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19 files changed

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-152
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‎nipype/info.py

Lines changed: 8 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -160,14 +160,14 @@ def get_nipype_gitversion():
160160
EXTRA_REQUIRES = {
161161
"data": ["datalad"],
162162
"doc": [
163-
'dipy',
164-
'ipython',
165-
'matplotlib',
166-
'nbsphinx',
167-
'sphinx-argparse',
168-
'sphinx>=2.1.2',
169-
'sphinxcontrib-apidoc',
170-
'sphinxcontrib-napoleon',
163+
"dipy",
164+
"ipython",
165+
"matplotlib",
166+
"nbsphinx",
167+
"sphinx-argparse",
168+
"sphinx>=2.1.2",
169+
"sphinxcontrib-apidoc",
170+
"sphinxcontrib-napoleon",
171171
],
172172
"duecredit": ["duecredit"],
173173
"nipy": ["nitime", "nilearn<0.5.0", "dipy", "nipy", "matplotlib"],

‎nipype/interfaces/afni/preprocess.py

Lines changed: 6 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -3483,7 +3483,8 @@ class QwarpInputSpec(AFNICommandInputSpec):
34833483
or the inverse can be computed as needed in 3dNwarpApply, like
34843484
3dNwarpApply -nwarp 'INV(Z_WARP+tlrc)' -source Dataset.nii ...
34853485
3486-
""")
3486+
""",
3487+
)
34873488
resample = traits.Bool(
34883489
desc="""\
34893490
This option simply resamples the source dataset to match the
@@ -3579,7 +3580,8 @@ class QwarpInputSpec(AFNICommandInputSpec):
35793580
use the option '-penold'.To be completely compatible with
35803581
the older 3dQwarp, you'll also have to use '-penfac 0.2'.
35813582
3582-
""")
3583+
""",
3584+
)
35833585
noweight = traits.Bool(
35843586
desc="If you want a binary weight (the old default), use this option."
35853587
"That is, each voxel in the base volume automask will be"
@@ -3624,7 +3626,7 @@ class QwarpInputSpec(AFNICommandInputSpec):
36243626
argstr="-wball %s",
36253627
minlen=5,
36263628
maxlen=5,
3627-
xor=['wmask'],
3629+
xor=["wmask"],
36283630
)
36293631
traits.Tuple((traits.Float(), traits.Float()), argstr="-bpass %f %f")
36303632
wmask = traits.Tuple(
@@ -3643,7 +3645,7 @@ class QwarpInputSpec(AFNICommandInputSpec):
36433645
36443646
""",
36453647
argstr="-wpass %s %f",
3646-
xor=['wball'],
3648+
xor=["wball"],
36473649
)
36483650
out_weight_file = File(
36493651
argstr="-wtprefix %s", desc="Write the weight volume to disk as a dataset"

‎nipype/interfaces/afni/utils.py

Lines changed: 15 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -1034,24 +1034,35 @@ class Edge3(AFNICommand):
10341034
input_spec = Edge3InputSpec
10351035
output_spec = AFNICommandOutputSpec
10361036
references_ = [
1037-
{'entry': BibTeX("""\
1037+
{
1038+
"entry": BibTeX(
1039+
"""\
10381040
@article{Deriche1987,
10391041
author={R. Deriche},
10401042
title={Optimal edge detection using recursive filtering},
10411043
journal={International Journal of Computer Vision},
10421044
volume={2},'
10431045
pages={167-187},
10441046
year={1987},
1045-
}"""), 'tags': ['method']},
1046-
{'entry': BibTeX("""\
1047+
}"""
1048+
),
1049+
"tags": ["method"],
1050+
},
1051+
{
1052+
"entry": BibTeX(
1053+
"""\
10471054
@article{MongaDericheMalandainCocquerez1991,
10481055
author={O. Monga, R. Deriche, G. Malandain, J.P. Cocquerez},
10491056
title={Recursive filtering and edge tracking: two primary tools for 3D edge detection},
10501057
journal={Image and vision computing},
10511058
volume={9},'
10521059
pages={203-214},
10531060
year={1991},
1054-
}"""), 'tags': ['method']}]
1061+
}"""
1062+
),
1063+
"tags": ["method"],
1064+
},
1065+
]
10551066

10561067

10571068
class EvalInputSpec(AFNICommandInputSpec):

‎nipype/interfaces/ants/segmentation.py

Lines changed: 8 additions & 14 deletions
Original file line numberDiff line numberDiff line change
@@ -610,9 +610,7 @@ class CorticalThicknessInputSpec(ANTSCommandInputSpec):
610610
0,
611611
1,
612612
argstr="-u %d",
613-
desc=(
614-
"Use random number generated from system clock in Atropos (default = 1)"
615-
),
613+
desc=("Use random number generated from system clock in Atropos (default = 1)"),
616614
)
617615
b_spline_smoothing = traits.Bool(
618616
argstr="-v",
@@ -855,9 +853,7 @@ class BrainExtractionInputSpec(ANTSCommandInputSpec):
855853
"highres001_",
856854
argstr="-o %s",
857855
usedefault=True,
858-
desc=(
859-
"Prefix that is prepended to all output files"
860-
),
856+
desc=("Prefix that is prepended to all output files"),
861857
)
862858

