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bpinsard
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Merge branch 'master' into enh/fsl/flirt6
* master: fix: fsl tests sty: white space fix: automask bug when apply_mask is not specified fix: updated test writer with additional metadata fix: remove unnecessary print statement fix: trim http link for code fix: github url generation fix: return full hash
2 parents 2acc46e + 47cdfdb commit ec592ea

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14 files changed

+50
-44
lines changed

14 files changed

+50
-44
lines changed

‎nipype/interfaces/afni/preprocess.py

Lines changed: 8 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -562,7 +562,9 @@ class AutomaskInputSpec(AFNITraitedSpec):
562562
hash_files=False)
563563

564564
apply_mask = File(desc="output file from 3dAutomask",
565-
argstr='-apply_prefix %s')
565+
argstr='-apply_prefix %s',
566+
genfile=True,
567+
hash_files=False)
566568

567569
clfrac = traits.Float(desc='sets the clip level fraction' +
568570
' (must be 0.1-0.9). ' +
@@ -610,8 +612,10 @@ class Automask(AFNICommand):
610612
output_spec = AutomaskOutputSpec
611613

612614
def _gen_filename(self, name):
613-
if name == 'out_file' or name == 'brain_file':
615+
if name == 'out_file':
614616
return self._list_outputs()[name]
617+
if name == 'apply_mask':
618+
return self._list_outputs()['brain_file']
615619
return None
616620

617621
def _list_outputs(self):
@@ -623,8 +627,8 @@ def _list_outputs(self):
623627
outputs['out_file'] = os.path.abspath(self.inputs.out_file)
624628

625629
if not isdefined(self.inputs.apply_mask):
626-
outputs['brain_file'] = self._gen_fname(
627-
self.inputs.in_file, suffix=self.inputs.apply_suffix)
630+
outputs['brain_file'] = self._gen_fname(self.inputs.in_file,
631+
suffix=self.inputs.apply_suffix)
628632
else:
629633
outputs['brain_file'] = os.path.abspath(self.inputs.apply_mask)
630634
return outputs

‎nipype/interfaces/afni/tests/test_preprocess.py

Lines changed: 6 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -356,17 +356,20 @@ def test_maskave():
356356
yield assert_equal, getattr(instance.inputs.traits()[key], metakey), value
357357

358358
def test_automask():
359-
input_map = dict(apply_mask = dict(argstr='-apply_prefix %s',),
359+
input_map = dict(apply_mask = dict(argstr='-apply_prefix %s',
360+
hash_files=False,genfile=True,),
361+
apply_suffix = dict(usedefault=True,),
360362
args = dict(argstr='%s',),
361363
clfrac = dict(argstr='-dilate %s',),
362364
dilate = dict(argstr='-dilate %s',),
363365
environ = dict(usedefault=True,),
364366
erode = dict(argstr='-erode %s',),
365367
ignore_exception = dict(usedefault=True,),
366368
in_file = dict(argstr='%s',mandatory=True,),
367-
out_file = dict(argstr='-prefix %s',),
369+
mask_suffix = dict(usedefault=True,),
370+
out_file = dict(hash_files=False,genfile=True,
371+
argstr='-prefix %s',),
368372
outputtype = dict(),
369-
suffix = dict(),
370373
)
371374
instance = afni.Automask()
372375
for key, metadata in input_map.items():

