diff --git a/nipype/algorithms/tests/test_auto_AddCSVColumn.py b/nipype/algorithms/tests/test_auto_AddCSVColumn.py index cf33aa14bb..aca82e442f 100644 --- a/nipype/algorithms/tests/test_auto_AddCSVColumn.py +++ b/nipype/algorithms/tests/test_auto_AddCSVColumn.py @@ -1,19 +1,21 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.algorithms.misc import AddCSVColumn + def test_AddCSVColumn_inputs(): input_map = dict(extra_column_heading=dict(), extra_field=dict(), - out_file=dict(usedefault=True, - ), in_file=dict(mandatory=True, ), + out_file=dict(usedefault=True, + ), ) inputs = AddCSVColumn.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_AddCSVColumn_outputs(): output_map = dict(csv_file=dict(), ) @@ -22,3 +24,4 @@ def test_AddCSVColumn_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/algorithms/tests/test_auto_ArtifactDetect.py b/nipype/algorithms/tests/test_auto_ArtifactDetect.py index 24b0b143d1..598bb0752b 100644 --- a/nipype/algorithms/tests/test_auto_ArtifactDetect.py +++ b/nipype/algorithms/tests/test_auto_ArtifactDetect.py @@ -1,46 +1,47 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.algorithms.rapidart import ArtifactDetect + def test_ArtifactDetect_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(bound_by_brainmask=dict(usedefault=True, ), - plot_type=dict(usedefault=True, + global_threshold=dict(usedefault=True, ), - mask_type=dict(mandatory=True, + ignore_exception=dict(nohash=True, + usedefault=True, ), + intersect_mask=dict(), + mask_file=dict(), mask_threshold=dict(), - parameter_source=dict(mandatory=True, + mask_type=dict(mandatory=True, ), - translation_threshold=dict(mandatory=True, - xor=['norm_threshold'], + norm_threshold=dict(mandatory=True, + xor=['rotation_threshold', 'translation_threshold'], ), - global_threshold=dict(usedefault=True, + parameter_source=dict(mandatory=True, ), - bound_by_brainmask=dict(usedefault=True, + plot_type=dict(usedefault=True, ), realigned_files=dict(mandatory=True, ), + realignment_parameters=dict(mandatory=True, + ), rotation_threshold=dict(mandatory=True, xor=['norm_threshold'], ), save_plot=dict(usedefault=True, ), - use_differences=dict(minlen=2, - maxlen=2, - usedefault=True, - ), - norm_threshold=dict(mandatory=True, - xor=['rotation_threshold', 'translation_threshold'], + translation_threshold=dict(mandatory=True, + xor=['norm_threshold'], ), - zintensity_threshold=dict(mandatory=True, + use_differences=dict(maxlen=2, + minlen=2, + usedefault=True, ), use_norm=dict(requires=['norm_threshold'], usedefault=True, ), - mask_file=dict(), - intersect_mask=dict(), - realignment_parameters=dict(mandatory=True, + zintensity_threshold=dict(mandatory=True, ), ) inputs = ArtifactDetect.input_spec() @@ -48,17 +49,19 @@ def test_ArtifactDetect_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ArtifactDetect_outputs(): output_map = dict(displacement_files=dict(), - outlier_files=dict(), - mask_files=dict(), intensity_files=dict(), + mask_files=dict(), norm_files=dict(), - statistic_files=dict(), + outlier_files=dict(), plot_files=dict(), + statistic_files=dict(), ) outputs = ArtifactDetect.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/algorithms/tests/test_auto_CalculateNormalizedMoments.py b/nipype/algorithms/tests/test_auto_CalculateNormalizedMoments.py index 35490271c4..f27766ea00 100644 --- a/nipype/algorithms/tests/test_auto_CalculateNormalizedMoments.py +++ b/nipype/algorithms/tests/test_auto_CalculateNormalizedMoments.py @@ -1,6 +1,7 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.algorithms.misc import CalculateNormalizedMoments + def test_CalculateNormalizedMoments_inputs(): input_map = dict(moment=dict(mandatory=True, ), @@ -12,6 +13,7 @@ def test_CalculateNormalizedMoments_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_CalculateNormalizedMoments_outputs(): output_map = dict(moments=dict(), ) @@ -20,3 +22,4 @@ def test_CalculateNormalizedMoments_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/algorithms/tests/test_auto_CreateNifti.py b/nipype/algorithms/tests/test_auto_CreateNifti.py index b7da739401..ead44c873e 100644 --- a/nipype/algorithms/tests/test_auto_CreateNifti.py +++ b/nipype/algorithms/tests/test_auto_CreateNifti.py @@ -1,21 +1,23 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.algorithms.misc import CreateNifti + def test_CreateNifti_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, - ), + input_map = dict(affine=dict(), data_file=dict(mandatory=True, ), - affine=dict(), header_file=dict(mandatory=True, ), + ignore_exception=dict(nohash=True, + usedefault=True, + ), ) inputs = CreateNifti.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_CreateNifti_outputs(): output_map = dict(nifti_file=dict(), ) @@ -24,3 +26,4 @@ def test_CreateNifti_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/algorithms/tests/test_auto_Distance.py b/nipype/algorithms/tests/test_auto_Distance.py index 65408d0208..dd6f682de2 100644 --- a/nipype/algorithms/tests/test_auto_Distance.py +++ b/nipype/algorithms/tests/test_auto_Distance.py @@ -1,15 +1,16 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.algorithms.misc import Distance + def test_Distance_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, ), - volume1=dict(mandatory=True, - ), + mask_volume=dict(), method=dict(usedefault=True, ), - mask_volume=dict(), + volume1=dict(mandatory=True, + ), volume2=dict(mandatory=True, ), ) @@ -18,14 +19,16 @@ def test_Distance_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Distance_outputs(): output_map = dict(distance=dict(), - point2=dict(), histogram=dict(), point1=dict(), + point2=dict(), ) outputs = Distance.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/algorithms/tests/test_auto_FuzzyOverlap.py b/nipype/algorithms/tests/test_auto_FuzzyOverlap.py index b7d3c87f0a..f9be02dc31 100644 --- a/nipype/algorithms/tests/test_auto_FuzzyOverlap.py +++ b/nipype/algorithms/tests/test_auto_FuzzyOverlap.py @@ -1,17 +1,18 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.algorithms.misc import FuzzyOverlap + def test_FuzzyOverlap_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, ), - weighting=dict(usedefault=True, + in_ref=dict(mandatory=True, ), in_tst=dict(mandatory=True, ), out_file=dict(usedefault=True, ), - in_ref=dict(mandatory=True, + weighting=dict(usedefault=True, ), ) inputs = FuzzyOverlap.input_spec() @@ -19,11 +20,12 @@ def test_FuzzyOverlap_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_FuzzyOverlap_outputs(): - output_map = dict(class_fji=dict(), - class_fdi=dict(), - diff_file=dict(), + output_map = dict(class_fdi=dict(), + class_fji=dict(), dice=dict(), + diff_file=dict(), jaccard=dict(), ) outputs = FuzzyOverlap.output_spec() @@ -31,3 +33,4 @@ def test_FuzzyOverlap_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/algorithms/tests/test_auto_Gunzip.py b/nipype/algorithms/tests/test_auto_Gunzip.py index e6d7c1e98e..eb665716a5 100644 --- a/nipype/algorithms/tests/test_auto_Gunzip.py +++ b/nipype/algorithms/tests/test_auto_Gunzip.py @@ -1,6 +1,7 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.algorithms.misc import Gunzip + def test_Gunzip_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, @@ -13,6 +14,7 @@ def test_Gunzip_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Gunzip_outputs(): output_map = dict(out_file=dict(), ) @@ -21,3 +23,4 @@ def test_Gunzip_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/algorithms/tests/test_auto_ICC.py b/nipype/algorithms/tests/test_auto_ICC.py index 421ef58e3e..cedefe009f 100644 --- a/nipype/algorithms/tests/test_auto_ICC.py +++ b/nipype/algorithms/tests/test_auto_ICC.py @@ -1,6 +1,7 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.algorithms.icc import ICC + def test_ICC_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, @@ -15,9 +16,10 @@ def test_ICC_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ICC_outputs(): - output_map = dict(session_var_map=dict(), - icc_map=dict(), + output_map = dict(icc_map=dict(), + session_var_map=dict(), subject_var_map=dict(), ) outputs = ICC.output_spec() @@ -25,3 +27,4 @@ def test_ICC_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/algorithms/tests/test_auto_Matlab2CSV.py b/nipype/algorithms/tests/test_auto_Matlab2CSV.py index 8bb5214674..bdf47a21b3 100644 --- a/nipype/algorithms/tests/test_auto_Matlab2CSV.py +++ b/nipype/algorithms/tests/test_auto_Matlab2CSV.py @@ -1,10 +1,11 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.algorithms.misc import Matlab2CSV + def test_Matlab2CSV_inputs(): - input_map = dict(reshape_matrix=dict(usedefault=True, + input_map = dict(in_file=dict(mandatory=True, ), - in_file=dict(mandatory=True, + reshape_matrix=dict(usedefault=True, ), ) inputs = Matlab2CSV.input_spec() @@ -12,6 +13,7 @@ def test_Matlab2CSV_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Matlab2CSV_outputs(): output_map = dict(csv_files=dict(), ) @@ -20,3 +22,4 @@ def test_Matlab2CSV_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/algorithms/tests/test_auto_MergeCSVFiles.py b/nipype/algorithms/tests/test_auto_MergeCSVFiles.py index 1c5e2c7e7c..fcdbd535d0 100644 --- a/nipype/algorithms/tests/test_auto_MergeCSVFiles.py +++ b/nipype/algorithms/tests/test_auto_MergeCSVFiles.py @@ -1,23 +1,25 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.algorithms.misc import MergeCSVFiles + def test_MergeCSVFiles_inputs(): - input_map = dict(out_file=dict(usedefault=True, - ), - column_headings=dict(), + input_map = dict(column_headings=dict(), + extra_column_heading=dict(), extra_field=dict(), - row_heading_title=dict(usedefault=True, - ), in_files=dict(mandatory=True, ), + out_file=dict(usedefault=True, + ), + row_heading_title=dict(usedefault=True, + ), row_headings=dict(), - extra_column_heading=dict(), ) inputs = MergeCSVFiles.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MergeCSVFiles_outputs(): output_map = dict(csv_file=dict(), ) @@ -26,3 +28,4 @@ def test_MergeCSVFiles_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/algorithms/tests/test_auto_ModifyAffine.py b/nipype/algorithms/tests/test_auto_ModifyAffine.py index d84ff08928..3186757ad8 100644 --- a/nipype/algorithms/tests/test_auto_ModifyAffine.py +++ b/nipype/algorithms/tests/test_auto_ModifyAffine.py @@ -1,12 +1,13 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.algorithms.misc import ModifyAffine + def test_ModifyAffine_inputs(): - input_map = dict(transformation_matrix=dict(usedefault=True, - ), - ignore_exception=dict(nohash=True, + input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, ), + transformation_matrix=dict(usedefault=True, + ), volumes=dict(mandatory=True, ), ) @@ -15,6 +16,7 @@ def test_ModifyAffine_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ModifyAffine_outputs(): output_map = dict(transformed_volumes=dict(), ) @@ -23,3 +25,4 @@ def test_ModifyAffine_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/algorithms/tests/test_auto_Overlap.py b/nipype/algorithms/tests/test_auto_Overlap.py index edab72a28a..331390e9b5 100644 --- a/nipype/algorithms/tests/test_auto_Overlap.py +++ b/nipype/algorithms/tests/test_auto_Overlap.py @@ -1,15 +1,16 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.algorithms.misc import Overlap + def test_Overlap_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, ), - volume1=dict(mandatory=True, - ), + mask_volume=dict(), out_file=dict(usedefault=True, ), - mask_volume=dict(), + volume1=dict(mandatory=True, + ), volume2=dict(mandatory=True, ), ) @@ -18,14 +19,16 @@ def test_Overlap_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Overlap_outputs(): - output_map = dict(volume_difference=dict(), + output_map = dict(dice=dict(), diff_file=dict(), - dice=dict(), jaccard=dict(), + volume_difference=dict(), ) outputs = Overlap.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/algorithms/tests/test_auto_P2PDistance.py b/nipype/algorithms/tests/test_auto_P2PDistance.py index a3542ba7b0..6f9a755f6b 100644 --- a/nipype/algorithms/tests/test_auto_P2PDistance.py +++ b/nipype/algorithms/tests/test_auto_P2PDistance.py @@ -1,14 +1,15 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.algorithms.mesh import P2PDistance + def test_P2PDistance_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, ), - surface2=dict(mandatory=True, - ), surface1=dict(mandatory=True, ), + surface2=dict(mandatory=True, + ), weighting=dict(usedefault=True, ), ) @@ -17,6 +18,7 @@ def test_P2PDistance_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_P2PDistance_outputs(): output_map = dict(distance=dict(), ) @@ -25,3 +27,4 @@ def test_P2PDistance_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/algorithms/tests/test_auto_PickAtlas.py b/nipype/algorithms/tests/test_auto_PickAtlas.py index be1391d81a..e4ad2e46be 100644 --- a/nipype/algorithms/tests/test_auto_PickAtlas.py +++ b/nipype/algorithms/tests/test_auto_PickAtlas.py @@ -1,25 +1,27 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.algorithms.misc import PickAtlas + def test_PickAtlas_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(atlas=dict(mandatory=True, ), - labels=dict(mandatory=True, + dilation_size=dict(usedefault=True, ), - output_file=dict(), hemi=dict(usedefault=True, ), - dilation_size=dict(usedefault=True, + ignore_exception=dict(nohash=True, + usedefault=True, ), - atlas=dict(mandatory=True, + labels=dict(mandatory=True, ), + output_file=dict(), ) inputs = PickAtlas.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_PickAtlas_outputs(): output_map = dict(mask_file=dict(), ) @@ -28,3 +30,4 @@ def test_PickAtlas_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/algorithms/tests/test_auto_SimpleThreshold.py b/nipype/algorithms/tests/test_auto_SimpleThreshold.py index ca2264553f..7a0c50ff10 100644 --- a/nipype/algorithms/tests/test_auto_SimpleThreshold.py +++ b/nipype/algorithms/tests/test_auto_SimpleThreshold.py @@ -1,12 +1,13 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.algorithms.misc import SimpleThreshold + def test_SimpleThreshold_inputs(): - input_map = dict(threshold=dict(mandatory=True, - ), - ignore_exception=dict(nohash=True, + input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, ), + threshold=dict(mandatory=True, + ), volumes=dict(mandatory=True, ), ) @@ -15,6 +16,7 @@ def test_SimpleThreshold_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_SimpleThreshold_outputs(): output_map = dict(thresholded_volumes=dict(), ) @@ -23,3 +25,4 @@ def test_SimpleThreshold_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/algorithms/tests/test_auto_SpecifyModel.py b/nipype/algorithms/tests/test_auto_SpecifyModel.py index 71fea1f25e..0160b69a1b 100644 --- a/nipype/algorithms/tests/test_auto_SpecifyModel.py +++ b/nipype/algorithms/tests/test_auto_SpecifyModel.py @@ -1,28 +1,29 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.algorithms.modelgen import SpecifyModel + def test_SpecifyModel_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(event_files=dict(mandatory=True, + xor=['subject_info'], ), functional_runs=dict(copyfile=False, mandatory=True, ), high_pass_filter_cutoff=dict(mandatory=True, ), - outlier_files=dict(copyfile=False, + ignore_exception=dict(nohash=True, + usedefault=True, ), - subject_info=dict(mandatory=True, - xor=['event_files'], + input_units=dict(mandatory=True, ), - time_repetition=dict(mandatory=True, + outlier_files=dict(copyfile=False, ), realignment_parameters=dict(copyfile=False, ), - event_files=dict(mandatory=True, - xor=['subject_info'], + subject_info=dict(mandatory=True, + xor=['event_files'], ), - input_units=dict(mandatory=True, + time_repetition=dict(mandatory=True, ), ) inputs = SpecifyModel.input_spec() @@ -30,6 +31,7 @@ def test_SpecifyModel_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_SpecifyModel_outputs(): output_map = dict(session_info=dict(), ) @@ -38,3 +40,4 @@ def test_SpecifyModel_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/algorithms/tests/test_auto_SpecifySPMModel.py b/nipype/algorithms/tests/test_auto_SpecifySPMModel.py index f3f4433f9c..de86a39a17 100644 --- a/nipype/algorithms/tests/test_auto_SpecifySPMModel.py +++ b/nipype/algorithms/tests/test_auto_SpecifySPMModel.py @@ -1,32 +1,33 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.algorithms.modelgen import SpecifySPMModel + def test_SpecifySPMModel_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(concatenate_runs=dict(usedefault=True, ), - subject_info=dict(mandatory=True, - xor=['event_files'], + event_files=dict(mandatory=True, + xor=['subject_info'], + ), + functional_runs=dict(copyfile=False, + mandatory=True, ), high_pass_filter_cutoff=dict(mandatory=True, ), - outlier_files=dict(copyfile=False, + ignore_exception=dict(nohash=True, + usedefault=True, ), - functional_runs=dict(copyfile=False, - mandatory=True, + input_units=dict(mandatory=True, ), - time_repetition=dict(mandatory=True, + outlier_files=dict(copyfile=False, ), output_units=dict(usedefault=True, ), realignment_parameters=dict(copyfile=False, ), - concatenate_runs=dict(usedefault=True, - ), - event_files=dict(mandatory=True, - xor=['subject_info'], + subject_info=dict(mandatory=True, + xor=['event_files'], ), - input_units=dict(mandatory=True, + time_repetition=dict(mandatory=True, ), ) inputs = SpecifySPMModel.input_spec() @@ -34,6 +35,7 @@ def test_SpecifySPMModel_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_SpecifySPMModel_outputs(): output_map = dict(session_info=dict(), ) @@ -42,3 +44,4 @@ def test_SpecifySPMModel_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/algorithms/tests/test_auto_SpecifySparseModel.py b/nipype/algorithms/tests/test_auto_SpecifySparseModel.py index a79c91f6bf..5a12f657cb 100644 --- a/nipype/algorithms/tests/test_auto_SpecifySparseModel.py +++ b/nipype/algorithms/tests/test_auto_SpecifySparseModel.py @@ -1,42 +1,43 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.algorithms.modelgen import SpecifySparseModel + def test_SpecifySparseModel_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(event_files=dict(mandatory=True, + xor=['subject_info'], ), - input_units=dict(mandatory=True, + functional_runs=dict(copyfile=False, + mandatory=True, ), high_pass_filter_cutoff=dict(mandatory=True, ), - outlier_files=dict(copyfile=False, + ignore_exception=dict(nohash=True, + usedefault=True, ), - scale_regressors=dict(usedefault=True, + input_units=dict(mandatory=True, ), model_hrf=dict(), - scan_onset=dict(usedefault=True, - ), - functional_runs=dict(copyfile=False, - mandatory=True, - ), - time_repetition=dict(mandatory=True, + outlier_files=dict(copyfile=False, ), - volumes_in_cluster=dict(usedefault=True, + realignment_parameters=dict(copyfile=False, ), save_plot=dict(), - realignment_parameters=dict(copyfile=False, + scale_regressors=dict(usedefault=True, + ), + scan_onset=dict(usedefault=True, ), stimuli_as_impulses=dict(usedefault=True, ), - use_temporal_deriv=dict(requires=['model_hrf'], + subject_info=dict(mandatory=True, + xor=['event_files'], ), time_acquisition=dict(mandatory=True, ), - subject_info=dict(mandatory=True, - xor=['event_files'], + time_repetition=dict(mandatory=True, ), - event_files=dict(mandatory=True, - xor=['subject_info'], + use_temporal_deriv=dict(requires=['model_hrf'], + ), + volumes_in_cluster=dict(usedefault=True, ), ) inputs = SpecifySparseModel.input_spec() @@ -44,13 +45,15 @@ def test_SpecifySparseModel_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_SpecifySparseModel_outputs(): - output_map = dict(sparse_png_file=dict(), + output_map = dict(session_info=dict(), + sparse_png_file=dict(), sparse_svg_file=dict(), - session_info=dict(), ) outputs = SpecifySparseModel.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/algorithms/tests/test_auto_StimulusCorrelation.py b/nipype/algorithms/tests/test_auto_StimulusCorrelation.py index eb8b82c98c..ad51cfdd2a 100644 --- a/nipype/algorithms/tests/test_auto_StimulusCorrelation.py +++ b/nipype/algorithms/tests/test_auto_StimulusCorrelation.py @@ -1,17 +1,18 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.algorithms.rapidart import StimulusCorrelation + def test_StimulusCorrelation_inputs(): - input_map = dict(intensity_values=dict(mandatory=True, + input_map = dict(concatenated_design=dict(mandatory=True, ), ignore_exception=dict(nohash=True, usedefault=True, ), - spm_mat_file=dict(mandatory=True, + intensity_values=dict(mandatory=True, ), realignment_parameters=dict(mandatory=True, ), - concatenated_design=dict(mandatory=True, + spm_mat_file=dict(mandatory=True, ), ) inputs = StimulusCorrelation.input_spec() @@ -19,6 +20,7 @@ def test_StimulusCorrelation_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_StimulusCorrelation_outputs(): output_map = dict(stimcorr_files=dict(), ) @@ -27,3 +29,4 @@ def test_StimulusCorrelation_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/algorithms/tests/test_auto_TSNR.py b/nipype/algorithms/tests/test_auto_TSNR.py index 8087960939..e3a7fc13cd 100644 --- a/nipype/algorithms/tests/test_auto_TSNR.py +++ b/nipype/algorithms/tests/test_auto_TSNR.py @@ -1,27 +1,30 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.algorithms.misc import TSNR + def test_TSNR_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, ), - regress_poly=dict(), in_file=dict(mandatory=True, ), + regress_poly=dict(), ) inputs = TSNR.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_TSNR_outputs(): output_map = dict(detrended_file=dict(), + mean_file=dict(), stddev_file=dict(), tsnr_file=dict(), - mean_file=dict(), ) outputs = TSNR.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/afni/tests/test_auto_AFNICommand.py b/nipype/interfaces/afni/tests/test_auto_AFNICommand.py index 191bc172da..6cc0b47d5b 100644 --- a/nipype/interfaces/afni/tests/test_auto_AFNICommand.py +++ b/nipype/interfaces/afni/tests/test_auto_AFNICommand.py @@ -1,26 +1,28 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.afni.base import AFNICommand + def test_AFNICommand_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + environ=dict(nohash=True, usedefault=True, ), - out_file=dict(name_source=['in_file'], - name_template='%s_afni', - argstr='-prefix %s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - args=dict(argstr='%s', + out_file=dict(argstr='-prefix %s', + name_source=['in_file'], + name_template='%s_afni', ), outputtype=dict(), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), ) inputs = AFNICommand.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/afni/tests/test_auto_AFNItoNIFTI.py b/nipype/interfaces/afni/tests/test_auto_AFNItoNIFTI.py index 1e6babe9cb..0a1ca00a38 100644 --- a/nipype/interfaces/afni/tests/test_auto_AFNItoNIFTI.py +++ b/nipype/interfaces/afni/tests/test_auto_AFNItoNIFTI.py @@ -1,34 +1,36 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.afni.preprocess import AFNItoNIFTI + def test_AFNItoNIFTI_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + environ=dict(nohash=True, usedefault=True, ), - out_file=dict(name_source='in_file', - name_template='%s.nii', - argstr='-prefix %s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - args=dict(argstr='%s', + in_file=dict(argstr='%s', + copyfile=False, + mandatory=True, + position=-1, + ), + out_file=dict(argstr='-prefix %s', + name_source='in_file', + name_template='%s.nii', ), outputtype=dict(), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - in_file=dict(copyfile=False, - mandatory=True, - position=-1, - argstr='%s', - ), ) inputs = AFNItoNIFTI.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_AFNItoNIFTI_outputs(): output_map = dict(out_file=dict(), ) @@ -37,3 +39,4 @@ def test_AFNItoNIFTI_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/afni/tests/test_auto_Allineate.py b/nipype/interfaces/afni/tests/test_auto_Allineate.py index afd797a72f..f29af550d6 100644 --- a/nipype/interfaces/afni/tests/test_auto_Allineate.py +++ b/nipype/interfaces/afni/tests/test_auto_Allineate.py @@ -1,107 +1,108 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.afni.preprocess import Allineate + def test_Allineate_inputs(): - input_map = dict(warp_type=dict(argstr='-warp %s', + input_map = dict(args=dict(argstr='%s', ), - fine_blur=dict(argstr='-fineblur %f', + autobox=dict(argstr='-autobox', ), - weight_file=dict(argstr='-weight %s', + automask=dict(argstr='-automask+%d', ), - reference=dict(argstr='-base %s', + autoweight=dict(argstr='-autoweight%s', ), - warpfreeze=dict(argstr='-warpfreeze', + center_of_mass=dict(argstr='-cmass%s', ), - zclip=dict(argstr='-zclip', + check=dict(argstr='-check %s', ), - usetemp=dict(argstr='-usetemp', + convergence=dict(argstr='-conv %f', ), cost=dict(argstr='-cost %s', ), - check=dict(argstr='-check %s', + environ=dict(nohash=True, + usedefault=True, ), - no_pad=dict(argstr='-nopad', + epi=dict(argstr='-EPI', ), - replacemeth=dict(argstr='-replacemeth %s', + final_interpolation=dict(argstr='-final %s', ), - replacebase=dict(argstr='-replacebase', + fine_blur=dict(argstr='-fineblur %f', ), - in_file=dict(copyfile=False, + ignore_exception=dict(nohash=True, + usedefault=True, + ), + in_file=dict(argstr='-source %s', + copyfile=False, mandatory=True, position=-1, - argstr='-source %s', - ), - nwarp_fixdep=dict(argstr='-nwarp_fixdep%s', ), - master=dict(argstr='-master %s', + in_matrix=dict(argstr='-1Dmatrix_apply %s', + position=-3, ), - center_of_mass=dict(argstr='-cmass%s', + in_param_file=dict(argstr='-1Dparam_apply %s', ), - nmatch=dict(argstr='-nmatch %d', + interpolation=dict(argstr='-interp %s', ), - final_interpolation=dict(argstr='-final %s', + master=dict(argstr='-master %s', ), - interpolation=dict(argstr='-interp %s', + newgrid=dict(argstr='-newgrid %f', ), - ignore_exception=dict(nohash=True, - usedefault=True, + nmatch=dict(argstr='-nmatch %d', ), - source_mask=dict(argstr='-source_mask %s', + no_pad=dict(argstr='-nopad', ), - one_pass=dict(argstr='-onepass', + nomask=dict(argstr='-nomask', ), - out_weight_file=dict(argstr='-wtprefix %s', + nwarp=dict(argstr='-nwarp %s', ), - automask=dict(argstr='-automask+%d', + nwarp_fixdep=dict(argstr='-nwarp_fixdep%s', ), - in_matrix=dict(position=-3, - argstr='-1Dmatrix_apply %s', + nwarp_fixmot=dict(argstr='-nwarp_fixmot%s', ), - args=dict(argstr='%s', + one_pass=dict(argstr='-onepass', ), - two_first=dict(argstr='-twofirst', + out_file=dict(argstr='-prefix %s', + genfile=True, + name_source='%s_allineate', + position=-2, ), out_matrix=dict(argstr='-1Dmatrix_save %s', ), - terminal_output=dict(mandatory=True, - nohash=True, + out_param_file=dict(argstr='-1Dparam_save %s', ), - source_automask=dict(argstr='-source_automask+%d', + out_weight_file=dict(argstr='-wtprefix %s', ), - newgrid=dict(argstr='-newgrid %f', + outputtype=dict(), + reference=dict(argstr='-base %s', ), - convergence=dict(argstr='-conv %f', + replacebase=dict(argstr='-replacebase', ), - autobox=dict(argstr='-autobox', + replacemeth=dict(argstr='-replacemeth %s', ), - nwarp_fixmot=dict(argstr='-nwarp_fixmot%s', + source_automask=dict(argstr='-source_automask+%d', ), - out_file=dict(name_source='%s_allineate', - genfile=True, - position=-2, - argstr='-prefix %s', + source_mask=dict(argstr='-source_mask %s', ), - nwarp=dict(argstr='-nwarp %s', + terminal_output=dict(mandatory=True, + nohash=True, ), - autoweight=dict(argstr='-autoweight%s', + two_best=dict(argstr='-twobest %d', ), - outputtype=dict(), - out_param_file=dict(argstr='-1Dparam_save %s', + two_blur=dict(argstr='-twoblur', ), - two_best=dict(argstr='-twobest %d', + two_first=dict(argstr='-twofirst', ), - environ=dict(nohash=True, - usedefault=True, + two_pass=dict(argstr='-twopass', ), - two_blur=dict(argstr='-twoblur', + usetemp=dict(argstr='-usetemp', ), - epi=dict(argstr='-EPI', + warp_type=dict(argstr='-warp %s', ), - in_param_file=dict(argstr='-1Dparam_apply %s', + warpfreeze=dict(argstr='-warpfreeze', ), - nomask=dict(argstr='-nomask', + weight_file=dict(argstr='-weight %s', ), - two_pass=dict(argstr='-twopass', + zclip=dict(argstr='-zclip', ), ) inputs = Allineate.input_spec() @@ -109,12 +110,14 @@ def test_Allineate_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Allineate_outputs(): - output_map = dict(out_file=dict(), - matrix=dict(), + output_map = dict(matrix=dict(), + out_file=dict(), ) outputs = Allineate.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/afni/tests/test_auto_AutoTcorrelate.py b/nipype/interfaces/afni/tests/test_auto_AutoTcorrelate.py index da90245a43..7f9eb5dfae 100644 --- a/nipype/interfaces/afni/tests/test_auto_AutoTcorrelate.py +++ b/nipype/interfaces/afni/tests/test_auto_AutoTcorrelate.py @@ -1,36 +1,37 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.afni.preprocess import AutoTcorrelate + def test_AutoTcorrelate_inputs(): - input_map = dict(polort=dict(argstr='-polort %d', + input_map = dict(args=dict(argstr='%s', ), - ignore_exception=dict(nohash=True, + environ=dict(nohash=True, usedefault=True, ), - mask_only_targets=dict(xor=['mask_source'], - argstr='-mask_only_targets', - ), - out_file=dict(name_source='in_file', - name_template='%s_similarity_matrix.1D', - argstr='-prefix %s', - ), eta2=dict(argstr='-eta2', ), - args=dict(argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, + ), + in_file=dict(argstr='%s', + copyfile=False, + mandatory=True, + position=-1, ), mask=dict(argstr='-mask %s', ), - outputtype=dict(), - mask_source=dict(xor=['mask_only_targets'], - argstr='-mask_source %s', + mask_only_targets=dict(argstr='-mask_only_targets', + xor=['mask_source'], ), - environ=dict(nohash=True, - usedefault=True, + mask_source=dict(argstr='-mask_source %s', + xor=['mask_only_targets'], ), - in_file=dict(copyfile=False, - mandatory=True, - position=-1, - argstr='%s', + out_file=dict(argstr='-prefix %s', + name_source='in_file', + name_template='%s_similarity_matrix.1D', + ), + outputtype=dict(), + polort=dict(argstr='-polort %d', ), terminal_output=dict(mandatory=True, nohash=True, @@ -41,6 +42,7 @@ def test_AutoTcorrelate_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_AutoTcorrelate_outputs(): output_map = dict(out_file=dict(), ) @@ -49,3 +51,4 @@ def test_AutoTcorrelate_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/afni/tests/test_auto_Autobox.py b/nipype/interfaces/afni/tests/test_auto_Autobox.py index 40c736610b..fe620d3842 100644 --- a/nipype/interfaces/afni/tests/test_auto_Autobox.py +++ b/nipype/interfaces/afni/tests/test_auto_Autobox.py @@ -1,14 +1,24 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.afni.preprocess import Autobox + def test_Autobox_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + environ=dict(nohash=True, usedefault=True, ), - out_file=dict(name_source='in_file', - argstr='-prefix %s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - args=dict(argstr='%s', + in_file=dict(argstr='-input %s', + copyfile=False, + mandatory=True, + ), + no_clustering=dict(argstr='-noclust', + ), + out_file=dict(argstr='-prefix %s', + name_source='in_file', ), outputtype=dict(), padding=dict(argstr='-npad %d', @@ -16,32 +26,25 @@ def test_Autobox_inputs(): terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - in_file=dict(copyfile=False, - mandatory=True, - argstr='-input %s', - ), - no_clustering=dict(argstr='-noclust', - ), ) inputs = Autobox.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Autobox_outputs(): - output_map = dict(y_min=dict(), + output_map = dict(out_file=dict(), + x_max=dict(), + x_min=dict(), y_max=dict(), + y_min=dict(), z_max=dict(), z_min=dict(), - x_max=dict(), - x_min=dict(), - out_file=dict(), ) outputs = Autobox.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/afni/tests/test_auto_Automask.py b/nipype/interfaces/afni/tests/test_auto_Automask.py index 7def2f45ba..c5bce5c2ef 100644 --- a/nipype/interfaces/afni/tests/test_auto_Automask.py +++ b/nipype/interfaces/afni/tests/test_auto_Automask.py @@ -1,37 +1,38 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.afni.preprocess import Automask + def test_Automask_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(args=dict(argstr='%s', ), - args=dict(argstr='%s', - ), - erode=dict(argstr='-erode %s', + brain_file=dict(argstr='-apply_prefix %s', + name_source='in_file', + name_template='%s_masked', ), - out_file=dict(name_source='in_file', - name_template='%s_mask', - argstr='-prefix %s', + clfrac=dict(argstr='-clfrac %s', ), dilate=dict(argstr='-dilate %s', ), - clfrac=dict(argstr='-clfrac %s', - ), - outputtype=dict(), - brain_file=dict(name_source='in_file', - name_template='%s_masked', - argstr='-apply_prefix %s', + environ=dict(nohash=True, + usedefault=True, ), - terminal_output=dict(mandatory=True, - nohash=True, + erode=dict(argstr='-erode %s', ), - environ=dict(nohash=True, + ignore_exception=dict(nohash=True, usedefault=True, ), - in_file=dict(copyfile=False, + in_file=dict(argstr='%s', + copyfile=False, mandatory=True, position=-1, - argstr='%s', + ), + out_file=dict(argstr='-prefix %s', + name_source='in_file', + name_template='%s_mask', + ), + outputtype=dict(), + terminal_output=dict(mandatory=True, + nohash=True, ), ) inputs = Automask.input_spec() @@ -39,12 +40,14 @@ def test_Automask_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Automask_outputs(): - output_map = dict(out_file=dict(), - brain_file=dict(), + output_map = dict(brain_file=dict(), + out_file=dict(), ) outputs = Automask.