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Merge pull request #1449 from satra/rel/0.12rc1
final changes before tagging release candidate
2 parents f316b8b + dbc1afe commit 09e91c8

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58 files changed

+145
-750
lines changed

‎CHANGES

+1-1
Original file line numberDiff line numberDiff line change
@@ -1,4 +1,4 @@
1-
Next release
1+
Release 0.12.0-rc1 (April 20, 2016)
22
============
33

44
* ENH: Add nipype_crash_search command (https://github.com/nipy/nipype/pull/1422)

‎nipype/info.py

+1-1
Original file line numberDiff line numberDiff line change
@@ -10,7 +10,7 @@
1010
_version_major = 0
1111
_version_minor = 12
1212
_version_micro = 0
13-
_version_extra = '-dev' # Remove -dev for release
13+
_version_extra = '-rc1' # Remove -dev for release
1414

1515

1616
def get_nipype_gitversion():

‎nipype/interfaces/afni/preprocess.py

+1-1
Original file line numberDiff line numberDiff line change
@@ -2178,7 +2178,7 @@ class FWHMxInputSpec(CommandLineInputSpec):
21782178
'is not given, the program picks q=NT/30. -detrend disables -demed, and includes '
21792179
'-unif.')
21802180
demed = traits.Bool(
2181-
False, argstr='-demed', xorg=['detrend'],
2181+
False, argstr='-demed', xor=['detrend'],
21822182
desc='If the input dataset has more than one sub-brick (e.g., has a time axis), then '
21832183
'subtract the median of each voxel\'s time series before processing FWHM. This will '
21842184
'tend to remove intrinsic spatial structure and leave behind the noise.')

‎nipype/interfaces/afni/tests/test_auto_FWHMx.py

+1-1
Original file line numberDiff line numberDiff line change
@@ -20,7 +20,7 @@ def test_FWHMx_inputs():
2020
compat=dict(argstr='-compat',
2121
),
2222
demed=dict(argstr='-demed',
23-
xorg=['detrend'],
23+
xor=['detrend'],
2424
),
2525
detrend=dict(argstr='-detrend',
2626
usedefault=True,

‎nipype/interfaces/dipy/reconstruction.py

+2-2
Original file line numberDiff line numberDiff line change
@@ -276,9 +276,9 @@ def _list_outputs(self):
276276
class CSDInputSpec(DipyBaseInterfaceInputSpec):
277277
in_mask = File(exists=True, desc=('input mask in which compute tensors'))
278278
response = File(exists=True, desc=('single fiber estimated response'))
279-
sh_order = traits.Int(8, exists=True, usedefault=True,
279+
sh_order = traits.Int(8, usedefault=True,
280280
desc=('maximal shperical harmonics order'))
281-
save_fods = traits.Bool(True, exists=True, usedefault=True,
281+
save_fods = traits.Bool(True, usedefault=True,
282282
desc=('save fODFs in file'))
283283
out_fods = File(desc=('fODFs output file name'))
284284

‎nipype/interfaces/dipy/tests/test_auto_CSD.py

+2-4
Original file line numberDiff line numberDiff line change
@@ -19,11 +19,9 @@ def test_CSD_inputs():
1919
out_fods=dict(),
2020
out_prefix=dict(),
2121
response=dict(),
22-
save_fods=dict(exists=True,
23-
usedefault=True,
22+
save_fods=dict(usedefault=True,
2423
),
25-
sh_order=dict(exists=True,
26-
usedefault=True,
24+
sh_order=dict(usedefault=True,
2725
),
2826
)
2927
inputs = CSD.input_spec()