‎nipype/interfaces/ants/registration.py

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -192,7 +192,7 @@ class RegistrationInputSpec(ANTSCommandInputSpec):
192192
requires=['sampling_strategy'], desc='')
193193
use_estimate_learning_rate_once = traits.List(traits.Bool(), desc='')
194194
use_histogram_matching = traits.List(traits.Bool(argstr='%s'), default=True, usedefault=True)
195-
# Interpolation flag
195+
# Interpolation flag
196196
interpolation = traits.Enum('Linear',
197197
'NearestNeighbor',
198198
'CosineWindowedSinc',
@@ -339,9 +339,9 @@ def _format_arg(self, opt, spec, val):
339339
if self.inputs.invert_initial_moving_transform:
340340
return '--initial-moving-transform [ %s, 1 ]' % self.inputs.initial_moving_transform
341341
else:
342-
return '--initial-moving-transform [ %s, 0 ]' % self.inputs.initial_moving_transform
343-
elif opt == 'interpolation':
344-
# TODO: handle multilabel, gaussian, and bspline options
342+
return '--initial-moving-transform [ %s, 0 ]' % self.inputs.initial_moving_transform
343+
elif opt == 'interpolation':
344+
# TODO: handle multilabel, gaussian, and bspline options
345345
return '--interpolation %s' % self.inputs.interpolation
346346
elif opt == 'output_transform_prefix':
347347
if isdefined(self.inputs.output_inverse_warped_image) and self.inputs.output_inverse_warped_image:

‎nipype/interfaces/ants/resampling.py

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -106,9 +106,9 @@ class WarpImageMultiTransformInputSpec(ANTSCommandInputSpec):
106106
input_image = File(argstr='%s', mandatory=True,
107107
desc=('image to apply transformation to (generally a '
108108
'coregistered functional)'), position=2)
109-
output_image = File(genfile=True, hash_files=False, argstr='%s',
109+
output_image = File(genfile=True, hash_files=False, argstr='%s',
110110
desc=('name of the output warped image'), position = 3, xor=['out_postfix'])
111-
out_postfix = File("_wimt", usedefault=True, hash_files=False,
111+
out_postfix = File("_wimt", usedefault=True, hash_files=False,
112112
desc=('Postfix that is prepended to all output '
113113
'files (default = _wimt)'), xor=['output_image'])
114114
reference_image = File(argstr='-R %s', xor=['tightest_box'],
@@ -166,7 +166,7 @@ class WarpImageMultiTransform(ANTSCommand):
166166
_cmd = 'WarpImageMultiTransform'
167167
input_spec = WarpImageMultiTransformInputSpec
168168
output_spec = WarpImageMultiTransformOutputSpec
169-
169+
170170
def _gen_filename(self, name):
171171
if name == 'output_image':
172172
_, name, ext = split_filename(os.path.abspath(self.inputs.input_image))

‎nipype/interfaces/fsl/preprocess.py

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -153,7 +153,7 @@ def _gen_outfilename(self):
153153
def _list_outputs(self):
154154
outputs = self.output_spec().get()
155155
outputs['out_file'] = self._gen_outfilename()
156-
if ((isdefined(self.inputs.mesh) and self.inputs.mesh) or
156+
if ((isdefined(self.inputs.mesh) and self.inputs.mesh) or
157157
(isdefined(self.inputs.surfaces) and self.inputs.surfaces)):
158158
outputs['meshfile'] = self._gen_fname(outputs['out_file'],
159159
suffix='_mesh.vtk',

‎nipype/interfaces/fsl/tests/test_base.py

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -15,7 +15,7 @@ def test_fslversion():
1515
if ver:
1616
# If ver is None, fsl is not installed
1717
ver = ver.split('.')
18-
yield assert_equal, ver[0], '4'
18+
yield assert_true, ver[0] in ['4', '5']
1919

2020
@skipif(no_fsl)#skip if fsl not installed)
2121
def test_fsloutputtype():

‎nipype/interfaces/fsl/tests/test_model.py

Lines changed: 7 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -299,29 +299,30 @@ def test_cluster():
299299
yield assert_equal, getattr(instance.inputs.traits()[key], metakey), value
300300