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/afni/tests/test_auto_Bandpass.py b/nipype/interfaces/afni/tests/test_auto_Bandpass.py index 1cb857f0a5..3170e8e6a2 100644 --- a/nipype/interfaces/afni/tests/test_auto_Bandpass.py +++ b/nipype/interfaces/afni/tests/test_auto_Bandpass.py @@ -1,62 +1,63 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.afni.preprocess import Bandpass + def test_Bandpass_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, - ), - localPV=dict(argstr='-localPV %f', - ), - orthogonalize_file=dict(argstr='-ort %s', + input_map = dict(args=dict(argstr='%s', ), - nfft=dict(argstr='-nfft %d', + automask=dict(argstr='-automask', ), - tr=dict(argstr='-dt %f', + blur=dict(argstr='-blur %f', ), despike=dict(argstr='-despike', ), - args=dict(argstr='%s', + environ=dict(nohash=True, + usedefault=True, ), - no_detrend=dict(argstr='-nodetrend', + highpass=dict(argstr='%f', + mandatory=True, + position=-3, ), - outputtype=dict(), - orthogonalize_dset=dict(argstr='-dsort %s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - highpass=dict(position=-3, + in_file=dict(argstr='%s', + copyfile=False, mandatory=True, - argstr='%f', + position=-1, ), - normalize=dict(argstr='-norm', + localPV=dict(argstr='-localPV %f', ), - terminal_output=dict(mandatory=True, - nohash=True, + lowpass=dict(argstr='%f', + mandatory=True, + position=-2, ), - notrans=dict(argstr='-notrans', + mask=dict(argstr='-mask %s', + position=2, ), - in_file=dict(copyfile=False, - mandatory=True, - position=-1, - argstr='%s', + nfft=dict(argstr='-nfft %d', ), - lowpass=dict(position=-2, - mandatory=True, - argstr='%f', + no_detrend=dict(argstr='-nodetrend', ), - blur=dict(argstr='-blur %f', + normalize=dict(argstr='-norm', ), - environ=dict(nohash=True, - usedefault=True, + notrans=dict(argstr='-notrans', ), - automask=dict(argstr='-automask', + orthogonalize_dset=dict(argstr='-dsort %s', ), - mask=dict(position=2, - argstr='-mask %s', + orthogonalize_file=dict(argstr='-ort %s', ), - out_file=dict(name_source='in_file', + out_file=dict(argstr='-prefix %s', genfile=True, + name_source='in_file', name_template='%s_bp', position=1, - argstr='-prefix %s', + ), + outputtype=dict(), + terminal_output=dict(mandatory=True, + nohash=True, + ), + tr=dict(argstr='-dt %f', ), ) inputs = Bandpass.input_spec() @@ -64,6 +65,7 @@ def test_Bandpass_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Bandpass_outputs(): output_map = dict(out_file=dict(), ) @@ -72,3 +74,4 @@ def test_Bandpass_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/afni/tests/test_auto_BlurInMask.py b/nipype/interfaces/afni/tests/test_auto_BlurInMask.py index 9e27f392eb..db3f926c47 100644 --- a/nipype/interfaces/afni/tests/test_auto_BlurInMask.py +++ b/nipype/interfaces/afni/tests/test_auto_BlurInMask.py @@ -1,44 +1,45 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.afni.preprocess import BlurInMask + def test_BlurInMask_inputs(): - input_map = dict(preserve=dict(argstr='-preserve', - ), - ignore_exception=dict(nohash=True, - usedefault=True, - ), - out_file=dict(name_source='in_file', - name_template='%s_blur', - position=-1, - argstr='-prefix %s', + input_map = dict(args=dict(argstr='%s', ), automask=dict(argstr='-automask', ), - args=dict(argstr='%s', - ), - mask=dict(argstr='-mask %s', + environ=dict(nohash=True, + usedefault=True, ), - outputtype=dict(), float_out=dict(argstr='-float', ), - terminal_output=dict(mandatory=True, - nohash=True, + fwhm=dict(argstr='-FWHM %f', + mandatory=True, ), - environ=dict(nohash=True, + ignore_exception=dict(nohash=True, usedefault=True, ), - in_file=dict(copyfile=False, + in_file=dict(argstr='-input %s', + copyfile=False, mandatory=True, position=1, - argstr='-input %s', + ), + mask=dict(argstr='-mask %s', ), multimask=dict(argstr='-Mmask %s', ), - fwhm=dict(mandatory=True, - argstr='-FWHM %f', + options=dict(argstr='%s', + position=2, + ), + out_file=dict(argstr='-prefix %s', + name_source='in_file', + name_template='%s_blur', + position=-1, + ), + outputtype=dict(), + preserve=dict(argstr='-preserve', ), - options=dict(position=2, - argstr='%s', + terminal_output=dict(mandatory=True, + nohash=True, ), ) inputs = BlurInMask.input_spec() @@ -46,6 +47,7 @@ def test_BlurInMask_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_BlurInMask_outputs(): output_map = dict(out_file=dict(), ) @@ -54,3 +56,4 @@ def test_BlurInMask_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/afni/tests/test_auto_BrickStat.py b/nipype/interfaces/afni/tests/test_auto_BrickStat.py index f1313e4d70..db6e422535 100644 --- a/nipype/interfaces/afni/tests/test_auto_BrickStat.py +++ b/nipype/interfaces/afni/tests/test_auto_BrickStat.py @@ -1,39 +1,41 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.afni.preprocess import BrickStat + def test_BrickStat_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + environ=dict(nohash=True, usedefault=True, ), - out_file=dict(name_source=['in_file'], - name_template='%s_afni', - argstr='-prefix %s', + ignore_exception=dict(nohash=True, + usedefault=True, + ), + in_file=dict(argstr='%s', + mandatory=True, + position=-1, ), - min=dict(position=1, - argstr='-min', + mask=dict(argstr='-mask %s', + position=2, ), - args=dict(argstr='%s', + min=dict(argstr='-min', + position=1, ), - mask=dict(position=2, - argstr='-mask %s', + out_file=dict(argstr='-prefix %s', + name_source=['in_file'], + name_template='%s_afni', ), outputtype=dict(), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - in_file=dict(position=-1, - mandatory=True, - argstr='%s', - ), ) inputs = BrickStat.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_BrickStat_outputs(): output_map = dict(min_val=dict(), ) @@ -42,3 +44,4 @@ def test_BrickStat_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/afni/tests/test_auto_Calc.py b/nipype/interfaces/afni/tests/test_auto_Calc.py index c69c834867..8c68f4f261 100644 --- a/nipype/interfaces/afni/tests/test_auto_Calc.py +++ b/nipype/interfaces/afni/tests/test_auto_Calc.py @@ -1,50 +1,52 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.afni.preprocess import Calc + def test_Calc_inputs(): - input_map = dict(stop_idx=dict(requires=['start_idx'], + input_map = dict(args=dict(argstr='%s', ), - ignore_exception=dict(nohash=True, + environ=dict(nohash=True, usedefault=True, ), - out_file=dict(name_source='in_file_a', - name_template='%s_calc', - argstr='-prefix %s', - ), - in_file_a=dict(position=0, + expr=dict(argstr='-expr "%s"', mandatory=True, - argstr='-a %s', + position=3, + ), + ignore_exception=dict(nohash=True, + usedefault=True, ), - expr=dict(position=3, + in_file_a=dict(argstr='-a %s', mandatory=True, - argstr='-expr "%s"', + position=0, + ), + in_file_b=dict(argstr=' -b %s', + position=1, ), - args=dict(argstr='%s', + in_file_c=dict(argstr=' -c %s', + position=2, + ), + other=dict(argstr='', + ), + out_file=dict(argstr='-prefix %s', + name_source='in_file_a', + name_template='%s_calc', ), outputtype=dict(), + single_idx=dict(), start_idx=dict(requires=['stop_idx'], ), - in_file_b=dict(position=1, - argstr=' -b %s', - ), - in_file_c=dict(position=2, - argstr=' -c %s', + stop_idx=dict(requires=['start_idx'], ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - other=dict(argstr='', - ), - single_idx=dict(), ) inputs = Calc.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Calc_outputs(): output_map = dict(out_file=dict(), ) @@ -53,3 +55,4 @@ def test_Calc_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/afni/tests/test_auto_Copy.py b/nipype/interfaces/afni/tests/test_auto_Copy.py index 29dc01dbd1..e7bf5d2fd7 100644 --- a/nipype/interfaces/afni/tests/test_auto_Copy.py +++ b/nipype/interfaces/afni/tests/test_auto_Copy.py @@ -1,34 +1,36 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.afni.preprocess import Copy + def test_Copy_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + environ=dict(nohash=True, usedefault=True, ), - out_file=dict(name_source='in_file', - name_template='%s_copy', - argstr='-prefix %s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - args=dict(argstr='%s', + in_file=dict(argstr='%s', + copyfile=False, + mandatory=True, + position=-2, + ), + out_file=dict(argstr='-prefix %s', + name_source='in_file', + name_template='%s_copy', ), outputtype=dict(), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - in_file=dict(copyfile=False, - mandatory=True, - position=-2, - argstr='%s', - ), ) inputs = Copy.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Copy_outputs(): output_map = dict(out_file=dict(), ) @@ -37,3 +39,4 @@ def test_Copy_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/afni/tests/test_auto_Despike.py b/nipype/interfaces/afni/tests/test_auto_Despike.py index 24ebce2568..96bc331f2a 100644 --- a/nipype/interfaces/afni/tests/test_auto_Despike.py +++ b/nipype/interfaces/afni/tests/test_auto_Despike.py @@ -1,34 +1,36 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.afni.preprocess import Despike + def test_Despike_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + environ=dict(nohash=True, usedefault=True, ), - out_file=dict(name_source='in_file', - name_template='%s_despike', - argstr='-prefix %s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - args=dict(argstr='%s', + in_file=dict(argstr='%s', + copyfile=False, + mandatory=True, + position=-1, + ), + out_file=dict(argstr='-prefix %s', + name_source='in_file', + name_template='%s_despike', ), outputtype=dict(), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - in_file=dict(copyfile=False, - mandatory=True, - position=-1, - argstr='%s', - ), ) inputs = Despike.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Despike_outputs(): output_map = dict(out_file=dict(), ) @@ -37,3 +39,4 @@ def test_Despike_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/afni/tests/test_auto_Detrend.py b/nipype/interfaces/afni/tests/test_auto_Detrend.py index 7f25a4105e..8e6159ee29 100644 --- a/nipype/interfaces/afni/tests/test_auto_Detrend.py +++ b/nipype/interfaces/afni/tests/test_auto_Detrend.py @@ -1,34 +1,36 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.afni.preprocess import Detrend + def test_Detrend_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + environ=dict(nohash=True, usedefault=True, ), - out_file=dict(name_source='in_file', - name_template='%s_detrend', - argstr='-prefix %s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - args=dict(argstr='%s', + in_file=dict(argstr='%s', + copyfile=False, + mandatory=True, + position=-1, + ), + out_file=dict(argstr='-prefix %s', + name_source='in_file', + name_template='%s_detrend', ), outputtype=dict(), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - in_file=dict(copyfile=False, - mandatory=True, - position=-1, - argstr='%s', - ), ) inputs = Detrend.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Detrend_outputs(): output_map = dict(out_file=dict(), ) @@ -37,3 +39,4 @@ def test_Detrend_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/afni/tests/test_auto_Fim.py b/nipype/interfaces/afni/tests/test_auto_Fim.py index 94b9f9c7f9..89fb674959 100644 --- a/nipype/interfaces/afni/tests/test_auto_Fim.py +++ b/nipype/interfaces/afni/tests/test_auto_Fim.py @@ -1,37 +1,38 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.afni.preprocess import Fim + def test_Fim_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(args=dict(argstr='%s', ), - out_file=dict(name_source='in_file', - name_template='%s_fim', - argstr='-bucket %s', - ), - args=dict(argstr='%s', + environ=dict(nohash=True, + usedefault=True, ), - outputtype=dict(), - fim_thr=dict(position=3, - argstr='-fim_thr %f', + fim_thr=dict(argstr='-fim_thr %f', + position=3, ), - ideal_file=dict(position=2, + ideal_file=dict(argstr='-ideal_file %s', mandatory=True, - argstr='-ideal_file %s', - ), - terminal_output=dict(mandatory=True, - nohash=True, + position=2, ), - environ=dict(nohash=True, + ignore_exception=dict(nohash=True, usedefault=True, ), - in_file=dict(copyfile=False, + in_file=dict(argstr=' -input %s', + copyfile=False, mandatory=True, position=1, - argstr=' -input %s', ), - out=dict(position=4, - argstr='-out %s', + out=dict(argstr='-out %s', + position=4, + ), + out_file=dict(argstr='-bucket %s', + name_source='in_file', + name_template='%s_fim', + ), + outputtype=dict(), + terminal_output=dict(mandatory=True, + nohash=True, ), ) inputs = Fim.input_spec() @@ -39,6 +40,7 @@ def test_Fim_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Fim_outputs(): output_map = dict(out_file=dict(), ) @@ -47,3 +49,4 @@ def test_Fim_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/afni/tests/test_auto_Fourier.py b/nipype/interfaces/afni/tests/test_auto_Fourier.py index 9177445294..56e5b469b6 100644 --- a/nipype/interfaces/afni/tests/test_auto_Fourier.py +++ b/nipype/interfaces/afni/tests/test_auto_Fourier.py @@ -1,35 +1,36 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.afni.preprocess import Fourier + def test_Fourier_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(args=dict(argstr='%s', ), - out_file=dict(name_source='in_file', - name_template='%s_fourier', - argstr='-prefix %s', - ), - args=dict(argstr='%s', + environ=dict(nohash=True, + usedefault=True, ), - outputtype=dict(), - highpass=dict(position=1, + highpass=dict(argstr='-highpass %f', mandatory=True, - argstr='-highpass %f', - ), - terminal_output=dict(mandatory=True, - nohash=True, + position=1, ), - environ=dict(nohash=True, + ignore_exception=dict(nohash=True, usedefault=True, ), - in_file=dict(copyfile=False, + in_file=dict(argstr='%s', + copyfile=False, mandatory=True, position=-1, - argstr='%s', ), - lowpass=dict(position=0, + lowpass=dict(argstr='-lowpass %f', mandatory=True, - argstr='-lowpass %f', + position=0, + ), + out_file=dict(argstr='-prefix %s', + name_source='in_file', + name_template='%s_fourier', + ), + outputtype=dict(), + terminal_output=dict(mandatory=True, + nohash=True, ), ) inputs = Fourier.input_spec() @@ -37,6 +38,7 @@ def test_Fourier_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Fourier_outputs(): output_map = dict(out_file=dict(), ) @@ -45,3 +47,4 @@ def test_Fourier_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/afni/tests/test_auto_Maskave.py b/nipype/interfaces/afni/tests/test_auto_Maskave.py index 9a544599ed..796a2528e1 100644 --- a/nipype/interfaces/afni/tests/test_auto_Maskave.py +++ b/nipype/interfaces/afni/tests/test_auto_Maskave.py @@ -1,42 +1,44 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.afni.preprocess import Maskave + def test_Maskave_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + environ=dict(nohash=True, usedefault=True, ), - out_file=dict(name_source='in_file', - name_template='%s_maskave.1D', - position=-1, - keep_extension=True, - argstr='> %s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - args=dict(argstr='%s', + in_file=dict(argstr='%s', + copyfile=False, + mandatory=True, + position=-2, ), - mask=dict(position=1, - argstr='-mask %s', + mask=dict(argstr='-mask %s', + position=1, + ), + out_file=dict(argstr='> %s', + keep_extension=True, + name_source='in_file', + name_template='%s_maskave.1D', + position=-1, ), outputtype=dict(), - quiet=dict(position=2, - argstr='-quiet', + quiet=dict(argstr='-quiet', + position=2, ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - in_file=dict(copyfile=False, - mandatory=True, - position=-2, - argstr='%s', - ), ) inputs = Maskave.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Maskave_outputs(): output_map = dict(out_file=dict(), ) @@ -45,3 +47,4 @@ def test_Maskave_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/afni/tests/test_auto_Merge.py b/nipype/interfaces/afni/tests/test_auto_Merge.py index e06ba52c31..e3eaf7e98e 100644 --- a/nipype/interfaces/afni/tests/test_auto_Merge.py +++ b/nipype/interfaces/afni/tests/test_auto_Merge.py @@ -1,39 +1,41 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.afni.preprocess import Merge + def test_Merge_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(args=dict(argstr='%s', ), - out_file=dict(name_source='in_file', - name_template='%s_merge', - argstr='-prefix %s', + blurfwhm=dict(argstr='-1blur_fwhm %d', + units='mm', + ), + doall=dict(argstr='-doall', ), - blurfwhm=dict(units='mm', - argstr='-1blur_fwhm %d', + environ=dict(nohash=True, + usedefault=True, ), - args=dict(argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - outputtype=dict(), - in_files=dict(copyfile=False, + in_files=dict(argstr='%s', + copyfile=False, mandatory=True, position=-1, - argstr='%s', ), + out_file=dict(argstr='-prefix %s', + name_source='in_file', + name_template='%s_merge', + ), + outputtype=dict(), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - doall=dict(argstr='-doall', - ), ) inputs = Merge.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Merge_outputs(): output_map = dict(out_file=dict(), ) @@ -42,3 +44,4 @@ def test_Merge_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/afni/tests/test_auto_ROIStats.py b/nipype/interfaces/afni/tests/test_auto_ROIStats.py index 56c6004865..11562fc00a 100644 --- a/nipype/interfaces/afni/tests/test_auto_ROIStats.py +++ b/nipype/interfaces/afni/tests/test_auto_ROIStats.py @@ -1,38 +1,40 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.afni.preprocess import ROIStats + def test_ROIStats_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + environ=dict(nohash=True, + usedefault=True, + ), + ignore_exception=dict(nohash=True, usedefault=True, ), - args=dict(argstr='%s', + in_file=dict(argstr='%s', + mandatory=True, + position=-1, + ), + mask=dict(argstr='-mask %s', + position=3, ), - mask=dict(position=3, - argstr='-mask %s', + mask_f2short=dict(argstr='-mask_f2short', + position=2, ), - quiet=dict(position=1, - argstr='-quiet', + quiet=dict(argstr='-quiet', + position=1, ), terminal_output=dict(mandatory=True, nohash=True, usedefault=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - in_file=dict(position=-1, - mandatory=True, - argstr='%s', - ), - mask_f2short=dict(position=2, - argstr='-mask_f2short', - ), ) inputs = ROIStats.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ROIStats_outputs(): output_map = dict(stats=dict(), ) @@ -41,3 +43,4 @@ def test_ROIStats_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/afni/tests/test_auto_Refit.py b/nipype/interfaces/afni/tests/test_auto_Refit.py index d961a429cc..288bcd1a8b 100644 --- a/nipype/interfaces/afni/tests/test_auto_Refit.py +++ b/nipype/interfaces/afni/tests/test_auto_Refit.py @@ -1,29 +1,30 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.afni.preprocess import Refit + def test_Refit_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(args=dict(argstr='%s', ), deoblique=dict(argstr='-deoblique', ), - args=dict(argstr='%s', - ), - yorigin=dict(argstr='-yorigin %s', - ), - terminal_output=dict(mandatory=True, - nohash=True, - ), environ=dict(nohash=True, usedefault=True, ), - in_file=dict(copyfile=True, + ignore_exception=dict(nohash=True, + usedefault=True, + ), + in_file=dict(argstr='%s', + copyfile=True, mandatory=True, position=-1, - argstr='%s', + ), + terminal_output=dict(mandatory=True, + nohash=True, ), xorigin=dict(argstr='-xorigin %s', ), + yorigin=dict(argstr='-yorigin %s', + ), zorigin=dict(argstr='-zorigin %s', ), ) @@ -32,6 +33,7 @@ def test_Refit_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Refit_outputs(): output_map = dict(out_file=dict(), ) @@ -40,3 +42,4 @@ def test_Refit_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/afni/tests/test_auto_Resample.py b/nipype/interfaces/afni/tests/test_auto_Resample.py index 3fea852e14..0c2384e897 100644 --- a/nipype/interfaces/afni/tests/test_auto_Resample.py +++ b/nipype/interfaces/afni/tests/test_auto_Resample.py @@ -1,35 +1,36 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.afni.preprocess import Resample + def test_Resample_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + environ=dict(nohash=True, usedefault=True, ), - out_file=dict(name_source='in_file', - name_template='%s_resample', - argstr='-prefix %s', + ignore_exception=dict(nohash=True, + usedefault=True, + ), + in_file=dict(argstr='-inset %s', + copyfile=False, + mandatory=True, + position=-1, + ), + master=dict(argstr='-master %s', ), - args=dict(argstr='%s', + orientation=dict(argstr='-orient %s', + ), + out_file=dict(argstr='-prefix %s', + name_source='in_file', + name_template='%s_resample', ), outputtype=dict(), resample_mode=dict(argstr='-rmode %s', ), - voxel_size=dict(argstr='-dxyz %f %f %f', - ), terminal_output=dict(mandatory=True, nohash=True, ), - master=dict(argstr='-master %s', - ), - in_file=dict(copyfile=False, - mandatory=True, - position=-1, - argstr='-inset %s', - ), - environ=dict(nohash=True, - usedefault=True, - ), - orientation=dict(argstr='-orient %s', + voxel_size=dict(argstr='-dxyz %f %f %f', ), ) inputs = Resample.input_spec() @@ -37,6 +38,7 @@ def test_Resample_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Resample_outputs(): output_map = dict(out_file=dict(), ) @@ -45,3 +47,4 @@ def test_Resample_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/afni/tests/test_auto_Retroicor.py b/nipype/interfaces/afni/tests/test_auto_Retroicor.py index 8e35ea4cf9..6b6ff48f86 100644 --- a/nipype/interfaces/afni/tests/test_auto_Retroicor.py +++ b/nipype/interfaces/afni/tests/test_auto_Retroicor.py @@ -1,47 +1,48 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.afni.preprocess import Retroicor + def test_Retroicor_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + card=dict(argstr='-card %s', + position=-2, + ), + cardphase=dict(argstr='-cardphase %s', + hash_files=False, + position=-6, + ), + environ=dict(nohash=True, usedefault=True, ), - out_file=dict(position=1, + ignore_exception=dict(nohash=True, + usedefault=True, + ), + in_file=dict(argstr='%s', + copyfile=False, mandatory=True, - argstr='-prefix %s', + position=-1, ), - resp=dict(position=-3, - argstr='-resp %s', + order=dict(argstr='-order %s', + position=-5, ), - args=dict(argstr='%s', + out_file=dict(argstr='-prefix %s', + mandatory=True, + position=1, ), outputtype=dict(), - cardphase=dict(position=-6, - hash_files=False, - argstr='-cardphase %s', + resp=dict(argstr='-resp %s', + position=-3, ), - respphase=dict(position=-7, + respphase=dict(argstr='-respphase %s', hash_files=False, - argstr='-respphase %s', + position=-7, ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - in_file=dict(copyfile=False, - mandatory=True, - position=-1, - argstr='%s', - ), - threshold=dict(position=-4, - argstr='-threshold %d', - ), - order=dict(position=-5, - argstr='-order %s', - ), - card=dict(position=-2, - argstr='-card %s', + threshold=dict(argstr='-threshold %d', + position=-4, ), ) inputs = Retroicor.input_spec() @@ -49,6 +50,7 @@ def test_Retroicor_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Retroicor_outputs(): output_map = dict(out_file=dict(), ) @@ -57,3 +59,4 @@ def test_Retroicor_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/afni/tests/test_auto_SkullStrip.py b/nipype/interfaces/afni/tests/test_auto_SkullStrip.py index fc23ee518a..71712e4d94 100644 --- a/nipype/interfaces/afni/tests/test_auto_SkullStrip.py +++ b/nipype/interfaces/afni/tests/test_auto_SkullStrip.py @@ -1,34 +1,36 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.afni.preprocess import SkullStrip + def test_SkullStrip_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + environ=dict(nohash=True, usedefault=True, ), - out_file=dict(name_source='in_file', - name_template='%s_skullstrip', - argstr='-prefix %s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - args=dict(argstr='%s', + in_file=dict(argstr='-input %s', + copyfile=False, + mandatory=True, + position=1, + ), + out_file=dict(argstr='-prefix %s', + name_source='in_file', + name_template='%s_skullstrip', ), outputtype=dict(), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - in_file=dict(copyfile=False, - mandatory=True, - position=1, - argstr='-input %s', - ), ) inputs = SkullStrip.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_SkullStrip_outputs(): output_map = dict(out_file=dict(), ) @@ -37,3 +39,4 @@ def test_SkullStrip_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/afni/tests/test_auto_TCat.py b/nipype/interfaces/afni/tests/test_auto_TCat.py index 5752aa8da2..95fd48b5cf 100644 --- a/nipype/interfaces/afni/tests/test_auto_TCat.py +++ b/nipype/interfaces/afni/tests/test_auto_TCat.py @@ -1,30 +1,31 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.afni.preprocess import TCat + def test_TCat_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(args=dict(argstr='%s', ), - out_file=dict(name_source='in_file', - name_template='%s_tcat', - argstr='-prefix %s', + environ=dict(nohash=True, + usedefault=True, ), - args=dict(argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - outputtype=dict(), - in_files=dict(copyfile=False, + in_files=dict(argstr=' %s', + copyfile=False, mandatory=True, position=-1, - argstr=' %s', ), - terminal_output=dict(mandatory=True, - nohash=True, + out_file=dict(argstr='-prefix %s', + name_source='in_file', + name_template='%s_tcat', ), - environ=dict(nohash=True, - usedefault=True, + outputtype=dict(), + rlt=dict(argstr='-rlt%s', + position=1, ), - rlt=dict(position=1, - argstr='-rlt%s', + terminal_output=dict(mandatory=True, + nohash=True, ), ) inputs = TCat.input_spec() @@ -32,6 +33,7 @@ def test_TCat_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_TCat_outputs(): output_map = dict(out_file=dict(), ) @@ -40,3 +42,4 @@ def test_TCat_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/afni/tests/test_auto_TCorr1D.py b/nipype/interfaces/afni/tests/test_auto_TCorr1D.py index e3426919c0..8c255bc0d6 100644 --- a/nipype/interfaces/afni/tests/test_auto_TCorr1D.py +++ b/nipype/interfaces/afni/tests/test_auto_TCorr1D.py @@ -1,48 +1,49 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.afni.preprocess import TCorr1D + def test_TCorr1D_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, - ), - spearman=dict(position=1, - xor=['pearson', 'quadrant', 'ktaub'], - argstr=' -spearman', + input_map = dict(args=dict(argstr='%s', ), - pearson=dict(position=1, - xor=['spearman', 'quadrant', 'ktaub'], - argstr=' -pearson', - ), - out_file=dict(name_source='xset', - argstr='-prefix %s', - name_template='%s_correlation.nii.gz', - keep_extension=True, + environ=dict(nohash=True, + usedefault=True, ), - y_1d=dict(position=-1, - mandatory=True, - argstr=' %s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - ktaub=dict(position=1, + ktaub=dict(argstr=' -ktaub', + position=1, xor=['pearson', 'spearman', 'quadrant'], - argstr=' -ktaub', ), - args=dict(argstr='%s', - ), - xset=dict(copyfile=False, - mandatory=True, - position=-2, - argstr=' %s', + out_file=dict(argstr='-prefix %s', + keep_extension=True, + name_source='xset', + name_template='%s_correlation.nii.gz', ), outputtype=dict(), - quadrant=dict(position=1, + pearson=dict(argstr=' -pearson', + position=1, + xor=['spearman', 'quadrant', 'ktaub'], + ), + quadrant=dict(argstr=' -quadrant', + position=1, xor=['pearson', 'spearman', 'ktaub'], - argstr=' -quadrant', + ), + spearman=dict(argstr=' -spearman', + position=1, + xor=['pearson', 'quadrant', 'ktaub'], ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, + xset=dict(argstr=' %s', + copyfile=False, + mandatory=True, + position=-2, + ), + y_1d=dict(argstr=' %s', + mandatory=True, + position=-1, ), ) inputs = TCorr1D.input_spec() @@ -50,6 +51,7 @@ def test_TCorr1D_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_TCorr1D_outputs(): output_map = dict(out_file=dict(), ) @@ -58,3 +60,4 @@ def test_TCorr1D_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/afni/tests/test_auto_TCorrMap.py b/nipype/interfaces/afni/tests/test_auto_TCorrMap.py index e90a8a9a41..4b574a60ad 100644 --- a/nipype/interfaces/afni/tests/test_auto_TCorrMap.py +++ b/nipype/interfaces/afni/tests/test_auto_TCorrMap.py @@ -1,103 +1,104 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.afni.preprocess import TCorrMap + def test_TCorrMap_inputs(): - input_map = dict(polort=dict(argstr='-polort %d', + input_map = dict(absolute_threshold=dict(argstr='-Thresh %f %s', + name_source='in_file', + suffix='_thresh', + xor=('absolute_threshold', 'var_absolute_threshold', 'var_absolute_threshold_normalize'), ), - zmean=dict(name_source='in_file', - suffix='_zmean', - argstr='-Zmean %s', + args=dict(argstr='%s', ), - correlation_maps_masked=dict(name_source='in_file', - argstr='-CorrMask %s', + automask=dict(argstr='-automask', ), - thresholds=dict(), - outputtype=dict(), - average_expr_nonzero=dict(name_source='in_file', + average_expr=dict(argstr='-Aexpr %s %s', + name_source='in_file', + suffix='_aexpr', xor=('average_expr', 'average_expr_nonzero', 'sum_expr'), + ), + average_expr_nonzero=dict(argstr='-Cexpr %s %s', + name_source='in_file', suffix='_cexpr', - argstr='-Cexpr %s %s', + xor=('average_expr', 'average_expr_nonzero', 'sum_expr'), ), - seeds_width=dict(xor='seeds', - argstr='-Mseed %f', + bandpass=dict(argstr='-bpass %f %f', ), - qmean=dict(name_source='in_file', - suffix='_qmean', - argstr='-Qmean %s', + blur_fwhm=dict(argstr='-Gblur %f', ), - pmean=dict(name_source='in_file', - suffix='_pmean', - argstr='-Pmean %s', + correlation_maps=dict(argstr='-CorrMap %s', + name_source='in_file', ), - in_file=dict(copyfile=False, - mandatory=True, - argstr='-input %s', + correlation_maps_masked=dict(argstr='-CorrMask %s', + name_source='in_file', ), - ignore_exception=dict(nohash=True, + environ=dict(nohash=True, usedefault=True, ), - var_absolute_threshold=dict(name_source='in_file', - xor=('absolute_threshold', 'var_absolute_threshold', 'var_absolute_threshold_normalize'), - suffix='_varthresh', - argstr='-VarThresh %f %f %f %s', + expr=dict(), + histogram=dict(argstr='-Hist %d %s', + name_source='in_file', + suffix='_hist', ), - absolute_threshold=dict(name_source='in_file', - xor=('absolute_threshold', 'var_absolute_threshold', 'var_absolute_threshold_normalize'), - suffix='_thresh', - argstr='-Thresh %f %s', + histogram_bin_numbers=dict(), + ignore_exception=dict(nohash=True, + usedefault=True, ), - automask=dict(argstr='-automask', + in_file=dict(argstr='-input %s', + copyfile=False, + mandatory=True, ), - args=dict(argstr='%s', + mask=dict(argstr='-mask %s', ), - histogram=dict(name_source='in_file', - suffix='_hist', - argstr='-Hist %d %s', + mean_file=dict(argstr='-Mean %s', + name_source='in_file', + suffix='_mean', ), - terminal_output=dict(mandatory=True, - nohash=True, + out_file=dict(argstr='-prefix %s', + name_source=['in_file'], + name_template='%s_afni', ), - average_expr=dict(name_source='in_file', - xor=('average_expr', 'average_expr_nonzero', 'sum_expr'), - suffix='_aexpr', - argstr='-Aexpr %s %s', + outputtype=dict(), + pmean=dict(argstr='-Pmean %s', + name_source='in_file', + suffix='_pmean', ), - blur_fwhm=dict(argstr='-Gblur %f', + polort=dict(argstr='-polort %d', ), - var_absolute_threshold_normalize=dict(name_source='in_file', - xor=('absolute_threshold', 'var_absolute_threshold', 'var_absolute_threshold_normalize'), - suffix='_varthreshn', - argstr='-VarThreshN %f %f %f %s', + qmean=dict(argstr='-Qmean %s', + name_source='in_file', + suffix='_qmean', ), - out_file=dict(name_source=['in_file'], - name_template='%s_afni', - argstr='-prefix %s', + regress_out_timeseries=dict(argstr='-ort %s', ), - expr=dict(), - mask=dict(argstr='-mask %s', + seeds=dict(argstr='-seed %s', + xor='seeds_width', ), - mean_file=dict(name_source='in_file', - suffix='_mean', - argstr='-Mean %s', + seeds_width=dict(argstr='-Mseed %f', + xor='seeds', ), - sum_expr=dict(name_source='in_file', - xor=('average_expr', 'average_expr_nonzero', 'sum_expr'), + sum_expr=dict(argstr='-Sexpr %s %s', + name_source='in_file', suffix='_sexpr', - argstr='-Sexpr %s %s', - ), - regress_out_timeseries=dict(argstr='-ort %s', + xor=('average_expr', 'average_expr_nonzero', 'sum_expr'), ), - seeds=dict(xor='seeds_width', - argstr='-seed %s', + terminal_output=dict(mandatory=True, + nohash=True, ), - environ=dict(nohash=True, - usedefault=True, + thresholds=dict(), + var_absolute_threshold=dict(argstr='-VarThresh %f %f %f %s', + name_source='in_file', + suffix='_varthresh', + xor=('absolute_threshold', 'var_absolute_threshold', 'var_absolute_threshold_normalize'), ), - correlation_maps=dict(name_source='in_file', - argstr='-CorrMap %s', + var_absolute_threshold_normalize=dict(argstr='-VarThreshN %f %f %f %s', + name_source='in_file', + suffix='_varthreshn', + xor=('absolute_threshold', 'var_absolute_threshold', 'var_absolute_threshold_normalize'), ), - histogram_bin_numbers=dict(), - bandpass=dict(argstr='-bpass %f %f', + zmean=dict(argstr='-Zmean %s', + name_source='in_file', + suffix='_zmean', ), ) inputs = TCorrMap.input_spec() @@ -105,23 +106,25 @@ def test_TCorrMap_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_TCorrMap_outputs(): output_map = dict(absolute_threshold=dict(), - zmean=dict(), - var_absolute_threshold_normalize=dict(), + average_expr=dict(), + average_expr_nonzero=dict(), + correlation_maps=dict(), correlation_maps_masked=dict(), - var_absolute_threshold=dict(), + histogram=dict(), mean_file=dict(), pmean=dict(), - histogram=dict(), - sum_expr=dict(), - average_expr_nonzero=dict(), - average_expr=dict(), - correlation_maps=dict(), qmean=dict(), + sum_expr=dict(), + var_absolute_threshold=dict(), + var_absolute_threshold_normalize=dict(), + zmean=dict(), ) outputs = TCorrMap.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/afni/tests/test_auto_TCorrelate.py b/nipype/interfaces/afni/tests/test_auto_TCorrelate.py index 22de450b4b..1388529b3e 100644 --- a/nipype/interfaces/afni/tests/test_auto_TCorrelate.py +++ b/nipype/interfaces/afni/tests/test_auto_TCorrelate.py @@ -1,38 +1,39 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.afni.preprocess import TCorrelate + def test_TCorrelate_inputs(): - input_map = dict(polort=dict(position=2, - argstr='-polort %d', + input_map = dict(args=dict(argstr='%s', ), - ignore_exception=dict(nohash=True, + environ=dict(nohash=True, usedefault=True, ), - pearson=dict(position=1, - argstr='-pearson', + ignore_exception=dict(nohash=True, + usedefault=True, ), - out_file=dict(name_source='xset', + out_file=dict(argstr='-prefix %s', + name_source='xset', name_template='%s_tcorr', - argstr='-prefix %s', ), - args=dict(argstr='%s', + outputtype=dict(), + pearson=dict(argstr='-pearson', + position=1, ), - xset=dict(copyfile=False, - mandatory=True, - position=-2, - argstr=' %s', + polort=dict(argstr='-polort %d', + position=2, ), - outputtype=dict(), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, + xset=dict(argstr=' %s', + copyfile=False, + mandatory=True, + position=-2, ), - yset=dict(copyfile=False, + yset=dict(argstr=' %s', + copyfile=False, mandatory=True, position=-1, - argstr=' %s', ), ) inputs = TCorrelate.input_spec() @@ -40,6 +41,7 @@ def test_TCorrelate_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_TCorrelate_outputs(): output_map = dict(out_file=dict(), ) @@ -48,3 +50,4 @@ def test_TCorrelate_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/afni/tests/test_auto_TShift.py b/nipype/interfaces/afni/tests/test_auto_TShift.py index 2e96fa5a32..b145d8a717 100644 --- a/nipype/interfaces/afni/tests/test_auto_TShift.py +++ b/nipype/interfaces/afni/tests/test_auto_TShift.py @@ -1,45 +1,46 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.afni.preprocess import TShift + def test_TShift_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(args=dict(argstr='%s', ), - tpattern=dict(argstr='-tpattern %s', + environ=dict(nohash=True, + usedefault=True, ), - out_file=dict(name_source='in_file', - name_template='%s_tshift', - argstr='-prefix %s', + ignore=dict(argstr='-ignore %s', ), - tr=dict(argstr='-TR %s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - args=dict(argstr='%s', + in_file=dict(argstr='%s', + copyfile=False, + mandatory=True, + position=-1, ), interp=dict(argstr='-%s', ), - outputtype=dict(), - tzero=dict(xor=['tslice'], - argstr='-tzero %s', + out_file=dict(argstr='-prefix %s', + name_source='in_file', + name_template='%s_tshift', ), - ignore=dict(argstr='-ignore %s', + outputtype=dict(), + rlt=dict(argstr='-rlt', ), rltplus=dict(argstr='-rlt+', ), terminal_output=dict(mandatory=True, nohash=True, ), - tslice=dict(xor=['tzero'], - argstr='-slice %s', + tpattern=dict(argstr='-tpattern %s', ), - in_file=dict(copyfile=False, - mandatory=True, - position=-1, - argstr='%s', + tr=dict(argstr='-TR %s', ), - rlt=dict(argstr='-rlt', + tslice=dict(argstr='-slice %s', + xor=['tzero'], ), - environ=dict(nohash=True, - usedefault=True, + tzero=dict(argstr='-tzero %s', + xor=['tslice'], ), ) inputs = TShift.input_spec() @@ -47,6 +48,7 @@ def test_TShift_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_TShift_outputs(): output_map = dict(out_file=dict(), ) @@ -55,3 +57,4 @@ def test_TShift_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/afni/tests/test_auto_TStat.py b/nipype/interfaces/afni/tests/test_auto_TStat.py index f5d653d68f..93f9c4500d 100644 --- a/nipype/interfaces/afni/tests/test_auto_TStat.py +++ b/nipype/interfaces/afni/tests/test_auto_TStat.py @@ -1,38 +1,40 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.afni.preprocess import TStat + def test_TStat_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + environ=dict(nohash=True, usedefault=True, ), - out_file=dict(name_source='in_file', - name_template='%s_tstat', - argstr='-prefix %s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - args=dict(argstr='%s', + in_file=dict(argstr='%s', + copyfile=False, + mandatory=True, + position=-1, ), mask=dict(argstr='-mask %s', ), + options=dict(argstr='%s', + ), + out_file=dict(argstr='-prefix %s', + name_source='in_file', + name_template='%s_tstat', + ), outputtype=dict(), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - in_file=dict(copyfile=False, - mandatory=True, - position=-1, - argstr='%s', - ), - options=dict(argstr='%s', - ), ) inputs = TStat.