Extended MRtrix3 interface

Author: matteomancini

.zenodo.json

@@ -538,6 +538,10 @@
       "affiliation": "MIT",
       "name": "Kaczmarzyk, Jakub",
       "orcid": "0000-0002-5544-7577"
+    },
+    {
+      "affiliation": "University College London"
+      "name": "Mancini, Matteo"
     }
   ],
   "keywords": [

doc/users/config_file.rst

@@ -74,11 +74,11 @@ Execution
 
 *display_variable*
 	Override the ``$DISPLAY`` environment variable for interfaces that require
-    an X server. This option is useful if there is a running X server, but 
-    ``$DISPLAY`` was not defined in nipype's environment. For example, if an X 
+    an X server. This option is useful if there is a running X server, but
+    ``$DISPLAY`` was not defined in nipype's environment. For example, if an X
     server is listening on the default port of 6000, set ``display_variable = :0``
-    to enable nipype interfaces to use it. It may also point to displays provided 
-    by VNC, `xnest <http://www.x.org/archive/X11R7.5/doc/man/man1/Xnest.1.html>`_ 
+    to enable nipype interfaces to use it. It may also point to displays provided
+    by VNC, `xnest <http://www.x.org/archive/X11R7.5/doc/man/man1/Xnest.1.html>`_
     or `Xvfb <http://www.x.org/archive/X11R6.8.1/doc/Xvfb.1.html>`_.
     If neither ``display_variable`` nor the ``$DISPLAY`` environment variable are
     set, nipype will try to configure a new virtual server using Xvfb.

doc/users/plugins.rst

@@ -82,9 +82,9 @@ Optional arguments::
   exceed the total amount of resources available (memory and threads), when
   ``False`` (default), only a warning will be issued.
 
-  maxtasksperchild : number of nodes to run on each process before refreshing 
+  maxtasksperchild : number of nodes to run on each process before refreshing
   the worker (default: 10).
-  
+
 
 To distribute processing on a multicore machine, simply call::
 

nipype/algorithms/tests/test_auto_CompCor.py

@@ -0,0 +1,53 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
+from ..confounds import CompCor
+
+
+def test_CompCor_inputs():
+    input_map = dict(components_file=dict(usedefault=True,
+    ),
+    header_prefix=dict(),
+    high_pass_cutoff=dict(usedefault=True,
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    ignore_initial_volumes=dict(usedefault=True,
+    ),
+    mask_files=dict(),
+    mask_index=dict(requires=['mask_files'],
+    xor=['merge_method'],
+    ),
+    merge_method=dict(requires=['mask_files'],
+    xor=['mask_index'],
+    ),
+    num_components=dict(usedefault=True,
+    ),
+    pre_filter=dict(usedefault=True,
+    ),
+    realigned_file=dict(mandatory=True,
+    ),
+    regress_poly_degree=dict(usedefault=True,
+    ),
+    repetition_time=dict(),
+    save_pre_filter=dict(),
+    use_regress_poly=dict(deprecated='0.15.0',
+    new_name='pre_filter',
+    ),
+    )
+    inputs = CompCor.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_CompCor_outputs():
+    output_map = dict(components_file=dict(),
+    pre_filter_file=dict(),
+    )
+    outputs = CompCor.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/algorithms/tests/test_auto_ErrorMap.py

@@ -0,0 +1,35 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
+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()):
+            assert 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()):
+            assert getattr(outputs.traits()[key], metakey) == value

nipype/algorithms/tests/test_auto_Overlap.py

@@ -0,0 +1,47 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
+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()):
+            assert 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()):
+            assert getattr(outputs.traits()[key], metakey) == value

nipype/algorithms/tests/test_auto_TSNR.py

@@ -0,0 +1,43 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
+from ..misc import TSNR
+
+
+def test_TSNR_inputs():
+    input_map = dict(detrended_file=dict(hash_files=False,
+    usedefault=True,
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    in_file=dict(mandatory=True,
+    ),
+    mean_file=dict(hash_files=False,
+    usedefault=True,
+    ),
+    regress_poly=dict(),
+    stddev_file=dict(hash_files=False,
+    usedefault=True,
+    ),
+    tsnr_file=dict(hash_files=False,
+    usedefault=True,
+    ),
+    )
+    inputs = TSNR.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_TSNR_outputs():
+    output_map = dict(detrended_file=dict(),
+    mean_file=dict(),
+    stddev_file=dict(),
+    tsnr_file=dict(),
+    )
+    outputs = TSNR.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/algorithms/tests/test_mesh_ops.py

@@ -15,7 +15,7 @@
 
 @pytest.mark.skipif(VTKInfo.no_tvtk(), reason="tvtk is not installed")
 def test_ident_distances(tmpdir):
-    tmpdir.chdir() 
+    tmpdir.chdir()
 
     in_surf = example_data('surf01.vtk')
     dist_ident = m.ComputeMeshWarp()

nipype/interfaces/afni/preprocess.py

@@ -3490,7 +3490,7 @@ class Qwarp(AFNICommand):
     >>> qwarp3.inputs.base_file = 'mni.nii'
     >>> qwarp3.inputs.allineate = True
     >>> qwarp3.inputs.allineate_opts = '-cose lpa -verb'
-    >>> qwarp3.cmdline
+    >>> qwarp3.cmdline  # doctest: +ALLOW_UNICODE
     "3dQwarp -allineate -allineate_opts '-cose lpa -verb' -base mni.nii -source structural.nii -prefix structural_QW"
     >>> res3 = qwarp3.run()  # doctest: +SKIP    """
     _cmd = '3dQwarp'

nipype/interfaces/afni/tests/test_auto_TCatSubBrick.py

@@ -0,0 +1,48 @@
+# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT
+from __future__ import unicode_literals
+from ..utils import TCatSubBrick
+
+
+def test_TCatSubBrick_inputs():
+    input_map = dict(args=dict(argstr='%s',
+    ),
+    environ=dict(nohash=True,
+    usedefault=True,
+    ),
+    ignore_exception=dict(nohash=True,
+    usedefault=True,
+    ),
+    in_files=dict(argstr='%s%s ...',
+    copyfile=False,
+    mandatory=True,
+    position=-1,
+    ),
+    num_threads=dict(nohash=True,
+    usedefault=True,
+    ),
+    out_file=dict(argstr='-prefix %s',
+    genfile=True,
+    ),
+    outputtype=dict(),
+    rlt=dict(argstr='-rlt%s',
+    position=1,
+    ),
+    terminal_output=dict(deprecated='1.0.0',
+    nohash=True,
+    ),
+    )
+    inputs = TCatSubBrick.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_TCatSubBrick_outputs():
+    output_map = dict(out_file=dict(),
+    )
+    outputs = TCatSubBrick.output_spec()
+
+    for key, metadata in list(output_map.items()):
+        for metakey, value in list(metadata.items()):
+            assert getattr(outputs.traits()[key], metakey) == value