‎nipype/interfaces/freesurfer/model.py

+7-8
Original file line numberDiff line numberDiff line change
@@ -654,7 +654,7 @@ class SegStatsInputSpec(FSTraitedSpec):
654654
wm_vol_from_surf = traits.Bool(argstr='--surf-wm-vol', desc='Compute wm volume from surf')
655655
cortex_vol_from_surf = traits.Bool(argstr='--surf-ctx-vol', desc='Compute cortex volume from surf')
656656
non_empty_only = traits.Bool(argstr='--nonempty', desc='Only report nonempty segmentations')
657-
empty = traits.Bool(argstr="--empty", mandatory=False,
657+
empty = traits.Bool(argstr="--empty",
658658
desc="Report on segmentations listed in the color table")
659659
mask_file = File(exists=True, argstr='--mask %s',
660660
desc='Mask volume (same size as seg')
@@ -690,7 +690,7 @@ class SegStatsInputSpec(FSTraitedSpec):
690690
desc="Compute volume of total gray matter")
691691
euler = traits.Bool(argstr="--euler",
692692
desc="Write out number of defect holes in orig.nofix based on the euler number")
693-
in_intensity = File(argstr="--in %s --in-intensity-name %s", mandatory=False,
693+
in_intensity = File(argstr="--in %s --in-intensity-name %s",
694694
desc="Undocumented input norm.mgz file")
695695
intensity_units = traits.Enum('MR', argstr="--in-intensity-units %s",
696696
requires=["in_intensity"], desc="Intensity units")
@@ -1083,14 +1083,13 @@ class Label2LabelInputSpec(FSTraitedSpec):
10831083
source_subject = traits.String(argstr="--srcsubject %s", mandatory=True,
10841084
desc="Source subject name")
10851085
# optional
1086-
out_file = File(argstr="--trglabel %s", mandatory=False,
1086+
out_file = File(argstr="--trglabel %s",
10871087
name_source=['source_label'], name_template='%s_converted',
10881088
hash_files=False, keep_extension=True,
10891089
desc="Target label")
10901090
registration_method = traits.Enum('surface', 'volume', usedefault=True,
10911091
argstr="--regmethod %s", desc="Registration method")
1092-
copy_inputs = traits.Bool(mandatory=False,
1093-
desc="If running as a node, set this to True." +
1092+
copy_inputs = traits.Bool(desc="If running as a node, set this to True." +
10941093
"This will copy the input files to the node " +
10951094
"directory.")
10961095

@@ -1180,11 +1179,11 @@ class Label2AnnotInputSpec(FSTraitedSpec):
11801179
orig = File(exists=True, mandatory=True,
11811180
desc="implicit {hemisphere}.orig")
11821181
# optional
1183-
keep_max = traits.Bool(argstr="--maxstatwinner", mandatory=False,
1182+
keep_max = traits.Bool(argstr="--maxstatwinner",
11841183
desc="Keep label with highest 'stat' value")
1185-
verbose_off = traits.Bool(argstr="--noverbose", mandatory=False,
1184+
verbose_off = traits.Bool(argstr="--noverbose",
11861185
desc="Turn off overlap and stat override messages")
1187-
color_table = File(argstr="--ctab %s", mandatory=False, exists=True,
1186+
color_table = File(argstr="--ctab %s", exists=True,
11881187
desc="File that defines the structure names, their indices, and their color")
11891188
copy_inputs = traits.Bool(desc="copy implicit inputs and create a temp subjects_dir")
11901189

‎nipype/interfaces/freesurfer/preprocess.py

+26-26
Original file line numberDiff line numberDiff line change
@@ -1502,11 +1502,11 @@ class NormalizeInputSpec(FSTraitedSpec):
15021502
# optional
15031503
gradient = traits.Int(1, argstr="-g %d", usedefault=False,
15041504
desc="use max intensity/mm gradient g (default=1)")
1505-
mask = File(argstr="-mask %s", mandatory=False, exists=True,
1505+
mask = File(argstr="-mask %s", exists=True,
15061506
desc="The input mask file for Normalize")
1507-
segmentation = File(argstr="-aseg %s", mandatory=False,
1507+
segmentation = File(argstr="-aseg %s",
15081508
exists=True, desc="The input segmentation for Normalize")
1509-
transform = File(exists=True, mandatory=False,
1509+
transform = File(exists=True,
15101510
desc="Tranform file from the header of the input file")
15111511