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_TStat_outputs(): output_map = dict(out_file=dict(), ) @@ -41,3 +43,4 @@ def test_TStat_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/afni/tests/test_auto_To3D.py b/nipype/interfaces/afni/tests/test_auto_To3D.py index 20ec653a50..08bedc93a3 100644 --- a/nipype/interfaces/afni/tests/test_auto_To3D.py +++ b/nipype/interfaces/afni/tests/test_auto_To3D.py @@ -1,36 +1,37 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.afni.preprocess import To3D + def test_To3D_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(args=dict(argstr='%s', ), - out_file=dict(name_source=['in_folder'], - name_template='%s', - argstr='-prefix %s', + assumemosaic=dict(argstr='-assume_dicom_mosaic', ), datatype=dict(argstr='-datum %s', ), - filetype=dict(argstr='-%s', - ), - args=dict(argstr='%s', + environ=dict(nohash=True, + usedefault=True, ), - outputtype=dict(), - assumemosaic=dict(argstr='-assume_dicom_mosaic', + filetype=dict(argstr='-%s', ), - terminal_output=dict(mandatory=True, - nohash=True, + funcparams=dict(argstr='-time:zt %s alt+z2', ), - environ=dict(nohash=True, + ignore_exception=dict(nohash=True, usedefault=True, ), - in_folder=dict(position=-1, + in_folder=dict(argstr='%s/*.dcm', mandatory=True, - argstr='%s/*.dcm', + position=-1, ), + out_file=dict(argstr='-prefix %s', + name_source=['in_folder'], + name_template='%s', + ), + outputtype=dict(), skipoutliers=dict(argstr='-skip_outliers', ), - funcparams=dict(argstr='-time:zt %s alt+z2', + terminal_output=dict(mandatory=True, + nohash=True, ), ) inputs = To3D.input_spec() @@ -38,6 +39,7 @@ def test_To3D_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_To3D_outputs(): output_map = dict(out_file=dict(), ) @@ -46,3 +48,4 @@ def test_To3D_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/afni/tests/test_auto_Volreg.py b/nipype/interfaces/afni/tests/test_auto_Volreg.py index 51f5fe15e8..7a63fd6402 100644 --- a/nipype/interfaces/afni/tests/test_auto_Volreg.py +++ b/nipype/interfaces/afni/tests/test_auto_Volreg.py @@ -1,50 +1,51 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.afni.preprocess import Volreg + def test_Volreg_inputs(): - input_map = dict(oned_file=dict(name_source='in_file', - argstr='-1Dfile %s', - name_template='%s.1D', - keep_extension=True, + input_map = dict(args=dict(argstr='%s', + ), + basefile=dict(argstr='-base %s', + position=-6, + ), + copyorigin=dict(argstr='-twodup', + ), + environ=dict(nohash=True, + usedefault=True, ), ignore_exception=dict(nohash=True, usedefault=True, ), - verbose=dict(argstr='-verbose', + in_file=dict(argstr='%s', + copyfile=False, + mandatory=True, + position=-1, ), - timeshift=dict(argstr='-tshift 0', + md1d_file=dict(argstr='-maxdisp1D %s', + keep_extension=True, + name_source='in_file', + name_template='%s_md.1D', + position=-4, ), - basefile=dict(position=-6, - argstr='-base %s', + oned_file=dict(argstr='-1Dfile %s', + keep_extension=True, + name_source='in_file', + name_template='%s.1D', ), - args=dict(argstr='%s', + out_file=dict(argstr='-prefix %s', + name_source='in_file', + name_template='%s_volreg', ), outputtype=dict(), - zpad=dict(position=-5, - argstr='-zpad %d', - ), terminal_output=dict(mandatory=True, nohash=True, ), - md1d_file=dict(name_source='in_file', - keep_extension=True, - position=-4, - name_template='%s_md.1D', - argstr='-maxdisp1D %s', - ), - in_file=dict(copyfile=False, - mandatory=True, - position=-1, - argstr='%s', - ), - copyorigin=dict(argstr='-twodup', + timeshift=dict(argstr='-tshift 0', ), - environ=dict(nohash=True, - usedefault=True, + verbose=dict(argstr='-verbose', ), - out_file=dict(name_source='in_file', - name_template='%s_volreg', - argstr='-prefix %s', + zpad=dict(argstr='-zpad %d', + position=-5, ), ) inputs = Volreg.input_spec() @@ -52,9 +53,10 @@ def test_Volreg_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Volreg_outputs(): - output_map = dict(oned_file=dict(), - md1d_file=dict(), + output_map = dict(md1d_file=dict(), + oned_file=dict(), out_file=dict(), ) outputs = Volreg.output_spec() @@ -62,3 +64,4 @@ def test_Volreg_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/afni/tests/test_auto_Warp.py b/nipype/interfaces/afni/tests/test_auto_Warp.py index df9aeab6d1..bd8eabf6b8 100644 --- a/nipype/interfaces/afni/tests/test_auto_Warp.py +++ b/nipype/interfaces/afni/tests/test_auto_Warp.py @@ -1,48 +1,50 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.afni.preprocess import Warp + def test_Warp_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(args=dict(argstr='%s', ), deoblique=dict(argstr='-deoblique', ), - out_file=dict(name_source='in_file', - name_template='%s_warp', - argstr='-prefix %s', + environ=dict(nohash=True, + usedefault=True, ), - matparent=dict(argstr='-matparent %s', + gridset=dict(argstr='-gridset %s', ), - args=dict(argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, + ), + in_file=dict(argstr='%s', + copyfile=False, + mandatory=True, + position=-1, ), interp=dict(argstr='-%s', ), - outputtype=dict(), - zpad=dict(argstr='-zpad %d', + matparent=dict(argstr='-matparent %s', ), mni2tta=dict(argstr='-mni2tta', ), + out_file=dict(argstr='-prefix %s', + name_source='in_file', + name_template='%s_warp', + ), + outputtype=dict(), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - in_file=dict(copyfile=False, - mandatory=True, - position=-1, - argstr='%s', - ), - gridset=dict(argstr='-gridset %s', - ), tta2mni=dict(argstr='-tta2mni', ), + zpad=dict(argstr='-zpad %d', + ), ) inputs = Warp.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Warp_outputs(): output_map = dict(out_file=dict(), ) @@ -51,3 +53,4 @@ def test_Warp_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/afni/tests/test_auto_ZCutUp.py b/nipype/interfaces/afni/tests/test_auto_ZCutUp.py index 8bd6cf82f0..e7755e5396 100644 --- a/nipype/interfaces/afni/tests/test_auto_ZCutUp.py +++ b/nipype/interfaces/afni/tests/test_auto_ZCutUp.py @@ -1,36 +1,38 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.afni.preprocess import ZCutUp + def test_ZCutUp_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + environ=dict(nohash=True, usedefault=True, ), - out_file=dict(name_source='in_file', - name_template='%s_zcupup', - argstr='-prefix %s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - args=dict(argstr='%s', + in_file=dict(argstr='%s', + copyfile=False, + mandatory=True, + position=-1, ), - outputtype=dict(), keep=dict(argstr='-keep %s', ), + out_file=dict(argstr='-prefix %s', + name_source='in_file', + name_template='%s_zcupup', + ), + outputtype=dict(), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - in_file=dict(copyfile=False, - mandatory=True, - position=-1, - argstr='%s', - ), ) inputs = ZCutUp.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ZCutUp_outputs(): output_map = dict(out_file=dict(), ) @@ -39,3 +41,4 @@ def test_ZCutUp_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/ants/tests/test_auto_ANTS.py b/nipype/interfaces/ants/tests/test_auto_ANTS.py index 300635b4f8..435c967656 100644 --- a/nipype/interfaces/ants/tests/test_auto_ANTS.py +++ b/nipype/interfaces/ants/tests/test_auto_ANTS.py @@ -1,92 +1,95 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.ants.registration import ANTS + def test_ANTS_inputs(): - input_map = dict(regularization_deformation_field_sigma=dict(requires=['regularization'], + input_map = dict(affine_gradient_descent_option=dict(argstr='%s', ), - fixed_image=dict(mandatory=True, + args=dict(argstr='%s', ), - regularization_gradient_field_sigma=dict(requires=['regularization'], + delta_time=dict(requires=['number_of_time_steps'], + ), + dimension=dict(argstr='%d', + position=1, + usedefault=False, ), - output_transform_prefix=dict(mandatory=True, - argstr='--output-naming %s', + environ=dict(nohash=True, usedefault=True, ), - moving_image=dict(mandatory=True, - argstr='%s', + fixed_image=dict(mandatory=True, ), - radius=dict(requires=['metric'], + gradient_step_length=dict(requires=['transformation_model'], + ), + ignore_exception=dict(nohash=True, + usedefault=True, + ), + metric=dict(mandatory=True, ), metric_weight=dict(requires=['metric'], ), - symmetry_type=dict(requires=['delta_time'], + mi_option=dict(argstr='--MI-option %s', + sep='x', ), - regularization=dict(argstr='%s', + moving_image=dict(argstr='%s', + mandatory=True, ), - mi_option=dict(sep='x', - argstr='--MI-option %s', + num_threads=dict(nohash=True, + usedefault=True, ), - number_of_affine_iterations=dict(sep='x', - argstr='--number-of-affine-iterations %s', + number_of_affine_iterations=dict(argstr='--number-of-affine-iterations %s', + sep='x', ), - metric=dict(mandatory=True, + number_of_iterations=dict(argstr='--number-of-iterations %s', + sep='x', ), - affine_gradient_descent_option=dict(argstr='%s', + number_of_time_steps=dict(requires=['gradient_step_length'], ), - ignore_exception=dict(nohash=True, + output_transform_prefix=dict(argstr='--output-naming %s', + mandatory=True, usedefault=True, ), - transformation_model=dict(mandatory=True, - argstr='%s', - ), - gradient_step_length=dict(requires=['transformation_model'], + radius=dict(requires=['metric'], ), - args=dict(argstr='%s', + regularization=dict(argstr='%s', ), - delta_time=dict(requires=['number_of_time_steps'], + regularization_deformation_field_sigma=dict(requires=['regularization'], ), - terminal_output=dict(mandatory=True, - nohash=True, + regularization_gradient_field_sigma=dict(requires=['regularization'], ), - subsampling_factors=dict(sep='x', - argstr='--subsampling-factors %s', + smoothing_sigmas=dict(argstr='--gaussian-smoothing-sigmas %s', + sep='x', ), - num_threads=dict(nohash=True, - usedefault=True, + subsampling_factors=dict(argstr='--subsampling-factors %s', + sep='x', ), - smoothing_sigmas=dict(sep='x', - argstr='--gaussian-smoothing-sigmas %s', + symmetry_type=dict(requires=['delta_time'], ), - number_of_iterations=dict(sep='x', - argstr='--number-of-iterations %s', + terminal_output=dict(mandatory=True, + nohash=True, ), - number_of_time_steps=dict(requires=['gradient_step_length'], + transformation_model=dict(argstr='%s', + mandatory=True, ), - environ=dict(nohash=True, + use_histogram_matching=dict(argstr='%s', usedefault=True, ), - use_histogram_matching=dict(usedefault=True, - argstr='%s', - ), - dimension=dict(position=1, - usedefault=False, - argstr='%d', - ), ) inputs = ANTS.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ANTS_outputs(): - output_map = dict(warp_transform=dict(), + output_map = dict(affine_transform=dict(), + inverse_warp_transform=dict(), metaheader=dict(), - affine_transform=dict(), metaheader_raw=dict(), - inverse_warp_transform=dict(), + warp_transform=dict(), ) outputs = ANTS.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/ants/tests/test_auto_ANTSCommand.py b/nipype/interfaces/ants/tests/test_auto_ANTSCommand.py index 5eef95b363..a30258af45 100644 --- a/nipype/interfaces/ants/tests/test_auto_ANTSCommand.py +++ b/nipype/interfaces/ants/tests/test_auto_ANTSCommand.py @@ -1,8 +1,14 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.ants.base import ANTSCommand + def test_ANTSCommand_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + environ=dict(nohash=True, + usedefault=True, + ), + ignore_exception=dict(nohash=True, usedefault=True, ), num_threads=dict(nohash=True, @@ -11,14 +17,10 @@ def test_ANTSCommand_inputs(): terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - args=dict(argstr='%s', - ), ) inputs = ANTSCommand.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/ants/tests/test_auto_ApplyTransforms.py b/nipype/interfaces/ants/tests/test_auto_ApplyTransforms.py index 61e12eb535..ab8433c4a8 100644 --- a/nipype/interfaces/ants/tests/test_auto_ApplyTransforms.py +++ b/nipype/interfaces/ants/tests/test_auto_ApplyTransforms.py @@ -1,55 +1,57 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.ants.resampling import ApplyTransforms + def test_ApplyTransforms_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(args=dict(argstr='%s', ), - num_threads=dict(nohash=True, + default_value=dict(argstr='--default-value %d', usedefault=True, ), - output_image=dict(argstr='--output %s', - hash_files=False, - genfile=True, + dimension=dict(argstr='--dimensionality %d', ), - out_postfix=dict(usedefault=True, + environ=dict(nohash=True, + usedefault=True, ), - args=dict(argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - print_out_composite_warp_file=dict(requires=['output_image'], + input_image=dict(argstr='--input %s', + mandatory=True, ), input_image_type=dict(argstr='--input-image-type %d', ), - terminal_output=dict(mandatory=True, - nohash=True, + interpolation=dict(argstr='%s', + usedefault=True, ), - environ=dict(nohash=True, + invert_transform_flags=dict(), + num_threads=dict(nohash=True, usedefault=True, ), - transforms=dict(mandatory=True, - argstr='%s', + out_postfix=dict(usedefault=True, ), - reference_image=dict(mandatory=True, - argstr='--reference-image %s', + output_image=dict(argstr='--output %s', + genfile=True, + hash_files=False, ), - interpolation=dict(usedefault=True, - argstr='%s', + print_out_composite_warp_file=dict(requires=['output_image'], ), - input_image=dict(mandatory=True, - argstr='--input %s', + reference_image=dict(argstr='--reference-image %s', + mandatory=True, ), - default_value=dict(usedefault=True, - argstr='--default-value %d', + terminal_output=dict(mandatory=True, + nohash=True, ), - dimension=dict(argstr='--dimensionality %d', + transforms=dict(argstr='%s', + mandatory=True, ), - invert_transform_flags=dict(), ) inputs = ApplyTransforms.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ApplyTransforms_outputs(): output_map = dict(output_image=dict(), ) @@ -58,3 +60,4 @@ def test_ApplyTransforms_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/ants/tests/test_auto_Atropos.py b/nipype/interfaces/ants/tests/test_auto_Atropos.py index 74acf25f58..8698879c7b 100644 --- a/nipype/interfaces/ants/tests/test_auto_Atropos.py +++ b/nipype/interfaces/ants/tests/test_auto_Atropos.py @@ -1,64 +1,65 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.ants.segmentation import Atropos + def test_Atropos_inputs(): - input_map = dict(icm_use_synchronous_update=dict(argstr='%s', - ), - prior_probability_images=dict(), - intensity_images=dict(mandatory=True, - argstr='--intensity-image %s...', - ), - prior_weighting=dict(), - out_classified_image_name=dict(hash_files=False, - genfile=True, - argstr='%s', - ), - mrf_smoothing_factor=dict(argstr='%s', + input_map = dict(args=dict(argstr='%s', ), convergence_threshold=dict(requires=['n_iterations'], ), - prior_probability_threshold=dict(requires=['prior_weighting'], + dimension=dict(argstr='--image-dimensionality %d', + usedefault=True, ), - save_posteriors=dict(), - maximum_number_of_icm_terations=dict(requires=['icm_use_synchronous_update'], + environ=dict(nohash=True, + usedefault=True, ), - use_mixture_model_proportions=dict(requires=['posterior_formulation'], + icm_use_synchronous_update=dict(argstr='%s', ), ignore_exception=dict(nohash=True, usedefault=True, ), - mask_image=dict(mandatory=True, - argstr='--mask-image %s', - ), - mrf_radius=dict(requires=['mrf_smoothing_factor'], - ), - initialization=dict(mandatory=True, + initialization=dict(argstr='%s', + mandatory=True, requires=['number_of_tissue_classes'], - argstr='%s', ), - args=dict(argstr='%s', + intensity_images=dict(argstr='--intensity-image %s...', + mandatory=True, ), likelihood_model=dict(argstr='--likelihood-model %s', ), - terminal_output=dict(mandatory=True, - nohash=True, + mask_image=dict(argstr='--mask-image %s', + mandatory=True, ), - output_posteriors_name_template=dict(usedefault=True, + maximum_number_of_icm_terations=dict(requires=['icm_use_synchronous_update'], + ), + mrf_radius=dict(requires=['mrf_smoothing_factor'], + ), + mrf_smoothing_factor=dict(argstr='%s', + ), + n_iterations=dict(argstr='%s', ), num_threads=dict(nohash=True, usedefault=True, ), number_of_tissue_classes=dict(mandatory=True, ), - n_iterations=dict(argstr='%s', + out_classified_image_name=dict(argstr='%s', + genfile=True, + hash_files=False, ), - environ=dict(nohash=True, - usedefault=True, + output_posteriors_name_template=dict(usedefault=True, ), posterior_formulation=dict(argstr='%s', ), - dimension=dict(usedefault=True, - argstr='--image-dimensionality %d', + prior_probability_images=dict(), + prior_probability_threshold=dict(requires=['prior_weighting'], + ), + prior_weighting=dict(), + save_posteriors=dict(), + terminal_output=dict(mandatory=True, + nohash=True, + ), + use_mixture_model_proportions=dict(requires=['posterior_formulation'], ), ) inputs = Atropos.input_spec() @@ -66,12 +67,14 @@ def test_Atropos_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Atropos_outputs(): - output_map = dict(posteriors=dict(), - classified_image=dict(), + output_map = dict(classified_image=dict(), + posteriors=dict(), ) outputs = Atropos.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/ants/tests/test_auto_AverageAffineTransform.py b/nipype/interfaces/ants/tests/test_auto_AverageAffineTransform.py index 23c88ec237..3885fa1f2a 100644 --- a/nipype/interfaces/ants/tests/test_auto_AverageAffineTransform.py +++ b/nipype/interfaces/ants/tests/test_auto_AverageAffineTransform.py @@ -1,40 +1,42 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.ants.utils import AverageAffineTransform + def test_AverageAffineTransform_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + dimension=dict(argstr='%d', + mandatory=True, + position=0, + usedefault=False, + ), + environ=dict(nohash=True, + usedefault=True, + ), + ignore_exception=dict(nohash=True, usedefault=True, ), num_threads=dict(nohash=True, usedefault=True, ), - output_affine_transform=dict(position=1, + output_affine_transform=dict(argstr='%s', mandatory=True, - argstr='%s', - ), - args=dict(argstr='%s', + position=1, ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), transforms=dict(argstr='%s', mandatory=True, position=3, ), - dimension=dict(mandatory=True, - usedefault=False, - position=0, - argstr='%d', - ), ) inputs = AverageAffineTransform.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_AverageAffineTransform_outputs(): output_map = dict(affine_transform=dict(), ) @@ -43,3 +45,4 @@ def test_AverageAffineTransform_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/ants/tests/test_auto_AverageImages.py b/nipype/interfaces/ants/tests/test_auto_AverageImages.py index dec50c828f..50df1bc36a 100644 --- a/nipype/interfaces/ants/tests/test_auto_AverageImages.py +++ b/nipype/interfaces/ants/tests/test_auto_AverageImages.py @@ -1,44 +1,46 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.ants.utils import AverageImages + def test_AverageImages_inputs(): - input_map = dict(normalize=dict(position=2, + input_map = dict(args=dict(argstr='%s', + ), + dimension=dict(argstr='%d', mandatory=True, - argstr='%d', + position=0, ), - num_threads=dict(nohash=True, + environ=dict(nohash=True, usedefault=True, ), ignore_exception=dict(nohash=True, usedefault=True, ), - args=dict(argstr='%s', + images=dict(argstr='%s', + mandatory=True, + position=3, + ), + normalize=dict(argstr='%d', + mandatory=True, + position=2, ), - output_average_image=dict(hash_files=False, + num_threads=dict(nohash=True, usedefault=True, + ), + output_average_image=dict(argstr='%s', + hash_files=False, position=1, - argstr='%s', + usedefault=True, ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - images=dict(argstr='%s', - mandatory=True, - position=3, - ), - dimension=dict(position=0, - mandatory=True, - argstr='%d', - ), ) inputs = AverageImages.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_AverageImages_outputs(): output_map = dict(output_average_image=dict(), ) @@ -47,3 +49,4 @@ def test_AverageImages_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/ants/tests/test_auto_GenWarpFields.py b/nipype/interfaces/ants/tests/test_auto_GenWarpFields.py index 2559740657..ddfe3d95d6 100644 --- a/nipype/interfaces/ants/tests/test_auto_GenWarpFields.py +++ b/nipype/interfaces/ants/tests/test_auto_GenWarpFields.py @@ -1,51 +1,52 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.ants.legacy import GenWarpFields + def test_GenWarpFields_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(args=dict(argstr='%s', ), - transformation_model=dict(usedefault=True, - argstr='-t %s', + bias_field_correction=dict(argstr='-n 1', ), - quality_check=dict(argstr='-q 1', + dimension=dict(argstr='-d %d', + position=1, + usedefault=True, ), - num_threads=dict(nohash=True, + environ=dict(nohash=True, usedefault=True, ), force_proceed=dict(argstr='-f 1', ), - args=dict(argstr='%s', - ), - out_prefix=dict(argstr='-o %s', + ignore_exception=dict(nohash=True, usedefault=True, ), - bias_field_correction=dict(argstr='-n 1', + input_image=dict(argstr='-i %s', + copyfile=False, + mandatory=True, ), - terminal_output=dict(mandatory=True, - nohash=True, + inverse_warp_template_labels=dict(argstr='-l', ), - environ=dict(nohash=True, + max_iterations=dict(argstr='-m %s', + sep='x', + ), + num_threads=dict(nohash=True, usedefault=True, ), - similarity_metric=dict(argstr='-s %s', + out_prefix=dict(argstr='-o %s', + usedefault=True, ), - reference_image=dict(copyfile=True, - mandatory=True, - argstr='-r %s', + quality_check=dict(argstr='-q 1', ), - input_image=dict(copyfile=False, + reference_image=dict(argstr='-r %s', + copyfile=True, mandatory=True, - argstr='-i %s', ), - inverse_warp_template_labels=dict(argstr='-l', + similarity_metric=dict(argstr='-s %s', ), - dimension=dict(position=1, - usedefault=True, - argstr='-d %d', + terminal_output=dict(mandatory=True, + nohash=True, ), - max_iterations=dict(sep='x', - argstr='-m %s', + transformation_model=dict(argstr='-t %s', + usedefault=True, ), ) inputs = GenWarpFields.input_spec() @@ -53,15 +54,17 @@ def test_GenWarpFields_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_GenWarpFields_outputs(): - output_map = dict(inverse_warp_field=dict(), + output_map = dict(affine_transformation=dict(), + input_file=dict(), + inverse_warp_field=dict(), output_file=dict(), warp_field=dict(), - affine_transformation=dict(), - input_file=dict(), ) outputs = GenWarpFields.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/ants/tests/test_auto_JacobianDeterminant.py b/nipype/interfaces/ants/tests/test_auto_JacobianDeterminant.py index b3b44d15a5..ca9a08d212 100644 --- a/nipype/interfaces/ants/tests/test_auto_JacobianDeterminant.py +++ b/nipype/interfaces/ants/tests/test_auto_JacobianDeterminant.py @@ -1,47 +1,48 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.ants.utils import JacobianDeterminant + def test_JacobianDeterminant_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + dimension=dict(argstr='%d', + mandatory=True, + position=0, + usedefault=False, + ), + environ=dict(nohash=True, usedefault=True, ), + ignore_exception=dict(nohash=True, + usedefault=True, + ), + norm_by_total=dict(argstr='%d', + position=5, + ), num_threads=dict(nohash=True, usedefault=True, ), - output_prefix=dict(hash_files=False, + output_prefix=dict(argstr='%s', genfile=True, + hash_files=False, position=2, - argstr='%s', ), - args=dict(argstr='%s', + projection_vector=dict(argstr='%s', + position=6, + sep='x', + ), + template_mask=dict(argstr='%s', + position=4, ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, + use_log=dict(argstr='%d', + position=3, ), - use_log=dict(position=3, - argstr='%d', - ), - warp_file=dict(position=1, + warp_file=dict(argstr='%s', mandatory=True, - argstr='%s', - ), - template_mask=dict(position=4, - argstr='%s', - ), - norm_by_total=dict(position=5, - argstr='%d', - ), - dimension=dict(mandatory=True, - usedefault=False, - position=0, - argstr='%d', - ), - projection_vector=dict(argstr='%s', - sep='x', - position=6, + position=1, ), ) inputs = JacobianDeterminant.input_spec() @@ -49,6 +50,7 @@ def test_JacobianDeterminant_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_JacobianDeterminant_outputs(): output_map = dict(jacobian_image=dict(), ) @@ -57,3 +59,4 @@ def test_JacobianDeterminant_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/ants/tests/test_auto_MultiplyImages.py b/nipype/interfaces/ants/tests/test_auto_MultiplyImages.py index da1449a89b..cdf1e43134 100644 --- a/nipype/interfaces/ants/tests/test_auto_MultiplyImages.py +++ b/nipype/interfaces/ants/tests/test_auto_MultiplyImages.py @@ -1,44 +1,46 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.ants.utils import MultiplyImages + def test_MultiplyImages_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(args=dict(argstr='%s', ), - num_threads=dict(nohash=True, + dimension=dict(argstr='%d', + mandatory=True, + position=0, + usedefault=False, + ), + environ=dict(nohash=True, usedefault=True, ), - second_input=dict(position=2, + first_input=dict(argstr='%s', mandatory=True, - argstr='%s', + position=1, + ), + ignore_exception=dict(nohash=True, + usedefault=True, ), - args=dict(argstr='%s', + num_threads=dict(nohash=True, + usedefault=True, ), - output_product_image=dict(position=3, + output_product_image=dict(argstr='%s', mandatory=True, - argstr='%s', + position=3, ), - first_input=dict(position=1, + second_input=dict(argstr='%s', mandatory=True, - argstr='%s', + position=2, ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - dimension=dict(mandatory=True, - usedefault=False, - position=0, - argstr='%d', - ), ) inputs = MultiplyImages.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MultiplyImages_outputs(): output_map = dict(output_product_image=dict(), ) @@ -47,3 +49,4 @@ def test_MultiplyImages_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/ants/tests/test_auto_N4BiasFieldCorrection.py b/nipype/interfaces/ants/tests/test_auto_N4BiasFieldCorrection.py index 84e43f8394..c47a59a68a 100644 --- a/nipype/interfaces/ants/tests/test_auto_N4BiasFieldCorrection.py +++ b/nipype/interfaces/ants/tests/test_auto_N4BiasFieldCorrection.py @@ -1,45 +1,46 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.ants.segmentation import N4BiasFieldCorrection + def test_N4BiasFieldCorrection_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(args=dict(argstr='%s', ), - num_threads=dict(nohash=True, - usedefault=True, + bspline_fitting_distance=dict(argstr='--bsline-fitting [%g]', ), - shrink_factor=dict(argstr='--shrink-factor %d', + convergence_threshold=dict(argstr=',%g]', + position=2, + requires=['n_iterations'], ), - mask_image=dict(argstr='--mask-image %s', + dimension=dict(argstr='--image-dimension %d', + usedefault=True, ), - output_image=dict(argstr='--output %s', - hash_files=False, - genfile=True, + environ=dict(nohash=True, + usedefault=True, ), - bspline_fitting_distance=dict(argstr='--bsline-fitting [%g]', + ignore_exception=dict(nohash=True, + usedefault=True, ), - convergence_threshold=dict(position=2, - requires=['n_iterations'], - argstr=',%g]', + input_image=dict(argstr='--input-image %s', + mandatory=True, ), - args=dict(argstr='%s', + mask_image=dict(argstr='--mask-image %s', ), - n_iterations=dict(sep='x', + n_iterations=dict(argstr='--convergence [ %s', position=1, requires=['convergence_threshold'], - argstr='--convergence [ %s', - ), - terminal_output=dict(mandatory=True, - nohash=True, + sep='x', ), - environ=dict(nohash=True, + num_threads=dict(nohash=True, usedefault=True, ), - input_image=dict(mandatory=True, - argstr='--input-image %s', + output_image=dict(argstr='--output %s', + genfile=True, + hash_files=False, + ), + shrink_factor=dict(argstr='--shrink-factor %d', ), - dimension=dict(usedefault=True, - argstr='--image-dimension %d', + terminal_output=dict(mandatory=True, + nohash=True, ), ) inputs = N4BiasFieldCorrection.input_spec() @@ -47,6 +48,7 @@ def test_N4BiasFieldCorrection_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_N4BiasFieldCorrection_outputs(): output_map = dict(output_image=dict(), ) @@ -55,3 +57,4 @@ def test_N4BiasFieldCorrection_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/ants/tests/test_auto_Registration.py b/nipype/interfaces/ants/tests/test_auto_Registration.py index 6c221e2ddb..1b78227c31 100644 --- a/nipype/interfaces/ants/tests/test_auto_Registration.py +++ b/nipype/interfaces/ants/tests/test_auto_Registration.py @@ -1,108 +1,109 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.ants.registration import Registration + def test_Registration_inputs(): - input_map = dict(convergence_window_size=dict(requires=['convergence_threshold'], - usedefault=True, + input_map = dict(args=dict(argstr='%s', ), - metric_item_trait=dict(), - metric_weight_item_trait=dict(), - output_inverse_warped_image=dict(requires=['output_warped_image'], - hash_files=False, - ), - metric_stage_trait=dict(), - metric=dict(mandatory=True, - ), - sampling_percentage_item_trait=dict(), - moving_image=dict(mandatory=True, - ), - initial_moving_transform=dict(xor=['initial_moving_transform_com'], - argstr='%s', - ), - sampling_percentage_stage_trait=dict(), - radius_bins_item_trait=dict(), - transforms=dict(mandatory=True, - argstr='%s', - ), - initial_moving_transform_com=dict(xor=['initial_moving_transform'], - argstr='%s', - ), - metric_weight=dict(mandatory=True, + collapse_linear_transforms_to_fixed_image_header=dict(argstr='%s', usedefault=True, - requires=['metric'], ), - dimension=dict(usedefault=True, - argstr='--dimensionality %d', - ), - sigma_units=dict(requires=['smoothing_sigmas'], - ), - invert_initial_moving_transform=dict(xor=['initial_moving_transform_com'], - requires=['initial_moving_transform'], - ), - winsorize_lower_quantile=dict(argstr='%s', + collapse_output_transforms=dict(argstr='--collapse-output-transforms %d', usedefault=True, ), - sampling_strategy_item_trait=dict(), convergence_threshold=dict(requires=['number_of_iterations'], usedefault=True, ), - sampling_strategy=dict(requires=['metric_weight'], + convergence_window_size=dict(requires=['convergence_threshold'], + usedefault=True, ), - shrink_factors=dict(mandatory=True, + dimension=dict(argstr='--dimensionality %d', + usedefault=True, ), - winsorize_upper_quantile=dict(argstr='%s', + environ=dict(nohash=True, usedefault=True, ), fixed_image=dict(mandatory=True, ), - output_transform_prefix=dict(argstr='%s', + fixed_image_mask=dict(argstr='%s', + ), + ignore_exception=dict(nohash=True, usedefault=True, ), - interpolation=dict(usedefault=True, - argstr='%s', + initial_moving_transform=dict(argstr='%s', + xor=['initial_moving_transform_com'], ), - ignore_exception=dict(nohash=True, + initial_moving_transform_com=dict(argstr='%s', + xor=['initial_moving_transform'], + ), + interpolation=dict(argstr='%s', usedefault=True, ), - radius_bins_stage_trait=dict(), - args=dict(argstr='%s', + invert_initial_moving_transform=dict(requires=['initial_moving_transform'], + xor=['initial_moving_transform_com'], ), - use_estimate_learning_rate_once=dict(), - terminal_output=dict(mandatory=True, - nohash=True, + metric=dict(mandatory=True, ), - metric_weight_stage_trait=dict(), - write_composite_transform=dict(argstr='--write-composite-transform %d', + metric_item_trait=dict(), + metric_stage_trait=dict(), + metric_weight=dict(mandatory=True, + requires=['metric'], usedefault=True, ), + metric_weight_item_trait=dict(), + metric_weight_stage_trait=dict(), + moving_image=dict(mandatory=True, + ), moving_image_mask=dict(requires=['fixed_image_mask'], ), num_threads=dict(nohash=True, usedefault=True, ), - output_warped_image=dict(hash_files=False, + number_of_iterations=dict(), + output_inverse_warped_image=dict(hash_files=False, + requires=['output_warped_image'], ), - sampling_percentage=dict(requires=['sampling_strategy'], + output_transform_prefix=dict(argstr='%s', + usedefault=True, ), - number_of_iterations=dict(), - fixed_image_mask=dict(argstr='%s', + output_warped_image=dict(hash_files=False, ), + radius_bins_item_trait=dict(), + radius_bins_stage_trait=dict(), radius_or_number_of_bins=dict(requires=['metric_weight'], usedefault=True, ), - environ=dict(nohash=True, - usedefault=True, + sampling_percentage=dict(requires=['sampling_strategy'], + ), + sampling_percentage_item_trait=dict(), + sampling_percentage_stage_trait=dict(), + sampling_strategy=dict(requires=['metric_weight'], + ), + sampling_strategy_item_trait=dict(), + sampling_strategy_stage_trait=dict(), + shrink_factors=dict(mandatory=True, + ), + sigma_units=dict(requires=['smoothing_sigmas'], ), smoothing_sigmas=dict(mandatory=True, ), - use_histogram_matching=dict(usedefault=True, + terminal_output=dict(mandatory=True, + nohash=True, ), transform_parameters=dict(), - collapse_linear_transforms_to_fixed_image_header=dict(argstr='%s', + transforms=dict(argstr='%s', + mandatory=True, + ), + use_estimate_learning_rate_once=dict(), + use_histogram_matching=dict(usedefault=True, + ), + winsorize_lower_quantile=dict(argstr='%s', usedefault=True, ), - sampling_strategy_stage_trait=dict(), - collapse_output_transforms=dict(argstr='--collapse-output-transforms %d', + winsorize_upper_quantile=dict(argstr='%s', + usedefault=True, + ), + write_composite_transform=dict(argstr='--write-composite-transform %d', usedefault=True, ), ) @@ -111,18 +112,20 @@ def test_Registration_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Registration_outputs(): - output_map = dict(reverse_invert_flags=dict(), + output_map = dict(composite_transform=dict(), + forward_invert_flags=dict(), + forward_transforms=dict(), inverse_composite_transform=dict(), - warped_image=dict(), inverse_warped_image=dict(), - forward_invert_flags=dict(), + reverse_invert_flags=dict(), reverse_transforms=dict(), - composite_transform=dict(), - forward_transforms=dict(), + warped_image=dict(), ) outputs = Registration.