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satrasatra
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Merge pull request #634 from yarikoptic/master
BF: according to Mark Jenkinson and FAQ all --long options should use = before the value
2 parents e7161f1 + b7fe287 commit d22219c

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+21
-21
lines changed

4 files changed

+21
-21
lines changed

‎nipype/interfaces/fsl/dti.py

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -345,7 +345,7 @@ class ProbTrackXInputSpec(FSLCommandInputSpec):
345345
loop_check = traits.Bool(argstr='--loopcheck', desc='perform loop_checks on paths -' +
346346
' slower, but allows lower curvature threshold')
347347
use_anisotropy = traits.Bool(argstr='--usef', desc='use anisotropy to constrain tracking')
348-
rand_fib = traits.Enum(0, 1, 2, 3, argstr='--randfib %d',
348+
rand_fib = traits.Enum(0, 1, 2, 3, argstr='--randfib=%d',
349349
desc='options: 0 - default, 1 - to randomly sample' +
350350
' initial fibres (with f > fibthresh), 2 - to sample in ' +
351351
'proportion fibres (with f>fibthresh) to f, 3 - to sample ALL ' +

‎nipype/interfaces/fsl/model.py

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -1661,7 +1661,7 @@ class GLMInputSpec(FSLCommandInputSpec):
16611661
+ ' contrasts'))
16621662
mask = File(exists=True, argstr='-m %s', desc=('mask image file name if'
16631663
+ ' input is image'))
1664-
dof = traits.Int(argstr='--dof %d', desc=('set degrees of freedom'
1664+
dof = traits.Int(argstr='--dof=%d', desc=('set degrees of freedom'
16651665
+ ' explicitly'))
16661666
des_norm = traits.Bool(argstr='--des_norm', desc=('switch on normalization'
16671667
+ ' of the design matrix'

‎nipype/interfaces/fsl/preprocess.py

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -803,10 +803,10 @@ class FNIRTInputSpec(FSLCommandInputSpec):
803803
apply_inmask = traits.List(
804804
traits.Enum(0, 1), argstr='--applyinmask=%s', xor=['skip_inmask'],
805805
desc='list of iterations to use input mask on (1 to use, 0 to skip)', sep=",")
806-
skip_implicit_ref_masking = traits.Bool(argstr='--imprefm 0',
806+
skip_implicit_ref_masking = traits.Bool(argstr='--imprefm=0',
807807
desc='skip implicit masking based on value'
808808
'in --ref image. Default = 0')
809-
skip_implicit_in_masking = traits.Bool(argstr='--impinm 0',
809+
skip_implicit_in_masking = traits.Bool(argstr='--impinm=0',
810810
desc='skip implicit masking based on value'
811811
'in --in image. Default = 0')
812812
refmask_val = traits.Float(argstr='--imprefval=%f',
@@ -836,7 +836,7 @@ class FNIRTInputSpec(FSLCommandInputSpec):
836836
regularization_lambda = traits.List(traits.Float, argstr='--lambda=%s',
837837
desc='Weight of regularisation, default depending on --ssqlambda and --regmod '
838838
'switches. See user documetation.', sep=",")
839-
skip_lambda_ssq = traits.Bool(argstr='--ssqlambda 0',
839+
skip_lambda_ssq = traits.Bool(argstr='--ssqlambda=0',
840840
desc='If true, lambda is not weighted by current ssq, default false')
841841
jacobian_range = traits.Tuple(traits.Float, traits.Float,
842842
argstr='--jacrange=%f,%f',

‎nipype/interfaces/fsl/tests/test_dti.py

Lines changed: 16 additions & 16 deletions
Original file line numberDiff line numberDiff line change
@@ -124,7 +124,7 @@ def test_probtrackx():
124124
os2t = dict(argstr='--os2t',),
125125
out_dir = dict(argstr='--dir=%s',),
126126
output_type = dict(),
127-
rand_fib = dict(argstr='--randfib %d',),
127+
rand_fib = dict(argstr='--randfib=%d',),
128128
random_seed = dict(argstr='--rseed',),
129129
s2tastext = dict(argstr='--s2tastext',),
130130
sample_random_points = dict(argstr='--sampvox',),
@@ -342,7 +342,7 @@ def test_randomise2():
342342
int_seed=4)
343343