15121512

@@ -1551,9 +1551,9 @@ class CANormalizeInputSpec(FSTraitedSpec):
15511551
transform = File(argstr='%s', exists=True, mandatory=True,
15521552
position=-2, desc="The tranform file in lta format")
15531553
# optional
1554-
mask = File(argstr='-mask %s', exists=True, mandatory=False,
1554+
mask = File(argstr='-mask %s', exists=True,
15551555
desc="Specifies volume to use as mask")
1556-
control_points = File(argstr='-c %s', mandatory=False,
1556+
control_points = File(argstr='-c %s',
15571557
desc="File name for the output control points")
15581558
long_file = File(argstr='-long %s',
15591559
desc='undocumented flag used in longitudinal processing')
@@ -1596,20 +1596,20 @@ class CARegisterInputSpec(FSTraitedSpecOpenMP):
15961596
#required
15971597
in_file = File(argstr='%s', exists=True, mandatory=True,
15981598
position=-3, desc="The input volume for CARegister")
1599-
out_file = File(argstr='%s', mandatory=False, position=-1,
1599+
out_file = File(argstr='%s', position=-1,
16001600
genfile=True, desc="The output volume for CARegister")
1601-
template = File(argstr='%s', exists=True, mandatory=False,
1601+
template = File(argstr='%s', exists=True,
16021602
position=-2, desc="The template file in gca format")
16031603
# optional
1604-
mask = File(argstr='-mask %s', exists=True, mandatory=False,
1604+
mask = File(argstr='-mask %s', exists=True,
16051605
desc="Specifies volume to use as mask")
1606-
invert_and_save = traits.Bool(argstr='-invert-and-save', mandatory=False, position=-4,
1606+
invert_and_save = traits.Bool(argstr='-invert-and-save', position=-4,
16071607
desc="Invert and save the .m3z multi-dimensional talaraich transform to x, y, and z .mgz files")
16081608
no_big_ventricles = traits.Bool(
1609-
argstr='-nobigventricles', mandatory=False, desc="No big ventricles")
1610-
transform = File(argstr='-T %s', exists=True, mandatory=False,
1609+
argstr='-nobigventricles', desc="No big ventricles")
1610+
transform = File(argstr='-T %s', exists=True,
16111611
desc="Specifies transform in lta format")
1612-
align = traits.String(argstr='-align-%s', mandatory=False,
1612+
align = traits.String(argstr='-align-%s',
16131613
desc="Specifies when to perform alignment")
16141614
levels = traits.Int(
16151615
argstr='-levels %d',
@@ -1675,17 +1675,18 @@ class CALabelInputSpec(FSTraitedSpecOpenMP):
16751675
intensities = File(argstr="-r %s", exists=True,
16761676
desc="input label intensities file(used in longitudinal processing)")
16771677
no_big_ventricles = traits.Bool(
1678-
argstr="-nobigventricles", mandatory=False, desc="No big ventricles")
1679-
align = traits.Bool(argstr="-align", mandatory=False, desc="Align CALabel")
1678+
argstr="-nobigventricles", desc="No big ventricles")
1679+
align = traits.Bool(argstr="-align", desc="Align CALabel")
16801680
prior = traits.Float(argstr="-prior %.1f",
1681-
mandatory=False, desc="Prior for CALabel")
1681+
desc="Prior for CALabel")
16821682
relabel_unlikely = traits.Tuple(traits.Int, traits.Float,
16831683
argstr="-relabel_unlikely %d %.1f",
1684-
desc="Reclassify voxels at least some std devs from the mean using some size Gaussian window",
1685-
mandatory=False)
1686-
label = traits.File(argstr="-l %s", mandatory=False, exists=True,
1684+
desc=("Reclassify voxels at least some std"
1685+
" devs from the mean using some size"
1686+
" Gaussian window"))
1687+
label = traits.File(argstr="-l %s", exists=True,
16871688
desc="Undocumented flag. Autorecon3 uses ../label/{hemisphere}.cortex.label as input file")
1688-
aseg = traits.File(argstr="-aseg %s", mandatory=False, exists=True,
1689+
aseg = traits.File(argstr="-aseg %s", exists=True,
16891690
desc="Undocumented flag. Autorecon3 uses ../mri/aseg.presurf.mgz as input file")
16901691