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/ants/tests/test_auto_WarpImageMultiTransform.py b/nipype/interfaces/ants/tests/test_auto_WarpImageMultiTransform.py index c7fb2cc9fa..0326973f4f 100644 --- a/nipype/interfaces/ants/tests/test_auto_WarpImageMultiTransform.py +++ b/nipype/interfaces/ants/tests/test_auto_WarpImageMultiTransform.py @@ -1,54 +1,55 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.ants.resampling import WarpImageMultiTransform + def test_WarpImageMultiTransform_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + dimension=dict(argstr='%d', + position=1, usedefault=True, ), - num_threads=dict(nohash=True, + environ=dict(nohash=True, usedefault=True, ), - invert_affine=dict(), - output_image=dict(hash_files=False, - genfile=True, - xor=['out_postfix'], - position=3, - argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - tightest_box=dict(xor=['reference_image'], - argstr='--tightest-bounding-box', + input_image=dict(argstr='%s', + mandatory=True, + position=2, ), - out_postfix=dict(xor=['output_image'], - hash_files=False, + invert_affine=dict(), + num_threads=dict(nohash=True, usedefault=True, ), - use_nearest=dict(argstr='--use-NN', + out_postfix=dict(hash_files=False, + usedefault=True, + xor=['output_image'], ), - args=dict(argstr='%s', + output_image=dict(argstr='%s', + genfile=True, + hash_files=False, + position=3, + xor=['out_postfix'], ), - dimension=dict(position=1, - usedefault=True, - argstr='%d', + reference_image=dict(argstr='-R %s', + xor=['tightest_box'], + ), + reslice_by_header=dict(argstr='--reslice-by-header', ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - reference_image=dict(xor=['tightest_box'], - argstr='-R %s', + tightest_box=dict(argstr='--tightest-bounding-box', + xor=['reference_image'], ), - input_image=dict(position=2, + transformation_series=dict(argstr='%s', mandatory=True, - argstr='%s', ), use_bspline=dict(argstr='--use-Bspline', ), - transformation_series=dict(mandatory=True, - argstr='%s', - ), - reslice_by_header=dict(argstr='--reslice-by-header', + use_nearest=dict(argstr='--use-NN', ), ) inputs = WarpImageMultiTransform.input_spec() @@ -56,6 +57,7 @@ def test_WarpImageMultiTransform_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_WarpImageMultiTransform_outputs(): output_map = dict(output_image=dict(), ) @@ -64,3 +66,4 @@ def test_WarpImageMultiTransform_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/ants/tests/test_auto_WarpTimeSeriesImageMultiTransform.py b/nipype/interfaces/ants/tests/test_auto_WarpTimeSeriesImageMultiTransform.py index fcbd5ba793..2934485819 100644 --- a/nipype/interfaces/ants/tests/test_auto_WarpTimeSeriesImageMultiTransform.py +++ b/nipype/interfaces/ants/tests/test_auto_WarpTimeSeriesImageMultiTransform.py @@ -1,48 +1,49 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.ants.resampling import WarpTimeSeriesImageMultiTransform + def test_WarpTimeSeriesImageMultiTransform_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + dimension=dict(argstr='%d', + position=1, usedefault=True, ), - num_threads=dict(nohash=True, + environ=dict(nohash=True, usedefault=True, ), - invert_affine=dict(), - reslice_by_header=dict(argstr='--reslice-by-header', + ignore_exception=dict(nohash=True, + usedefault=True, + ), + input_image=dict(argstr='%s', + copyfile=True, + mandatory=True, ), - tightest_box=dict(xor=['reference_image'], - argstr='--tightest-bounding-box', + invert_affine=dict(), + num_threads=dict(nohash=True, + usedefault=True, ), out_postfix=dict(argstr='%s', usedefault=True, ), - use_nearest=dict(argstr='--use-NN', + reference_image=dict(argstr='-R %s', + xor=['tightest_box'], ), - args=dict(argstr='%s', + reslice_by_header=dict(argstr='--reslice-by-header', ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - reference_image=dict(xor=['tightest_box'], - argstr='-R %s', + tightest_box=dict(argstr='--tightest-bounding-box', + xor=['reference_image'], ), - input_image=dict(copyfile=True, + transformation_series=dict(argstr='%s', + copyfile=False, mandatory=True, - argstr='%s', ), use_bspline=dict(argstr='--use-Bspline', ), - transformation_series=dict(copyfile=False, - mandatory=True, - argstr='%s', - ), - dimension=dict(position=1, - usedefault=True, - argstr='%d', + use_nearest=dict(argstr='--use-NN', ), ) inputs = WarpTimeSeriesImageMultiTransform.input_spec() @@ -50,6 +51,7 @@ def test_WarpTimeSeriesImageMultiTransform_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_WarpTimeSeriesImageMultiTransform_outputs(): output_map = dict(output_image=dict(), ) @@ -58,3 +60,4 @@ def test_WarpTimeSeriesImageMultiTransform_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/ants/tests/test_auto_antsIntroduction.py b/nipype/interfaces/ants/tests/test_auto_antsIntroduction.py index 1702141c1b..de5d80e08f 100644 --- a/nipype/interfaces/ants/tests/test_auto_antsIntroduction.py +++ b/nipype/interfaces/ants/tests/test_auto_antsIntroduction.py @@ -1,51 +1,52 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.ants.legacy import antsIntroduction + def test_antsIntroduction_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(args=dict(argstr='%s', ), - transformation_model=dict(usedefault=True, - argstr='-t %s', + bias_field_correction=dict(argstr='-n 1', ), - quality_check=dict(argstr='-q 1', + dimension=dict(argstr='-d %d', + position=1, + usedefault=True, ), - num_threads=dict(nohash=True, + environ=dict(nohash=True, usedefault=True, ), force_proceed=dict(argstr='-f 1', ), - args=dict(argstr='%s', - ), - out_prefix=dict(argstr='-o %s', + ignore_exception=dict(nohash=True, usedefault=True, ), - bias_field_correction=dict(argstr='-n 1', + input_image=dict(argstr='-i %s', + copyfile=False, + mandatory=True, ), - terminal_output=dict(mandatory=True, - nohash=True, + inverse_warp_template_labels=dict(argstr='-l', ), - environ=dict(nohash=True, + max_iterations=dict(argstr='-m %s', + sep='x', + ), + num_threads=dict(nohash=True, usedefault=True, ), - similarity_metric=dict(argstr='-s %s', + out_prefix=dict(argstr='-o %s', + usedefault=True, ), - reference_image=dict(copyfile=True, - mandatory=True, - argstr='-r %s', + quality_check=dict(argstr='-q 1', ), - input_image=dict(copyfile=False, + reference_image=dict(argstr='-r %s', + copyfile=True, mandatory=True, - argstr='-i %s', ), - inverse_warp_template_labels=dict(argstr='-l', + similarity_metric=dict(argstr='-s %s', ), - dimension=dict(position=1, - usedefault=True, - argstr='-d %d', + terminal_output=dict(mandatory=True, + nohash=True, ), - max_iterations=dict(sep='x', - argstr='-m %s', + transformation_model=dict(argstr='-t %s', + usedefault=True, ), ) inputs = antsIntroduction.input_spec() @@ -53,15 +54,17 @@ def test_antsIntroduction_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_antsIntroduction_outputs(): - output_map = dict(inverse_warp_field=dict(), + output_map = dict(affine_transformation=dict(), + input_file=dict(), + inverse_warp_field=dict(), output_file=dict(), warp_field=dict(), - affine_transformation=dict(), - input_file=dict(), ) outputs = antsIntroduction.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/ants/tests/test_auto_buildtemplateparallel.py b/nipype/interfaces/ants/tests/test_auto_buildtemplateparallel.py index fc324e147c..fec9f76e11 100644 --- a/nipype/interfaces/ants/tests/test_auto_buildtemplateparallel.py +++ b/nipype/interfaces/ants/tests/test_auto_buildtemplateparallel.py @@ -1,69 +1,72 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.ants.legacy import buildtemplateparallel + def test_buildtemplateparallel_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + bias_field_correction=dict(argstr='-n 1', + ), + dimension=dict(argstr='-d %d', + position=1, usedefault=True, ), - gradient_step_size=dict(argstr='-g %f', + environ=dict(nohash=True, + usedefault=True, ), - rigid_body_registration=dict(argstr='-r 1', + gradient_step_size=dict(argstr='-g %f', ), - num_threads=dict(nohash=True, + ignore_exception=dict(nohash=True, usedefault=True, ), - transformation_model=dict(usedefault=True, - argstr='-t %s', + in_files=dict(argstr='%s', + mandatory=True, + position=-1, + ), + iteration_limit=dict(argstr='-i %d', + usedefault=True, ), - parallelization=dict(usedefault=True, - argstr='-c %d', + max_iterations=dict(argstr='-m %s', + sep='x', ), - args=dict(argstr='%s', + num_cores=dict(argstr='-j %d', + requires=['parallelization'], ), - num_cores=dict(requires=['parallelization'], - argstr='-j %d', + num_threads=dict(nohash=True, + usedefault=True, ), out_prefix=dict(argstr='-o %s', usedefault=True, ), - iteration_limit=dict(argstr='-i %d', + parallelization=dict(argstr='-c %d', usedefault=True, ), - in_files=dict(mandatory=True, - position=-1, - argstr='%s', + rigid_body_registration=dict(argstr='-r 1', ), - bias_field_correction=dict(argstr='-n 1', + similarity_metric=dict(argstr='-s %s', ), terminal_output=dict(mandatory=True, nohash=True, ), - use_first_as_target=dict(), - similarity_metric=dict(argstr='-s %s', - ), - environ=dict(nohash=True, - usedefault=True, - ), - dimension=dict(position=1, + transformation_model=dict(argstr='-t %s', usedefault=True, - argstr='-d %d', - ), - max_iterations=dict(sep='x', - argstr='-m %s', ), + use_first_as_target=dict(), ) inputs = buildtemplateparallel.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_buildtemplateparallel_outputs(): - output_map = dict(subject_outfiles=dict(), + output_map = dict(final_template_file=dict(), + subject_outfiles=dict(), template_files=dict(), - final_template_file=dict(), ) outputs = buildtemplateparallel.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/camino/tests/test_auto_AnalyzeHeader.py b/nipype/interfaces/camino/tests/test_auto_AnalyzeHeader.py index ae94aecf4a..51588b12c3 100644 --- a/nipype/interfaces/camino/tests/test_auto_AnalyzeHeader.py +++ b/nipype/interfaces/camino/tests/test_auto_AnalyzeHeader.py @@ -1,82 +1,83 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.camino.convert import AnalyzeHeader + def test_AnalyzeHeader_inputs(): - input_map = dict(scaleinter=dict(units='NA', - argstr='-scaleinter %d', - ), - printintelbyteorder=dict(position=3, - argstr='-printintelbyteorder %s', - ), - data_dims=dict(units='voxels', - argstr='-datadims %s', - ), - centre=dict(units='mm', - argstr='-centre %s', + input_map = dict(args=dict(argstr='%s', ), - scaleslope=dict(units='NA', - argstr='-scaleslope %d', + centre=dict(argstr='-centre %s', + units='mm', ), - scheme_file=dict(position=2, - argstr='%s', + data_dims=dict(argstr='-datadims %s', + units='voxels', ), - in_file=dict(position=1, + datatype=dict(argstr='-datatype %s', mandatory=True, - argstr='< %s', ), - intelbyteorder=dict(argstr='-intelbyteorder', + description=dict(argstr='-description %s', ), - nimages=dict(units='NA', - argstr='-nimages %d', + environ=dict(nohash=True, + usedefault=True, ), - voxel_dims=dict(units='mm', - argstr='-voxeldims %s', + greylevels=dict(argstr='-gl %s', + units='NA', ), ignore_exception=dict(nohash=True, usedefault=True, ), - description=dict(argstr='-description %s', + in_file=dict(argstr='< %s', + mandatory=True, + position=1, ), - printprogargs=dict(position=3, - argstr='-printprogargs %s', + initfromheader=dict(argstr='-initfromheader %s', + position=3, ), - args=dict(argstr='%s', + intelbyteorder=dict(argstr='-intelbyteorder', ), - readheader=dict(position=3, - argstr='-readheader %s', + networkbyteorder=dict(argstr='-networkbyteorder', ), - terminal_output=dict(mandatory=True, - nohash=True, + nimages=dict(argstr='-nimages %d', + units='NA', ), - offset=dict(units='NA', - argstr='-offset %d', + offset=dict(argstr='-offset %d', + units='NA', ), - printbigendian=dict(position=3, - argstr='-printbigendian %s', + out_file=dict(argstr='> %s', + genfile=True, + position=-1, ), - picoseed=dict(units='mm', - argstr='-picoseed %s', + picoseed=dict(argstr='-picoseed %s', + units='mm', ), - initfromheader=dict(position=3, - argstr='-initfromheader %s', + printbigendian=dict(argstr='-printbigendian %s', + position=3, ), - out_file=dict(position=-1, - genfile=True, - argstr='> %s', + printimagedims=dict(argstr='-printimagedims %s', + position=3, ), - datatype=dict(mandatory=True, - argstr='-datatype %s', + printintelbyteorder=dict(argstr='-printintelbyteorder %s', + position=3, ), - networkbyteorder=dict(argstr='-networkbyteorder', + printprogargs=dict(argstr='-printprogargs %s', + position=3, ), - greylevels=dict(units='NA', - argstr='-gl %s', + readheader=dict(argstr='-readheader %s', + position=3, ), - environ=dict(nohash=True, - usedefault=True, + scaleinter=dict(argstr='-scaleinter %d', + units='NA', + ), + scaleslope=dict(argstr='-scaleslope %d', + units='NA', ), - printimagedims=dict(position=3, - argstr='-printimagedims %s', + scheme_file=dict(argstr='%s', + position=2, + ), + terminal_output=dict(mandatory=True, + nohash=True, + ), + voxel_dims=dict(argstr='-voxeldims %s', + units='mm', ), ) inputs = AnalyzeHeader.input_spec() @@ -84,6 +85,7 @@ def test_AnalyzeHeader_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_AnalyzeHeader_outputs(): output_map = dict(header=dict(), ) @@ -92,3 +94,4 @@ def test_AnalyzeHeader_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/camino/tests/test_auto_ComputeEigensystem.py b/nipype/interfaces/camino/tests/test_auto_ComputeEigensystem.py index 29810ba137..da2e383342 100644 --- a/nipype/interfaces/camino/tests/test_auto_ComputeEigensystem.py +++ b/nipype/interfaces/camino/tests/test_auto_ComputeEigensystem.py @@ -1,32 +1,33 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.camino.dti import ComputeEigensystem + def test_ComputeEigensystem_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(args=dict(argstr='%s', ), - out_file=dict(position=-1, - genfile=True, - argstr='> %s', + environ=dict(nohash=True, + usedefault=True, ), - inputmodel=dict(argstr='-inputmodel %s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - outputdatatype=dict(usedefault=True, - argstr='-outputdatatype %s', + in_file=dict(argstr='< %s', + mandatory=True, + position=1, ), - args=dict(argstr='%s', + inputdatatype=dict(argstr='-inputdatatype %s', + usedefault=True, ), - inputdatatype=dict(usedefault=True, - argstr='-inputdatatype %s', + inputmodel=dict(argstr='-inputmodel %s', ), maxcomponents=dict(argstr='-maxcomponents %d', ), - environ=dict(nohash=True, - usedefault=True, + out_file=dict(argstr='> %s', + genfile=True, + position=-1, ), - in_file=dict(position=1, - mandatory=True, - argstr='< %s', + outputdatatype=dict(argstr='-outputdatatype %s', + usedefault=True, ), terminal_output=dict(mandatory=True, nohash=True, @@ -37,6 +38,7 @@ def test_ComputeEigensystem_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ComputeEigensystem_outputs(): output_map = dict(eigen=dict(), ) @@ -45,3 +47,4 @@ def test_ComputeEigensystem_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/camino/tests/test_auto_ComputeFractionalAnisotropy.py b/nipype/interfaces/camino/tests/test_auto_ComputeFractionalAnisotropy.py index ba1c7ff17a..adc16bd07a 100644 --- a/nipype/interfaces/camino/tests/test_auto_ComputeFractionalAnisotropy.py +++ b/nipype/interfaces/camino/tests/test_auto_ComputeFractionalAnisotropy.py @@ -1,34 +1,35 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.camino.dti import ComputeFractionalAnisotropy + def test_ComputeFractionalAnisotropy_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, - ), - out_file=dict(position=-1, - genfile=True, - argstr='> %s', + input_map = dict(args=dict(argstr='%s', ), - scheme_file=dict(position=2, - argstr='%s', + environ=dict(nohash=True, + usedefault=True, ), - outputdatatype=dict(argstr='-outputdatatype %s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - args=dict(argstr='%s', + in_file=dict(argstr='< %s', + mandatory=True, + position=1, ), inputdatatype=dict(argstr='-inputdatatype %s', ), - terminal_output=dict(mandatory=True, - nohash=True, + inputmodel=dict(argstr='-inputmodel %s', ), - environ=dict(nohash=True, - usedefault=True, + out_file=dict(argstr='> %s', + genfile=True, + position=-1, ), - in_file=dict(position=1, - mandatory=True, - argstr='< %s', + outputdatatype=dict(argstr='-outputdatatype %s', ), - inputmodel=dict(argstr='-inputmodel %s', + scheme_file=dict(argstr='%s', + position=2, + ), + terminal_output=dict(mandatory=True, + nohash=True, ), ) inputs = ComputeFractionalAnisotropy.input_spec() @@ -36,6 +37,7 @@ def test_ComputeFractionalAnisotropy_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ComputeFractionalAnisotropy_outputs(): output_map = dict(fa=dict(), ) @@ -44,3 +46,4 @@ def test_ComputeFractionalAnisotropy_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/camino/tests/test_auto_ComputeMeanDiffusivity.py b/nipype/interfaces/camino/tests/test_auto_ComputeMeanDiffusivity.py index b2f0f1071b..b1fcee3747 100644 --- a/nipype/interfaces/camino/tests/test_auto_ComputeMeanDiffusivity.py +++ b/nipype/interfaces/camino/tests/test_auto_ComputeMeanDiffusivity.py @@ -1,34 +1,35 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.camino.dti import ComputeMeanDiffusivity + def test_ComputeMeanDiffusivity_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, - ), - out_file=dict(position=-1, - genfile=True, - argstr='> %s', + input_map = dict(args=dict(argstr='%s', ), - scheme_file=dict(position=2, - argstr='%s', + environ=dict(nohash=True, + usedefault=True, ), - outputdatatype=dict(argstr='-outputdatatype %s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - args=dict(argstr='%s', + in_file=dict(argstr='< %s', + mandatory=True, + position=1, ), inputdatatype=dict(argstr='-inputdatatype %s', ), - terminal_output=dict(mandatory=True, - nohash=True, + inputmodel=dict(argstr='-inputmodel %s', ), - environ=dict(nohash=True, - usedefault=True, + out_file=dict(argstr='> %s', + genfile=True, + position=-1, ), - in_file=dict(position=1, - mandatory=True, - argstr='< %s', + outputdatatype=dict(argstr='-outputdatatype %s', ), - inputmodel=dict(argstr='-inputmodel %s', + scheme_file=dict(argstr='%s', + position=2, + ), + terminal_output=dict(mandatory=True, + nohash=True, ), ) inputs = ComputeMeanDiffusivity.input_spec() @@ -36,6 +37,7 @@ def test_ComputeMeanDiffusivity_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ComputeMeanDiffusivity_outputs(): output_map = dict(md=dict(), ) @@ -44,3 +46,4 @@ def test_ComputeMeanDiffusivity_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/camino/tests/test_auto_ComputeTensorTrace.py b/nipype/interfaces/camino/tests/test_auto_ComputeTensorTrace.py index a801f59bad..ab09b91dba 100644 --- a/nipype/interfaces/camino/tests/test_auto_ComputeTensorTrace.py +++ b/nipype/interfaces/camino/tests/test_auto_ComputeTensorTrace.py @@ -1,34 +1,35 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.camino.dti import ComputeTensorTrace + def test_ComputeTensorTrace_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, - ), - out_file=dict(position=-1, - genfile=True, - argstr='> %s', + input_map = dict(args=dict(argstr='%s', ), - scheme_file=dict(position=2, - argstr='%s', + environ=dict(nohash=True, + usedefault=True, ), - outputdatatype=dict(argstr='-outputdatatype %s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - args=dict(argstr='%s', + in_file=dict(argstr='< %s', + mandatory=True, + position=1, ), inputdatatype=dict(argstr='-inputdatatype %s', ), - terminal_output=dict(mandatory=True, - nohash=True, + inputmodel=dict(argstr='-inputmodel %s', ), - environ=dict(nohash=True, - usedefault=True, + out_file=dict(argstr='> %s', + genfile=True, + position=-1, ), - in_file=dict(position=1, - mandatory=True, - argstr='< %s', + outputdatatype=dict(argstr='-outputdatatype %s', ), - inputmodel=dict(argstr='-inputmodel %s', + scheme_file=dict(argstr='%s', + position=2, + ), + terminal_output=dict(mandatory=True, + nohash=True, ), ) inputs = ComputeTensorTrace.input_spec() @@ -36,6 +37,7 @@ def test_ComputeTensorTrace_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ComputeTensorTrace_outputs(): output_map = dict(trace=dict(), ) @@ -44,3 +46,4 @@ def test_ComputeTensorTrace_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/camino/tests/test_auto_Conmat.py b/nipype/interfaces/camino/tests/test_auto_Conmat.py index fe28c09adc..d1f380fc42 100644 --- a/nipype/interfaces/camino/tests/test_auto_Conmat.py +++ b/nipype/interfaces/camino/tests/test_auto_Conmat.py @@ -1,39 +1,40 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.camino.connectivity import Conmat + def test_Conmat_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + environ=dict(nohash=True, usedefault=True, ), - target_file=dict(position=2, - mandatory=True, - argstr='-targetfile %s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - args=dict(argstr='%s', + in_file=dict(argstr='-inputfile %s', + mandatory=True, + position=1, ), - targetname_file=dict(position=4, - argstr='-targetnamefile %s', + output_root=dict(argstr='-outputroot %s', + genfile=True, ), - scalar_file=dict(position=3, - argstr='-scalarfile %s', + scalar_file=dict(argstr='-scalarfile %s', + position=3, requires=['tract_stat'], ), - tract_stat=dict(units='NA', - requires=['scalar_file'], - argstr='-tractstat %s', + target_file=dict(argstr='-targetfile %s', + mandatory=True, + position=2, + ), + targetname_file=dict(argstr='-targetnamefile %s', + position=4, ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - in_file=dict(position=1, - mandatory=True, - argstr='-inputfile %s', - ), - output_root=dict(argstr='-outputroot %s', - genfile=True, + tract_stat=dict(argstr='-tractstat %s', + requires=['scalar_file'], + units='NA', ), ) inputs = Conmat.input_spec() @@ -41,6 +42,7 @@ def test_Conmat_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Conmat_outputs(): output_map = dict(conmat_sc=dict(), conmat_ts=dict(), @@ -50,3 +52,4 @@ def test_Conmat_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/camino/tests/test_auto_DT2NIfTI.py b/nipype/interfaces/camino/tests/test_auto_DT2NIfTI.py index 3ee4ca6f5f..c242578985 100644 --- a/nipype/interfaces/camino/tests/test_auto_DT2NIfTI.py +++ b/nipype/interfaces/camino/tests/test_auto_DT2NIfTI.py @@ -1,26 +1,27 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.camino.convert import DT2NIfTI + def test_DT2NIfTI_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(args=dict(argstr='%s', ), - args=dict(argstr='%s', + environ=dict(nohash=True, + usedefault=True, ), - header_file=dict(position=3, + header_file=dict(argstr='-header %s', mandatory=True, - argstr='-header %s', + position=3, ), - environ=dict(nohash=True, + ignore_exception=dict(nohash=True, usedefault=True, ), - in_file=dict(position=1, + in_file=dict(argstr='-inputfile %s', mandatory=True, - argstr='-inputfile %s', + position=1, ), - output_root=dict(position=2, + output_root=dict(argstr='-outputroot %s', genfile=True, - argstr='-outputroot %s', + position=2, ), terminal_output=dict(mandatory=True, nohash=True, @@ -31,13 +32,15 @@ def test_DT2NIfTI_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_DT2NIfTI_outputs(): output_map = dict(dt=dict(), - lns0=dict(), exitcode=dict(), + lns0=dict(), ) outputs = DT2NIfTI.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/camino/tests/test_auto_DTIFit.py b/nipype/interfaces/camino/tests/test_auto_DTIFit.py index 218c18ca2f..7f92084b0b 100644 --- a/nipype/interfaces/camino/tests/test_auto_DTIFit.py +++ b/nipype/interfaces/camino/tests/test_auto_DTIFit.py @@ -1,34 +1,35 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.camino.dti import DTIFit + def test_DTIFit_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(args=dict(argstr='%s', ), - out_file=dict(position=-1, - genfile=True, - argstr='> %s', + bgmask=dict(argstr='-bgmask %s', ), - args=dict(argstr='%s', + environ=dict(nohash=True, + usedefault=True, ), - non_linear=dict(position=3, - argstr='-nonlinear', + ignore_exception=dict(nohash=True, + usedefault=True, ), - scheme_file=dict(position=2, + in_file=dict(argstr='%s', mandatory=True, - argstr='%s', + position=1, ), - terminal_output=dict(mandatory=True, - nohash=True, + non_linear=dict(argstr='-nonlinear', + position=3, ), - environ=dict(nohash=True, - usedefault=True, + out_file=dict(argstr='> %s', + genfile=True, + position=-1, ), - in_file=dict(position=1, + scheme_file=dict(argstr='%s', mandatory=True, - argstr='%s', + position=2, ), - bgmask=dict(argstr='-bgmask %s', + terminal_output=dict(mandatory=True, + nohash=True, ), ) inputs = DTIFit.input_spec() @@ -36,6 +37,7 @@ def test_DTIFit_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_DTIFit_outputs(): output_map = dict(tensor_fitted=dict(), ) @@ -44,3 +46,4 @@ def test_DTIFit_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/camino/tests/test_auto_DTLUTGen.py b/nipype/interfaces/camino/tests/test_auto_DTLUTGen.py index 2002a25759..8d763288da 100644 --- a/nipype/interfaces/camino/tests/test_auto_DTLUTGen.py +++ b/nipype/interfaces/camino/tests/test_auto_DTLUTGen.py @@ -1,54 +1,55 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.camino.dti import DTLUTGen + def test_DTLUTGen_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(acg=dict(argstr='-acg', ), - inversion=dict(units='NA', - argstr='-inversion %d', + args=dict(argstr='%s', + ), + bingham=dict(argstr='-bingham', + ), + environ=dict(nohash=True, + usedefault=True, ), frange=dict(argstr='-frange %s', - units='NA', position=1, + units='NA', ), - acg=dict(argstr='-acg', + ignore_exception=dict(nohash=True, + usedefault=True, ), - out_file=dict(position=-1, - genfile=True, - argstr='> %s', + inversion=dict(argstr='-inversion %d', + units='NA', ), - trace=dict(units='NA', - argstr='-trace %G', + lrange=dict(argstr='-lrange %s', + position=1, + units='NA', ), - args=dict(argstr='%s', + out_file=dict(argstr='> %s', + genfile=True, + position=-1, ), - watson=dict(argstr='-watson', + samples=dict(argstr='-samples %d', + units='NA', ), - scheme_file=dict(position=2, + scheme_file=dict(argstr='-schemefile %s', mandatory=True, - argstr='-schemefile %s', + position=2, ), - step=dict(units='NA', - argstr='-step %f', + snr=dict(argstr='-snr %f', + units='NA', + ), + step=dict(argstr='-step %f', + units='NA', ), terminal_output=dict(mandatory=True, nohash=True, ), - snr=dict(units='NA', - argstr='-snr %f', - ), - lrange=dict(argstr='-lrange %s', + trace=dict(argstr='-trace %G', units='NA', - position=1, ), - samples=dict(units='NA', - argstr='-samples %d', - ), - environ=dict(nohash=True, - usedefault=True, - ), - bingham=dict(argstr='-bingham', + watson=dict(argstr='-watson', ), ) inputs = DTLUTGen.input_spec() @@ -56,6 +57,7 @@ def test_DTLUTGen_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_DTLUTGen_outputs(): output_map = dict(dtLUT=dict(), ) @@ -64,3 +66,4 @@ def test_DTLUTGen_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/camino/tests/test_auto_DTMetric.py b/nipype/interfaces/camino/tests/test_auto_DTMetric.py index b823803921..fae80561ab 100644 --- a/nipype/interfaces/camino/tests/test_auto_DTMetric.py +++ b/nipype/interfaces/camino/tests/test_auto_DTMetric.py @@ -1,34 +1,35 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.camino.dti import DTMetric + def test_DTMetric_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(args=dict(argstr='%s', ), - outputfile=dict(argstr='-outputfile %s', - genfile=True, + data_header=dict(argstr='-header %s', ), - outputdatatype=dict(usedefault=True, - argstr='-outputdatatype %s', + eigen_data=dict(argstr='-inputfile %s', + mandatory=True, ), - metric=dict(mandatory=True, - argstr='-stat %s', + environ=dict(nohash=True, + usedefault=True, ), - args=dict(argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - inputdatatype=dict(usedefault=True, - argstr='-inputdatatype %s', + inputdatatype=dict(argstr='-inputdatatype %s', + usedefault=True, ), - terminal_output=dict(mandatory=True, - nohash=True, + metric=dict(argstr='-stat %s', + mandatory=True, ), - environ=dict(nohash=True, + outputdatatype=dict(argstr='-outputdatatype %s', usedefault=True, ), - eigen_data=dict(mandatory=True, - argstr='-inputfile %s', + outputfile=dict(argstr='-outputfile %s', + genfile=True, ), - data_header=dict(argstr='-header %s', + terminal_output=dict(mandatory=True, + nohash=True, ), ) inputs = DTMetric.input_spec() @@ -36,6 +37,7 @@ def test_DTMetric_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_DTMetric_outputs(): output_map = dict(metric_stats=dict(), ) @@ -44,3 +46,4 @@ def test_DTMetric_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/camino/tests/test_auto_FSL2Scheme.py b/nipype/interfaces/camino/tests/test_auto_FSL2Scheme.py index b05ea08801..2068dd23ac 100644 --- a/nipype/interfaces/camino/tests/test_auto_FSL2Scheme.py +++ b/nipype/interfaces/camino/tests/test_auto_FSL2Scheme.py @@ -1,48 +1,49 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.camino.convert import FSL2Scheme + def test_FSL2Scheme_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(args=dict(argstr='%s', ), - numscans=dict(units='NA', - argstr='-numscans %d', + bscale=dict(argstr='-bscale %d', + units='NA', ), - args=dict(argstr='%s', + bval_file=dict(argstr='-bvalfile %s', + mandatory=True, + position=2, ), - flipz=dict(argstr='-flipz', + bvec_file=dict(argstr='-bvecfile %s', + mandatory=True, + position=1, ), - usegradmod=dict(argstr='-usegradmod', + diffusiontime=dict(argstr='-diffusiontime %f', + units='NA', + ), + environ=dict(nohash=True, + usedefault=True, ), flipx=dict(argstr='-flipx', ), flipy=dict(argstr='-flipy', ), - bval_file=dict(position=2, - mandatory=True, - argstr='-bvalfile %s', + flipz=dict(argstr='-flipz', ), - diffusiontime=dict(units='NA', - argstr='-diffusiontime %f', + ignore_exception=dict(nohash=True, + usedefault=True, ), interleave=dict(argstr='-interleave', ), - terminal_output=dict(mandatory=True, - nohash=True, - ), - environ=dict(nohash=True, - usedefault=True, + numscans=dict(argstr='-numscans %d', + units='NA', ), - bvec_file=dict(position=1, - mandatory=True, - argstr='-bvecfile %s', + out_file=dict(argstr='> %s', + genfile=True, + position=-1, ), - bscale=dict(units='NA', - argstr='-bscale %d', + terminal_output=dict(mandatory=True, + nohash=True, ), - out_file=dict(position=-1, - genfile=True, - argstr='> %s', + usegradmod=dict(argstr='-usegradmod', ), ) inputs = FSL2Scheme.input_spec() @@ -50,6 +51,7 @@ def test_FSL2Scheme_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_FSL2Scheme_outputs(): output_map = dict(scheme=dict(), ) @@ -58,3 +60,4 @@ def test_FSL2Scheme_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/camino/tests/test_auto_Image2Voxel.py b/nipype/interfaces/camino/tests/test_auto_Image2Voxel.py index 32b4244f6c..d8ca211846 100644 --- a/nipype/interfaces/camino/tests/test_auto_Image2Voxel.py +++ b/nipype/interfaces/camino/tests/test_auto_Image2Voxel.py @@ -1,36 +1,38 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.camino.convert import Image2Voxel + def test_Image2Voxel_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + environ=dict(nohash=True, usedefault=True, ), - args=dict(argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - out_file=dict(position=-1, + in_file=dict(argstr='-4dimage %s', + mandatory=True, + position=1, + ), + out_file=dict(argstr='> %s', genfile=True, - argstr='> %s', + position=-1, ), - out_type=dict(position=2, + out_type=dict(argstr='-outputdatatype %s', + position=2, usedefault=True, - argstr='-outputdatatype %s', ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - in_file=dict(position=1, - mandatory=True, - argstr='-4dimage %s', - ), ) inputs = Image2Voxel.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Image2Voxel_outputs(): output_map = dict(voxel_order=dict(), ) @@ -39,3 +41,4 @@ def test_Image2Voxel_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/camino/tests/test_auto_LinRecon.py b/nipype/interfaces/camino/tests/test_auto_LinRecon.py index ec54f7fc44..0b97834ab8 100644 --- a/nipype/interfaces/camino/tests/test_auto_LinRecon.py +++ b/nipype/interfaces/camino/tests/test_auto_LinRecon.py @@ -1,39 +1,40 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.camino.odf import LinRecon + def test_LinRecon_inputs(): - input_map = dict(normalize=dict(argstr='-normalize', + input_map = dict(args=dict(argstr='%s', + ), + bgmask=dict(argstr='-bgmask %s', + ), + environ=dict(nohash=True, + usedefault=True, ), ignore_exception=dict(nohash=True, usedefault=True, ), - qball_mat=dict(position=3, + in_file=dict(argstr='%s', mandatory=True, - argstr='%s', + position=1, ), log=dict(argstr='-log', ), - args=dict(argstr='%s', - ), - scheme_file=dict(position=2, - mandatory=True, - argstr='%s', - ), - terminal_output=dict(mandatory=True, - nohash=True, + normalize=dict(argstr='-normalize', ), - environ=dict(nohash=True, - usedefault=True, + out_file=dict(argstr='> %s', + genfile=True, + position=-1, ), - in_file=dict(position=1, + qball_mat=dict(argstr='%s', mandatory=True, - argstr='%s', + position=3, ), - bgmask=dict(argstr='-bgmask %s', + scheme_file=dict(argstr='%s', + mandatory=True, + position=2, ), - out_file=dict(position=-1, - genfile=True, - argstr='> %s', + terminal_output=dict(mandatory=True, + nohash=True, ), ) inputs = LinRecon.input_spec() @@ -41,6 +42,7 @@ def test_LinRecon_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_LinRecon_outputs(): output_map = dict(recon_data=dict(), ) @@ -49,3 +51,4 @@ def test_LinRecon_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/camino/tests/test_auto_ModelFit.py b/nipype/interfaces/camino/tests/test_auto_ModelFit.py index 08196a8f49..33c3ecb0a7 100644 --- a/nipype/interfaces/camino/tests/test_auto_ModelFit.py +++ b/nipype/interfaces/camino/tests/test_auto_ModelFit.py @@ -1,61 +1,63 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.camino.dti import ModelFit + def test_ModelFit_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(args=dict(argstr='%s', ), - tau=dict(argstr='-tau %G', + bgmask=dict(argstr='-bgmask %s', ), - outputfile=dict(argstr='-outputfile %s', + bgthresh=dict(argstr='-bgthresh %G', ), - out_file=dict(position=-1, - genfile=True, - argstr='> %s', + cfthresh=dict(argstr='-csfthresh %G', ), - outlier=dict(argstr='-outliermap %s', + environ=dict(nohash=True, + usedefault=True, ), fixedbvalue=dict(argstr='-fixedbvalue %s', ), - scheme_file=dict(mandatory=True, - argstr='-schemefile %s', - ), - args=dict(argstr='%s', - ), - noisemap=dict(argstr='-noisemap %s', + fixedmodq=dict(argstr='-fixedmod %s', ), - cfthresh=dict(argstr='-csfthresh %G', + ignore_exception=dict(nohash=True, + usedefault=True, ), - residualmap=dict(argstr='-residualmap %s', + in_file=dict(argstr='-inputfile %s', + mandatory=True, ), inputdatatype=dict(argstr='-inputdatatype %s', ), - terminal_output=dict(mandatory=True, - nohash=True, + model=dict(argstr='-model %s', + mandatory=True, ), - environ=dict(nohash=True, - usedefault=True, + noisemap=dict(argstr='-noisemap %s', ), - in_file=dict(mandatory=True, - argstr='-inputfile %s', + out_file=dict(argstr='> %s', + genfile=True, + position=-1, ), - fixedmodq=dict(argstr='-fixedmod %s', + outlier=dict(argstr='-outliermap %s', ), - bgthresh=dict(argstr='-bgthresh %G', + outputfile=dict(argstr='-outputfile %s', ), - model=dict(mandatory=True, - argstr='-model %s', + residualmap=dict(argstr='-residualmap %s', ), - bgmask=dict(argstr='-bgmask %s', + scheme_file=dict(argstr='-schemefile %s', + mandatory=True, ), sigma=dict(argstr='-sigma %G', ), + tau=dict(argstr='-tau %G', + ), + terminal_output=dict(mandatory=True, + nohash=True, + ), ) inputs = ModelFit.