changing tests (to be able to pass the after changes...)

Author: djarecka

nipype/interfaces/afni/utils.py

@@ -1671,7 +1671,7 @@ class NwarpApply(AFNICommandBase):
     >>> nwarp.inputs.master = 'NWARP'
     >>> nwarp.inputs.warp = "'Fred_WARP+tlrc Fred.Xaff12.1D'"
     >>> nwarp.cmdline
-    "3dNwarpApply -source Fred+orig -master NWARP -prefix Fred+orig_Nwarp -nwarp \'Fred_WARP+tlrc Fred.Xaff12.1D\'"
+    "3dNwarpApply -ainterp wsinc5 -source Fred+orig -interp wsinc5 -master NWARP -prefix Fred+orig_Nwarp -nwarp \'Fred_WARP+tlrc Fred.Xaff12.1D\'"
     >>> res = nwarp.run()  # doctest: +SKIP
 
     """
@@ -1765,7 +1765,7 @@ class NwarpCat(AFNICommand):
     >>> nwarpcat.inputs.in_files = ['Q25_warp+tlrc.HEAD', ('IDENT', 'structural.nii')]
     >>> nwarpcat.inputs.out_file = 'Fred_total_WARP'
     >>> nwarpcat.cmdline
-    "3dNwarpCat -prefix Fred_total_WARP Q25_warp+tlrc.HEAD 'IDENT(structural.nii)'"
+    "3dNwarpCat -interp wsinc5 -prefix Fred_total_WARP Q25_warp+tlrc.HEAD 'IDENT(structural.nii)'"
     >>> res = nwarpcat.run()  # doctest: +SKIP
 
     """

nipype/interfaces/ants/resampling.py

@@ -381,7 +381,7 @@ class ApplyTransforms(ANTSCommand):
     >>> at.inputs.reference_image = 'fixed1.nii'
     >>> at.inputs.transforms = 'identity'
     >>> at.cmdline
-    'antsApplyTransforms --default-value 0 --input moving1.nii \
+    'antsApplyTransforms --default-value 0 --float 0 --input moving1.nii \
 --interpolation Linear --output moving1_trans.nii \
 --reference-image fixed1.nii -t identity'
 
@@ -395,9 +395,9 @@ class ApplyTransforms(ANTSCommand):
     >>> at.inputs.transforms = ['ants_Warp.nii.gz', 'trans.mat']
     >>> at.inputs.invert_transform_flags = [False, False]
     >>> at.cmdline
-    'antsApplyTransforms --default-value 0 --dimensionality 3 --input moving1.nii --interpolation Linear \
---output deformed_moving1.nii --reference-image fixed1.nii --transform [ ants_Warp.nii.gz, 0 ] \
---transform [ trans.mat, 0 ]'
+    'antsApplyTransforms --default-value 0 --dimensionality 3 --float 0 --input moving1.nii \
+--interpolation Linear --output deformed_moving1.nii --reference-image fixed1.nii \
+--transform [ ants_Warp.nii.gz, 0 ] --transform [ trans.mat, 0 ]'
 
     >>> at1 = ApplyTransforms()
     >>> at1.inputs.dimension = 3
@@ -410,9 +410,9 @@ class ApplyTransforms(ANTSCommand):
     >>> at1.inputs.transforms = ['ants_Warp.nii.gz', 'trans.mat']
     >>> at1.inputs.invert_transform_flags = [False, False]
     >>> at1.cmdline
-    'antsApplyTransforms --default-value 0 --dimensionality 3 --input moving1.nii --interpolation BSpline[ 5 ] \
---output deformed_moving1.nii --reference-image fixed1.nii --transform [ ants_Warp.nii.gz, 0 ] \
---transform [ trans.mat, 0 ]'
+    'antsApplyTransforms --default-value 0 --dimensionality 3 --float 0 --input moving1.nii \
+--interpolation BSpline[ 5 ] --output deformed_moving1.nii --reference-image fixed1.nii \
+--transform [ ants_Warp.nii.gz, 0 ] --transform [ trans.mat, 0 ]'
     """
     _cmd = 'antsApplyTransforms'
     input_spec = ApplyTransformsInputSpec

nipype/interfaces/base/tests/test_core.py

@@ -174,7 +174,7 @@ def __init__(self, **inputs):
     assert {} == check_dict(data_dict, tsthash2.inputs.get_traitsfree())
 
     _, hashvalue = tsthash.inputs.get_hashval(hash_method='timestamp')
-    assert 'ec5755e07287e04a4b409e03b77a517c' == hashvalue
+    assert '269f084898fab793e270f9d6de7ef0c2' == hashvalue
 
 
 class MinVerInputSpec(nib.TraitedSpec):

nipype/interfaces/niftyseg/em.py

@@ -143,7 +143,8 @@ class EM(NiftySegCommand):
     >>> node.inputs.in_file = 'im1.nii'
     >>> node.inputs.no_prior = 4
     >>> node.cmdline
-    'seg_EM -in im1.nii -nopriors 4 -bc_out im1_bc_em.nii.gz -out im1_em.nii.gz -out_outlier im1_outlier_em.nii.gz'
+    'seg_EM -in im1.nii -bc_order 3 -bc_thresh 0 -max_iter 100 -min_iter 0 -nopriors 4 \
+-bc_out im1_bc_em.nii.gz -out im1_em.nii.gz -out_outlier im1_outlier_em.nii.gz'
 
     """
     _cmd = get_custom_path('seg_EM', env_dir='NIFTYSEGDIR')