16911692

@@ -1742,11 +1743,11 @@ class MRIsCALabelInputSpec(FSTraitedSpecOpenMP):
17421743
hash_files=False, name_template="%s.aparc.annot",
17431744
desc="Annotated surface output file")
17441745
# optional
1745-
label = traits.File(argstr="-l %s", mandatory=False, exists=True,
1746+
label = traits.File(argstr="-l %s", exists=True,
17461747
desc="Undocumented flag. Autorecon3 uses ../label/{hemisphere}.cortex.label as input file")
1747-
aseg = traits.File(argstr="-aseg %s", mandatory=False, exists=True,
1748+
aseg = traits.File(argstr="-aseg %s", exists=True,
17481749
desc="Undocumented flag. Autorecon3 uses ../mri/aseg.presurf.mgz as input file")
1749-
seed = traits.Int(argstr="-seed %d", mandatory=False,
1750+
seed = traits.Int(argstr="-seed %d",
17501751
desc="")
17511752
copy_inputs = traits.Bool(desc="Copies implicit inputs to node directory " +
17521753
"and creates a temp subjects_directory. " +
@@ -1835,8 +1836,7 @@ class SegmentCCInputSpec(FSTraitedSpec):
18351836
subject_id = traits.String('subject_id', argstr="%s", mandatory=True,
18361837
position=-1, usedefault=True,
18371838
desc="Subject name")
1838-
copy_inputs = traits.Bool(mandatory=False,
1839-
desc="If running as a node, set this to True." +
1839+
copy_inputs = traits.Bool(desc="If running as a node, set this to True." +
18401840
"This will copy the input files to the node " +
18411841
"directory.")
18421842

@@ -1979,10 +1979,10 @@ class EditWMwithAsegInputSpec(FSTraitedSpec):
19791979
desc="Input brain/T1 file")
19801980
seg_file = File(argstr="%s", position=-2, mandatory=True, exists=True,
19811981
desc="Input presurf segmentation file")
1982-
out_file = File(argstr="%s", position=-1, mandtaory=True, exists=False,
1982+
out_file = File(argstr="%s", position=-1, mandatory=True, exists=False,
19831983
desc="File to be written as output")
19841984
# optional
1985-
keep_in = traits.Bool(argstr="-keep-in", mandatory=False,
1985+
keep_in = traits.Bool(argstr="-keep-in",
19861986
desc="Keep edits as found in input volume")
19871987

19881988
class EditWMwithAsegOutputSpec(TraitedSpec):

‎nipype/interfaces/freesurfer/registration.py

+7-8
Original file line numberDiff line numberDiff line change
@@ -113,8 +113,8 @@ class RegisterAVItoTalairachInputSpec(FSTraitedSpec):
113113
position=1, desc="The target file")
114114
vox2vox = File(argstr='%s', exists=True, mandatory=True,
115115
position=2, desc="The vox2vox file")
116-
out_file = File('talairach.auto.xfm', usedfault=True,
117-
argstr='%s', mandatory=False,
116+
out_file = File('talairach.auto.xfm', usedefault=True,
117+
argstr='%s',
118118
position=3, desc="The transform output")
119119

120120

@@ -179,10 +179,10 @@ class EMRegisterInputSpec(FSTraitedSpecOpenMP):
179179
skull = traits.Bool(
180180
argstr="-skull", desc="align to atlas containing skull (uns=5)")
181181
mask = File(argstr="-mask %s", exists=True,
182-
mandatory=False, desc="use volume as a mask")
183-
nbrspacing = traits.Int(argstr="-uns %d", mandatory=False,
182+
desc="use volume as a mask")
183+
nbrspacing = traits.Int(argstr="-uns %d",
184184
desc="align to atlas containing skull setting unknown_nbr_spacing = nbrspacing")
185-
transform = File(argstr="-t %s", exists=True, mandatory=False,
185+
transform = File(argstr="-t %s", exists=True,
186186
desc="Previously computed transform")
187187

188188

@@ -287,9 +287,8 @@ class PaintInputSpec(FSTraitedSpec):
287287
template = File(argstr="%s", exists=True, mandatory=True, position=-3,
288288
desc="Template file")
289289
# optional
290-
template_param = traits.Int(
291-
mandatory=False, desc="Frame number of the input template")
292-
averages = traits.Int(argstr="-a %d", mandatory=False,
290+
template_param = traits.Int(desc="Frame number of the input template")
291+
averages = traits.Int(argstr="-a %d",
293292
desc="Average curvature patterns")
294293
out_file = File(argstr="%s", exists=False, position=-1,
295294
name_template="%s.avg_curv", hash_files=False,