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ModelFit_outputs(): output_map = dict(fitted_data=dict(), ) @@ -64,3 +66,4 @@ def test_ModelFit_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/camino/tests/test_auto_NIfTIDT2Camino.py b/nipype/interfaces/camino/tests/test_auto_NIfTIDT2Camino.py index 74782cfe27..7e563b8403 100644 --- a/nipype/interfaces/camino/tests/test_auto_NIfTIDT2Camino.py +++ b/nipype/interfaces/camino/tests/test_auto_NIfTIDT2Camino.py @@ -1,37 +1,38 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.camino.convert import NIfTIDT2Camino + def test_NIfTIDT2Camino_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + bgmask=dict(argstr='-bgmask %s', + ), + environ=dict(nohash=True, usedefault=True, ), - scaleinter=dict(argstr='-scaleinter %s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - out_file=dict(position=-1, + in_file=dict(argstr='-inputfile %s', + mandatory=True, + position=1, + ), + lns0_file=dict(argstr='-lns0 %s', + ), + out_file=dict(argstr='> %s', genfile=True, - argstr='> %s', + position=-1, ), - args=dict(argstr='%s', + s0_file=dict(argstr='-s0 %s', ), - uppertriangular=dict(argstr='-uppertriangular %s', + scaleinter=dict(argstr='-scaleinter %s', ), scaleslope=dict(argstr='-scaleslope %s', ), - lns0_file=dict(argstr='-lns0 %s', - ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - in_file=dict(position=1, - mandatory=True, - argstr='-inputfile %s', - ), - s0_file=dict(argstr='-s0 %s', - ), - bgmask=dict(argstr='-bgmask %s', + uppertriangular=dict(argstr='-uppertriangular %s', ), ) inputs = NIfTIDT2Camino.input_spec() @@ -39,6 +40,7 @@ def test_NIfTIDT2Camino_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_NIfTIDT2Camino_outputs(): output_map = dict(out_file=dict(), ) @@ -47,3 +49,4 @@ def test_NIfTIDT2Camino_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/camino/tests/test_auto_PicoPDFs.py b/nipype/interfaces/camino/tests/test_auto_PicoPDFs.py index 773da9bc9e..650e8e30cb 100644 --- a/nipype/interfaces/camino/tests/test_auto_PicoPDFs.py +++ b/nipype/interfaces/camino/tests/test_auto_PicoPDFs.py @@ -1,41 +1,42 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.camino.dti import PicoPDFs + def test_PicoPDFs_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(args=dict(argstr='%s', ), - luts=dict(mandatory=True, - argstr='-luts %s', - ), - out_file=dict(position=-1, - genfile=True, - argstr='> %s', + directmap=dict(argstr='-directmap', ), - args=dict(argstr='%s', + environ=dict(nohash=True, + usedefault=True, ), - inputmodel=dict(position=2, + ignore_exception=dict(nohash=True, usedefault=True, - argstr='-inputmodel %s', ), - maxcomponents=dict(units='NA', - argstr='-maxcomponents %d', + in_file=dict(argstr='< %s', + mandatory=True, + position=1, ), - environ=dict(nohash=True, + inputmodel=dict(argstr='-inputmodel %s', + position=2, usedefault=True, ), - in_file=dict(position=1, + luts=dict(argstr='-luts %s', mandatory=True, - argstr='< %s', ), - directmap=dict(argstr='-directmap', + maxcomponents=dict(argstr='-maxcomponents %d', + units='NA', ), - numpds=dict(units='NA', - argstr='-numpds %d', + numpds=dict(argstr='-numpds %d', + units='NA', ), - pdf=dict(position=4, + out_file=dict(argstr='> %s', + genfile=True, + position=-1, + ), + pdf=dict(argstr='-pdf %s', + position=4, usedefault=True, - argstr='-pdf %s', ), terminal_output=dict(mandatory=True, nohash=True, @@ -46,6 +47,7 @@ def test_PicoPDFs_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_PicoPDFs_outputs(): output_map = dict(pdfs=dict(), ) @@ -54,3 +56,4 @@ def test_PicoPDFs_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/camino/tests/test_auto_ProcStreamlines.py b/nipype/interfaces/camino/tests/test_auto_ProcStreamlines.py index c88cb3d6c7..ab5653a408 100644 --- a/nipype/interfaces/camino/tests/test_auto_ProcStreamlines.py +++ b/nipype/interfaces/camino/tests/test_auto_ProcStreamlines.py @@ -1,98 +1,99 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.camino.convert import ProcStreamlines + def test_ProcStreamlines_inputs(): - input_map = dict(outputsc=dict(argstr='-outputsc', + input_map = dict(allowmultitargets=dict(argstr='-allowmultitargets', ), - mintractlength=dict(units='mm', - argstr='-mintractlength %d', + args=dict(argstr='%s', ), - datadims=dict(units='voxels', - argstr='-datadims %s', + datadims=dict(argstr='-datadims %s', + units='voxels', ), - truncateloops=dict(argstr='-truncateloops', + directional=dict(argstr='-directional %s', + units='NA', ), - mintractpoints=dict(units='NA', - argstr='-mintractpoints %d', + discardloops=dict(argstr='-discardloops', ), - maxtractlength=dict(units='mm', - argstr='-maxtractlength %d', + endpointfile=dict(argstr='-endpointfile %s', ), - waypointfile=dict(argstr='-waypointfile %s', + environ=dict(nohash=True, + usedefault=True, ), - outputcbs=dict(argstr='-outputcbs', + exclusionfile=dict(argstr='-exclusionfile %s', ), - iterations=dict(units='NA', - argstr='-iterations %d', + gzip=dict(argstr='-gzip', ), - outputtracts=dict(argstr='-outputtracts', + ignore_exception=dict(nohash=True, + usedefault=True, ), - directional=dict(units='NA', - argstr='-directional %s', + in_file=dict(argstr='-inputfile %s', + mandatory=True, + position=1, ), - seedfile=dict(argstr='-seedfile %s', + inputmodel=dict(argstr='-inputmodel %s', + usedefault=True, ), - seedpointmm=dict(units='mm', - argstr='-seedpointmm %s', + iterations=dict(argstr='-iterations %d', + units='NA', ), - in_file=dict(position=1, - mandatory=True, - argstr='-inputfile %s', + maxtractlength=dict(argstr='-maxtractlength %d', + units='mm', ), - truncateinexclusion=dict(argstr='-truncateinexclusion', + maxtractpoints=dict(argstr='-maxtractpoints %d', + units='NA', ), - ignore_exception=dict(nohash=True, - usedefault=True, + mintractlength=dict(argstr='-mintractlength %d', + units='mm', ), - endpointfile=dict(argstr='-endpointfile %s', + mintractpoints=dict(argstr='-mintractpoints %d', + units='NA', ), - args=dict(argstr='%s', + noresample=dict(argstr='-noresample', ), - outputroot=dict(argstr='-outputroot %s', + out_file=dict(argstr='> %s', + genfile=True, + position=-1, ), - maxtractpoints=dict(units='NA', - argstr='-maxtractpoints %d', + outputacm=dict(argstr='-outputacm', ), - targetfile=dict(argstr='-targetfile %s', + outputcbs=dict(argstr='-outputcbs', ), - inputmodel=dict(usedefault=True, - argstr='-inputmodel %s', + outputcp=dict(argstr='-outputcp', ), - terminal_output=dict(mandatory=True, - nohash=True, + outputroot=dict(argstr='-outputroot %s', ), - seedpointvox=dict(units='voxels', - argstr='-seedpointvox %s', + outputsc=dict(argstr='-outputsc', ), - regionindex=dict(units='mm', - argstr='-regionindex %d', + outputtracts=dict(argstr='-outputtracts', ), - out_file=dict(position=-1, - genfile=True, - argstr='> %s', + regionindex=dict(argstr='-regionindex %d', + units='mm', ), - voxeldims=dict(units='mm', - argstr='-voxeldims %s', + resamplestepsize=dict(argstr='-resamplestepsize %d', + units='NA', ), - outputcp=dict(argstr='-outputcp', + seedfile=dict(argstr='-seedfile %s', ), - noresample=dict(argstr='-noresample', + seedpointmm=dict(argstr='-seedpointmm %s', + units='mm', ), - discardloops=dict(argstr='-discardloops', + seedpointvox=dict(argstr='-seedpointvox %s', + units='voxels', ), - outputacm=dict(argstr='-outputacm', + targetfile=dict(argstr='-targetfile %s', ), - exclusionfile=dict(argstr='-exclusionfile %s', + terminal_output=dict(mandatory=True, + nohash=True, ), - allowmultitargets=dict(argstr='-allowmultitargets', + truncateinexclusion=dict(argstr='-truncateinexclusion', ), - environ=dict(nohash=True, - usedefault=True, + truncateloops=dict(argstr='-truncateloops', ), - gzip=dict(argstr='-gzip', + voxeldims=dict(argstr='-voxeldims %s', + units='mm', ), - resamplestepsize=dict(units='NA', - argstr='-resamplestepsize %d', + waypointfile=dict(argstr='-waypointfile %s', ), ) inputs = ProcStreamlines.input_spec() @@ -100,6 +101,7 @@ def test_ProcStreamlines_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ProcStreamlines_outputs(): output_map = dict(proc=dict(), ) @@ -108,3 +110,4 @@ def test_ProcStreamlines_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/camino/tests/test_auto_QBallMX.py b/nipype/interfaces/camino/tests/test_auto_QBallMX.py index d020baf61c..19ac843f74 100644 --- a/nipype/interfaces/camino/tests/test_auto_QBallMX.py +++ b/nipype/interfaces/camino/tests/test_auto_QBallMX.py @@ -1,46 +1,48 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.camino.odf import QBallMX + def test_QBallMX_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + basistype=dict(argstr='-basistype %s', + usedefault=True, + ), + environ=dict(nohash=True, + usedefault=True, + ), + ignore_exception=dict(nohash=True, usedefault=True, ), - rbfpointset=dict(units='NA', - argstr='-rbfpointset %d', + order=dict(argstr='-order %d', + units='NA', ), - out_file=dict(position=-1, + out_file=dict(argstr='> %s', genfile=True, - argstr='> %s', + position=-1, ), - rbfsigma=dict(units='NA', - argstr='-rbfsigma %f', + rbfpointset=dict(argstr='-rbfpointset %d', + units='NA', ), - args=dict(argstr='%s', + rbfsigma=dict(argstr='-rbfsigma %f', + units='NA', ), - smoothingsigma=dict(units='NA', - argstr='-smoothingsigma %f', + scheme_file=dict(argstr='-schemefile %s', + mandatory=True, ), - scheme_file=dict(mandatory=True, - argstr='-schemefile %s', + smoothingsigma=dict(argstr='-smoothingsigma %f', + units='NA', ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - basistype=dict(usedefault=True, - argstr='-basistype %s', - ), - order=dict(units='NA', - argstr='-order %d', - ), ) inputs = QBallMX.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_QBallMX_outputs(): output_map = dict(qmat=dict(), ) @@ -49,3 +51,4 @@ def test_QBallMX_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/camino/tests/test_auto_SFLUTGen.py b/nipype/interfaces/camino/tests/test_auto_SFLUTGen.py index a19003749f..4842209a4a 100644 --- a/nipype/interfaces/camino/tests/test_auto_SFLUTGen.py +++ b/nipype/interfaces/camino/tests/test_auto_SFLUTGen.py @@ -1,44 +1,45 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.camino.calib import SFLUTGen + def test_SFLUTGen_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(args=dict(argstr='%s', ), - out_file=dict(position=-1, - genfile=True, - argstr='> %s', + binincsize=dict(argstr='-binincsize %d', + units='NA', ), - minvectsperbin=dict(units='NA', - argstr='-minvectsperbin %d', + directmap=dict(argstr='-directmap', ), - args=dict(argstr='%s', + environ=dict(nohash=True, + usedefault=True, ), - terminal_output=dict(mandatory=True, - nohash=True, + ignore_exception=dict(nohash=True, + usedefault=True, ), - binincsize=dict(units='NA', - argstr='-binincsize %d', + in_file=dict(argstr='-inputfile %s', + mandatory=True, ), - in_file=dict(mandatory=True, - argstr='-inputfile %s', + info_file=dict(argstr='-infofile %s', + mandatory=True, ), - directmap=dict(argstr='-directmap', + minvectsperbin=dict(argstr='-minvectsperbin %d', + units='NA', ), - pdf=dict(usedefault=True, - argstr='-pdf %s', + order=dict(argstr='-order %d', + units='NA', ), - environ=dict(nohash=True, - usedefault=True, + out_file=dict(argstr='> %s', + genfile=True, + position=-1, ), outputstem=dict(argstr='-outputstem %s', usedefault=True, ), - info_file=dict(mandatory=True, - argstr='-infofile %s', + pdf=dict(argstr='-pdf %s', + usedefault=True, ), - order=dict(units='NA', - argstr='-order %d', + terminal_output=dict(mandatory=True, + nohash=True, ), ) inputs = SFLUTGen.input_spec() @@ -46,12 +47,14 @@ def test_SFLUTGen_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_SFLUTGen_outputs(): - output_map = dict(lut_two_fibres=dict(), - lut_one_fibre=dict(), + output_map = dict(lut_one_fibre=dict(), + lut_two_fibres=dict(), ) outputs = SFLUTGen.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/camino/tests/test_auto_SFPICOCalibData.py b/nipype/interfaces/camino/tests/test_auto_SFPICOCalibData.py index aec90dac62..5e252b07f5 100644 --- a/nipype/interfaces/camino/tests/test_auto_SFPICOCalibData.py +++ b/nipype/interfaces/camino/tests/test_auto_SFPICOCalibData.py @@ -1,62 +1,63 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.camino.calib import SFPICOCalibData + def test_SFPICOCalibData_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + environ=dict(nohash=True, usedefault=True, ), - twodtfastep=dict(units='NA', - argstr='-twodtfastep %f', + ignore_exception=dict(nohash=True, + usedefault=True, ), - out_file=dict(position=-1, + info_file=dict(argstr='-infooutputfile %s', genfile=True, - argstr='> %s', - ), - trace=dict(units='NA', - argstr='-trace %f', + hash_files=False, + mandatory=True, ), - args=dict(argstr='%s', + onedtfarange=dict(argstr='-onedtfarange %s', + units='NA', ), - twodtmixmax=dict(units='NA', - argstr='-twodtmixmax %f', + onedtfastep=dict(argstr='-onedtfastep %f', + units='NA', ), - twodtmixstep=dict(units='NA', - argstr='-twodtmixstep %f', + out_file=dict(argstr='> %s', + genfile=True, + position=-1, ), - twodtfarange=dict(units='NA', - argstr='-twodtfarange %s', + scheme_file=dict(argstr='-schemefile %s', + mandatory=True, ), - scheme_file=dict(mandatory=True, - argstr='-schemefile %s', + seed=dict(argstr='-seed %f', + units='NA', ), - onedtfarange=dict(units='NA', - argstr='-onedtfarange %s', + snr=dict(argstr='-snr %f', + units='NA', ), - seed=dict(units='NA', - argstr='-seed %f', + terminal_output=dict(mandatory=True, + nohash=True, ), - snr=dict(units='NA', - argstr='-snr %f', + trace=dict(argstr='-trace %f', + units='NA', ), - onedtfastep=dict(units='NA', - argstr='-onedtfastep %f', + twodtanglerange=dict(argstr='-twodtanglerange %s', + units='NA', ), - environ=dict(nohash=True, - usedefault=True, + twodtanglestep=dict(argstr='-twodtanglestep %f', + units='NA', ), - info_file=dict(hash_files=False, - genfile=True, - mandatory=True, - argstr='-infooutputfile %s', + twodtfarange=dict(argstr='-twodtfarange %s', + units='NA', ), - twodtanglerange=dict(units='NA', - argstr='-twodtanglerange %s', + twodtfastep=dict(argstr='-twodtfastep %f', + units='NA', ), - terminal_output=dict(mandatory=True, - nohash=True, + twodtmixmax=dict(argstr='-twodtmixmax %f', + units='NA', ), - twodtanglestep=dict(units='NA', - argstr='-twodtanglestep %f', + twodtmixstep=dict(argstr='-twodtmixstep %f', + units='NA', ), ) inputs = SFPICOCalibData.input_spec() @@ -64,6 +65,7 @@ def test_SFPICOCalibData_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_SFPICOCalibData_outputs(): output_map = dict(PICOCalib=dict(), calib_info=dict(), @@ -73,3 +75,4 @@ def test_SFPICOCalibData_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/camino/tests/test_auto_SFPeaks.py b/nipype/interfaces/camino/tests/test_auto_SFPeaks.py index 61c92b2cd6..99a1561eaa 100644 --- a/nipype/interfaces/camino/tests/test_auto_SFPeaks.py +++ b/nipype/interfaces/camino/tests/test_auto_SFPeaks.py @@ -1,58 +1,59 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.camino.odf import SFPeaks + def test_SFPeaks_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(args=dict(argstr='%s', ), - stdsfrommean=dict(units='NA', - argstr='-stdsfrommean %f', + density=dict(argstr='-density %d', + units='NA', ), - mepointset=dict(units='NA', - argstr='-mepointset %d', + environ=dict(nohash=True, + usedefault=True, ), - rbfpointset=dict(units='NA', - argstr='-rbfpointset %d', + ignore_exception=dict(nohash=True, + usedefault=True, ), - out_file=dict(position=-1, - genfile=True, - argstr='> %s', + in_file=dict(argstr='-inputfile %s', + mandatory=True, ), - density=dict(units='NA', - argstr='-density %d', + inputmodel=dict(argstr='-inputmodel %s', + mandatory=True, ), - scheme_file=dict(argstr='%s', + mepointset=dict(argstr='-mepointset %d', + units='NA', ), - args=dict(argstr='%s', + noconsistencycheck=dict(argstr='-noconsistencycheck', ), - pdthresh=dict(units='NA', - argstr='-pdthresh %f', + numpds=dict(argstr='-numpds %d', + units='NA', ), - inputmodel=dict(mandatory=True, - argstr='-inputmodel %s', + order=dict(argstr='-order %d', + units='NA', ), - pointset=dict(units='NA', - argstr='-pointset %d', + out_file=dict(argstr='> %s', + genfile=True, + position=-1, ), - terminal_output=dict(mandatory=True, - nohash=True, + pdthresh=dict(argstr='-pdthresh %f', + units='NA', ), - environ=dict(nohash=True, - usedefault=True, + pointset=dict(argstr='-pointset %d', + units='NA', ), - in_file=dict(mandatory=True, - argstr='-inputfile %s', + rbfpointset=dict(argstr='-rbfpointset %d', + units='NA', ), - numpds=dict(units='NA', - argstr='-numpds %d', + scheme_file=dict(argstr='%s', ), - searchradius=dict(units='NA', - argstr='-searchradius %f', + searchradius=dict(argstr='-searchradius %f', + units='NA', ), - noconsistencycheck=dict(argstr='-noconsistencycheck', + stdsfrommean=dict(argstr='-stdsfrommean %f', + units='NA', ), - order=dict(units='NA', - argstr='-order %d', + terminal_output=dict(mandatory=True, + nohash=True, ), ) inputs = SFPeaks.input_spec() @@ -60,6 +61,7 @@ def test_SFPeaks_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_SFPeaks_outputs(): output_map = dict(peaks=dict(), ) @@ -68,3 +70,4 @@ def test_SFPeaks_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/camino/tests/test_auto_Track.py b/nipype/interfaces/camino/tests/test_auto_Track.py index abe4a3a796..4109e5caf2 100644 --- a/nipype/interfaces/camino/tests/test_auto_Track.py +++ b/nipype/interfaces/camino/tests/test_auto_Track.py @@ -1,60 +1,61 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.camino.dti import Track + def test_Track_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, - ), - seed_file=dict(position=2, - argstr='-seedfile %s', - ), - data_dims=dict(units='voxels', - argstr='-datadims %s', - ), - out_file=dict(position=-1, - genfile=True, - argstr='-outputfile %s', - ), - outputtracts=dict(argstr='-outputtracts %s', + input_map = dict(anisfile=dict(argstr='-anisfile %s', ), - inputdatatype=dict(argstr='-inputdatatype %s', + anisthresh=dict(argstr='-anisthresh %f', ), args=dict(argstr='%s', ), curvethresh=dict(argstr='-curvethresh %f', ), - output_root=dict(position=-1, - argstr='-outputroot %s', + data_dims=dict(argstr='-datadims %s', + units='voxels', ), - maxcomponents=dict(units='NA', - argstr='-maxcomponents %d', - ), - inputmodel=dict(usedefault=True, - argstr='-inputmodel %s', + environ=dict(nohash=True, + usedefault=True, ), - terminal_output=dict(mandatory=True, - nohash=True, + gzip=dict(argstr='-gzip', ), - environ=dict(nohash=True, + ignore_exception=dict(nohash=True, usedefault=True, ), - in_file=dict(position=1, + in_file=dict(argstr='-inputfile %s', mandatory=True, - argstr='-inputfile %s', + position=1, + ), + inputdatatype=dict(argstr='-inputdatatype %s', + ), + inputmodel=dict(argstr='-inputmodel %s', + usedefault=True, ), ipthresh=dict(argstr='-ipthresh %f', ), - gzip=dict(argstr='-gzip', + maxcomponents=dict(argstr='-maxcomponents %d', + units='NA', ), - numpds=dict(units='NA', - argstr='-numpds %d', + numpds=dict(argstr='-numpds %d', + units='NA', ), - voxel_dims=dict(units='mm', - argstr='-voxeldims %s', + out_file=dict(argstr='-outputfile %s', + genfile=True, + position=-1, ), - anisthresh=dict(argstr='-anisthresh %f', + output_root=dict(argstr='-outputroot %s', + position=-1, ), - anisfile=dict(argstr='-anisfile %s', + outputtracts=dict(argstr='-outputtracts %s', + ), + seed_file=dict(argstr='-seedfile %s', + position=2, + ), + terminal_output=dict(mandatory=True, + nohash=True, + ), + voxel_dims=dict(argstr='-voxeldims %s', + units='mm', ), ) inputs = Track.input_spec() @@ -62,6 +63,7 @@ def test_Track_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Track_outputs(): output_map = dict(tracked=dict(), ) @@ -70,3 +72,4 @@ def test_Track_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/camino/tests/test_auto_TrackBallStick.py b/nipype/interfaces/camino/tests/test_auto_TrackBallStick.py index 2bd4606cab..55a14ba560 100644 --- a/nipype/interfaces/camino/tests/test_auto_TrackBallStick.py +++ b/nipype/interfaces/camino/tests/test_auto_TrackBallStick.py @@ -1,60 +1,61 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.camino.dti import TrackBallStick + def test_TrackBallStick_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, - ), - seed_file=dict(position=2, - argstr='-seedfile %s', - ), - data_dims=dict(units='voxels', - argstr='-datadims %s', - ), - out_file=dict(position=-1, - genfile=True, - argstr='-outputfile %s', - ), - outputtracts=dict(argstr='-outputtracts %s', + input_map = dict(anisfile=dict(argstr='-anisfile %s', ), - inputdatatype=dict(argstr='-inputdatatype %s', + anisthresh=dict(argstr='-anisthresh %f', ), args=dict(argstr='%s', ), curvethresh=dict(argstr='-curvethresh %f', ), - output_root=dict(position=-1, - argstr='-outputroot %s', + data_dims=dict(argstr='-datadims %s', + units='voxels', ), - maxcomponents=dict(units='NA', - argstr='-maxcomponents %d', - ), - inputmodel=dict(usedefault=True, - argstr='-inputmodel %s', + environ=dict(nohash=True, + usedefault=True, ), - terminal_output=dict(mandatory=True, - nohash=True, + gzip=dict(argstr='-gzip', ), - environ=dict(nohash=True, + ignore_exception=dict(nohash=True, usedefault=True, ), - in_file=dict(position=1, + in_file=dict(argstr='-inputfile %s', mandatory=True, - argstr='-inputfile %s', + position=1, + ), + inputdatatype=dict(argstr='-inputdatatype %s', + ), + inputmodel=dict(argstr='-inputmodel %s', + usedefault=True, ), ipthresh=dict(argstr='-ipthresh %f', ), - gzip=dict(argstr='-gzip', + maxcomponents=dict(argstr='-maxcomponents %d', + units='NA', ), - numpds=dict(units='NA', - argstr='-numpds %d', + numpds=dict(argstr='-numpds %d', + units='NA', ), - voxel_dims=dict(units='mm', - argstr='-voxeldims %s', + out_file=dict(argstr='-outputfile %s', + genfile=True, + position=-1, ), - anisthresh=dict(argstr='-anisthresh %f', + output_root=dict(argstr='-outputroot %s', + position=-1, ), - anisfile=dict(argstr='-anisfile %s', + outputtracts=dict(argstr='-outputtracts %s', + ), + seed_file=dict(argstr='-seedfile %s', + position=2, + ), + terminal_output=dict(mandatory=True, + nohash=True, + ), + voxel_dims=dict(argstr='-voxeldims %s', + units='mm', ), ) inputs = TrackBallStick.input_spec() @@ -62,6 +63,7 @@ def test_TrackBallStick_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_TrackBallStick_outputs(): output_map = dict(tracked=dict(), ) @@ -70,3 +72,4 @@ def test_TrackBallStick_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/camino/tests/test_auto_TrackBayesDirac.py b/nipype/interfaces/camino/tests/test_auto_TrackBayesDirac.py index 8299e36d96..bd9eaa67b0 100644 --- a/nipype/interfaces/camino/tests/test_auto_TrackBayesDirac.py +++ b/nipype/interfaces/camino/tests/test_auto_TrackBayesDirac.py @@ -1,80 +1,81 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.camino.dti import TrackBayesDirac + def test_TrackBayesDirac_inputs(): - input_map = dict(anisthresh=dict(argstr='-anisthresh %f', - ), - pointset=dict(argstr='-pointset %s', + input_map = dict(anisfile=dict(argstr='-anisfile %s', ), - iterations=dict(units='NA', - argstr='-iterations %d', + anisthresh=dict(argstr='-anisthresh %f', ), - numpds=dict(units='NA', - argstr='-numpds %d', + args=dict(argstr='%s', ), curvepriorg=dict(argstr='-curvepriorg %G', ), - data_dims=dict(units='voxels', - argstr='-datadims %s', + curvepriork=dict(argstr='-curvepriork %G', ), - outputtracts=dict(argstr='-outputtracts %s', + curvethresh=dict(argstr='-curvethresh %f', ), - scheme_file=dict(mandatory=True, - argstr='-schemefile %s', + data_dims=dict(argstr='-datadims %s', + units='voxels', ), - curvepriork=dict(argstr='-curvepriork %G', + datamodel=dict(argstr='-datamodel %s', + ), + environ=dict(nohash=True, + usedefault=True, ), - seed_file=dict(position=2, - argstr='-seedfile %s', + extpriordatatype=dict(argstr='-extpriordatatype %s', ), - maxcomponents=dict(units='NA', - argstr='-maxcomponents %d', + extpriorfile=dict(argstr='-extpriorfile %s', ), - in_file=dict(position=1, - mandatory=True, - argstr='-inputfile %s', + gzip=dict(argstr='-gzip', ), - ipthresh=dict(argstr='-ipthresh %f', + ignore_exception=dict(nohash=True, + usedefault=True, ), - voxel_dims=dict(units='mm', - argstr='-voxeldims %s', + in_file=dict(argstr='-inputfile %s', + mandatory=True, + position=1, ), - output_root=dict(position=-1, - argstr='-outputroot %s', + inputdatatype=dict(argstr='-inputdatatype %s', ), - ignore_exception=dict(nohash=True, + inputmodel=dict(argstr='-inputmodel %s', usedefault=True, ), - args=dict(argstr='%s', + ipthresh=dict(argstr='-ipthresh %f', ), - inputmodel=dict(usedefault=True, - argstr='-inputmodel %s', + iterations=dict(argstr='-iterations %d', + units='NA', ), - terminal_output=dict(mandatory=True, - nohash=True, + maxcomponents=dict(argstr='-maxcomponents %d', + units='NA', ), - anisfile=dict(argstr='-anisfile %s', + numpds=dict(argstr='-numpds %d', + units='NA', ), - out_file=dict(position=-1, + out_file=dict(argstr='-outputfile %s', genfile=True, - argstr='-outputfile %s', + position=-1, ), - curvethresh=dict(argstr='-curvethresh %f', + output_root=dict(argstr='-outputroot %s', + position=-1, ), - extpriordatatype=dict(argstr='-extpriordatatype %s', + outputtracts=dict(argstr='-outputtracts %s', ), - inputdatatype=dict(argstr='-inputdatatype %s', + pdf=dict(argstr='-pdf %s', ), - environ=dict(nohash=True, - usedefault=True, + pointset=dict(argstr='-pointset %s', ), - gzip=dict(argstr='-gzip', + scheme_file=dict(argstr='-schemefile %s', + mandatory=True, ), - pdf=dict(argstr='-pdf %s', + seed_file=dict(argstr='-seedfile %s', + position=2, ), - extpriorfile=dict(argstr='-extpriorfile %s', + terminal_output=dict(mandatory=True, + nohash=True, ), - datamodel=dict(argstr='-datamodel %s', + voxel_dims=dict(argstr='-voxeldims %s', + units='mm', ), ) inputs = TrackBayesDirac.input_spec() @@ -82,6 +83,7 @@ def test_TrackBayesDirac_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_TrackBayesDirac_outputs(): output_map = dict(tracked=dict(), ) @@ -90,3 +92,4 @@ def test_TrackBayesDirac_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/camino/tests/test_auto_TrackBootstrap.py b/nipype/interfaces/camino/tests/test_auto_TrackBootstrap.py index 5e1367ec22..ce8d945667 100644 --- a/nipype/interfaces/camino/tests/test_auto_TrackBootstrap.py +++ b/nipype/interfaces/camino/tests/test_auto_TrackBootstrap.py @@ -1,73 +1,74 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.camino.dti import TrackBootstrap + def test_TrackBootstrap_inputs(): - input_map = dict(bsdatafiles=dict(mandatory=True, - argstr='-bsdatafile %s', + input_map = dict(anisfile=dict(argstr='-anisfile %s', ), - iterations=dict(units='NA', - argstr='-iterations %d', + anisthresh=dict(argstr='-anisthresh %f', ), - numpds=dict(units='NA', - argstr='-numpds %d', + args=dict(argstr='%s', ), - data_dims=dict(units='voxels', - argstr='-datadims %s', + bgmask=dict(argstr='-bgmask %s', ), - outputtracts=dict(argstr='-outputtracts %s', + bsdatafiles=dict(argstr='-bsdatafile %s', + mandatory=True, ), - scheme_file=dict(mandatory=True, - argstr='-schemefile %s', + curvethresh=dict(argstr='-curvethresh %f', ), - seed_file=dict(position=2, - argstr='-seedfile %s', + data_dims=dict(argstr='-datadims %s', + units='voxels', ), - maxcomponents=dict(units='NA', - argstr='-maxcomponents %d', + environ=dict(nohash=True, + usedefault=True, ), - in_file=dict(position=1, - mandatory=True, - argstr='-inputfile %s', + gzip=dict(argstr='-gzip', ), - ipthresh=dict(argstr='-ipthresh %f', + ignore_exception=dict(nohash=True, + usedefault=True, ), - voxel_dims=dict(units='mm', - argstr='-voxeldims %s', + in_file=dict(argstr='-inputfile %s', + mandatory=True, + position=1, ), - output_root=dict(position=-1, - argstr='-outputroot %s', + inputdatatype=dict(argstr='-inputdatatype %s', ), - ignore_exception=dict(nohash=True, + inputmodel=dict(argstr='-inputmodel %s', usedefault=True, ), - args=dict(argstr='%s', + inversion=dict(argstr='-inversion %s', ), - inputmodel=dict(usedefault=True, - argstr='-inputmodel %s', + ipthresh=dict(argstr='-ipthresh %f', ), - terminal_output=dict(mandatory=True, - nohash=True, + iterations=dict(argstr='-iterations %d', + units='NA', ), - anisfile=dict(argstr='-anisfile %s', + maxcomponents=dict(argstr='-maxcomponents %d', + units='NA', ), - inversion=dict(argstr='-inversion %s', + numpds=dict(argstr='-numpds %d', + units='NA', ), - out_file=dict(position=-1, + out_file=dict(argstr='-outputfile %s', genfile=True, - argstr='-outputfile %s', + position=-1, ), - curvethresh=dict(argstr='-curvethresh %f', + output_root=dict(argstr='-outputroot %s', + position=-1, ), - inputdatatype=dict(argstr='-inputdatatype %s', + outputtracts=dict(argstr='-outputtracts %s', ), - environ=dict(nohash=True, - usedefault=True, + scheme_file=dict(argstr='-schemefile %s', + mandatory=True, ), - gzip=dict(argstr='-gzip', + seed_file=dict(argstr='-seedfile %s', + position=2, ), - bgmask=dict(argstr='-bgmask %s', + terminal_output=dict(mandatory=True, + nohash=True, ), - anisthresh=dict(argstr='-anisthresh %f', + voxel_dims=dict(argstr='-voxeldims %s', + units='mm', ), ) inputs = TrackBootstrap.input_spec() @@ -75,6 +76,7 @@ def test_TrackBootstrap_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_TrackBootstrap_outputs(): output_map = dict(tracked=dict(), ) @@ -83,3 +85,4 @@ def test_TrackBootstrap_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/camino/tests/test_auto_TrackDT.py b/nipype/interfaces/camino/tests/test_auto_TrackDT.py index f93e545fa6..ffb33f3e2c 100644 --- a/nipype/interfaces/camino/tests/test_auto_TrackDT.py +++ b/nipype/interfaces/camino/tests/test_auto_TrackDT.py @@ -1,60 +1,61 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.camino.dti import TrackDT + def test_TrackDT_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, - ), - seed_file=dict(position=2, - argstr='-seedfile %s', - ), - data_dims=dict(units='voxels', - argstr='-datadims %s', - ), - out_file=dict(position=-1, - genfile=True, - argstr='-outputfile %s', - ), - outputtracts=dict(argstr='-outputtracts %s', + input_map = dict(anisfile=dict(argstr='-anisfile %s', ), - inputdatatype=dict(argstr='-inputdatatype %s', + anisthresh=dict(argstr='-anisthresh %f', ), args=dict(argstr='%s', ), curvethresh=dict(argstr='-curvethresh %f', ), - output_root=dict(position=-1, - argstr='-outputroot %s', + data_dims=dict(argstr='-datadims %s', + units='voxels', ), - maxcomponents=dict(units='NA', - argstr='-maxcomponents %d', - ), - inputmodel=dict(usedefault=True, - argstr='-inputmodel %s', + environ=dict(nohash=True, + usedefault=True, ), - terminal_output=dict(mandatory=True, - nohash=True, + gzip=dict(argstr='-gzip', ), - environ=dict(nohash=True, + ignore_exception=dict(nohash=True, usedefault=True, ), - in_file=dict(position=1, + in_file=dict(argstr='-inputfile %s', mandatory=True, - argstr='-inputfile %s', + position=1, + ), + inputdatatype=dict(argstr='-inputdatatype %s', + ), + inputmodel=dict(argstr='-inputmodel %s', + usedefault=True, ), ipthresh=dict(argstr='-ipthresh %f', ), - gzip=dict(argstr='-gzip', + maxcomponents=dict(argstr='-maxcomponents %d', + units='NA', ), - numpds=dict(units='NA', - argstr='-numpds %d', + numpds=dict(argstr='-numpds %d', + units='NA', ), - voxel_dims=dict(units='mm', - argstr='-voxeldims %s', + out_file=dict(argstr='-outputfile %s', + genfile=True, + position=-1, ), - anisthresh=dict(argstr='-anisthresh %f', + output_root=dict(argstr='-outputroot %s', + position=-1, ), - anisfile=dict(argstr='-anisfile %s', + outputtracts=dict(argstr='-outputtracts %s', + ), + seed_file=dict(argstr='-seedfile %s', + position=2, + ), + terminal_output=dict(mandatory=True, + nohash=True, + ), + voxel_dims=dict(argstr='-voxeldims %s', + units='mm', ), ) inputs = TrackDT.input_spec() @@ -62,6 +63,7 @@ def test_TrackDT_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_TrackDT_outputs(): output_map = dict(tracked=dict(), ) @@ -70,3 +72,4 @@ def test_TrackDT_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/camino/tests/test_auto_TrackPICo.py b/nipype/interfaces/camino/tests/test_auto_TrackPICo.py index 451d02d601..35049b1318 100644 --- a/nipype/interfaces/camino/tests/test_auto_TrackPICo.py +++ b/nipype/interfaces/camino/tests/test_auto_TrackPICo.py @@ -1,65 +1,66 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.camino.dti import TrackPICo + def test_TrackPICo_inputs(): - input_map = dict(iterations=dict(units='NA', - argstr='-iterations %d', + input_map = dict(anisfile=dict(argstr='-anisfile %s', ), - numpds=dict(units='NA', - argstr='-numpds %d', + anisthresh=dict(argstr='-anisthresh %f', ), - data_dims=dict(units='voxels', - argstr='-datadims %s', + args=dict(argstr='%s', ), - outputtracts=dict(argstr='-outputtracts %s', + curvethresh=dict(argstr='-curvethresh %f', ), - seed_file=dict(position=2, - argstr='-seedfile %s', + data_dims=dict(argstr='-datadims %s', + units='voxels', ), - maxcomponents=dict(units='NA', - argstr='-maxcomponents %d', + environ=dict(nohash=True, + usedefault=True, ), - in_file=dict(position=1, - mandatory=True, - argstr='-inputfile %s', + gzip=dict(argstr='-gzip', ), - ipthresh=dict(argstr='-ipthresh %f', + ignore_exception=dict(nohash=True, + usedefault=True, ), - voxel_dims=dict(units='mm', - argstr='-voxeldims %s', + in_file=dict(argstr='-inputfile %s', + mandatory=True, + position=1, ), - output_root=dict(position=-1, - argstr='-outputroot %s', + inputdatatype=dict(argstr='-inputdatatype %s', ), - ignore_exception=dict(nohash=True, + inputmodel=dict(argstr='-inputmodel %s', usedefault=True, ), - args=dict(argstr='%s', + ipthresh=dict(argstr='-ipthresh %f', ), - inputmodel=dict(usedefault=True, - argstr='-inputmodel %s', + iterations=dict(argstr='-iterations %d', + units='NA', ), - terminal_output=dict(mandatory=True, - nohash=True, + maxcomponents=dict(argstr='-maxcomponents %d', + units='NA', ), - anisfile=dict(argstr='-anisfile %s', + numpds=dict(argstr='-numpds %d', + units='NA', ), - out_file=dict(position=-1, + out_file=dict(argstr='-outputfile %s', genfile=True, - argstr='-outputfile %s', + position=-1, ), - curvethresh=dict(argstr='-curvethresh %f', + output_root=dict(argstr='-outputroot %s', + position=-1, ), - inputdatatype=dict(argstr='-inputdatatype %s', + outputtracts=dict(argstr='-outputtracts %s', ), - environ=dict(nohash=True, - usedefault=True, + pdf=dict(argstr='-pdf %s', ), - gzip=dict(argstr='-gzip', + seed_file=dict(argstr='-seedfile %s', + position=2, ), - pdf=dict(argstr='-pdf %s', + terminal_output=dict(mandatory=True, + nohash=True, ), - anisthresh=dict(argstr='-anisthresh %f', + voxel_dims=dict(argstr='-voxeldims %s', + units='mm', ), ) inputs = TrackPICo.input_spec() @@ -67,6 +68,7 @@ def test_TrackPICo_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_TrackPICo_outputs(): output_map = dict(tracked=dict(), ) @@ -75,3 +77,4 @@ def test_TrackPICo_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/camino/tests/test_auto_TractShredder.py