863859
extraction_registration_mask = File(
@@ -879,9 +875,7 @@ class BrainExtractionInputSpec(ANTSCommandInputSpec):
879875
0,
880876
1,
881877
argstr="-u %d",
882-
desc=(
883-
"Use random number generated from system clock in Atropos (default = 1)"
884-
),
878+
desc=("Use random number generated from system clock in Atropos (default = 1)"),
885879
)
886880
keep_temporary_files = traits.Int(
887881
argstr="-k %d",
@@ -1156,9 +1150,7 @@ class JointFusionInputSpec(ANTSCommandInputSpec):
11561150
minlen=3,
11571151
maxlen=3,
11581152
argstr="-rp %s",
1159-
desc=(
1160-
"Patch radius for similarity measures, scalar or vector. Default: 2x2x2"
1161-
),
1153+
desc=("Patch radius for similarity measures, scalar or vector. Default: 2x2x2"),
11621154
)
11631155
search_radius = traits.ListInt(
11641156
minlen=3, maxlen=3, argstr="-rs %s", desc="Local search radius. Default: 3x3x3"
@@ -1816,7 +1808,8 @@ class KellyKapowski(ANTSCommand):
18161808

18171809
references_ = [
18181810
{
1819-
"entry": BibTeX("""\
1811+
"entry": BibTeX(
1812+
"""\
18201813
@book{Das2009867,
18211814
author={Sandhitsu R. Das and Brian B. Avants and Murray Grossman and James C. Gee},
18221815
title={Registration based cortical thickness measurement.},
@@ -1828,7 +1821,8 @@ class KellyKapowski(ANTSCommand):
18281821
issn={1053-8119},
18291822
url={http://www.sciencedirect.com/science/article/pii/S1053811908012780},
18301823
doi={https://doi.org/10.1016/j.neuroimage.2008.12.016}
1831-
}"""),
1824+
}"""
1825+
),
18321826
"description": "The details on the implementation of DiReCT.",
18331827
"tags": ["implementation"],
18341828
}

‎nipype/interfaces/ants/visualization.py

Lines changed: 17 additions & 8 deletions
Original file line numberDiff line numberDiff line change
@@ -32,8 +32,21 @@ class ConvertScalarImageToRGBInputSpec(ANTSCommandInputSpec):
3232
"none", argstr="%s", exists=True, desc="mask image", position=3, usedefault=True
3333
)
3434
colormap = traits.Enum(
35-
"grey", "red", "green", "blue", "copper", "jet", "hsv", "spring", "summer",
36-
"autumn", "winter", "hot", "cool", "overunder", "custom",
35+
"grey",
36+
"red",
37+
"green",
38+
"blue",
39+
"copper",
40+
"jet",
41+
"hsv",
42+
"spring",
43+
"summer",
44+
"autumn",
45+
"winter",
46+
"hot",
47+
"cool",
48+
"overunder",
49+
"custom",
3750
argstr="%s",
3851
desc="Select a colormap",
3952
mandatory=True,
@@ -48,12 +61,8 @@ class ConvertScalarImageToRGBInputSpec(ANTSCommandInputSpec):
4861
maximum_input = traits.Int(
4962
argstr="%d", desc="maximum input", mandatory=True, position=7
5063
)
51-
minimum_RGB_output = traits.Int(
52-
0, usedefault=True, argstr="%d", position=8
53-
)
54-
maximum_RGB_output = traits.Int(
55-
255, usedefault=True, argstr="%d", position=9
56-
)
64+
minimum_RGB_output = traits.Int(0, usedefault=True, argstr="%d", position=8)
65+
maximum_RGB_output = traits.Int(255, usedefault=True, argstr="%d", position=9)
5766

5867

5968
class ConvertScalarImageToRGBOutputSpec(TraitedSpec):

‎nipype/interfaces/diffusion_toolkit/dti.py

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -210,12 +210,12 @@ class DTITrackerInputSpec(CommandLineInputSpec):
210210
)
211211
angle_threshold_weight = traits.Float(
212212
desc="set angle threshold weighting factor. weighting will be be applied "
213-
"on top of the angle_threshold",
213+
"on top of the angle_threshold",
214214
argstr="-atw %f",
215215
)
216216
random_seed = traits.Int(
217217
desc="use random location in a voxel instead of the center of the voxel "
218-
"to seed. can also define number of seed per voxel. default is 1",
218+
"to seed. can also define number of seed per voxel. default is 1",
219219
argstr="-rseed %d",
220220
)
221221
invert_x = traits.Bool(desc="invert x component of the vector", argstr="-ix")
@@ -229,13 +229,13 @@ class DTITrackerInputSpec(CommandLineInputSpec):
229229
)
230230
mask1_threshold = traits.Float(
231231
desc="threshold value for the first mask image, if not given, the program will "
232-
"try automatically find the threshold",
232+
"try automatically find the threshold",
233233
position=3,
234234
)
235235
mask2_file = File(desc="second mask image", argstr="-m2 %s", position=4)
236236
mask2_threshold = traits.Float(
237237
desc="threshold value for the second mask image, if not given, the program will "
238-
"try automatically find the threshold",
238+
"try automatically find the threshold",
239239
position=5,
240240
)
241241
input_data_prefix = traits.Str(