‎nipype/interfaces/freesurfer/tests/test_auto_Aparc2Aseg.py

+1-8
Original file line numberDiff line numberDiff line change
@@ -9,25 +9,20 @@ def test_Aparc2Aseg_inputs():
99
args=dict(argstr='%s',
1010
),
1111
aseg=dict(argstr='--aseg %s',
12-
mandatory=False,
13-
),
14-
copy_inputs=dict(mandatory=False,
1512
),
13+
copy_inputs=dict(),
1614
ctxseg=dict(argstr='--ctxseg %s',
17-
mandatory=False,
1815
),
1916
environ=dict(nohash=True,
2017
usedefault=True,
2118
),
2219
filled=dict(),
2320
hypo_wm=dict(argstr='--hypo-as-wm',
24-
mandatory=False,
2521
),
2622
ignore_exception=dict(nohash=True,
2723
usedefault=True,
2824
),
2925
label_wm=dict(argstr='--labelwm',
30-
mandatory=False,
3126
),
3227
lh_annotation=dict(mandatory=True,
3328
),
@@ -51,7 +46,6 @@ def test_Aparc2Aseg_inputs():
5146
ribbon=dict(mandatory=True,
5247
),
5348
rip_unknown=dict(argstr='--rip-unknown',
54-
mandatory=False,
5549
),
5650
subject_id=dict(argstr='--s %s',
5751
mandatory=True,
@@ -61,7 +55,6 @@ def test_Aparc2Aseg_inputs():
6155
terminal_output=dict(nohash=True,
6256
),
6357
volmask=dict(argstr='--volmask',
64-
mandatory=False,
6558
),
6659
)
6760
inputs = Aparc2Aseg.input_spec()

‎nipype/interfaces/freesurfer/tests/test_auto_Apas2Aseg.py

-1
Original file line numberDiff line numberDiff line change
@@ -31,7 +31,6 @@ def test_Apas2Aseg_inputs():
3131

3232
def test_Apas2Aseg_outputs():
3333
output_map = dict(out_file=dict(argstr='%s',
34-
mandatory=False,
3534
),
3635
)
3736
outputs = Apas2Aseg.output_spec()

‎nipype/interfaces/freesurfer/tests/test_auto_CALabel.py

-6
Original file line numberDiff line numberDiff line change
@@ -5,12 +5,10 @@
55

66
def test_CALabel_inputs():
77
input_map = dict(align=dict(argstr='-align',
8-
mandatory=False,
98
),
109
args=dict(argstr='%s',
1110
),
1211
aseg=dict(argstr='-aseg %s',
13-
mandatory=False,
1412
),
1513
environ=dict(nohash=True,
1614
usedefault=True,
@@ -27,21 +25,17 @@ def test_CALabel_inputs():
2725
intensities=dict(argstr='-r %s',
2826
),
2927
label=dict(argstr='-l %s',
30-
mandatory=False,
3128
),
3229
no_big_ventricles=dict(argstr='-nobigventricles',
33-
mandatory=False,
3430
),
3531
num_threads=dict(),
3632
out_file=dict(argstr='%s',
3733
mandatory=True,
3834
position=-1,
3935
),
4036
prior=dict(argstr='-prior %.1f',
41-
mandatory=False,
4237
),
4338
relabel_unlikely=dict(argstr='-relabel_unlikely %d %.1f',
44-
mandatory=False,
4539
),
4640
subjects_dir=dict(),
4741
template=dict(argstr='%s',

‎nipype/interfaces/freesurfer/tests/test_auto_CANormalize.py

-2
Original file line numberDiff line numberDiff line change
@@ -11,7 +11,6 @@ def test_CANormalize_inputs():
1111
position=-3,
1212
),
1313
control_points=dict(argstr='-c %s',
14-
mandatory=False,
1514
),
1615
environ=dict(nohash=True,
1716
usedefault=True,
@@ -26,7 +25,6 @@ def test_CANormalize_inputs():
2625
long_file=dict(argstr='-long %s',
2726
),
2827
mask=dict(argstr='-mask %s',
29-
mandatory=False,
3028
),
3129
out_file=dict(argstr='%s',
3230
hash_files=False,

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