b/nipype/interfaces/camino/tests/test_auto_TractShredder.py index c75d049c94..a45888ac99 100644 --- a/nipype/interfaces/camino/tests/test_auto_TractShredder.py +++ b/nipype/interfaces/camino/tests/test_auto_TractShredder.py @@ -1,37 +1,38 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.camino.convert import TractShredder + def test_TractShredder_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, - ), - out_file=dict(position=-1, - genfile=True, - argstr='> %s', - ), - space=dict(units='NA', - position=3, - argstr='%d', + input_map = dict(args=dict(argstr='%s', ), - args=dict(argstr='%s', - ), - bunchsize=dict(units='NA', + bunchsize=dict(argstr='%d', position=2, - argstr='%d', - ), - terminal_output=dict(mandatory=True, - nohash=True, + units='NA', ), environ=dict(nohash=True, usedefault=True, ), - in_file=dict(position=-2, + ignore_exception=dict(nohash=True, + usedefault=True, + ), + in_file=dict(argstr='< %s', mandatory=True, - argstr='< %s', + position=-2, ), - offset=dict(units='NA', + offset=dict(argstr='%d', position=1, - argstr='%d', + units='NA', + ), + out_file=dict(argstr='> %s', + genfile=True, + position=-1, + ), + space=dict(argstr='%d', + position=3, + units='NA', + ), + terminal_output=dict(mandatory=True, + nohash=True, ), ) inputs = TractShredder.input_spec() @@ -39,6 +40,7 @@ def test_TractShredder_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_TractShredder_outputs(): output_map = dict(shredded=dict(), ) @@ -47,3 +49,4 @@ def test_TractShredder_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/camino/tests/test_auto_VtkStreamlines.py b/nipype/interfaces/camino/tests/test_auto_VtkStreamlines.py index c8b011f287..cf2db2298e 100644 --- a/nipype/interfaces/camino/tests/test_auto_VtkStreamlines.py +++ b/nipype/interfaces/camino/tests/test_auto_VtkStreamlines.py @@ -1,47 +1,48 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.camino.convert import VtkStreamlines + def test_VtkStreamlines_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, - ), - voxeldims=dict(argstr='-voxeldims %s', - units='mm', - position=4, + input_map = dict(args=dict(argstr='%s', ), colourorient=dict(argstr='-colourorient', ), - out_file=dict(position=-1, - genfile=True, - argstr='> %s', + environ=dict(nohash=True, + usedefault=True, ), - target_file=dict(position=2, - argstr='-targetfile %s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - args=dict(argstr='%s', + in_file=dict(argstr=' < %s', + mandatory=True, + position=-2, ), - interpolate=dict(argstr='-interpolate', + inputmodel=dict(argstr='-inputmodel %s', + usedefault=True, ), - inputmodel=dict(usedefault=True, - argstr='-inputmodel %s', + interpolate=dict(argstr='-interpolate', ), interpolatescalars=dict(argstr='-interpolatescalars', ), - terminal_output=dict(mandatory=True, - nohash=True, + out_file=dict(argstr='> %s', + genfile=True, + position=-1, ), - seed_file=dict(position=1, - argstr='-seedfile %s', + scalar_file=dict(argstr='-scalarfile %s', + position=3, ), - scalar_file=dict(position=3, - argstr='-scalarfile %s', + seed_file=dict(argstr='-seedfile %s', + position=1, ), - environ=dict(nohash=True, - usedefault=True, + target_file=dict(argstr='-targetfile %s', + position=2, ), - in_file=dict(position=-2, - mandatory=True, - argstr=' < %s', + terminal_output=dict(mandatory=True, + nohash=True, + ), + voxeldims=dict(argstr='-voxeldims %s', + position=4, + units='mm', ), ) inputs = VtkStreamlines.input_spec() @@ -49,6 +50,7 @@ def test_VtkStreamlines_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_VtkStreamlines_outputs(): output_map = dict(vtk=dict(), ) @@ -57,3 +59,4 @@ def test_VtkStreamlines_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/camino2trackvis/tests/test_auto_Camino2Trackvis.py b/nipype/interfaces/camino2trackvis/tests/test_auto_Camino2Trackvis.py index ed8c9e8171..6e31714e83 100644 --- a/nipype/interfaces/camino2trackvis/tests/test_auto_Camino2Trackvis.py +++ b/nipype/interfaces/camino2trackvis/tests/test_auto_Camino2Trackvis.py @@ -1,46 +1,47 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.camino2trackvis.convert import Camino2Trackvis + def test_Camino2Trackvis_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, - ), - min_length=dict(units='mm', - position=3, - argstr='-l %d', + input_map = dict(args=dict(argstr='%s', ), - data_dims=dict(mandatory=True, - sep=',', + data_dims=dict(argstr='-d %s', + mandatory=True, position=4, - argstr='-d %s', + sep=',', ), - out_file=dict(position=2, - genfile=True, - argstr='-o %s', + environ=dict(nohash=True, + usedefault=True, ), - args=dict(argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - voxel_order=dict(position=6, + in_file=dict(argstr='-i %s', mandatory=True, - argstr='--voxel-order %s', + position=1, + ), + min_length=dict(argstr='-l %d', + position=3, + units='mm', + ), + nifti_file=dict(argstr='--nifti %s', + position=7, + ), + out_file=dict(argstr='-o %s', + genfile=True, + position=2, ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - in_file=dict(position=1, + voxel_dims=dict(argstr='-x %s', mandatory=True, - argstr='-i %s', - ), - voxel_dims=dict(mandatory=True, - sep=',', position=5, - argstr='-x %s', + sep=',', ), - nifti_file=dict(position=7, - argstr='--nifti %s', + voxel_order=dict(argstr='--voxel-order %s', + mandatory=True, + position=6, ), ) inputs = Camino2Trackvis.input_spec() @@ -48,6 +49,7 @@ def test_Camino2Trackvis_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Camino2Trackvis_outputs(): output_map = dict(trackvis=dict(), ) @@ -56,3 +58,4 @@ def test_Camino2Trackvis_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/camino2trackvis/tests/test_auto_Trackvis2Camino.py b/nipype/interfaces/camino2trackvis/tests/test_auto_Trackvis2Camino.py index 5e081e8fe0..99dd28b123 100644 --- a/nipype/interfaces/camino2trackvis/tests/test_auto_Trackvis2Camino.py +++ b/nipype/interfaces/camino2trackvis/tests/test_auto_Trackvis2Camino.py @@ -1,28 +1,29 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.camino2trackvis.convert import Trackvis2Camino + def test_Trackvis2Camino_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, - ), - out_file=dict(position=2, - genfile=True, - argstr='-o %s', - ), - append_file=dict(position=2, - argstr='-a %s', + input_map = dict(append_file=dict(argstr='-a %s', + position=2, ), args=dict(argstr='%s', ), - terminal_output=dict(mandatory=True, - nohash=True, - ), environ=dict(nohash=True, usedefault=True, ), - in_file=dict(position=1, + ignore_exception=dict(nohash=True, + usedefault=True, + ), + in_file=dict(argstr='-i %s', mandatory=True, - argstr='-i %s', + position=1, + ), + out_file=dict(argstr='-o %s', + genfile=True, + position=2, + ), + terminal_output=dict(mandatory=True, + nohash=True, ), ) inputs = Trackvis2Camino.input_spec() @@ -30,6 +31,7 @@ def test_Trackvis2Camino_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Trackvis2Camino_outputs(): output_map = dict(camino=dict(), ) @@ -38,3 +40,4 @@ def test_Trackvis2Camino_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/cmtk/tests/test_auto_AverageNetworks.py b/nipype/interfaces/cmtk/tests/test_auto_AverageNetworks.py index e92ce7d7c9..9194faa30c 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_AverageNetworks.py +++ b/nipype/interfaces/cmtk/tests/test_auto_AverageNetworks.py @@ -1,30 +1,33 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.cmtk.nx import AverageNetworks + def test_AverageNetworks_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(group_id=dict(usedefault=True, + ), + ignore_exception=dict(nohash=True, usedefault=True, ), - resolution_network_file=dict(), - out_gexf_groupavg=dict(), in_files=dict(mandatory=True, ), + out_gexf_groupavg=dict(), out_gpickled_groupavg=dict(), - group_id=dict(usedefault=True, - ), + resolution_network_file=dict(), ) inputs = AverageNetworks.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_AverageNetworks_outputs(): - output_map = dict(matlab_groupavgs=dict(), - gexf_groupavg=dict(), + output_map = dict(gexf_groupavg=dict(), gpickled_groupavg=dict(), + matlab_groupavgs=dict(), ) outputs = AverageNetworks.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/cmtk/tests/test_auto_CFFConverter.py b/nipype/interfaces/cmtk/tests/test_auto_CFFConverter.py index e411c46a32..e89ac62c60 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_CFFConverter.py +++ b/nipype/interfaces/cmtk/tests/test_auto_CFFConverter.py @@ -1,39 +1,41 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.cmtk.convert import CFFConverter + def test_CFFConverter_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, - ), - publisher=dict(), - gifti_labels=dict(), - timeseries_files=dict(), + input_map = dict(creator=dict(), + data_files=dict(), description=dict(usedefault=True, ), - gpickled_networks=dict(), - creator=dict(), - title=dict(), - tract_files=dict(), - script_files=dict(), - graphml_networks=dict(), email=dict(), - references=dict(), - rights=dict(), + gifti_labels=dict(), gifti_surfaces=dict(), + gpickled_networks=dict(), + graphml_networks=dict(), + ignore_exception=dict(nohash=True, + usedefault=True, + ), license=dict(), - data_files=dict(), nifti_volumes=dict(), - species=dict(usedefault=True, + out_file=dict(usedefault=True, ), + publisher=dict(), + references=dict(), relation=dict(), - out_file=dict(usedefault=True, + rights=dict(), + script_files=dict(), + species=dict(usedefault=True, ), + timeseries_files=dict(), + title=dict(), + tract_files=dict(), ) inputs = CFFConverter.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_CFFConverter_outputs(): output_map = dict(connectome_file=dict(), ) @@ -42,3 +44,4 @@ def test_CFFConverter_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/cmtk/tests/test_auto_CreateMatrix.py b/nipype/interfaces/cmtk/tests/test_auto_CreateMatrix.py index 88c6cb8f4d..4f697009fe 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_CreateMatrix.py +++ b/nipype/interfaces/cmtk/tests/test_auto_CreateMatrix.py @@ -1,28 +1,29 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.cmtk.cmtk import CreateMatrix + def test_CreateMatrix_inputs(): - input_map = dict(resolution_network_file=dict(mandatory=True, + input_map = dict(count_region_intersections=dict(usedefault=True, ), - out_intersection_matrix_mat_file=dict(genfile=True, + out_endpoint_array_name=dict(genfile=True, ), - out_median_fiber_length_matrix_mat_file=dict(genfile=True, + out_fiber_length_std_matrix_mat_file=dict(genfile=True, ), - tract_file=dict(mandatory=True, + out_intersection_matrix_mat_file=dict(genfile=True, ), out_matrix_file=dict(genfile=True, ), out_matrix_mat_file=dict(usedefault=True, ), - count_region_intersections=dict(usedefault=True, + out_mean_fiber_length_matrix_mat_file=dict(genfile=True, ), - out_endpoint_array_name=dict(genfile=True, + out_median_fiber_length_matrix_mat_file=dict(genfile=True, ), - roi_file=dict(mandatory=True, + resolution_network_file=dict(mandatory=True, ), - out_fiber_length_std_matrix_mat_file=dict(genfile=True, + roi_file=dict(mandatory=True, ), - out_mean_fiber_length_matrix_mat_file=dict(genfile=True, + tract_file=dict(mandatory=True, ), ) inputs = CreateMatrix.input_spec() @@ -30,28 +31,30 @@ def test_CreateMatrix_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_CreateMatrix_outputs(): - output_map = dict(matrix_file=dict(), - median_fiber_length_matrix_mat_file=dict(), + output_map = dict(endpoint_file=dict(), + endpoint_file_mm=dict(), + fiber_label_file=dict(), fiber_labels_noorphans=dict(), - matlab_matrix_files=dict(), + fiber_length_file=dict(), + fiber_length_std_matrix_mat_file=dict(), filtered_tractographies=dict(), filtered_tractography=dict(), - fiber_length_std_matrix_mat_file=dict(), - fiber_label_file=dict(), - endpoint_file_mm=dict(), - mean_fiber_length_matrix_mat_file=dict(), - matrix_files=dict(), - intersection_matrix_mat_file=dict(), filtered_tractography_by_intersections=dict(), + intersection_matrix_file=dict(), + intersection_matrix_mat_file=dict(), + matlab_matrix_files=dict(), + matrix_file=dict(), + matrix_files=dict(), matrix_mat_file=dict(), - endpoint_file=dict(), - fiber_length_file=dict(), + mean_fiber_length_matrix_mat_file=dict(), + median_fiber_length_matrix_mat_file=dict(), stats_file=dict(), - intersection_matrix_file=dict(), ) outputs = CreateMatrix.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/cmtk/tests/test_auto_CreateNodes.py b/nipype/interfaces/cmtk/tests/test_auto_CreateNodes.py index 4fe5d9204b..98adc0800b 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_CreateNodes.py +++ b/nipype/interfaces/cmtk/tests/test_auto_CreateNodes.py @@ -1,12 +1,13 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.cmtk.cmtk import CreateNodes + def test_CreateNodes_inputs(): - input_map = dict(out_filename=dict(usedefault=True, - ), - ignore_exception=dict(nohash=True, + input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, ), + out_filename=dict(usedefault=True, + ), resolution_network_file=dict(mandatory=True, ), roi_file=dict(mandatory=True, @@ -17,6 +18,7 @@ def test_CreateNodes_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_CreateNodes_outputs(): output_map = dict(node_network=dict(), ) @@ -25,3 +27,4 @@ def test_CreateNodes_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/cmtk/tests/test_auto_MergeCNetworks.py b/nipype/interfaces/cmtk/tests/test_auto_MergeCNetworks.py index f5ae3d35dc..a00bc45664 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_MergeCNetworks.py +++ b/nipype/interfaces/cmtk/tests/test_auto_MergeCNetworks.py @@ -1,6 +1,7 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.cmtk.convert import MergeCNetworks + def test_MergeCNetworks_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, @@ -15,6 +16,7 @@ def test_MergeCNetworks_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MergeCNetworks_outputs(): output_map = dict(connectome_file=dict(), ) @@ -23,3 +25,4 @@ def test_MergeCNetworks_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/cmtk/tests/test_auto_NetworkBasedStatistic.py b/nipype/interfaces/cmtk/tests/test_auto_NetworkBasedStatistic.py index 22eedb538d..706386d3e8 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_NetworkBasedStatistic.py +++ b/nipype/interfaces/cmtk/tests/test_auto_NetworkBasedStatistic.py @@ -1,38 +1,41 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.cmtk.nbs import NetworkBasedStatistic + def test_NetworkBasedStatistic_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(edge_key=dict(usedefault=True, ), - t_tail=dict(usedefault=True, + ignore_exception=dict(nohash=True, + usedefault=True, ), - edge_key=dict(usedefault=True, + in_group1=dict(mandatory=True, ), in_group2=dict(mandatory=True, ), - out_nbs_network=dict(), + node_position_network=dict(), number_of_permutations=dict(usedefault=True, ), - threshold=dict(usedefault=True, + out_nbs_network=dict(), + out_nbs_pval_network=dict(), + t_tail=dict(usedefault=True, ), - in_group1=dict(mandatory=True, + threshold=dict(usedefault=True, ), - node_position_network=dict(), - out_nbs_pval_network=dict(), ) inputs = NetworkBasedStatistic.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_NetworkBasedStatistic_outputs(): output_map = dict(nbs_network=dict(), - network_files=dict(), nbs_pval_network=dict(), + network_files=dict(), ) outputs = NetworkBasedStatistic.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/cmtk/tests/test_auto_NetworkXMetrics.py b/nipype/interfaces/cmtk/tests/test_auto_NetworkXMetrics.py index ec4fbb076d..19b8b60203 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_NetworkXMetrics.py +++ b/nipype/interfaces/cmtk/tests/test_auto_NetworkXMetrics.py @@ -1,29 +1,30 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.cmtk.nx import NetworkXMetrics + def test_NetworkXMetrics_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(compute_clique_related_measures=dict(usedefault=True, ), - treat_as_weighted_graph=dict(usedefault=True, + ignore_exception=dict(nohash=True, + usedefault=True, ), - out_node_metrics_matlab=dict(genfile=True, + in_file=dict(mandatory=True, ), out_edge_metrics_matlab=dict(genfile=True, ), - out_k_shell=dict(usedefault=True, + out_global_metrics_matlab=dict(genfile=True, ), - compute_clique_related_measures=dict(usedefault=True, + out_k_core=dict(usedefault=True, ), out_k_crust=dict(usedefault=True, ), - out_k_core=dict(usedefault=True, + out_k_shell=dict(usedefault=True, ), - in_file=dict(mandatory=True, + out_node_metrics_matlab=dict(genfile=True, ), out_pickled_extra_measures=dict(usedefault=True, ), - out_global_metrics_matlab=dict(genfile=True, + treat_as_weighted_graph=dict(usedefault=True, ), ) inputs = NetworkXMetrics.input_spec() @@ -31,23 +32,25 @@ def test_NetworkXMetrics_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_NetworkXMetrics_outputs(): - output_map = dict(k_networks=dict(), + output_map = dict(edge_measure_networks=dict(), edge_measures_matlab=dict(), - node_measure_networks=dict(), - pickled_extra_measures=dict(), - matlab_matrix_files=dict(), - k_crust=dict(), - node_measures_matlab=dict(), - gpickled_network_files=dict(), - k_shell=dict(), - edge_measure_networks=dict(), global_measures_matlab=dict(), + gpickled_network_files=dict(), k_core=dict(), + k_crust=dict(), + k_networks=dict(), + k_shell=dict(), matlab_dict_measures=dict(), + matlab_matrix_files=dict(), + node_measure_networks=dict(), + node_measures_matlab=dict(), + pickled_extra_measures=dict(), ) outputs = NetworkXMetrics.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/cmtk/tests/test_auto_Parcellate.py b/nipype/interfaces/cmtk/tests/test_auto_Parcellate.py index 051de231e1..4d3d1a4cbd 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_Parcellate.py +++ b/nipype/interfaces/cmtk/tests/test_auto_Parcellate.py @@ -1,38 +1,41 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.cmtk.parcellation import Parcellate + def test_Parcellate_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, - ), - subject_id=dict(mandatory=True, + input_map = dict(dilation=dict(usedefault=True, ), freesurfer_dir=dict(), - subjects_dir=dict(), - out_roi_file=dict(genfile=True, + ignore_exception=dict(nohash=True, + usedefault=True, ), - dilation=dict(usedefault=True, + out_roi_file=dict(genfile=True, ), parcellation_name=dict(usedefault=True, ), + subject_id=dict(mandatory=True, + ), + subjects_dir=dict(), ) inputs = Parcellate.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Parcellate_outputs(): output_map = dict(aseg_file=dict(), - ribbon_file=dict(), - roiv_file=dict(), - roi_file_in_structural_space=dict(), - white_matter_mask_file=dict(), cc_unknown_file=dict(), dilated_roi_file_in_structural_space=dict(), + ribbon_file=dict(), roi_file=dict(), + roi_file_in_structural_space=dict(), + roiv_file=dict(), + white_matter_mask_file=dict(), ) outputs = Parcellate.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/cmtk/tests/test_auto_ROIGen.py b/nipype/interfaces/cmtk/tests/test_auto_ROIGen.py index a84bd551d6..5651bd99f2 100644 --- a/nipype/interfaces/cmtk/tests/test_auto_ROIGen.py +++ b/nipype/interfaces/cmtk/tests/test_auto_ROIGen.py @@ -1,28 +1,30 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.cmtk.cmtk import ROIGen + def test_ROIGen_inputs(): input_map = dict(LUT_file=dict(xor=['use_freesurfer_LUT'], ), + aparc_aseg_file=dict(mandatory=True, + ), + freesurfer_dir=dict(requires=['use_freesurfer_LUT'], + ), ignore_exception=dict(nohash=True, usedefault=True, ), out_dict_file=dict(genfile=True, ), - use_freesurfer_LUT=dict(xor=['LUT_file'], - ), - freesurfer_dir=dict(requires=['use_freesurfer_LUT'], - ), - aparc_aseg_file=dict(mandatory=True, - ), out_roi_file=dict(genfile=True, ), + use_freesurfer_LUT=dict(xor=['LUT_file'], + ), ) inputs = ROIGen.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ROIGen_outputs(): output_map = dict(dict_file=dict(), roi_file=dict(), @@ -32,3 +34,4 @@ def test_ROIGen_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTIRecon.py b/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTIRecon.py index c3abad7b72..d8de600172 100644 --- a/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTIRecon.py +++ b/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTIRecon.py @@ -1,41 +1,42 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.diffusion_toolkit.dti import DTIRecon + def test_DTIRecon_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, - ), - bvecs=dict(mandatory=True, - argstr='-gm %s', + input_map = dict(DWI=dict(argstr='%s', + mandatory=True, + position=1, ), args=dict(argstr='%s', ), - oblique_correction=dict(argstr='-oc', + b0_threshold=dict(argstr='-b0_th', ), bvals=dict(mandatory=True, ), - out_prefix=dict(position=2, - usedefault=True, - argstr='%s', - ), - DWI=dict(position=1, + bvecs=dict(argstr='-gm %s', mandatory=True, - argstr='%s', - ), - terminal_output=dict(mandatory=True, - nohash=True, ), environ=dict(nohash=True, usedefault=True, ), - image_orientation_vectors=dict(argstr='-iop %f', + ignore_exception=dict(nohash=True, + usedefault=True, ), - output_type=dict(usedefault=True, - argstr='-ot %s', + image_orientation_vectors=dict(argstr='-iop %f', ), n_averages=dict(argstr='-nex %s', ), - b0_threshold=dict(argstr='-b0_th', + oblique_correction=dict(argstr='-oc', + ), + out_prefix=dict(argstr='%s', + position=2, + usedefault=True, + ), + output_type=dict(argstr='-ot %s', + usedefault=True, + ), + terminal_output=dict(mandatory=True, + nohash=True, ), ) inputs = DTIRecon.input_spec() @@ -43,22 +44,24 @@ def test_DTIRecon_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_DTIRecon_outputs(): - output_map = dict(tensor=dict(), + output_map = dict(ADC=dict(), + B0=dict(), FA=dict(), FA_color=dict(), + L1=dict(), + L2=dict(), + L3=dict(), V1=dict(), V2=dict(), V3=dict(), - L2=dict(), - L3=dict(), exp=dict(), - L1=dict(), - B0=dict(), - ADC=dict(), + tensor=dict(), ) outputs = DTIRecon.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTITracker.py b/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTITracker.py index a910a8a9ee..dc1d9db5b4 100644 --- a/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTITracker.py +++ b/nipype/interfaces/diffusion_toolkit/tests/test_auto_DTITracker.py @@ -1,65 +1,66 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.diffusion_toolkit.dti import DTITracker + def test_DTITracker_inputs(): - input_map = dict(mask2_threshold=dict(position=5, + input_map = dict(angle_threshold=dict(argstr='-at %f', + ), + angle_threshold_weight=dict(argstr='-atw %f', + ), + args=dict(argstr='%s', + ), + environ=dict(nohash=True, + usedefault=True, ), - input_data_prefix=dict(position=0, + ignore_exception=dict(nohash=True, usedefault=True, - argstr='%s', ), - mask2_file=dict(position=4, - argstr='-m2 %s', + input_data_prefix=dict(argstr='%s', + position=0, + usedefault=True, ), - invert_y=dict(argstr='-iy', + input_type=dict(argstr='-it %s', ), invert_x=dict(argstr='-ix', ), + invert_y=dict(argstr='-iy', + ), invert_z=dict(argstr='-iz', ), - tensor_file=dict(), - input_type=dict(argstr='-it %s', + mask1_file=dict(argstr='-m %s', + mandatory=True, + position=2, ), mask1_threshold=dict(position=3, ), - output_file=dict(position=1, - usedefault=True, - argstr='%s', + mask2_file=dict(argstr='-m2 %s', + position=4, ), - tracking_method=dict(argstr='-%s', + mask2_threshold=dict(position=5, ), - step_length=dict(argstr='-l %f', + output_file=dict(argstr='%s', + position=1, + usedefault=True, ), output_mask=dict(argstr='-om %s', ), primary_vector=dict(argstr='-%s', ), - ignore_exception=dict(nohash=True, - usedefault=True, - ), random_seed=dict(argstr='-rseed', ), - args=dict(argstr='%s', - ), - angle_threshold_weight=dict(argstr='-atw %f', - ), - terminal_output=dict(mandatory=True, - nohash=True, + step_length=dict(argstr='-l %f', ), - mask1_file=dict(position=2, - mandatory=True, - argstr='-m %s', + swap_xy=dict(argstr='-sxy', ), - angle_threshold=dict(argstr='-at %f', + swap_yz=dict(argstr='-syz', ), swap_zx=dict(argstr='-szx', ), - swap_xy=dict(argstr='-sxy', - ), - environ=dict(nohash=True, - usedefault=True, + tensor_file=dict(), + terminal_output=dict(mandatory=True, + nohash=True, ), - swap_yz=dict(argstr='-syz', + tracking_method=dict(argstr='-%s', ), ) inputs = DTITracker.input_spec() @@ -67,12 +68,14 @@ def test_DTITracker_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_DTITracker_outputs(): - output_map = dict(track_file=dict(), - mask_file=dict(), + output_map = dict(mask_file=dict(), + track_file=dict(), ) outputs = DTITracker.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/diffusion_toolkit/tests/test_auto_HARDIMat.py b/nipype/interfaces/diffusion_toolkit/tests/test_auto_HARDIMat.py index 45e3777280..ef71d23b97 100644 --- a/nipype/interfaces/diffusion_toolkit/tests/test_auto_HARDIMat.py +++ b/nipype/interfaces/diffusion_toolkit/tests/test_auto_HARDIMat.py @@ -1,46 +1,48 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.diffusion_toolkit.odf import HARDIMat + def test_HARDIMat_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(args=dict(argstr='%s', + ), + bvals=dict(mandatory=True, ), - bvecs=dict(position=1, + bvecs=dict(argstr='%s', mandatory=True, - argstr='%s', + position=1, ), - bvals=dict(mandatory=True, + environ=dict(nohash=True, + usedefault=True, ), - out_file=dict(position=2, + ignore_exception=dict(nohash=True, usedefault=True, - argstr='%s', ), - oblique_correction=dict(argstr='-oc', + image_info=dict(argstr='-info %s', ), - args=dict(argstr='%s', + image_orientation_vectors=dict(argstr='-iop %f', ), - image_info=dict(argstr='-info %s', + oblique_correction=dict(argstr='-oc', ), odf_file=dict(argstr='-odf %s', ), - terminal_output=dict(mandatory=True, - nohash=True, + order=dict(argstr='-order %s', ), - environ=dict(nohash=True, + out_file=dict(argstr='%s', + position=2, usedefault=True, ), - image_orientation_vectors=dict(argstr='-iop %f', - ), - order=dict(argstr='-order %s', - ), reference_file=dict(argstr='-ref %s', ), + terminal_output=dict(mandatory=True, + nohash=True, + ), ) inputs = HARDIMat.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_HARDIMat_outputs(): output_map = dict(out_file=dict(), ) @@ -49,3 +51,4 @@ def test_HARDIMat_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFRecon.py b/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFRecon.py index 542987cd21..9c855a4bc1 100644 --- a/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFRecon.py +++ b/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFRecon.py @@ -1,56 +1,57 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.diffusion_toolkit.odf import ODFRecon + def test_ODFRecon_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(DWI=dict(argstr='%s', + mandatory=True, + position=1, + ), + args=dict(argstr='%s', + ), + dsi=dict(argstr='-dsi', + ), + environ=dict(nohash=True, usedefault=True, ), filter=dict(argstr='-f', ), - dsi=dict(argstr='-dsi', + ignore_exception=dict(nohash=True, + usedefault=True, ), - n_b0=dict(mandatory=True, - argstr='-b0 %s', + image_orientation_vectors=dict(argstr='-iop %f', ), - matrix=dict(mandatory=True, - argstr='-mat %s', + matrix=dict(argstr='-mat %s', + mandatory=True, ), - n_output_directions=dict(position=3, + n_b0=dict(argstr='-b0 %s', mandatory=True, - argstr='%s', ), - oblique_correction=dict(argstr='-oc', + n_directions=dict(argstr='%s', + mandatory=True, + position=2, ), - args=dict(argstr='%s', + n_output_directions=dict(argstr='%s', + mandatory=True, + position=3, ), - sharpness=dict(argstr='-s %f', + oblique_correction=dict(argstr='-oc', ), - out_prefix=dict(position=4, + out_prefix=dict(argstr='%s', + position=4, usedefault=True, - argstr='%s', - ), - subtract_background=dict(argstr='-bg', ), output_entropy=dict(argstr='-oe', ), - terminal_output=dict(mandatory=True, - nohash=True, - ), - environ=dict(nohash=True, + output_type=dict(argstr='-ot %s', usedefault=True, ), - n_directions=dict(position=2, - mandatory=True, - argstr='%s', - ), - image_orientation_vectors=dict(argstr='-iop %f', + sharpness=dict(argstr='-s %f', ), - output_type=dict(usedefault=True, - argstr='-ot %s', + subtract_background=dict(argstr='-bg', ), - DWI=dict(position=1, - mandatory=True, - argstr='%s', + terminal_output=dict(mandatory=True, + nohash=True, ), ) inputs = ODFRecon.input_spec() @@ -58,15 +59,17 @@ def test_ODFRecon_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ODFRecon_outputs(): - output_map = dict(max=dict(), + output_map = dict(B0=dict(), DWI=dict(), - B0=dict(), ODF=dict(), entropy=dict(), + max=dict(), ) outputs = ODFRecon.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFTracker.py b/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFTracker.py index b57e42ab0f..a7d383002d 100644 --- a/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFTracker.py +++ b/nipype/interfaces/diffusion_toolkit/tests/test_auto_ODFTracker.py @@ -1,75 +1,76 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.diffusion_toolkit.odf import ODFTracker + def test_ODFTracker_inputs(): - input_map = dict(mask2_threshold=dict(position=5, - ), - input_data_prefix=dict(position=0, - usedefault=True, - argstr='%s', - ), - disc=dict(argstr='-disc', - ), - mask2_file=dict(position=4, - argstr='-m2 %s', - ), - slice_order=dict(argstr='-sorder %d', + input_map = dict(ODF=dict(mandatory=True, ), - invert_y=dict(argstr='-iy', - ), - invert_x=dict(argstr='-ix', - ), - invert_z=dict(argstr='-iz', + angle_threshold=dict(argstr='-at %f', ), - swap_yz=dict(argstr='-syz', + args=dict(argstr='%s', ), - step_length=dict(argstr='-l %f', + disc=dict(argstr='-disc', ), dsi=dict(argstr='-dsi', ), environ=dict(nohash=True, usedefault=True, ), - ODF=dict(mandatory=True, - ), ignore_exception=dict(nohash=True, usedefault=True, ), - random_seed=dict(argstr='-rseed %s', + image_orientation_vectors=dict(argstr='-iop %f', ), - max=dict(mandatory=True, + input_data_prefix=dict(argstr='%s', + position=0, + usedefault=True, ), - args=dict(argstr='%s', + input_output_type=dict(argstr='-it %s', + usedefault=True, ), - voxel_order=dict(argstr='-vorder %s', + invert_x=dict(argstr='-ix', ), - terminal_output=dict(mandatory=True, - nohash=True, + invert_y=dict(argstr='-iy', + ), + invert_z=dict(argstr='-iz', + ), + limit=dict(argstr='-limit %d', ), - mask1_file=dict(position=2, + mask1_file=dict(argstr='-m %s', mandatory=True, - argstr='-m %s', + position=2, ), - image_orientation_vectors=dict(argstr='-iop %f', + mask1_threshold=dict(position=3, + ), + mask2_file=dict(argstr='-m2 %s', + position=4, ), - out_file=dict(position=1, + mask2_threshold=dict(position=5, + ), + max=dict(mandatory=True, + ), + out_file=dict(argstr='%s', + position=1, usedefault=True, - argstr='%s', ), - angle_threshold=dict(argstr='-at %f', + random_seed=dict(argstr='-rseed %s', ), - swap_zx=dict(argstr='-szx', + runge_kutta2=dict(argstr='-rk2', + ), + slice_order=dict(argstr='-sorder %d', + ), + step_length=dict(argstr='-l %f', ), swap_xy=dict(argstr='-sxy', ), - input_output_type=dict(usedefault=True, - argstr='-it %s', + swap_yz=dict(argstr='-syz', ), - runge_kutta2=dict(argstr='-rk2', + swap_zx=dict(argstr='-szx', ), - limit=dict(argstr='-limit %d', + terminal_output=dict(mandatory=True, + nohash=True, ), - mask1_threshold=dict(position=3, + voxel_order=dict(argstr='-vorder %s', ), ) inputs = ODFTracker.input_spec() @@ -77,6 +78,7 @@ def test_ODFTracker_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ODFTracker_outputs(): output_map = dict(track_file=dict(), ) @@ -85,3 +87,4 @@ def test_ODFTracker_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/diffusion_toolkit/tests/test_auto_SplineFilter.py b/nipype/interfaces/diffusion_toolkit/tests/test_auto_SplineFilter.py index 27cd4e10de..89761eafad 100644 --- a/nipype/interfaces/diffusion_toolkit/tests/test_auto_SplineFilter.py +++ b/nipype/interfaces/diffusion_toolkit/tests/test_auto_SplineFilter.py @@ -1,29 +1,30 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.diffusion_toolkit.postproc import SplineFilter + def test_SplineFilter_inputs(): - input_map = dict(track_file=dict(position=0, - mandatory=True, - argstr='%s', + input_map = dict(args=dict(argstr='%s', + ), + environ=dict(nohash=True, + usedefault=True, ), ignore_exception=dict(nohash=True, usedefault=True, ), - output_file=dict(position=2, + output_file=dict(argstr='%s', + position=2, usedefault=True, - argstr='%s', ), - args=dict(argstr='%s', + step_length=dict(argstr='%f', + mandatory=True, + position=1, ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - step_length=dict(position=1, + track_file=dict(argstr='%s', mandatory=True, - argstr='%f', + position=0, ), ) inputs = SplineFilter.input_spec() @@ -31,6 +32,7 @@ def test_SplineFilter_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_SplineFilter_outputs(): output_map = dict(smoothed_track_file=dict(), ) @@ -39,3 +41,4 @@ def test_SplineFilter_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/dipy/tests/test_auto_TensorMode.py b/nipype/interfaces/dipy/tests/test_auto_TensorMode.py index 4c5898fe48..d20e0eded9 100644 --- a/nipype/interfaces/dipy/tests/test_auto_TensorMode.py +++ b/nipype/interfaces/dipy/tests/test_auto_TensorMode.py @@ -1,21 +1,23 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.dipy.tensors import TensorMode + def test_TensorMode_inputs(): - input_map = dict(out_filename=dict(genfile=True, + input_map = dict(bvals=dict(mandatory=True, ), bvecs=dict(mandatory=True, ), - bvals=dict(mandatory=True, - ), in_file=dict(mandatory=True, ), + out_filename=dict(genfile=True, + ), ) inputs = TensorMode.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_TensorMode_outputs(): output_map = dict(out_file=dict(), ) @@ -24,3 +26,4 @@ def test_TensorMode_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/dipy/tests/test_auto_TrackDensityMap.py b/nipype/interfaces/dipy/tests/test_auto_TrackDensityMap.py index 14a502365d..763929ca5d 100644 --- a/nipype/interfaces/dipy/tests/test_auto_TrackDensityMap.py +++ b/nipype/interfaces/dipy/tests/test_auto_TrackDensityMap.py @@ -1,19 +1,21 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.dipy.tracks import TrackDensityMap + def test_TrackDensityMap_inputs(): - input_map = dict(out_filename=dict(usedefault=True, - ), - data_dims=dict(), - voxel_dims=dict(), + input_map = dict(data_dims=dict(), in_file=dict(mandatory=True, ), + out_filename=dict(usedefault=True, + ), + voxel_dims=dict(), ) inputs = TrackDensityMap.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_TrackDensityMap_outputs(): output_map = dict(out_file=dict(), ) @@ -22,3 +24,4 @@ def test_TrackDensityMap_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ApplyMask.py b/nipype/interfaces/freesurfer/tests/test_auto_ApplyMask.py index f5bb24c98a..a2a1c4fa49 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ApplyMask.