301301
@skipif(no_fsl)
302-
def test_randomise1():
302+
def test_randomise():
303303
input_map = dict(args = dict(argstr='%s',),
304-
base_name = dict(argstr='-o %s',),
304+
base_name = dict(argstr='-o "%s"',usedefault=True,),
305305
c_thresh = dict(argstr='-c %.2f',),
306306
cm_thresh = dict(argstr='-C %.2f',),
307307
demean = dict(argstr='-D',),
308-
design_mat = dict(argstr='-d %s',mandatory=True,),
309-
environ = dict(),
308+
design_mat = dict(argstr='-d %s',),
309+
environ = dict(usedefault=True,),
310310
f_c_thresh = dict(argstr='-F %.2f',),
311311
f_cm_thresh = dict(argstr='-S %.2f',),
312312
f_only = dict(argstr='--f_only',),
313313
fcon = dict(argstr='-f %s',),
314+
ignore_exception = dict(usedefault=True,),
314315
in_file = dict(argstr='-i %s',mandatory=True,),
315316
mask = dict(argstr='-m %s',),
316317
num_perm = dict(argstr='-n %d',),
317-
one_sample_group_mean = dict(argstr='-l',),
318+
one_sample_group_mean = dict(argstr='-1',),
318319
output_type = dict(),
319320
p_vec_n_dist_files = dict(argstr='-P',),
320321
raw_stats_imgs = dict(argstr='-R',),
321322
seed = dict(argstr='--seed %d',),
322323
show_info_parallel_mode = dict(argstr='-Q',),
323324
show_total_perms = dict(argstr='-q',),
324-
tcon = dict(argstr='-t %s',mandatory=True,),
325+
tcon = dict(argstr='-t %s',),
325326
tfce = dict(argstr='-T',),
326327
tfce2D = dict(argstr='--T2',),
327328
tfce_C = dict(argstr='--tfce_C %.2f',),

‎nipype/interfaces/fsl/utils.py

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -1151,14 +1151,14 @@ def _list_outputs(self):
11511151
outputs['exf_mask'] = self._gen_fname(cwd=self.inputs.tmpdir,
11521152
basename='maskexf')
11531153
return outputs
1154-
1154+
11551155
class Reorient2StdInputSpec(FSLCommandInputSpec):
11561156
in_file = File(exists=True, mandatory=True, argstr="%s")
11571157
out_file = File(genfile=True, hash_files=False, argstr="%s")
1158-
1158+
11591159
class Reorient2StdOutputSpec(TraitedSpec):
11601160
out_file = File(exists=True)
1161-
1161+
11621162
class Reorient2Std(FSLCommand):
11631163
"""fslreorient2std is a tool for reorienting the image to match the
11641164
approximate orientation of the standard template images (MNI152).
@@ -1180,7 +1180,7 @@ def _gen_filename(self, name):
11801180
return self._gen_fname(self.inputs.in_file,
11811181
suffix="_reoriented")
11821182
return None
1183-
1183+
11841184
def _list_outputs(self):
11851185
outputs = self.output_spec().get()
11861186
if not isdefined(self.inputs.out_file):

‎nipype/pkg_info.py

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -48,7 +48,7 @@ def pkg_commit_hash(pkg_path):
4848
if install_subst != '':
4949
return 'installation', install_subst
5050
# maybe we are in a repository
51-
proc = subprocess.Popen('git rev-parse --short HEAD',
51+
proc = subprocess.Popen('git rev-parse HEAD',
5252
stdout=subprocess.PIPE,
5353
stderr=subprocess.PIPE,
5454
cwd=pkg_path, shell=True)

‎nipype/workflows/smri/ants/ANTSBuildTemplate.py

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -98,14 +98,14 @@ def ANTSTemplateBuildSingleIterationWF(iterationPhasePrefix=''):
9898
Inputs::
9999
100100
inputspec.images :
101-
inputspec.fixed_image :
101+
inputspec.fixed_image :
102102
inputspec.ListOfPassiveImagesDictionaries :
103103
104104
Outputs::
105105
106106
outputspec.template :
107107
outputspec.transforms_list :
108-
outputspec.passive_deformed_templates :
108+
outputspec.passive_deformed_templates :
109109
"""
110110

111111

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