344344
actualCmdline = sorted(rand2.cmdline.split())
345-
cmd = 'randomise -i infile2 -o outfile2 -1 -f infile.f --seed 4'
345+
cmd = 'randomise -i infile2 -o outfile2 -1 -f infile.f --seed=4'
346346
desiredCmdline = sorted(cmd.split())
347347
yield assert_equal, actualCmdline, desiredCmdline
348348

@@ -379,13 +379,13 @@ def test_randomise2():
379379
'diagnostics_off': ('--quiet', True),
380380
'output_raw': ('-R', True),
381381
'output_perm_vect': ('-P', True),
382-
'int_seed': ('--seed 20', 20),
383-
'TFCE_height_param': ('--tfce_H 0.11', 0.11),
384-
'TFCE_extent_param': ('--tfce_E 0.50', 0.50),
385-
'TFCE_connectivity': ('--tfce_C 0.30', 0.30),
386-
'list_num_voxel_EVs_pos': ('--vxl 1,2,3,4',
382+
'int_seed': ('--seed=20', 20),
383+
'TFCE_height_param': ('--tfce_H=0.11', 0.11),
384+
'TFCE_extent_param': ('--tfce_E=0.50', 0.50),
385+
'TFCE_connectivity': ('--tfce_C=0.30', 0.30),
386+
'list_num_voxel_EVs_pos': ('--vxl=1,2,3,4',
387387
'1,2,3,4'),
388-
'list_img_voxel_EVs': ('--vxf 6,7,8,9,3',
388+
'list_img_voxel_EVs': ('--vxf=6,7,8,9,3',
389389
'6,7,8,9,3')}
390390

391391
for name, settings in opt_map.items():
@@ -423,7 +423,7 @@ def test_Randomise_parallel():
423423
int_seed=4)
424424

425425
actualCmdline = sorted(rand2.cmdline.split())
426-
cmd = 'randomise_parallel -i infile2 -o outfile2 -1 -f infile.f --seed 4'
426+
cmd = 'randomise_parallel -i infile2 -o outfile2 -1 -f infile.f --seed=4'
427427
desiredCmdline = sorted(cmd.split())
428428
yield assert_equal, actualCmdline, desiredCmdline
429429

@@ -460,14 +460,14 @@ def test_Randomise_parallel():
460460
'diagnostics_off': ('--quiet', True),
461461
'output_raw': ('-R', True),
462462
'output_perm_vect': ('-P', True),
463-
'int_seed': ('--seed 20', 20),
464-
'TFCE_height_param': ('--tfce_H 0.11', 0.11),
465-
'TFCE_extent_param': ('--tfce_E 0.50', 0.50),
466-
'TFCE_connectivity': ('--tfce_C 0.30', 0.30),
467-
'list_num_voxel_EVs_pos': ('--vxl ' \
463+
'int_seed': ('--seed=20', 20),
464+
'TFCE_height_param': ('--tfce_H=0.11', 0.11),
465+
'TFCE_extent_param': ('--tfce_E=0.50', 0.50),
466+
'TFCE_connectivity': ('--tfce_C=0.30', 0.30),
467+
'list_num_voxel_EVs_pos': ('--vxl=' \
468468
+ repr([1, 2, 3, 4]),
469469
repr([1, 2, 3, 4])),
470-
'list_img_voxel_EVs': ('--vxf ' \
470+
'list_img_voxel_EVs': ('--vxf=' \
471471
+ repr([6, 7, 8, 9, 3]),
472472
repr([6, 7, 8, 9, 3]))}
473473

@@ -584,7 +584,7 @@ def test_Vec_reg():
584584
'tensor': ('--tensor', True),
585585
'affineTmat': ('-t Tmat', 'Tmat'),
586586
'warpFile': ('-w wrpFile', 'wrpFile'),
587-
'interpolation': ('--interp sinc', 'sinc'),
587+
'interpolation': ('--interp=sinc', 'sinc'),
588588
'brainMask': ('-m mask', 'mask')}
589589

590590
for name, settings in opt_map.items():

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