‎nipype/interfaces/diffusion_toolkit/odf.py

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -297,13 +297,13 @@ class ODFTrackerInputSpec(CommandLineInputSpec):
297297
)
298298
mask1_threshold = traits.Float(
299299
desc="threshold value for the first mask image, if not given, the program will "
300-
"try automatically find the threshold",
300+
"try automatically find the threshold",
301301
position=3,
302302
)
303303
mask2_file = File(desc="second mask image", argstr="-m2 %s", position=4)
304304
mask2_threshold = traits.Float(
305305
desc="threshold value for the second mask image, if not given, the program will "
306-
"try automatically find the threshold",
306+
"try automatically find the threshold",
307307
position=5,
308308
)
309309
limit = traits.Int(

‎nipype/interfaces/freesurfer/model.py

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -175,8 +175,8 @@ class MRISPreprocReconAllInputSpec(MRISPreprocInputSpec):
175175
)
176176
copy_inputs = traits.Bool(
177177
desc="If running as a node, set this to True "
178-
"this will copy some implicit inputs to the "
179-
"node directory."
178+
"this will copy some implicit inputs to the "
179+
"node directory."
180180
)
181181

182182

@@ -1073,8 +1073,8 @@ class SegStatsReconAllInputSpec(SegStatsInputSpec):
10731073
aseg = File(exists=True, desc="Mandatory implicit input in 5.3")
10741074
copy_inputs = traits.Bool(
10751075
desc="If running as a node, set this to True "
1076-
"otherwise, this will copy the implicit inputs "
1077-
"to the node directory."
1076+
"otherwise, this will copy the implicit inputs "
1077+
"to the node directory."
10781078
)
10791079

10801080

‎nipype/interfaces/freesurfer/utils.py

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -1685,7 +1685,7 @@ class SmoothTessellationInputSpec(FSTraitedSpec):
16851685
argstr="-n %d", desc="Number of smoothing iterations (default=10)"
16861686
)
16871687
snapshot_writing_iterations = traits.Int(
1688-
argstr="-w %d", desc='Write snapshot every *n* iterations'
1688+
argstr="-w %d", desc="Write snapshot every *n* iterations"
16891689
)
16901690

16911691
use_gaussian_curvature_smoothing = traits.Bool(
@@ -3835,8 +3835,8 @@ class Aparc2AsegInputSpec(FSTraitedSpec):
38353835
a2009s = traits.Bool(argstr="--a2009s", desc="Using the a2009s atlas")
38363836
copy_inputs = traits.Bool(
38373837
desc="If running as a node, set this to True."
3838-
"This will copy the input files to the node "
3839-
"directory."
3838+
"This will copy the input files to the node "
3839+
"directory."
38403840
)
38413841

38423842

‎nipype/interfaces/niftyseg/maths.py

Lines changed: 11 additions & 5 deletions
Original file line numberDiff line numberDiff line change
@@ -149,7 +149,8 @@ class UnaryMathsInput(MathsInput):
149149
* 4to5 - Flip the 4th and 5th dimension.
150150
* range - Reset the image range to the min max.
151151
152-
""")
152+
""",
153+
)
153154

154155

155156
class UnaryMaths(MathsCommand):
@@ -406,7 +407,8 @@ class BinaryMathsInputInteger(MathsInput):
406407
* crop - <int> - Crop <int> voxels around each 3D volume.
407408
* pad - <int> - Pad <int> voxels with NaN value around each 3D volume.
408409
409-
""")
410+
""",
411+
)
410412

411413
operand_value = traits.Int(
412414
argstr="%d",
@@ -475,7 +477,8 @@ class TupleMathsInput(MathsInput):
475477
* lssd <file> <std> Local SSD between current img and <file> on a kernel with <std>
476478
* lltsnorm <file_norm> <float> Linear LTS normalisation assuming <float> percent outliers
477479
478-
""")
480+
""",
481+
)
479482

480483
operand_file1 = File(
481484
exists=True,
@@ -559,8 +562,11 @@ class MergeInput(MathsInput):
559562

560563
dimension = traits.Int(mandatory=True, desc="Dimension to merge the images.")
561564
merge_files = traits.List(
562-
File(exists=True), argstr="%s", mandatory=True, position=4,
563-
desc="List of images to merge to the working image <input>."
565+
File(exists=True),
566+
argstr="%s",
567+
mandatory=True,
568+
position=4,
569+
desc="List of images to merge to the working image <input>.",
564570
)
565571

566572

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