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doc: fix rst formatting
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‎doc/devel/testing_nipype.rst‎

Lines changed: 1 addition & 1 deletion
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@@ -89,7 +89,7 @@ To enable the tests depending on these data, just unpack the targz file and set
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variable to point to that folder.
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Xfail tests
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~~~~~~~~~~
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~~~~~~~~~~~
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Some tests are expect to fail until the code will be changed or for other reasons.
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‎nipype/interfaces/base.py‎

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@@ -386,14 +386,6 @@ def _generate_handlers(self):
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"""Find all traits with the 'xor' metadata and attach an event
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handler to them.
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"""
389-
has_xor = dict(xor=lambda t: t is not None)
390-
xors = self.trait_names(**has_xor)
391-
for elem in xors:
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self.on_trait_change(self._xor_warn, elem)
393-
has_requires = dict(requires=lambda t: t is not None)
394-
requires = self.trait_names(**has_requires)
395-
for elem in requires:
396-
self.on_trait_change(self._requires_warn, elem)
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has_deprecation = dict(deprecated=lambda t: t is not None)
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deprecated = self.trait_names(**has_deprecation)
399391
for elem in deprecated:

‎nipype/interfaces/mipav/developer.py‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -658,7 +658,7 @@ class MedicAlgorithmSPECTRE2010(SEMLikeCommandLine):
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category: Developer Tools
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description: Simple Paradigm for Extra-Cranial Tissue REmoval
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################################################
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Algorithm Version: 1.6
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GUI Version: 1.10
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‎nipype/interfaces/niftyseg/em.py‎

Lines changed: 4 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -117,9 +117,8 @@ class EM(NiftySegCommand):
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it's simplest form, it takes in one 2D or 3D image and segments it in n
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classes.
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For source code, see http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg
121-
For Documentation, see:
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http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg_documentation
120+
`Source code <http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg>`_ |
121+
`Documentation <http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg_documentation>`_
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Examples
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--------
@@ -128,8 +127,8 @@ class EM(NiftySegCommand):
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>>> node.inputs.in_file = 'im1.nii'
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>>> node.inputs.no_prior = 4
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>>> node.cmdline # doctest: +ALLOW_UNICODE
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'seg_EM -in im1.nii -nopriors 4 -bc_out im1_bc_em.nii.gz \
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-out im1_em.nii.gz -out_outlier im1_outlier_em.nii.gz'
130+
'seg_EM -in im1.nii -nopriors 4 -bc_out im1_bc_em.nii.gz
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-out im1_em.nii.gz -out_outlier im1_outlier_em.nii.gz'
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"""
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_cmd = get_custom_path('seg_EM', env_dir='NIFTYSEGDIR')

‎nipype/interfaces/niftyseg/label_fusion.py‎

Lines changed: 3 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -133,9 +133,8 @@ class LabelFusion(NiftySegCommand):
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FusedSegmentation.nii -STEPS 2 15 TargetImage.nii \
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4D_Propagated_Intensities.nii
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136-
For source code, see http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg
137-
For Documentation, see:
138-
http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg_documentation
136+
`Source code <http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg>`_ |
137+
`Documentation <http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg_documentation>`_
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Examples
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--------
@@ -148,8 +147,7 @@ class LabelFusion(NiftySegCommand):
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>>> node.inputs.template_num = 2
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>>> node.inputs.classifier_type = 'STEPS'
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>>> node.cmdline # doctest: +ALLOW_UNICODE
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'seg_LabFusion -in im1.nii -STEPS 2.000000 2 im2.nii im3.nii -out \
152-
im1_steps.nii'
150+
'seg_LabFusion -in im1.nii -STEPS 2.000000 2 im2.nii im3.nii -out im1_steps.nii'
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"""
155153
_cmd = get_custom_path('seg_LabFusion', env_dir='NIFTYSEGDIR')

‎nipype/interfaces/niftyseg/lesions.py‎

Lines changed: 2 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -99,9 +99,8 @@ class FillLesions(NiftySegCommand):
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Fill all the masked lesions with WM intensity average.
101101
102-
For source code, see http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg
103-
For Documentation, see:
104-
http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg_documentation
102+
`Source code <http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg>`_ |
103+
`Documentation <http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg_documentation>`_
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Examples
107106
--------

