From e8c9c86c4b230e6d7c41bf9017108d62963151b6 Mon Sep 17 00:00:00 2001 From: Xihe Xie Date: Wed, 15 Dec 2021 13:43:47 -0500 Subject: [PATCH 1/3] add GenericLabel to antsRegistration interpolation input --- nipype/interfaces/ants/registration.py | 3 +++ 1 file changed, 3 insertions(+) diff --git a/nipype/interfaces/ants/registration.py b/nipype/interfaces/ants/registration.py index b9bd38f2df..83a9b36046 100644 --- a/nipype/interfaces/ants/registration.py +++ b/nipype/interfaces/ants/registration.py @@ -418,6 +418,7 @@ class RegistrationInputSpec(ANTSCommandInputSpec): "BSpline", "MultiLabel", "Gaussian", + "GenericLabel", argstr="%s", usedefault=True, ) @@ -426,6 +427,7 @@ class RegistrationInputSpec(ANTSCommandInputSpec): traits.Tuple( traits.Float(), traits.Float() # Gaussian/MultiLabel (sigma, alpha) ), + traits.Tuple(traits.Str()), # GenericLabel (interpolator) ) write_composite_transform = traits.Bool( @@ -1297,6 +1299,7 @@ def _format_arg(self, opt, spec, val): "BSpline", "MultiLabel", "Gaussian", + "GenericLabel", ] and isdefined(self.inputs.interpolation_parameters) ): From 7df16faa7d505f61e380cff78ef7015553b65404 Mon Sep 17 00:00:00 2001 From: Xihe Xie Date: Wed, 15 Dec 2021 14:03:22 -0500 Subject: [PATCH 2/3] make check-before-commit deleted test --- nipype/interfaces/tests/test_auto_Dcm2nii.py | 107 ------------------- 1 file changed, 107 deletions(-) delete mode 100644 nipype/interfaces/tests/test_auto_Dcm2nii.py diff --git a/nipype/interfaces/tests/test_auto_Dcm2nii.py b/nipype/interfaces/tests/test_auto_Dcm2nii.py deleted file mode 100644 index 948aafa083..0000000000 --- a/nipype/interfaces/tests/test_auto_Dcm2nii.py +++ /dev/null @@ -1,107 +0,0 @@ -# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT -from ..dcm2nii import Dcm2nii - - -def test_Dcm2nii_inputs(): - input_map = dict( - anonymize=dict( - argstr="-a", - usedefault=True, - ), - args=dict( - argstr="%s", - ), - collapse_folders=dict( - argstr="-c", - usedefault=True, - ), - config_file=dict( - argstr="-b %s", - extensions=None, - genfile=True, - ), - convert_all_pars=dict( - argstr="-v", - usedefault=True, - ), - date_in_filename=dict( - argstr="-d", - usedefault=True, - ), - environ=dict( - nohash=True, - usedefault=True, - ), - events_in_filename=dict( - argstr="-e", - usedefault=True, - ), - gzip_output=dict( - argstr="-g", - usedefault=True, - ), - id_in_filename=dict( - argstr="-i", - usedefault=True, - ), - nii_output=dict( - argstr="-n", - usedefault=True, - ), - output_dir=dict( - argstr="-o %s", - genfile=True, - ), - protocol_in_filename=dict( - argstr="-p", - usedefault=True, - ), - reorient=dict( - argstr="-r", - ), - reorient_and_crop=dict( - argstr="-x", - usedefault=True, - ), - source_dir=dict( - argstr="%s", - mandatory=True, - position=-1, - xor=["source_names"], - ), - source_in_filename=dict( - argstr="-f", - usedefault=True, - ), - source_names=dict( - argstr="%s", - copyfile=False, - mandatory=True, - position=-1, - xor=["source_dir"], - ), - spm_analyze=dict( - argstr="-s", - xor=["nii_output"], - ), - ) - inputs = Dcm2nii.input_spec() - - for key, metadata in list(input_map.items()): - for metakey, value in list(metadata.items()): - assert getattr(inputs.traits()[key], metakey) == value - - -def test_Dcm2nii_outputs(): - output_map = dict( - bvals=dict(), - bvecs=dict(), - converted_files=dict(), - reoriented_and_cropped_files=dict(), - reoriented_files=dict(), - ) - outputs = Dcm2nii.output_spec() - - for key, metadata in list(output_map.items()): - for metakey, value in list(metadata.items()): - assert getattr(outputs.traits()[key], metakey) == value From 01e4a5ea5fa037faa3afc4e3518bfa152e01d66c Mon Sep 17 00:00:00 2001 From: Xihe Xie Date: Wed, 15 Dec 2021 14:48:21 -0500 Subject: [PATCH 3/3] Revert "make check-before-commit deleted test" This reverts commit 7df16faa7d505f61e380cff78ef7015553b65404. --- nipype/interfaces/tests/test_auto_Dcm2nii.py | 107 +++++++++++++++++++ 1 file changed, 107 insertions(+) create mode 100644 nipype/interfaces/tests/test_auto_Dcm2nii.py diff --git a/nipype/interfaces/tests/test_auto_Dcm2nii.py b/nipype/interfaces/tests/test_auto_Dcm2nii.py new file mode 100644 index 0000000000..948aafa083 --- /dev/null +++ b/nipype/interfaces/tests/test_auto_Dcm2nii.py @@ -0,0 +1,107 @@ +# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT +from ..dcm2nii import Dcm2nii + + +def test_Dcm2nii_inputs(): + input_map = dict( + anonymize=dict( + argstr="-a", + usedefault=True, + ), + args=dict( + argstr="%s", + ), + collapse_folders=dict( + argstr="-c", + usedefault=True, + ), + config_file=dict( + argstr="-b %s", + extensions=None, + genfile=True, + ), + convert_all_pars=dict( + argstr="-v", + usedefault=True, + ), + date_in_filename=dict( + argstr="-d", + usedefault=True, + ), + environ=dict( + nohash=True, + usedefault=True, + ), + events_in_filename=dict( + argstr="-e", + usedefault=True, + ), + gzip_output=dict( + argstr="-g", + usedefault=True, + ), + id_in_filename=dict( + argstr="-i", + usedefault=True, + ), + nii_output=dict( + argstr="-n", + usedefault=True, + ), + output_dir=dict( + argstr="-o %s", + genfile=True, + ), + protocol_in_filename=dict( + argstr="-p", + usedefault=True, + ), + reorient=dict( + argstr="-r", + ), + reorient_and_crop=dict( + argstr="-x", + usedefault=True, + ), + source_dir=dict( + argstr="%s", + mandatory=True, + position=-1, + xor=["source_names"], + ), + source_in_filename=dict( + argstr="-f", + usedefault=True, + ), + source_names=dict( + argstr="%s", + copyfile=False, + mandatory=True, + position=-1, + xor=["source_dir"], + ), + spm_analyze=dict( + argstr="-s", + xor=["nii_output"], + ), + ) + inputs = Dcm2nii.input_spec() + + for key, metadata in list(input_map.items()): + for metakey, value in list(metadata.items()): + assert getattr(inputs.traits()[key], metakey) == value + + +def test_Dcm2nii_outputs(): + output_map = dict( + bvals=dict(), + bvecs=dict(), + converted_files=dict(), + reoriented_and_cropped_files=dict(), + reoriented_files=dict(), + ) + outputs = Dcm2nii.output_spec() + + for key, metadata in list(output_map.items()): + for metakey, value in list(metadata.items()): + assert getattr(outputs.traits()[key], metakey) == value