSpec(CommandLineInputSpec):
     feat_dir = Directory(exists=True, mandatory=True,
                          argstr='-feat %s',

nipype/interfaces/fsl/fix.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 """The fix module provides classes for interfacing with the `FSL FIX
@@ -53,8 +54,9 @@
 outgraph = fix_pipeline.run()
 
 """
+from __future__ import print_function, division, unicode_literals, absolute_import
 
-from nipype.interfaces.base import (
+from ..base import (
     TraitedSpec,
     CommandLineInputSpec,
     CommandLine,
@@ -64,13 +66,10 @@
     BaseInterfaceInputSpec,
     traits
 )
-from nipype.interfaces.traits_extension import (
-    Directory,
-    File,
-    isdefined
-)
+from ..traits_extension import Directory, File, isdefined
 import os
 
+
 class TrainingSetCreatorInputSpec(BaseInterfaceInputSpec):
     mel_icas_in = InputMultiPath(Directory(exists=True), copyfile=False,
                               desc='Melodic output directories',

nipype/interfaces/niftyseg/base.py

@@ -1,3 +1,4 @@
+# -*- coding: utf-8 -*-
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
 
@@ -15,9 +16,10 @@
 --------
 See the docstrings of the individual classes for examples.
 """
+from __future__ import print_function, division, unicode_literals, absolute_import
 
-from nipype.interfaces.niftyreg.base import no_nifty_package
-from nipype.interfaces.niftyfit.base import NiftyFitCommand
+from ..niftyreg.base import no_nifty_package
+from ..niftyfit.base import NiftyFitCommand
 import subprocess
 import warnings
 

nipype/interfaces/petpvc.py

@@ -13,7 +13,8 @@
 import os
 
 from .base import TraitedSpec, CommandLineInputSpec, CommandLine, File, isdefined, traits
-from ..external.due import due, Doi, BibTeX
+from ..utils.filemanip import fname_presuffix
+from ..external.due import BibTeX
 
 pvc_methods = ['GTM',
                'IY',
@@ -200,8 +201,6 @@ def _gen_fname(self, basename, cwd=None, suffix=None, change_ext=True,
             New filename based on given parameters.
 
         """
-        from nipype.utils.filemanip import fname_presuffix
-
         if basename == '':
             msg = 'Unable to generate filename for command %s. ' % self.cmd
             msg += 'basename is not set!'

nipype/interfaces/utility/wrappers.py

@@ -19,9 +19,9 @@
 
 from builtins import str, bytes
 
-from nipype import logging
+from ... import logging
 from ..base import (traits, DynamicTraitedSpec, Undefined, isdefined, runtime_profile,
-                    BaseInterfaceInputSpec)
+                    BaseInterfaceInputSpec, get_max_resources_used)
 from ..io import IOBase, add_traits
 from ...utils.filemanip import filename_to_list
 from ...utils.misc import getsource, create_function_from_source
@@ -138,7 +138,6 @@ def _add_output_traits(self, base):
 
     def _run_interface(self, runtime):
         # Get workflow logger for runtime profile error reporting
-        from nipype import logging
         logger = logging.getLogger('workflow')
 
         # Create function handle
@@ -163,7 +162,6 @@ def _function_handle_wrapper(queue, **kwargs):
 
         # Profile resources if set
         if runtime_profile:
-            from nipype.interfaces.base import get_max_resources_used
             import multiprocessing
             # Init communication queue and proc objs
             queue = multiprocessing.Queue()

nipype/pipeline/engine/utils.py

@@ -1,4 +1,3 @@
-#!/usr/bin/env python
 # -*- coding: utf-8 -*-
 # emacs: -*- mode: python; py-indent-offset: 4; indent-tabs-mode: nil -*-
 # vi: set ft=python sts=4 ts=4 sw=4 et:
@@ -24,7 +23,7 @@
 import pickle
 from functools import reduce
 import numpy as np
-from nipype.utils.misc import package_check
+from ...utils.misc import package_check
 
 package_check('networkx', '1.3')
 

nipype/pipeline/plugins/pbs.py

@@ -49,8 +49,13 @@ def _is_pending(self, taskid):
                              environ=dict(os.environ),
                              terminal_output='allatonce',
                              ignore_exception=True).run()
+        stderr = result.runtime.stderr
         errmsg = 'Unknown Job Id'  # %s' % taskid
-        return errmsg not in result.runtime.stderr
+        success = 'Job has finished'
+        if success in e:  # Fix for my PBS
+            return False
+        else:
+            return errmsg not in e
 
     def _submit_batchtask(self, scriptfile, node):
         cmd = CommandLine('qsub', environ=dict(os.environ),

nipype/utils/__init__.py

@@ -1,6 +1,6 @@
 # -*- coding: utf-8 -*-
 from __future__ import absolute_import
 
-from nipype.utils.config import NUMPY_MMAP
-from nipype.utils.onetime import OneTimeProperty, setattr_on_read
-from nipype.utils.tmpdirs import TemporaryDirectory, InTemporaryDirectory
+from .config import NUMPY_MMAP
+from .onetime import OneTimeProperty, setattr_on_read
+from .tmpdirs import TemporaryDirectory, InTemporaryDirectory