‎nipype/interfaces/niftyseg/maths.py‎

Lines changed: 21 additions & 21 deletions
Original file line numberDiff line numberDiff line change
@@ -102,7 +102,8 @@ class UnaryMaths(MathsCommand):
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"""Interface for executable seg_maths from NiftySeg platform.
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Interface to use any unary mathematical operations that can be performed
105-
with the seg_maths command-line program. See below for those operations:
105+
with the seg_maths command-line program. See below for those operations::
106+
106107
-sqrt Square root of the image.
107108
-exp Exponential root of the image.
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-log Log of the image.
@@ -133,9 +134,8 @@ class UnaryMaths(MathsCommand):
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-4to5 Flip the 4th and 5th dimension.
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-range Reset the image range to the min max
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For source code, see http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg
137-
For Documentation, see:
138-
http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg_documentation
137+
`Source code <http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg>`_ |
138+
`Documentation <http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg_documentation>`_
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Examples
141141
--------
@@ -216,7 +216,8 @@ class BinaryMaths(MathsCommand):
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"""Interface for executable seg_maths from NiftySeg platform.
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Interface to use any binary mathematical operations that can be performed
219-
with the seg_maths command-line program. See below for those operations:
219+
with the seg_maths command-line program. See below for those operations::
220+
220221
-mul <float/file> Multiply image <float> value or by other image.
221222
-div <float/file> Divide image by <float> or by other image.
222223
-add <float/file> Add image by <float> or by other image.
@@ -248,9 +249,8 @@ class BinaryMaths(MathsCommand):
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-splitinter <x/y/z> Split interleaved slices in direction <x/y/z>
249250
into separate time points
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251-
For source code, see http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg
252-
For Documentation, see:
253-
http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg_documentation
252+
`Source code <http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg>`_ |
253+
`Documentation <http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg_documentation>`_
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Examples
256256
--------
@@ -348,8 +348,9 @@ class BinaryMathsInteger(MathsCommand):
348348
"""Interface for executable seg_maths from NiftySeg platform.
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350350
Interface to use any integer mathematical operations that can be performed
351-
with the seg_maths command-line program. See below for those operations:
352-
(requiring integer values)
351+
with the seg_maths command-line program. See below for those operations::
352+
353+
(requiring integer values)
353354
-equal <int> Get voxels equal to <int>
354355
-dil <int> Dilate the image <int> times (in voxels).
355356
-ero <int> Erode the image <int> times (in voxels).
@@ -358,9 +359,8 @@ class BinaryMathsInteger(MathsCommand):
358359
-pad <int> Pad <int> voxels with NaN value around each 3D
359360
volume.
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For source code, see http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg
362-
For Documentation, see:
363-
http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg_documentation
362+
`Source code <http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg>`_ |
363+
`Documentation <http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg_documentation>`_
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365365
Examples
366366
--------
@@ -436,17 +436,17 @@ class TupleMaths(MathsCommand):
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"""Interface for executable seg_maths from NiftySeg platform.
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Interface to use any tuple mathematical operations that can be performed
439-
with the seg_maths command-line program. See below for those operations:
439+
with the seg_maths command-line program. See below for those operations::
440+
440441
-lncc <file> <std> Local CC between current img and <file>
441442
on a kernel with <std>
442443
-lssd <file> <std> Local SSD between current img and <file>
443444
on a kernel with <std>
444445
-lltsnorm <file_norm> <float> Linear LTS normalisation assuming
445446
<float> percent outliers
446447
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For source code, see http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg
448-
For Documentation, see:
449-
http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg_documentation
448+
`Source code <http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg>`_ |
449+
`Documentation <http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg_documentation>`_
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Examples
452452
--------
@@ -504,13 +504,13 @@ class Merge(MathsCommand):
504504
"""Interface for executable seg_maths from NiftySeg platform.
505505
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Interface to use the merge operation that can be performed
507-
with the seg_maths command-line program. See below for this option:
507+
with the seg_maths command-line program. See below for this option::
508+
508509
-merge <i> <d> <files> Merge <i> images and the working image in the
509510
<d> dimension
510511
511-
For source code, see http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg
512-
For Documentation, see:
513-
http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg_documentation
512+
`Source code <http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg>`_ |
513+
`Documentation <http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg_documentation>`_
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Examples
516516
--------

‎nipype/interfaces/niftyseg/patchmatch.py‎

Lines changed: 2 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -96,9 +96,8 @@ class PatchMatch(NiftySegCommand):
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volumes than the input image allowing to propagate multiple labels
9797
in the same execution.
9898
99-
For source code, see http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg
100-
For Documentation, see:
101-
http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg_documentation
99+
`Source code <http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg>`_ |
100+
`Documentation <http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg_documentation>`_
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Examples
104103
--------

‎nipype/interfaces/niftyseg/stats.py‎

Lines changed: 8 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -103,7 +103,8 @@ class UnaryStats(StatsCommand):
103103
Interface for executable seg_stats from NiftySeg platform.
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Interface to use any unary statistical operations that can be performed
106-
with the seg_stats command-line program. See below for those operations:
106+
with the seg_stats command-line program. See below for those operations::
107+
107108
-r | The range <min max> of all voxels.
108109
-R | The robust range (assuming 2% outliers on both sides)
109110
| of all voxels
@@ -130,9 +131,8 @@ class UnaryStats(StatsCommand):
130131
-xdim | Output the voxel dimention in the x direction.
131132
| Replace x with y/z for other directions.
132133
133-
For source code, see http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg
134-
For Documentation, see:
135-
http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg_documentation
134+
`Source code <http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg>`_ |
135+
`Documentation <http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg_documentation>`_
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137137
Examples
138138
--------
@@ -191,7 +191,8 @@ class BinaryStats(StatsCommand):
191191
Interface for executable seg_stats from NiftySeg platform.
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193193
Interface to use any binary statistical operations that can be performed
194-
with the seg_stats command-line program. See below for those operations:
194+
with the seg_stats command-line program. See below for those operations::
195+
195196
-p <float> | The <float>th percentile of all voxels intensity
196197
| (float=[0,100])
197198
-sa <ax> | Average of all voxels
@@ -206,9 +207,8 @@ class BinaryStats(StatsCommand):
206207
-Vl <csv> | Volume of each integer label <in>. Save to <csv>file.
207208
-Nl <csv> | Count of each label <in>. Save to <csv> file.
208209
209-
For source code, see http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg
210-
For Documentation, see:
211-
http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg_documentation
210+
`Source code <http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg>`_ |
211+
`Documentation <http://cmictig.cs.ucl.ac.uk/wiki/index.php/NiftySeg_documentation>`_
212212
213213
Examples
214214
--------

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