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ApplyMask.py @@ -1,49 +1,51 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.freesurfer.utils import ApplyMask + def test_ApplyMask_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + environ=dict(nohash=True, usedefault=True, ), - xfm_file=dict(argstr='-xform %s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - use_abs=dict(argstr='-abs', + in_file=dict(argstr='%s', + mandatory=True, + position=-3, ), - out_file=dict(position=-1, - genfile=True, - argstr='%s', + invert_xfm=dict(argstr='-invert', ), - args=dict(argstr='%s', + mask_file=dict(argstr='%s', + mandatory=True, + position=-2, ), - xfm_target=dict(argstr='-lta_dst %s', + mask_thresh=dict(argstr='-T %.4f', ), - invert_xfm=dict(argstr='-invert', + out_file=dict(argstr='%s', + genfile=True, + position=-1, ), + subjects_dir=dict(), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - in_file=dict(position=-3, - mandatory=True, - argstr='%s', - ), - mask_thresh=dict(argstr='-T %.4f', + use_abs=dict(argstr='-abs', ), - subjects_dir=dict(), - mask_file=dict(position=-2, - mandatory=True, - argstr='%s', + xfm_file=dict(argstr='-xform %s', ), xfm_source=dict(argstr='-lta_src %s', ), + xfm_target=dict(argstr='-lta_dst %s', + ), ) inputs = ApplyMask.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ApplyMask_outputs(): output_map = dict(out_file=dict(), ) @@ -52,3 +54,4 @@ def test_ApplyMask_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ApplyVolTransform.py b/nipype/interfaces/freesurfer/tests/test_auto_ApplyVolTransform.py index 10a2baad32..b77a4c9a65 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ApplyVolTransform.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ApplyVolTransform.py @@ -1,74 +1,75 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.freesurfer.preprocess import ApplyVolTransform + def test_ApplyVolTransform_inputs(): - input_map = dict(no_ded_m3z_path=dict(requires=['m3z_file'], - argstr='--noDefM3zPath', - ), - reg_file=dict(xor=('reg_file', 'fsl_reg_file', 'xfm_reg_file', 'reg_header', 'subject'), - mandatory=True, - argstr='--reg %s', - ), - interp=dict(argstr='--interp %s', + input_map = dict(args=dict(argstr='%s', ), - source_file=dict(copyfile=False, - mandatory=True, - argstr='--mov %s', + environ=dict(nohash=True, + usedefault=True, ), - fs_target=dict(xor=('target_file', 'tal', 'fs_target'), + fs_target=dict(argstr='--fstarg', mandatory=True, requires=['reg_file'], - argstr='--fstarg', + xor=('target_file', 'tal', 'fs_target'), ), - tal=dict(xor=('target_file', 'tal', 'fs_target'), + fsl_reg_file=dict(argstr='--fsl %s', mandatory=True, - argstr='--tal', + xor=('reg_file', 'fsl_reg_file', 'xfm_reg_file', 'reg_header', 'subject'), ), - no_resample=dict(argstr='--no-resample', + ignore_exception=dict(nohash=True, + usedefault=True, ), - subject=dict(xor=('reg_file', 'fsl_reg_file', 'xfm_reg_file', 'reg_header', 'subject'), - mandatory=True, - argstr='--s %s', + interp=dict(argstr='--interp %s', ), inverse=dict(argstr='--inv', ), - invert_morph=dict(requires=['m3z_file'], - argstr='--inv-morph', + invert_morph=dict(argstr='--inv-morph', + requires=['m3z_file'], ), - reg_header=dict(xor=('reg_file', 'fsl_reg_file', 'xfm_reg_file', 'reg_header', 'subject'), - mandatory=True, - argstr='--regheader', + m3z_file=dict(argstr='--m3z %s', ), - xfm_reg_file=dict(xor=('reg_file', 'fsl_reg_file', 'xfm_reg_file', 'reg_header', 'subject'), - mandatory=True, - argstr='--xfm %s', + no_ded_m3z_path=dict(argstr='--noDefM3zPath', + requires=['m3z_file'], ), - m3z_file=dict(argstr='--m3z %s', + no_resample=dict(argstr='--no-resample', ), - ignore_exception=dict(nohash=True, - usedefault=True, + reg_file=dict(argstr='--reg %s', + mandatory=True, + xor=('reg_file', 'fsl_reg_file', 'xfm_reg_file', 'reg_header', 'subject'), ), - args=dict(argstr='%s', + reg_header=dict(argstr='--regheader', + mandatory=True, + xor=('reg_file', 'fsl_reg_file', 'xfm_reg_file', 'reg_header', 'subject'), ), - terminal_output=dict(mandatory=True, - nohash=True, + source_file=dict(argstr='--mov %s', + copyfile=False, + mandatory=True, + ), + subject=dict(argstr='--s %s', + mandatory=True, + xor=('reg_file', 'fsl_reg_file', 'xfm_reg_file', 'reg_header', 'subject'), ), subjects_dir=dict(), - fsl_reg_file=dict(xor=('reg_file', 'fsl_reg_file', 'xfm_reg_file', 'reg_header', 'subject'), + tal=dict(argstr='--tal', mandatory=True, - argstr='--fsl %s', + xor=('target_file', 'tal', 'fs_target'), + ), + tal_resolution=dict(argstr='--talres %.10f', ), - target_file=dict(xor=('target_file', 'tal', 'fs_target'), + target_file=dict(argstr='--targ %s', mandatory=True, - argstr='--targ %s', + xor=('target_file', 'tal', 'fs_target'), ), - transformed_file=dict(genfile=True, - argstr='--o %s', + terminal_output=dict(mandatory=True, + nohash=True, ), - environ=dict(nohash=True, - usedefault=True, + transformed_file=dict(argstr='--o %s', + genfile=True, ), - tal_resolution=dict(argstr='--talres %.10f', + xfm_reg_file=dict(argstr='--xfm %s', + mandatory=True, + xor=('reg_file', 'fsl_reg_file', 'xfm_reg_file', 'reg_header', 'subject'), ), ) inputs = ApplyVolTransform.input_spec() @@ -76,6 +77,7 @@ def test_ApplyVolTransform_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ApplyVolTransform_outputs(): output_map = dict(transformed_file=dict(), ) @@ -84,3 +86,4 @@ def test_ApplyVolTransform_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/freesurfer/tests/test_auto_BBRegister.py b/nipype/interfaces/freesurfer/tests/test_auto_BBRegister.py index e17d008d2e..d05874fba1 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_BBRegister.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_BBRegister.py @@ -1,69 +1,72 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.freesurfer.preprocess import BBRegister + def test_BBRegister_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(args=dict(argstr='%s', ), - init_reg_file=dict(xor=['init'], + contrast_type=dict(argstr='--%s', mandatory=True, ), - reg_frame=dict(xor=['reg_middle_frame'], - argstr='--frame %d', + environ=dict(nohash=True, + usedefault=True, ), - registered_file=dict(argstr='--o %s', + epi_mask=dict(argstr='--epi-mask', ), - out_fsl_file=dict(argstr='--fslmat %s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - contrast_type=dict(mandatory=True, - argstr='--%s', + init=dict(argstr='--init-%s', + mandatory=True, + xor=['init_reg_file'], + ), + init_reg_file=dict(mandatory=True, + xor=['init'], ), - subject_id=dict(mandatory=True, - argstr='--s %s', + intermediate_file=dict(argstr='--int %s', ), - args=dict(argstr='%s', + out_fsl_file=dict(argstr='--fslmat %s', ), out_reg_file=dict(argstr='--reg %s', genfile=True, ), - intermediate_file=dict(argstr='--int %s', - ), - init=dict(xor=['init_reg_file'], - mandatory=True, - argstr='--init-%s', + reg_frame=dict(argstr='--frame %d', + xor=['reg_middle_frame'], ), - source_file=dict(copyfile=False, - mandatory=True, - argstr='--mov %s', + reg_middle_frame=dict(argstr='--mid-frame', + xor=['reg_frame'], ), - reg_middle_frame=dict(xor=['reg_frame'], - argstr='--mid-frame', + registered_file=dict(argstr='--o %s', ), - subjects_dir=dict(), - environ=dict(nohash=True, - usedefault=True, + source_file=dict(argstr='--mov %s', + copyfile=False, + mandatory=True, ), spm_nifti=dict(argstr='--spm-nii', ), + subject_id=dict(argstr='--s %s', + mandatory=True, + ), + subjects_dir=dict(), terminal_output=dict(mandatory=True, nohash=True, ), - epi_mask=dict(argstr='--epi-mask', - ), ) inputs = BBRegister.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_BBRegister_outputs(): - output_map = dict(out_reg_file=dict(), - min_cost_file=dict(), - registered_file=dict(), + output_map = dict(min_cost_file=dict(), out_fsl_file=dict(), + out_reg_file=dict(), + registered_file=dict(), ) outputs = BBRegister.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Binarize.py b/nipype/interfaces/freesurfer/tests/test_auto_Binarize.py index 2892386e18..59d814e481 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Binarize.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Binarize.py @@ -1,76 +1,77 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.freesurfer.model import Binarize + def test_Binarize_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(abs=dict(argstr='--abs', ), - binary_file=dict(argstr='--o %s', - genfile=True, + args=dict(argstr='%s', ), - count_file=dict(argstr='--count %s', + bin_col_num=dict(argstr='--bincol', ), - frame_no=dict(argstr='--frame %s', + bin_val=dict(argstr='--binval %d', ), bin_val_not=dict(argstr='--binvalnot %d', ), - zero_edges=dict(argstr='--zero-edges', + binary_file=dict(argstr='--o %s', + genfile=True, ), - bin_val=dict(argstr='--binval %d', + count_file=dict(argstr='--count %s', ), - rmin=dict(argstr='--rmin %f', + dilate=dict(argstr='--dilate %d', ), - min=dict(xor=['wm_ven_csf'], - argstr='--min %f', + environ=dict(nohash=True, + usedefault=True, ), - invert=dict(argstr='--inv', + erode=dict(argstr='--erode %d', ), erode2d=dict(argstr='--erode2d %d', ), - abs=dict(argstr='--abs', + frame_no=dict(argstr='--frame %s', + ), + ignore_exception=dict(nohash=True, + usedefault=True, ), - in_file=dict(copyfile=False, + in_file=dict(argstr='--i %s', + copyfile=False, mandatory=True, - argstr='--i %s', ), - match=dict(argstr='--match %d...', + invert=dict(argstr='--inv', ), - zero_slice_edge=dict(argstr='--zero-slice-edges', + mask_file=dict(argstr='--mask maskvol', ), - out_type=dict(argstr='', + mask_thresh=dict(argstr='--mask-thresh %f', ), - erode=dict(argstr='--erode %d', + match=dict(argstr='--match %d...', ), - max=dict(xor=['wm_ven_csf'], - argstr='--max %f', + max=dict(argstr='--max %f', + xor=['wm_ven_csf'], ), - wm=dict(argstr='--wm', + merge_file=dict(argstr='--merge %s', ), - args=dict(argstr='%s', + min=dict(argstr='--min %f', + xor=['wm_ven_csf'], + ), + out_type=dict(argstr='', ), rmax=dict(argstr='--rmax %f', ), + rmin=dict(argstr='--rmin %f', + ), + subjects_dir=dict(), terminal_output=dict(mandatory=True, nohash=True, ), - wm_ven_csf=dict(xor=['min', 'max'], - argstr='--wm+vcsf', - ), - subjects_dir=dict(), ventricles=dict(argstr='--ventricles', ), - bin_col_num=dict(argstr='--bincol', - ), - dilate=dict(argstr='--dilate %d', - ), - merge_file=dict(argstr='--merge %s', + wm=dict(argstr='--wm', ), - environ=dict(nohash=True, - usedefault=True, + wm_ven_csf=dict(argstr='--wm+vcsf', + xor=['min', 'max'], ), - mask_thresh=dict(argstr='--mask-thresh %f', + zero_edges=dict(argstr='--zero-edges', ), - mask_file=dict(argstr='--mask maskvol', + zero_slice_edge=dict(argstr='--zero-slice-edges', ), ) inputs = Binarize.input_spec() @@ -78,12 +79,14 @@ def test_Binarize_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Binarize_outputs(): - output_map = dict(count_file=dict(), - binary_file=dict(), + output_map = dict(binary_file=dict(), + count_file=dict(), ) outputs = Binarize.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Concatenate.py b/nipype/interfaces/freesurfer/tests/test_auto_Concatenate.py index c1d078efc8..e7781ca7bb 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Concatenate.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Concatenate.py @@ -1,54 +1,55 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.freesurfer.model import Concatenate + def test_Concatenate_inputs(): - input_map = dict(sort=dict(argstr='--sort', + input_map = dict(add_val=dict(argstr='--add %f', ), - sign=dict(argstr='--%s', + args=dict(argstr='%s', ), - vote=dict(argstr='--vote', + combine=dict(argstr='--combine', ), - gmean=dict(argstr='--gmean %d', + concatenated_file=dict(argstr='--o %s', + genfile=True, ), - mean_div_n=dict(argstr='--mean-div-n', + environ=dict(nohash=True, + usedefault=True, ), - stats=dict(argstr='--%s', + gmean=dict(argstr='--gmean %d', ), - concatenated_file=dict(genfile=True, - argstr='--o %s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - combine=dict(argstr='--combine', + in_files=dict(argstr='--i %s...', + mandatory=True, ), - environ=dict(nohash=True, - usedefault=True, + keep_dtype=dict(argstr='--keep-datatype', ), - paired_stats=dict(argstr='--paired-%s', + mask_file=dict(argstr='--mask %s', ), - multiply_by=dict(argstr='--mul %f', + max_bonfcor=dict(argstr='--max-bonfcor', ), - ignore_exception=dict(nohash=True, - usedefault=True, + max_index=dict(argstr='--max-index', ), - args=dict(argstr='%s', + mean_div_n=dict(argstr='--mean-div-n', ), - terminal_output=dict(mandatory=True, - nohash=True, + multiply_by=dict(argstr='--mul %f', ), - subjects_dir=dict(), multiply_matrix_file=dict(argstr='--mtx %s', ), - in_files=dict(mandatory=True, - argstr='--i %s...', + paired_stats=dict(argstr='--paired-%s', ), - add_val=dict(argstr='--add %f', + sign=dict(argstr='--%s', ), - max_bonfcor=dict(argstr='--max-bonfcor', + sort=dict(argstr='--sort', ), - keep_dtype=dict(argstr='--keep-datatype', + stats=dict(argstr='--%s', ), - mask_file=dict(argstr='--mask %s', + subjects_dir=dict(), + terminal_output=dict(mandatory=True, + nohash=True, ), - max_index=dict(argstr='--max-index', + vote=dict(argstr='--vote', ), ) inputs = Concatenate.input_spec() @@ -56,6 +57,7 @@ def test_Concatenate_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Concatenate_outputs(): output_map = dict(concatenated_file=dict(), ) @@ -64,3 +66,4 @@ def test_Concatenate_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/freesurfer/tests/test_auto_DICOMConvert.py b/nipype/interfaces/freesurfer/tests/test_auto_DICOMConvert.py index 20de953757..e3a3421031 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_DICOMConvert.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_DICOMConvert.py @@ -1,37 +1,39 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.freesurfer.preprocess import DICOMConvert + def test_DICOMConvert_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + base_output_dir=dict(mandatory=True, + ), + dicom_dir=dict(mandatory=True, + ), + dicom_info=dict(), + environ=dict(nohash=True, usedefault=True, ), - args=dict(argstr='%s', + file_mapping=dict(), + ignore_exception=dict(nohash=True, + usedefault=True, ), ignore_single_slice=dict(requires=['dicom_info'], ), - base_output_dir=dict(mandatory=True, - ), out_type=dict(usedefault=True, ), seq_list=dict(requires=['dicom_info'], ), - terminal_output=dict(mandatory=True, - nohash=True, - ), - environ=dict(nohash=True, - usedefault=True, - ), - subjects_dir=dict(), - dicom_dir=dict(mandatory=True, - ), subject_dir_template=dict(usedefault=True, ), - file_mapping=dict(), subject_id=dict(), - dicom_info=dict(), + subjects_dir=dict(), + terminal_output=dict(mandatory=True, + nohash=True, + ), ) inputs = DICOMConvert.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ExtractMainComponent.py b/nipype/interfaces/freesurfer/tests/test_auto_ExtractMainComponent.py index 8faa19eef5..3fa114358c 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ExtractMainComponent.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ExtractMainComponent.py @@ -1,33 +1,35 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.freesurfer.utils import ExtractMainComponent + def test_ExtractMainComponent_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + environ=dict(nohash=True, + usedefault=True, + ), + ignore_exception=dict(nohash=True, usedefault=True, ), - out_file=dict(name_source='in_file', + in_file=dict(argstr='%s', + mandatory=True, + position=1, + ), + out_file=dict(argstr='%s', + name_source='in_file', name_template='%s.maincmp', position=2, - argstr='%s', - ), - args=dict(argstr='%s', ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - in_file=dict(position=1, - mandatory=True, - argstr='%s', - ), ) inputs = ExtractMainComponent.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ExtractMainComponent_outputs(): output_map = dict(out_file=dict(), ) @@ -36,3 +38,4 @@ def test_ExtractMainComponent_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/freesurfer/tests/test_auto_FSCommand.py b/nipype/interfaces/freesurfer/tests/test_auto_FSCommand.py index 1217063bf9..facdcf3c75 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_FSCommand.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_FSCommand.py @@ -1,22 +1,24 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.freesurfer.base import FSCommand + def test_FSCommand_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, - ), - terminal_output=dict(mandatory=True, - nohash=True, + input_map = dict(args=dict(argstr='%s', ), environ=dict(nohash=True, usedefault=True, ), - args=dict(argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, ), subjects_dir=dict(), + terminal_output=dict(mandatory=True, + nohash=True, + ), ) inputs = FSCommand.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/freesurfer/tests/test_auto_FitMSParams.py b/nipype/interfaces/freesurfer/tests/test_auto_FitMSParams.py index 9eb5bf794d..3a26b51be6 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_FitMSParams.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_FitMSParams.py @@ -1,44 +1,47 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.freesurfer.preprocess import FitMSParams + def test_FitMSParams_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + environ=dict(nohash=True, usedefault=True, ), flip_list=dict(), - out_dir=dict(position=-1, - genfile=True, - argstr='%s', - ), - args=dict(argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, ), in_files=dict(argstr='%s', mandatory=True, position=-2, ), + out_dir=dict(argstr='%s', + genfile=True, + position=-1, + ), + subjects_dir=dict(), + te_list=dict(), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - xfm_list=dict(), - subjects_dir=dict(), tr_list=dict(), - te_list=dict(), + xfm_list=dict(), ) inputs = FitMSParams.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_FitMSParams_outputs(): - output_map = dict(t2star_image=dict(), - pd_image=dict(), + output_map = dict(pd_image=dict(), t1_image=dict(), + t2star_image=dict(), ) outputs = FitMSParams.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/freesurfer/tests/test_auto_GLMFit.py b/nipype/interfaces/freesurfer/tests/test_auto_GLMFit.py index 4a27b950b7..6b2ea7b1ae 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_GLMFit.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_GLMFit.py @@ -1,139 +1,140 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.freesurfer.model import GLMFit + def test_GLMFit_inputs(): - input_map = dict(surf=dict(requires=['subject_id', 'hemi'], - argstr='--surf %s %s %s', + input_map = dict(allow_ill_cond=dict(argstr='--illcond', ), - save_residual=dict(argstr='--eres-save', + allow_repeated_subjects=dict(argstr='--allowsubjrep', ), - invert_mask=dict(argstr='--mask-inv', + args=dict(argstr='%s', ), - save_res_corr_mtx=dict(argstr='--eres-scm', + calc_AR1=dict(argstr='--tar1', ), - weight_file=dict(xor=['weighted_ls'], + check_opts=dict(argstr='--checkopts', ), - allow_repeated_subjects=dict(argstr='--allowsubjrep', + compute_log_y=dict(argstr='--logy', ), - no_est_fwhm=dict(argstr='--no-est-fwhm', + contrast=dict(argstr='--C %s...', ), - seed=dict(argstr='--seed %d', + cortex=dict(argstr='--cortex', + xor=['label_file'], ), - design=dict(xor=('fsgd', 'design', 'one_sample'), - argstr='--X %s', + debug=dict(argstr='--debug', ), - no_prune=dict(xor=['prunethresh'], - argstr='--no-prune', + design=dict(argstr='--X %s', + xor=('fsgd', 'design', 'one_sample'), ), - surf_geo=dict(usedefault=True, + diag=dict(), + diag_cluster=dict(argstr='--diag-cluster', ), - fwhm=dict(argstr='--fwhm %f', + environ=dict(nohash=True, + usedefault=True, ), - fixed_fx_dof=dict(xor=['fixed_fx_dof_file'], - argstr='--ffxdof %d', + fixed_fx_dof=dict(argstr='--ffxdof %d', + xor=['fixed_fx_dof_file'], ), - per_voxel_reg=dict(argstr='--pvr %s...', + fixed_fx_dof_file=dict(argstr='--ffxdofdat %d', + xor=['fixed_fx_dof'], ), - fixed_fx_dof_file=dict(xor=['fixed_fx_dof'], - argstr='--ffxdofdat %d', + fixed_fx_var=dict(argstr='--yffxvar %s', ), - diag_cluster=dict(argstr='--diag-cluster', + force_perm=dict(argstr='--perm-force', ), - check_opts=dict(argstr='--checkopts', + fsgd=dict(argstr='--fsgd %s %s', + xor=('fsgd', 'design', 'one_sample'), ), - self_reg=dict(argstr='--selfreg %d %d %d', + fwhm=dict(argstr='--fwhm %f', ), - weight_inv=dict(xor=['weighted_ls'], - argstr='--w-inv', + glm_dir=dict(argstr='--glmdir %s', + genfile=True, ), - uniform=dict(argstr='--uniform %f %f', + hemi=dict(), + ignore_exception=dict(nohash=True, + usedefault=True, ), - in_file=dict(copyfile=False, + in_file=dict(argstr='--y %s', + copyfile=False, mandatory=True, - argstr='--y %s', ), - var_fwhm=dict(argstr='--var-fwhm %f', + invert_mask=dict(argstr='--mask-inv', ), - synth=dict(argstr='--synth', + label_file=dict(argstr='--label %s', + xor=['cortex'], ), - prune_thresh=dict(xor=['noprune'], - argstr='--prune_thr %f', + mask_file=dict(argstr='--mask %s', ), - pca=dict(argstr='--pca', + no_contrast_sok=dict(argstr='--no-contrasts-ok', ), - contrast=dict(argstr='--C %s...', + no_est_fwhm=dict(argstr='--no-est-fwhm', ), - label_file=dict(xor=['cortex'], - argstr='--label %s', + no_mask_smooth=dict(argstr='--no-mask-smooth', ), - profile=dict(argstr='--profile %d', + no_prune=dict(argstr='--no-prune', + xor=['prunethresh'], ), - compute_log_y=dict(argstr='--logy', + one_sample=dict(argstr='--osgm', + xor=('one_sample', 'fsgd', 'design', 'contrast'), ), - hemi=dict(), - vox_dump=dict(argstr='--voxdump %d %d %d', + pca=dict(argstr='--pca', ), - save_estimate=dict(argstr='--yhat-save', + per_voxel_reg=dict(argstr='--pvr %s...', ), - save_cond=dict(argstr='--save-cond', + profile=dict(argstr='--profile %d', ), - calc_AR1=dict(argstr='--tar1', + prune=dict(argstr='--prune', ), - args=dict(argstr='%s', + prune_thresh=dict(argstr='--prune_thr %f', + xor=['noprune'], ), - fsgd=dict(xor=('fsgd', 'design', 'one_sample'), - argstr='--fsgd %s %s', + resynth_test=dict(argstr='--resynthtest %d', ), - mask_file=dict(argstr='--mask %s', + save_cond=dict(argstr='--save-cond', ), - terminal_output=dict(mandatory=True, - nohash=True, + save_estimate=dict(argstr='--yhat-save', ), - subjects_dir=dict(), - sim_sign=dict(argstr='--sim-sign %s', + save_res_corr_mtx=dict(argstr='--eres-scm', ), - allow_ill_cond=dict(argstr='--illcond', + save_residual=dict(argstr='--eres-save', ), - force_perm=dict(argstr='--perm-force', + seed=dict(argstr='--seed %d', ), - one_sample=dict(xor=('one_sample', 'fsgd', 'design', 'contrast'), - argstr='--osgm', + self_reg=dict(argstr='--selfreg %d %d %d', ), - prune=dict(argstr='--prune', + sim_done_file=dict(argstr='--sim-done %s', ), - ignore_exception=dict(nohash=True, - usedefault=True, + sim_sign=dict(argstr='--sim-sign %s', ), - no_contrast_sok=dict(argstr='--no-contrasts-ok', + simulation=dict(argstr='--sim %s %d %f %s', ), - fixed_fx_var=dict(argstr='--yffxvar %s', + subject_id=dict(), + subjects_dir=dict(), + surf=dict(argstr='--surf %s %s %s', + requires=['subject_id', 'hemi'], ), - no_mask_smooth=dict(argstr='--no-mask-smooth', + surf_geo=dict(usedefault=True, ), - simulation=dict(argstr='--sim %s %d %f %s', + synth=dict(argstr='--synth', ), - environ=dict(nohash=True, - usedefault=True, + terminal_output=dict(mandatory=True, + nohash=True, ), - cortex=dict(xor=['label_file'], - argstr='--cortex', + uniform=dict(argstr='--uniform %f %f', ), - weight_sqrt=dict(xor=['weighted_ls'], - argstr='--w-sqrt', + var_fwhm=dict(argstr='--var-fwhm %f', ), - diag=dict(), - debug=dict(argstr='--debug', + vox_dump=dict(argstr='--voxdump %d %d %d', ), - weighted_ls=dict(xor=('weight_file', 'weight_inv', 'weight_sqrt'), - argstr='--wls %s', + weight_file=dict(xor=['weighted_ls'], ), - glm_dir=dict(argstr='--glmdir %s', - genfile=True, + weight_inv=dict(argstr='--w-inv', + xor=['weighted_ls'], ), - subject_id=dict(), - resynth_test=dict(argstr='--resynthtest %d', + weight_sqrt=dict(argstr='--w-sqrt', + xor=['weighted_ls'], ), - sim_done_file=dict(argstr='--sim-done %s', + weighted_ls=dict(argstr='--wls %s', + xor=('weight_file', 'weight_inv', 'weight_sqrt'), ), ) inputs = GLMFit.input_spec() @@ -141,27 +142,29 @@ def test_GLMFit_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_GLMFit_outputs(): - output_map = dict(frame_eigenvectors=dict(), - spatial_eigenvectors=dict(), - gamma_var_file=dict(), + output_map = dict(beta_file=dict(), + dof_file=dict(), + error_file=dict(), + error_stddev_file=dict(), error_var_file=dict(), - fwhm_file=dict(), + estimate_file=dict(), + frame_eigenvectors=dict(), ftest_file=dict(), - beta_file=dict(), - error_stddev_file=dict(), - error_file=dict(), + fwhm_file=dict(), gamma_file=dict(), - sig_file=dict(), - mask_file=dict(), - svd_stats_file=dict(), + gamma_var_file=dict(), glm_dir=dict(), - dof_file=dict(), + mask_file=dict(), + sig_file=dict(), singular_values=dict(), - estimate_file=dict(), + spatial_eigenvectors=dict(), + svd_stats_file=dict(), ) outputs = GLMFit.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ImageInfo.py b/nipype/interfaces/freesurfer/tests/test_auto_ImageInfo.py index 940b36cb43..729f04c9fb 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ImageInfo.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ImageInfo.py @@ -1,43 +1,46 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.freesurfer.utils import ImageInfo + def test_ImageInfo_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, - ), - args=dict(argstr='%s', - ), - terminal_output=dict(mandatory=True, - nohash=True, + input_map = dict(args=dict(argstr='%s', ), environ=dict(nohash=True, usedefault=True, ), - in_file=dict(position=1, - argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, + ), + in_file=dict(argstr='%s', + position=1, ), subjects_dir=dict(), + terminal_output=dict(mandatory=True, + nohash=True, + ), ) inputs = ImageInfo.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ImageInfo_outputs(): - output_map = dict(info=dict(), - orientation=dict(), + output_map = dict(TE=dict(), + TI=dict(), + TR=dict(), data_type=dict(), + dimensions=dict(), file_format=dict(), + info=dict(), + orientation=dict(), + out_file=dict(), ph_enc_dir=dict(), - TR=dict(), - dimensions=dict(), - TI=dict(), - TE=dict(), vox_sizes=dict(), - out_file=dict(), ) outputs = ImageInfo.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Label2Vol.py b/nipype/interfaces/freesurfer/tests/test_auto_Label2Vol.py index f1f92ccfbd..2771245fbf 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Label2Vol.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Label2Vol.py @@ -1,74 +1,75 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.freesurfer.model import Label2Vol + def test_Label2Vol_inputs(): - input_map = dict(reg_file=dict(xor=('reg_file', 'reg_header', 'identity'), - argstr='--reg %s', + input_map = dict(annot_file=dict(argstr='--annot %s', + copyfile=False, + mandatory=True, + requires=('subject_id', 'hemi'), + xor=('label_file', 'annot_file', 'seg_file', 'aparc_aseg'), ), - template_file=dict(mandatory=True, - argstr='--temp %s', + aparc_aseg=dict(argstr='--aparc+aseg', + mandatory=True, + xor=('label_file', 'annot_file', 'seg_file', 'aparc_aseg'), ), - surface=dict(argstr='--surf %s', + args=dict(argstr='%s', ), - label_voxel_volume=dict(argstr='--labvoxvol %f', + environ=dict(nohash=True, + usedefault=True, ), - native_vox2ras=dict(argstr='--native-vox2ras', + fill_thresh=dict(argstr='--fillthresh %.f', ), - vol_label_file=dict(argstr='--o %s', - genfile=True, + hemi=dict(argstr='--hemi %s', ), - subject_id=dict(argstr='--subject %s', + identity=dict(argstr='--identity', + xor=('reg_file', 'reg_header', 'identity'), + ), + ignore_exception=dict(nohash=True, + usedefault=True, ), invert_mtx=dict(argstr='--invertmtx', ), - label_hit_file=dict(argstr='--hits %s', + label_file=dict(argstr='--label %s...', + copyfile=False, + mandatory=True, + xor=('label_file', 'annot_file', 'seg_file', 'aparc_aseg'), ), - proj=dict(requires=('subject_id', 'hemi'), - argstr='--proj %s %f %f %f', + label_hit_file=dict(argstr='--hits %s', ), - reg_header=dict(xor=('reg_file', 'reg_header', 'identity'), - argstr='--regheader %s', + label_voxel_volume=dict(argstr='--labvoxvol %f', ), - ignore_exception=dict(nohash=True, - usedefault=True, + map_label_stat=dict(argstr='--label-stat %s', ), - hemi=dict(argstr='--hemi %s', + native_vox2ras=dict(argstr='--native-vox2ras', ), - args=dict(argstr='%s', + proj=dict(argstr='--proj %s %f %f %f', + requires=('subject_id', 'hemi'), ), - map_label_stat=dict(argstr='--label-stat %s', + reg_file=dict(argstr='--reg %s', + xor=('reg_file', 'reg_header', 'identity'), ), - terminal_output=dict(mandatory=True, - nohash=True, + reg_header=dict(argstr='--regheader %s', + xor=('reg_file', 'reg_header', 'identity'), ), - seg_file=dict(copyfile=False, + seg_file=dict(argstr='--seg %s', + copyfile=False, mandatory=True, xor=('label_file', 'annot_file', 'seg_file', 'aparc_aseg'), - argstr='--seg %s', - ), - subjects_dir=dict(), - fill_thresh=dict(argstr='--fillthresh %.f', ), - identity=dict(xor=('reg_file', 'reg_header', 'identity'), - argstr='--identity', + subject_id=dict(argstr='--subject %s', ), - environ=dict(nohash=True, - usedefault=True, + subjects_dir=dict(), + surface=dict(argstr='--surf %s', ), - label_file=dict(copyfile=False, - xor=('label_file', 'annot_file', 'seg_file', 'aparc_aseg'), + template_file=dict(argstr='--temp %s', mandatory=True, - argstr='--label %s...', ), - aparc_aseg=dict(xor=('label_file', 'annot_file', 'seg_file', 'aparc_aseg'), - mandatory=True, - argstr='--aparc+aseg', + terminal_output=dict(mandatory=True, + nohash=True, ), - annot_file=dict(copyfile=False, - mandatory=True, - xor=('label_file', 'annot_file', 'seg_file', 'aparc_aseg'), - argstr='--annot %s', - requires=('subject_id', 'hemi'), + vol_label_file=dict(argstr='--o %s', + genfile=True, ), ) inputs = Label2Vol.input_spec() @@ -76,6 +77,7 @@ def test_Label2Vol_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Label2Vol_outputs(): output_map = dict(vol_label_file=dict(), ) @@ -84,3 +86,4 @@ def test_Label2Vol_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIConvert.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIConvert.py index 9f566eea5a..2a385fcc68 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIConvert.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIConvert.py @@ -1,179 +1,180 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.freesurfer.preprocess import MRIConvert + def test_MRIConvert_inputs(): - input_map = dict(conform_min=dict(argstr='--conform_min', - ), - no_change=dict(argstr='--nochange', + input_map = dict(apply_inv_transform=dict(argstr='--apply_inverse_transform %s', ), - no_scale=dict(argstr='--no_scale 1', + apply_transform=dict(argstr='--apply_transform %s', ), - force_ras=dict(argstr='--force_ras_good', + args=dict(argstr='%s', ), - ignore_exception=dict(nohash=True, - usedefault=True, + ascii=dict(argstr='--ascii', ), - fwhm=dict(argstr='--fwhm %f', + autoalign_matrix=dict(argstr='--autoalign %s', ), - in_like=dict(argstr='--in_like %s', + color_file=dict(argstr='--color_file %s', ), conform=dict(argstr='--conform', ), - args=dict(argstr='%s', + conform_min=dict(argstr='--conform_min', ), - in_center=dict(argstr='--in_center %s', + conform_size=dict(argstr='--conform_size %s', ), - devolve_transform=dict(argstr='--devolvexfm %s', + crop_center=dict(argstr='--crop %d %d %d', ), - no_translate=dict(argstr='--no_translate', + crop_gdf=dict(argstr='--crop_gdf', ), - zero_ge_z_offset=dict(argstr='--zero_ge_z_offset', + crop_size=dict(argstr='--cropsize %d %d %d', ), - out_j_count=dict(argstr='--out_j_count %d', + cut_ends=dict(argstr='--cutends %d', ), - color_file=dict(argstr='--color_file %s', + devolve_transform=dict(argstr='--devolvexfm %s', ), - apply_transform=dict(argstr='--apply_transform %s', + drop_n=dict(argstr='--ndrop %d', ), - in_info=dict(argstr='--in_info', + environ=dict(nohash=True, + usedefault=True, ), - out_i_dir=dict(argstr='--out_i_direction %f %f %f', + fill_parcellation=dict(argstr='--fill_parcellation', ), - resample_type=dict(argstr='--resample_type %s', + force_ras=dict(argstr='--force_ras_good', ), - unwarp_gradient=dict(argstr='--unwarp_gradient_nonlinearity', + frame=dict(argstr='--frame %d', ), - out_k_size=dict(argstr='--out_k_size %d', + frame_subsample=dict(argstr='--fsubsample %d %d %d', ), - subject_name=dict(argstr='--subject_name %s', + fwhm=dict(argstr='--fwhm %f', ), - drop_n=dict(argstr='--ndrop %d', + ignore_exception=dict(nohash=True, + usedefault=True, ), - in_j_size=dict(argstr='--in_j_size %d', + in_center=dict(argstr='--in_center %s', ), - slice_bias=dict(argstr='--slice-bias %f', + in_file=dict(argstr='--input_volume %s', + mandatory=True, + position=-2, ), - out_orientation=dict(argstr='--out_orientation %s', + in_i_dir=dict(argstr='--in_i_direction %f %f %f', ), - slice_crop=dict(argstr='--slice-crop %d %d', + in_i_size=dict(argstr='--in_i_size %d', ), - conform_size=dict(argstr='--conform_size %s', + in_info=dict(argstr='--in_info', ), - out_i_count=dict(argstr='--out_i_count %d', + in_j_dir=dict(argstr='--in_j_direction %f %f %f', ), - ascii=dict(argstr='--ascii', + in_j_size=dict(argstr='--in_j_size %d', ), - out_center=dict(argstr='--out_center %f %f %f', + in_k_dir=dict(argstr='--in_k_direction %f %f %f', ), - slice_reverse=dict(argstr='--slice-reverse', + in_k_size=dict(argstr='--in_k_size %d', ), - zero_outlines=dict(argstr='--zero_outlines', + in_like=dict(argstr='--in_like %s', ), - in_j_dir=dict(argstr='--in_j_direction %f %f %f', + in_matrix=dict(argstr='--in_matrix', ), - out_k_dir=dict(argstr='--out_k_direction %f %f %f', + in_orientation=dict(argstr='--in_orientation %s', ), - template_type=dict(argstr='--template_type %s', + in_scale=dict(argstr='--scale %f', ), - split=dict(argstr='--split', + in_stats=dict(argstr='--in_stats', ), - crop_gdf=dict(argstr='--crop_gdf', + in_type=dict(argstr='--in_type %s', ), - in_i_dir=dict(argstr='--in_i_direction %f %f %f', + invert_contrast=dict(argstr='--invert_contrast %f', ), - cut_ends=dict(argstr='--cutends %d', + midframe=dict(argstr='--mid-frame', ), - crop_size=dict(argstr='--cropsize %d %d %d', + no_change=dict(argstr='--nochange', ), - frame=dict(argstr='--frame %d', + no_scale=dict(argstr='--no_scale 1', ), - reorder=dict(argstr='--reorder %d %d %d', + no_translate=dict(argstr='--no_translate', ), - in_file=dict(position=-2, - mandatory=True, - argstr='--input_volume %s', + no_write=dict(argstr='--no_write', ), - skip_n=dict(argstr='--nskip %d', + out_center=dict(argstr='--out_center %f %f %f', ), - midframe=dict(argstr='--mid-frame', + out_datatype=dict(argstr='--out_data_type %s', ), - fill_parcellation=dict(argstr='--fill_parcellation', + out_file=dict(argstr='--output_volume %s', + genfile=True, + position=-1, + ), + out_i_count=dict(argstr='--out_i_count %d', + ), + out_i_dir=dict(argstr='--out_i_direction %f %f %f', + ), + out_i_size=dict(argstr='--out_i_size %d', ), out_info=dict(argstr='--out_info', ), - in_stats=dict(argstr='--in_stats', + out_j_count=dict(argstr='--out_j_count %d', ), - in_matrix=dict(argstr='--in_matrix', + out_j_dir=dict(argstr='--out_j_direction %f %f %f', ), - out_type=dict(argstr='--out_type %s', + out_j_size=dict(argstr='--out_j_size %d', ), out_k_count=dict(argstr='--out_k_count %d', ), - in_scale=dict(argstr='--scale %f', + out_k_dir=dict(argstr='--out_k_direction %f %f %f', + ), + out_k_size=dict(argstr='--out_k_size %d', ), out_matrix=dict(argstr='--out_matrix', ), - read_only=dict(argstr='--read_only', + out_orientation=dict(argstr='--out_orientation %s', ), - template_info=dict(), out_scale=dict(argstr='--out-scale %d', ), - subjects_dir=dict(), - status_file=dict(argstr='--status %s', - ), - crop_center=dict(argstr='--crop %d %d %d', + out_stats=dict(argstr='--out_stats', ), - invert_contrast=dict(argstr='--invert_contrast %f', + out_type=dict(argstr='--out_type %s', ), parse_only=dict(argstr='--parse_only', ), - vox_size=dict(argstr='-voxsize %f %f %f', + read_only=dict(argstr='--read_only', ), - apply_inv_transform=dict(argstr='--apply_inverse_transform %s', + reorder=dict(argstr='--reorder %d %d %d', ), - out_j_dir=dict(argstr='--out_j_direction %f %f %f', + resample_type=dict(argstr='--resample_type %s', ), reslice_like=dict(argstr='--reslice_like %s', ), - sphinx=dict(argstr='--sphinx', + sdcm_list=dict(argstr='--sdcmlist %s', ), - out_file=dict(position=-1, - genfile=True, - argstr='--output_volume %s', + skip_n=dict(argstr='--nskip %d', ), - in_type=dict(argstr='--in_type %s', + slice_bias=dict(argstr='--slice-bias %f', ), - out_i_size=dict(argstr='--out_i_size %d', + slice_crop=dict(argstr='--slice-crop %d %d', ), - in_k_size=dict(argstr='--in_k_size %d', + slice_reverse=dict(argstr='--slice-reverse', ), - out_j_size=dict(argstr='--out_j_size %d', + smooth_parcellation=dict(argstr='--smooth_parcellation', ), - in_k_dir=dict(argstr='--in_k_direction %f %f %f', + sphinx=dict(argstr='--sphinx', ), - no_write=dict(argstr='--no_write', + split=dict(argstr='--split', ), - sdcm_list=dict(argstr='--sdcmlist %s', + status_file=dict(argstr='--status %s', ), - autoalign_matrix=dict(argstr='--autoalign %s', + subject_name=dict(argstr='--subject_name %s', + ), + subjects_dir=dict(), + template_info=dict(), + template_type=dict(argstr='--template_type %s', ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - in_i_size=dict(argstr='--in_i_size %d', - ), - in_orientation=dict(argstr='--in_orientation %s', - ), - out_stats=dict(argstr='--out_stats', + unwarp_gradient=dict(argstr='--unwarp_gradient_nonlinearity', ), - frame_subsample=dict(argstr='--fsubsample %d %d %d', + vox_size=dict(argstr='-voxsize %f %f %f', ), - smooth_parcellation=dict(argstr='--smooth_parcellation', + zero_ge_z_offset=dict(argstr='--zero_ge_z_offset', ), - out_datatype=dict(argstr='--out_data_type %s', + zero_outlines=dict(argstr='--zero_outlines', ), ) inputs = MRIConvert.input_spec() @@ -181,6 +182,7 @@ def test_MRIConvert_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MRIConvert_outputs(): output_map = dict(out_file=dict(), ) @@ -189,3 +191,4 @@ def test_MRIConvert_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIMarchingCubes.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIMarchingCubes.py index 67bf3320e6..112831578f 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIMarchingCubes.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIMarchingCubes.py @@ -1,41 +1,43 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.freesurfer.utils import MRIMarchingCubes + def test_MRIMarchingCubes_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + connectivity_value=dict(argstr='%d', + position=-1, usedefault=True, ), - connectivity_value=dict(position=-1, - argstr='%d', + environ=dict(nohash=True, usedefault=True, ), - args=dict(argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - out_file=dict(position=-2, - genfile=True, - argstr='./%s', + in_file=dict(argstr='%s', + mandatory=True, + position=1, ), - label_value=dict(position=2, + label_value=dict(argstr='%d', mandatory=True, - argstr='%d', + position=2, + ), + out_file=dict(argstr='./%s', + genfile=True, + position=-2, ), + subjects_dir=dict(), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - in_file=dict(position=1, - mandatory=True, - argstr='%s', - ), - subjects_dir=dict(), ) inputs = MRIMarchingCubes.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MRIMarchingCubes_outputs(): output_map = dict(surface=dict(), ) @@ -44,3 +46,4 @@ def test_MRIMarchingCubes_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRISPreproc.py b/nipype/interfaces/freesurfer/tests/test_auto_MRISPreproc.py index b20b401b3c..62a95a7ec4 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRISPreproc.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRISPreproc.py @@ -1,67 +1,68 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.freesurfer.model import MRISPreproc + def test_MRISPreproc_inputs(): - input_map = dict(surf_dir=dict(argstr='--surfdir %s', + input_map = dict(args=dict(argstr='%s', ), - vol_measure_file=dict(argstr='--iv %s %s...', + environ=dict(nohash=True, + usedefault=True, ), - fsgd_file=dict(xor=('subjects', 'fsgd_file', 'subject_file'), - argstr='--fsgd %s', + fsgd_file=dict(argstr='--fsgd %s', + xor=('subjects', 'fsgd_file', 'subject_file'), ), - fwhm=dict(xor=['num_iters'], - argstr='--fwhm %f', + fwhm=dict(argstr='--fwhm %f', + xor=['num_iters'], ), - fwhm_source=dict(xor=['num_iters_source'], - argstr='--fwhm-src %f', + fwhm_source=dict(argstr='--fwhm-src %f', + xor=['num_iters_source'], ), - surf_measure=dict(xor=('surf_measure', 'surf_measure_file', 'surf_area'), - argstr='--meas %s', + hemi=dict(argstr='--hemi %s', + mandatory=True, ), - subject_file=dict(xor=('subjects', 'fsgd_file', 'subject_file'), - argstr='--f %s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - surf_measure_file=dict(xor=('surf_measure', 'surf_measure_file', 'surf_area'), - argstr='--is %s...', + num_iters=dict(argstr='--niters %d', + xor=['fwhm'], ), - source_format=dict(argstr='--srcfmt %s', + num_iters_source=dict(argstr='--niterssrc %d', + xor=['fwhm_source'], ), - subjects=dict(xor=('subjects', 'fsgd_file', 'subject_file'), - argstr='--s %s...', + out_file=dict(argstr='--out %s', + genfile=True, ), - ignore_exception=dict(nohash=True, - usedefault=True, + proj_frac=dict(argstr='--projfrac %s', ), - hemi=dict(mandatory=True, - argstr='--hemi %s', + smooth_cortex_only=dict(argstr='--smooth-cortex-only', ), - surf_area=dict(xor=('surf_measure', 'surf_measure_file', 'surf_area'), - argstr='--area %s', + source_format=dict(argstr='--srcfmt %s', ), - args=dict(argstr='%s', + subject_file=dict(argstr='--f %s', + xor=('subjects', 'fsgd_file', 'subject_file'), ), - terminal_output=dict(mandatory=True, - nohash=True, + subjects=dict(argstr='--s %s...', + xor=('subjects', 'fsgd_file', 'subject_file'), ), - num_iters_source=dict(xor=['fwhm_source'], - argstr='--niterssrc %d', + subjects_dir=dict(), + surf_area=dict(argstr='--area %s', + xor=('surf_measure', 'surf_measure_file', 'surf_area'), ), - smooth_cortex_only=dict(argstr='--smooth-cortex-only', + surf_dir=dict(argstr='--surfdir %s', ), - subjects_dir=dict(), - num_iters=dict(xor=['fwhm'], - argstr='--niters %d', + surf_measure=dict(argstr='--meas %s', + xor=('surf_measure', 'surf_measure_file', 'surf_area'), ), - proj_frac=dict(argstr='--projfrac %s', + surf_measure_file=dict(argstr='--is %s...', + xor=('surf_measure', 'surf_measure_file', 'surf_area'), ), - target=dict(mandatory=True, - argstr='--target %s', + target=dict(argstr='--target %s', + mandatory=True, ), - out_file=dict(argstr='--out %s', - genfile=True, + terminal_output=dict(mandatory=True, + nohash=True, ), - environ=dict(nohash=True, - usedefault=True, + vol_measure_file=dict(argstr='--iv %s %s...', ), ) inputs = MRISPreproc.input_spec() @@ -69,6 +70,7 @@ def test_MRISPreproc_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MRISPreproc_outputs(): output_map = dict(out_file=dict(), ) @@ -77,3 +79,4 @@ def test_MRISPreproc_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRITessellate.py b/nipype/interfaces/freesurfer/tests/test_auto_MRITessellate.py index 0aa0e4b6a0..24cef4872b 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRITessellate.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRITessellate.py @@ -1,33 +1,34 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.freesurfer.utils import MRITessellate + def test_MRITessellate_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(args=dict(argstr='%s', ), - args=dict(argstr='%s', + environ=dict(nohash=True, + usedefault=True, ), - tesselate_all_voxels=dict(argstr='-a', + ignore_exception=dict(nohash=True, + usedefault=True, ), - out_file=dict(position=-1, - genfile=True, - argstr='./%s', + in_file=dict(argstr='%s', + mandatory=True, + position=-3, ), - label_value=dict(position=-2, + label_value=dict(argstr='%d', mandatory=True, - argstr='%d', + position=-2, + ), + out_file=dict(argstr='./%s', + genfile=True, + position=-1, ), + subjects_dir=dict(), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - in_file=dict(position=-3, - mandatory=True, - argstr='%s', + tesselate_all_voxels=dict(argstr='-a', ), - subjects_dir=dict(), use_real_RAS_coordinates=dict(argstr='-n', ), ) @@ -36,6 +37,7 @@ def test_MRITessellate_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MRITessellate_outputs(): output_map = dict(surface=dict(), ) @@ -44,3 +46,4 @@ def test_MRITessellate_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MRIsConvert.py b/nipype/interfaces/freesurfer/tests/test_auto_MRIsConvert.py index 44896d3d53..5bd2c238a0 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MRIsConvert.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MRIsConvert.py @@ -1,58 +1,59 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.freesurfer.utils import MRIsConvert + def test_MRIsConvert_inputs(): - input_map = dict(out_datatype=dict(mandatory=True, - ), - scale=dict(argstr='-s %.3f', + input_map = dict(annot_file=dict(argstr='--annot %s', ), - functional_file=dict(argstr='-f %s', + args=dict(argstr='%s', ), - labelstats_outfile=dict(argstr='--labelstats %s', + dataarray_num=dict(argstr='--da_num %d', ), - in_file=dict(position=-2, - mandatory=True, - argstr='%s', + environ=dict(nohash=True, + usedefault=True, ), - talairachxfm_subjid=dict(argstr='-t %s', + functional_file=dict(argstr='-f %s', ), ignore_exception=dict(nohash=True, usedefault=True, ), - origname=dict(argstr='-o %s', - ), - normal=dict(argstr='-n', + in_file=dict(argstr='%s', + mandatory=True, + position=-2, ), - rescale=dict(argstr='-r', + label_file=dict(argstr='--label %s', ), - args=dict(argstr='%s', + labelstats_outfile=dict(argstr='--labelstats %s', ), - vertex=dict(argstr='-v', + normal=dict(argstr='-n', ), - terminal_output=dict(mandatory=True, - nohash=True, + origname=dict(argstr='-o %s', ), - subjects_dir=dict(), - xyz_ascii=dict(argstr='-a', + out_datatype=dict(mandatory=True, ), - out_file=dict(position=-1, + out_file=dict(argstr='./%s', genfile=True, - argstr='./%s', + position=-1, + ), + parcstats_file=dict(argstr='--parcstats %s', ), patch=dict(argstr='-p', ), - environ=dict(nohash=True, - usedefault=True, + rescale=dict(argstr='-r', ), - label_file=dict(argstr='--label %s', + scalarcurv_file=dict(argstr='-c %s', ), - parcstats_file=dict(argstr='--parcstats %s', + scale=dict(argstr='-s %.3f', ), - annot_file=dict(argstr='--annot %s', + subjects_dir=dict(), + talairachxfm_subjid=dict(argstr='-t %s', ), - scalarcurv_file=dict(argstr='-c %s', + terminal_output=dict(mandatory=True, + nohash=True, ), - dataarray_num=dict(argstr='--da_num %d', + vertex=dict(argstr='-v', + ), + xyz_ascii=dict(argstr='-a', ), ) inputs = MRIsConvert.input_spec() @@ -60,6 +61,7 @@ def test_MRIsConvert_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MRIsConvert_outputs(): output_map = dict(converted=dict(), ) @@ -68,3 +70,4 @@ def test_MRIsConvert_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MS_LDA.py b/nipype/interfaces/freesurfer/tests/test_auto_MS_LDA.py index 8933064c00..6654a606a9 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MS_LDA.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MS_LDA.py @@ -1,43 +1,44 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.freesurfer.model import MS_LDA + def test_MS_LDA_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(args=dict(argstr='%s', ), conform=dict(argstr='-conform', ), - weight_file=dict(mandatory=True, - argstr='-weight %s', + environ=dict(nohash=True, + usedefault=True, ), - lda_labels=dict(mandatory=True, - sep=' ', - argstr='-lda %s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - vol_synth_file=dict(mandatory=True, - argstr='-synth %s', + images=dict(argstr='%s', + copyfile=False, + mandatory=True, + position=-1, ), - shift=dict(argstr='-shift %d', + label_file=dict(argstr='-label %s', ), - args=dict(argstr='%s', + lda_labels=dict(argstr='-lda %s', + mandatory=True, + sep=' ', ), mask_file=dict(argstr='-mask %s', ), + shift=dict(argstr='-shift %d', + ), + subjects_dir=dict(), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - label_file=dict(argstr='-label %s', + use_weights=dict(argstr='-W', ), - subjects_dir=dict(), - images=dict(copyfile=False, + vol_synth_file=dict(argstr='-synth %s', mandatory=True, - position=-1, - argstr='%s', ), - use_weights=dict(argstr='-W', + weight_file=dict(argstr='-weight %s', + mandatory=True, ), ) inputs = MS_LDA.input_spec() @@ -45,12 +46,14 @@ def test_MS_LDA_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MS_LDA_outputs(): - output_map = dict(weight_file=dict(), - vol_synth_file=dict(), + output_map = dict(vol_synth_file=dict(), + weight_file=dict(), ) outputs = MS_LDA.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/freesurfer/tests/test_auto_MakeAverageSubject.py b/nipype/interfaces/freesurfer/tests/test_auto_MakeAverageSubject.py index 631d8db199..e384324c4b 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_MakeAverageSubject.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_MakeAverageSubject.py @@ -1,18 +1,16 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.freesurfer.utils import MakeAverageSubject + def test_MakeAverageSubject_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, - ), - args=dict(argstr='%s', - ), - terminal_output=dict(mandatory=True, - nohash=True, + input_map = dict(args=dict(argstr='%s', ), environ=dict(nohash=True, usedefault=True, ), + ignore_exception=dict(nohash=True, + usedefault=True, + ), out_name=dict(argstr='--out %s', usedefault=True, ), @@ -21,12 +19,16 @@ def test_MakeAverageSubject_inputs(): mandatory=True, sep=' ', ), + terminal_output=dict(mandatory=True, + nohash=True, + ), ) inputs = MakeAverageSubject.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MakeAverageSubject_outputs(): output_map = dict(average_subject_name=dict(), ) @@ -35,3 +37,4 @@ def test_MakeAverageSubject_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/freesurfer/tests/test_auto_OneSampleTTest.py b/nipype/interfaces/freesurfer/tests/test_auto_OneSampleTTest.py index 5d132da3a0..12b26354bc 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_OneSampleTTest.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_OneSampleTTest.py @@ -1,139 +1,140 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.freesurfer.model import OneSampleTTest + def test_OneSampleTTest_inputs(): - input_map = dict(surf=dict(requires=['subject_id', 'hemi'], - argstr='--surf %s %s %s', + input_map = dict(allow_ill_cond=dict(argstr='--illcond', ), - save_residual=dict(argstr='--eres-save', + allow_repeated_subjects=dict(argstr='--allowsubjrep', ), - invert_mask=dict(argstr='--mask-inv', + args=dict(argstr='%s', ), - save_res_corr_mtx=dict(argstr='--eres-scm', + calc_AR1=dict(argstr='--tar1', ), - weight_file=dict(xor=['weighted_ls'], + check_opts=dict(argstr='--checkopts', ), - allow_repeated_subjects=dict(argstr='--allowsubjrep', + compute_log_y=dict(argstr='--logy', ), - no_est_fwhm=dict(argstr='--no-est-fwhm', + contrast=dict(argstr='--C %s...', ), - seed=dict(argstr='--seed %d', + cortex=dict(argstr='--cortex', + xor=['label_file'], ), - design=dict(xor=('fsgd', 'design', 'one_sample'), - argstr='--X %s', + debug=dict(argstr='--debug', ), - no_prune=dict(xor=['prunethresh'], - argstr='--no-prune', + design=dict(argstr='--X %s', + xor=('fsgd', 'design', 'one_sample'), ), - surf_geo=dict(usedefault=True, + diag=dict(), + diag_cluster=dict(argstr='--diag-cluster', ), - fwhm=dict(argstr='--fwhm %f', + environ=dict(nohash=True, + usedefault=True, ), - fixed_fx_dof=dict(xor=['fixed_fx_dof_file'], - argstr='--ffxdof %d', + fixed_fx_dof=dict(argstr='--ffxdof %d', + xor=['fixed_fx_dof_file'], ), - per_voxel_reg=dict(argstr='--pvr %s...', + fixed_fx_dof_file=dict(argstr='--ffxdofdat %d', + xor=['fixed_fx_dof'], ), - fixed_fx_dof_file=dict(xor=['fixed_fx_dof'], - argstr='--ffxdofdat %d', + fixed_fx_var=dict(argstr='--yffxvar %s', ), - diag_cluster=dict(argstr='--diag-cluster', + force_perm=dict(argstr='--perm-force', ), - check_opts=dict(argstr='--checkopts', + fsgd=dict(argstr='--fsgd %s %s', + xor=('fsgd', 'design', 'one_sample'), ), - self_reg=dict(argstr='--selfreg %d %d %d', + fwhm=dict(argstr='--fwhm %f', ), - weight_inv=dict(xor=['weighted_ls'], - argstr='--w-inv', + glm_dir=dict(argstr='--glmdir %s', + genfile=True, ), - uniform=dict(argstr='--uniform %f %f', + hemi=dict(), + ignore_exception=dict(nohash=True, + usedefault=True, ), - in_file=dict(copyfile=False, + in_file=dict(argstr='--y %s', + copyfile=False, mandatory=True, - argstr='--y %s', ), - var_fwhm=dict(argstr='--var-fwhm %f', + invert_mask=dict(argstr='--mask-inv', ), - synth=dict(argstr='--synth', + label_file=dict(argstr='--label %s', + xor=['cortex'], ), - prune_thresh=dict(xor=['noprune'], - argstr='--prune_thr %f', + mask_file=dict(argstr='--mask %s', ), - pca=dict(argstr='--pca', + no_contrast_sok=dict(argstr='--no-contrasts-ok', ), - contrast=dict(argstr='--C %s...', + no_est_fwhm=dict(argstr='--no-est-fwhm', ), - label_file=dict(xor=['cortex'], - argstr='--label %s', + no_mask_smooth=dict(argstr='--no-mask-smooth', ), - profile=dict(argstr='--profile %d', + no_prune=dict(argstr='--no-prune', + xor=['prunethresh'], ), - compute_log_y=dict(argstr='--logy', + one_sample=dict(argstr='--osgm', + xor=('one_sample', 'fsgd', 'design', 'contrast'), ), - hemi=dict(), - vox_dump=dict(argstr='--voxdump %d %d %d', + pca=dict(argstr='--pca', ), - save_estimate=dict(argstr='--yhat-save', + per_voxel_reg=dict(argstr='--pvr %s...', ), - save_cond=dict(argstr='--save-cond', + profile=dict(argstr='--profile %d', ), - calc_AR1=dict(argstr='--tar1', + prune=dict(argstr='--prune', ), - args=dict(argstr='%s', + prune_thresh=dict(argstr='--prune_thr %f', + xor=['noprune'], ), - fsgd=dict(xor=('fsgd', 'design', 'one_sample'), - argstr='--fsgd %s %s', + resynth_test=dict(argstr='--resynthtest %d', ), - mask_file=dict(argstr='--mask %s', + save_cond=dict(argstr='--save-cond', ), - terminal_output=dict(mandatory=True, - nohash=True, + save_estimate=dict(argstr='--yhat-save', ), - subjects_dir=dict(), - sim_sign=dict(argstr='--sim-sign %s', + save_res_corr_mtx=dict(argstr='--eres-scm', ), - allow_ill_cond=dict(argstr='--illcond', + save_residual=dict(argstr='--eres-save', ), - force_perm=dict(argstr='--perm-force', + seed=dict(argstr='--seed %d', ), - one_sample=dict(xor=('one_sample', 'fsgd', 'design', 'contrast'), - argstr='--osgm', + self_reg=dict(argstr='--selfreg %d %d %d', ), - prune=dict(argstr='--prune', + sim_done_file=dict(argstr='--sim-done %s', ), - ignore_exception=dict(nohash=True, - usedefault=True, + sim_sign=dict(argstr='--sim-sign %s', ), - no_contrast_sok=dict(argstr='--no-contrasts-ok', + simulation=dict(argstr='--sim %s %d %f %s', ), - fixed_fx_var=dict(argstr='--yffxvar %s', + subject_id=dict(), + subjects_dir=dict(), + surf=dict(argstr='--surf %s %s %s', + requires=['subject_id', 'hemi'], ), - no_mask_smooth=dict(argstr='--no-mask-smooth', + surf_geo=dict(usedefault=True, ), - simulation=dict(argstr='--sim %s %d %f %s', + synth=dict(argstr='--synth', ), - environ=dict(nohash=True, - usedefault=True, + terminal_output=dict(mandatory=True, + nohash=True, ), - cortex=dict(xor=['label_file'], - argstr='--cortex', + uniform=dict(argstr='--uniform %f %f', ), - weight_sqrt=dict(xor=['weighted_ls'], - argstr='--w-sqrt', + var_fwhm=dict(argstr='--var-fwhm %f', ), - diag=dict(), - debug=dict(argstr='--debug', + vox_dump=dict(argstr='--voxdump %d %d %d', ), - weighted_ls=dict(xor=('weight_file', 'weight_inv', 'weight_sqrt'), - argstr='--wls %s', + weight_file=dict(xor=['weighted_ls'], ), - glm_dir=dict(argstr='--glmdir %s', - genfile=True, + weight_inv=dict(argstr='--w-inv', + xor=['weighted_ls'], ), - subject_id=dict(), - resynth_test=dict(argstr='--resynthtest %d', + weight_sqrt=dict(argstr='--w-sqrt', + xor=['weighted_ls'], ), - sim_done_file=dict(argstr='--sim-done %s', + weighted_ls=dict(argstr='--wls %s', + xor=('weight_file', 'weight_inv', 'weight_sqrt'), ), ) inputs = OneSampleTTest.input_spec() @@ -141,27 +142,29 @@ def test_OneSampleTTest_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_OneSampleTTest_outputs(): - output_map = dict(frame_eigenvectors=dict(), - spatial_eigenvectors=dict(), - gamma_var_file=dict(), + output_map = dict(beta_file=dict(), + dof_file=dict(), + error_file=dict(), + error_stddev_file=dict(), error_var_file=dict(), - fwhm_file=dict(), + estimate_file=dict(), + frame_eigenvectors=dict(), ftest_file=dict(), - beta_file=dict(), - error_stddev_file=dict(), - error_file=dict(), + fwhm_file=dict(), gamma_file=dict(), - sig_file=dict(), - mask_file=dict(), - svd_stats_file=dict(), + gamma_var_file=dict(), glm_dir=dict(), - dof_file=dict(), + mask_file=dict(), + sig_file=dict(), singular_values=dict(), - estimate_file=dict(), + spatial_eigenvectors=dict(), + svd_stats_file=dict(), ) outputs = OneSampleTTest.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ParseDICOMDir.py b/nipype/interfaces/freesurfer/tests/test_auto_ParseDICOMDir.py index 35b3d53329..7b695e48f8 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ParseDICOMDir.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ParseDICOMDir.py @@ -1,11 +1,12 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.freesurfer.preprocess import ParseDICOMDir + def test_ParseDICOMDir_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(args=dict(argstr='%s', ), - args=dict(argstr='%s', + dicom_dir=dict(argstr='--d %s', + mandatory=True, ), dicom_info_file=dict(argstr='--o %s', usedefault=True, @@ -13,14 +14,14 @@ def test_ParseDICOMDir_inputs(): environ=dict(nohash=True, usedefault=True, ), - subjects_dir=dict(), - dicom_dir=dict(mandatory=True, - argstr='--d %s', - ), - summarize=dict(argstr='--summarize', + ignore_exception=dict(nohash=True, + usedefault=True, ), sortbyrun=dict(argstr='--sortbyrun', ), + subjects_dir=dict(), + summarize=dict(argstr='--summarize', + ), terminal_output=dict(mandatory=True, nohash=True, ), @@ -30,6 +31,7 @@ def test_ParseDICOMDir_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ParseDICOMDir_outputs(): output_map = dict(dicom_info_file=dict(), ) @@ -38,3 +40,4 @@ def test_ParseDICOMDir_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/freesurfer/tests/test_auto_ReconAll.py b/nipype/interfaces/freesurfer/tests/test_auto_ReconAll.py index 2ae853a630..4c65baec14 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_ReconAll.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_ReconAll.py @@ -1,39 +1,40 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.freesurfer.preprocess import ReconAll + def test_ReconAll_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(T1_files=dict(argstr='-i %s...', ), - hemi=dict(argstr='-hemi %s', + T2_file=dict(argstr='-T2 %s', + min_ver='5.3.0', ), - T1_files=dict(argstr='-i %s...', + args=dict(argstr='%s', ), - directive=dict(position=0, + directive=dict(argstr='-%s', + position=0, usedefault=True, - argstr='-%s', ), - subject_id=dict(argstr='-subjid %s', + environ=dict(nohash=True, usedefault=True, ), - args=dict(argstr='%s', + flags=dict(argstr='%s', ), - terminal_output=dict(mandatory=True, - nohash=True, + hemi=dict(argstr='-hemi %s', ), - environ=dict(nohash=True, + ignore_exception=dict(nohash=True, usedefault=True, ), - subjects_dir=dict(argstr='-sd %s', - hash_files=False, - genfile=True, + openmp=dict(argstr='-openmp %d', ), - flags=dict(argstr='%s', + subject_id=dict(argstr='-subjid %s', + usedefault=True, ), - openmp=dict(argstr='-openmp %d', + subjects_dir=dict(argstr='-sd %s', + genfile=True, + hash_files=False, ), - T2_file=dict(argstr='-T2 %s', - min_ver='5.3.0', + terminal_output=dict(mandatory=True, + nohash=True, ), ) inputs = ReconAll.input_spec() @@ -41,88 +42,90 @@ def test_ReconAll_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ReconAll_outputs(): - output_map = dict(curv=dict(loc='surf', - ), - curv_stats=dict(altkey='curv', + output_map = dict(BA_stats=dict(altkey='BA', loc='stats', ), - sphere=dict(loc='surf', + T1=dict(loc='mri', ), - label=dict(altkey='*label', + annot=dict(altkey='*annot', loc='label', ), - BA_stats=dict(altkey='BA', + aparc_a2009s_stats=dict(altkey='aparc.a2009s', loc='stats', ), - sphere_reg=dict(altkey='sphere.reg', - loc='surf', + aparc_aseg=dict(altkey='aparc*aseg', + loc='mri', ), - orig=dict(loc='mri', + aparc_stats=dict(altkey='aparc', + loc='stats', ), - entorhinal_exvivo_stats=dict(altkey='entorhinal_exvivo', + aseg=dict(loc='mri', + ), + aseg_stats=dict(altkey='aseg', loc='stats', ), - subject_id=dict(), + brain=dict(loc='mri', + ), brainmask=dict(loc='mri', ), - thickness=dict(loc='surf', + curv=dict(loc='surf', ), - ribbon=dict(altkey='*ribbon', - loc='mri', + curv_stats=dict(altkey='curv', + loc='stats', ), - rawavg=dict(loc='mri', + entorhinal_exvivo_stats=dict(altkey='entorhinal_exvivo', + loc='stats', ), - white=dict(loc='surf', + filled=dict(loc='mri', ), - sulc=dict(loc='surf', + inflated=dict(loc='surf', ), - nu=dict(loc='mri', + label=dict(altkey='*label', + loc='label', ), norm=dict(loc='mri', ), - inflated=dict(loc='surf', + nu=dict(loc='mri', ), - wm=dict(loc='mri', + orig=dict(loc='mri', ), - wmparc=dict(loc='mri', + pial=dict(loc='surf', ), - T1=dict(loc='mri', + rawavg=dict(loc='mri', ), - volume=dict(loc='surf', + ribbon=dict(altkey='*ribbon', + loc='mri', ), - subjects_dir=dict(), - aseg=dict(loc='mri', + smoothwm=dict(loc='surf', ), - aparc_stats=dict(altkey='aparc', - loc='stats', + sphere=dict(loc='surf', ), - brain=dict(loc='mri', + sphere_reg=dict(altkey='sphere.reg', + loc='surf', ), - aparc_a2009s_stats=dict(altkey='aparc.a2009s', - loc='stats', + subject_id=dict(), + subjects_dir=dict(), + sulc=dict(loc='surf', ), - annot=dict(altkey='*annot', - loc='label', + thickness=dict(loc='surf', ), - aseg_stats=dict(altkey='aseg', - loc='stats', + volume=dict(loc='surf', ), - filled=dict(loc='mri', + white=dict(loc='surf', ), - pial=dict(loc='surf', + wm=dict(loc='mri', + ), + wmparc=dict(loc='mri', ), wmparc_stats=dict(altkey='wmparc', loc='stats', ), - aparc_aseg=dict(altkey='aparc*aseg', - loc='mri', - ), - smoothwm=dict(loc='surf', - ), ) outputs = ReconAll.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Resample.py b/nipype/interfaces/freesurfer/tests/test_auto_Resample.py index 486446ca7c..50a3736ae0 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Resample.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Resample.py @@ -1,36 +1,38 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.freesurfer.preprocess import Resample + def test_Resample_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + environ=dict(nohash=True, usedefault=True, ), - resampled_file=dict(position=-1, - genfile=True, - argstr='-o %s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - args=dict(argstr='%s', + in_file=dict(argstr='-i %s', + mandatory=True, + position=-2, ), - voxel_size=dict(mandatory=True, - argstr='-vs %.2f %.2f %.2f', + resampled_file=dict(argstr='-o %s', + genfile=True, + position=-1, ), + subjects_dir=dict(), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - in_file=dict(position=-2, + voxel_size=dict(argstr='-vs %.2f %.2f %.2f', mandatory=True, - argstr='-i %s', ), - subjects_dir=dict(), ) inputs = Resample.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Resample_outputs(): output_map = dict(resampled_file=dict(), ) @@ -39,3 +41,4 @@ def test_Resample_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/freesurfer/tests/test_auto_RobustRegister.py b/nipype/interfaces/freesurfer/tests/test_auto_RobustRegister.py index fb54bb9e7b..201b297593 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_RobustRegister.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_RobustRegister.py @@ -1,83 +1,84 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.freesurfer.preprocess import RobustRegister + def test_RobustRegister_inputs(): - input_map = dict(no_init=dict(argstr='--noinit', - ), - init_orient=dict(argstr='--initorient', + input_map = dict(args=dict(argstr='%s', ), - auto_sens=dict(xor=['outlier_sens'], + auto_sens=dict(argstr='--satit', mandatory=True, - argstr='--satit', - ), - source_file=dict(mandatory=True, - argstr='--mov %s', - ), - outlier_limit=dict(argstr='--wlimit %.3f', - ), - force_float=dict(argstr='--floattype', + xor=['outlier_sens'], ), - half_targ=dict(argstr='--halfdst %s', + environ=dict(nohash=True, + usedefault=True, ), - max_iterations=dict(argstr='--maxit %d', + est_int_scale=dict(argstr='--iscale', ), - write_vo2vox=dict(argstr='--vox2vox', + force_double=dict(argstr='--doubleprec', ), - high_iterations=dict(argstr='--highit %d', + force_float=dict(argstr='--floattype', ), half_source=dict(argstr='--halfmov %s', ), - force_double=dict(argstr='--doubleprec', + half_source_xfm=dict(argstr='--halfmovlta %s', ), - out_reg_file=dict(argstr='--lta %s', - genfile=True, + half_targ=dict(argstr='--halfdst %s', ), - half_source_xfm=dict(argstr='--halfmovlta %s', + half_targ_xfm=dict(argstr='--halfdstlta %s', ), - subsample_thresh=dict(argstr='--subsample %d', + half_weights=dict(argstr='--halfweights %s', ), - no_multi=dict(argstr='--nomulti', + high_iterations=dict(argstr='--highit %d', ), ignore_exception=dict(nohash=True, usedefault=True, ), - trans_only=dict(argstr='--transonly', - ), in_xfm_file=dict(argstr='--transform', ), - registered_file=dict(argstr='--warp %s', + init_orient=dict(argstr='--initorient', ), - least_squares=dict(argstr='--leastsquares', + iteration_thresh=dict(argstr='--epsit %.3f', ), - args=dict(argstr='%s', + least_squares=dict(argstr='--leastsquares', ), mask_source=dict(argstr='--maskmov %s', ), - outlier_sens=dict(xor=['auto_sens'], - mandatory=True, - argstr='--sat %.4f', - ), - subjects_dir=dict(), mask_target=dict(argstr='--maskdst %s', ), - half_weights=dict(argstr='--halfweights %s', + max_iterations=dict(argstr='--maxit %d', ), - target_file=dict(mandatory=True, - argstr='--dst %s', + no_init=dict(argstr='--noinit', ), - est_int_scale=dict(argstr='--iscale', + no_multi=dict(argstr='--nomulti', ), - weights_file=dict(argstr='--weights %s', + out_reg_file=dict(argstr='--lta %s', + genfile=True, ), - half_targ_xfm=dict(argstr='--halfdstlta %s', + outlier_limit=dict(argstr='--wlimit %.3f', ), - iteration_thresh=dict(argstr='--epsit %.3f', + outlier_sens=dict(argstr='--sat %.4f', + mandatory=True, + xor=['auto_sens'], + ), + registered_file=dict(argstr='--warp %s', + ), + source_file=dict(argstr='--mov %s', + mandatory=True, + ), + subjects_dir=dict(), + subsample_thresh=dict(argstr='--subsample %d', + ), + target_file=dict(argstr='--dst %s', + mandatory=True, ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, + trans_only=dict(argstr='--transonly', + ), + weights_file=dict(argstr='--weights %s', + ), + write_vo2vox=dict(argstr='--vox2vox', ), ) inputs = RobustRegister.input_spec() @@ -85,18 +86,20 @@ def test_RobustRegister_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_RobustRegister_outputs(): - output_map = dict(out_reg_file=dict(), + output_map = dict(half_source=dict(), + half_source_xfm=dict(), + half_targ=dict(), + half_targ_xfm=dict(), half_weights=dict(), + out_reg_file=dict(), registered_file=dict(), - half_source=dict(), - half_targ=dict(), weights_file=dict(), - half_targ_xfm=dict(), - half_source_xfm=dict(), ) outputs = RobustRegister.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SampleToSurface.py b/nipype/interfaces/freesurfer/tests/test_auto_SampleToSurface.py index c9332c7d86..7d43a72908 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SampleToSurface.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SampleToSurface.py @@ -1,106 +1,107 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.freesurfer.utils import SampleToSurface + def test_SampleToSurface_inputs(): - input_map = dict(reg_file=dict(mandatory=True, - argstr='--reg %s', - xor=['reg_file', 'reg_header', 'mni152reg'], - ), - sampling_units=dict(), - vox_file=dict(argstr='--nvox %s', - ), - frame=dict(argstr='--frame %d', + input_map = dict(apply_rot=dict(argstr='--rot %.3f %.3f %.3f', ), apply_trans=dict(argstr='--trans %.3f %.3f %.3f', ), - surface=dict(argstr='--surf %s', - ), - fix_tk_reg=dict(argstr='--fixtkreg', - ), - source_file=dict(mandatory=True, - argstr='--mov %s', - ), - interp_method=dict(argstr='--interp %s', + args=dict(argstr='%s', ), - scale_input=dict(argstr='--scale %.3f', + cortex_mask=dict(argstr='--cortex', + xor=['mask_label'], ), - reshape_slices=dict(argstr='--rf %d', + environ=dict(nohash=True, + usedefault=True, ), - args=dict(argstr='%s', + fix_tk_reg=dict(argstr='--fixtkreg', ), - reshape=dict(xor=['no_reshape'], - argstr='--reshape', + float2int_method=dict(argstr='--float2int %s', ), - subject_id=dict(), - sampling_method=dict(xor=['projection_stem'], - mandatory=True, - argstr='%s', - requires=['sampling_range', 'sampling_units'], + frame=dict(argstr='--frame %d', ), - reg_header=dict(xor=['reg_file', 'reg_header', 'mni152reg'], + hemi=dict(argstr='--hemi %s', mandatory=True, - requires=['subject_id'], - argstr='--regheader %s', ), hits_file=dict(argstr='--srchit %s', ), - reference_file=dict(argstr='--ref %s', + hits_type=dict(argstr='--srchit_type', ), - override_reg_subj=dict(requires=['subject_id'], - argstr='--srcsubject %s', + ico_order=dict(argstr='--icoorder %d', + requires=['target_subject'], ), ignore_exception=dict(nohash=True, usedefault=True, ), - ico_order=dict(requires=['target_subject'], - argstr='--icoorder %d', + interp_method=dict(argstr='--interp %s', ), - hits_type=dict(argstr='--srchit_type', + mask_label=dict(argstr='--mask %s', + xor=['cortex_mask'], + ), + mni152reg=dict(argstr='--mni152reg', + mandatory=True, + xor=['reg_file', 'reg_header', 'mni152reg'], + ), + no_reshape=dict(argstr='--noreshape', + xor=['reshape'], + ), + out_file=dict(argstr='--o %s', + genfile=True, ), - sampling_range=dict(), out_type=dict(argstr='--out_type %s', ), - terminal_output=dict(mandatory=True, - nohash=True, + override_reg_subj=dict(argstr='--srcsubject %s', + requires=['subject_id'], ), - no_reshape=dict(xor=['reshape'], - argstr='--noreshape', + projection_stem=dict(mandatory=True, + xor=['sampling_method'], ), - mni152reg=dict(mandatory=True, - argstr='--mni152reg', - xor=['reg_file', 'reg_header', 'mni152reg'], + reference_file=dict(argstr='--ref %s', ), - smooth_vol=dict(argstr='--fwhm %.3f', + reg_file=dict(argstr='--reg %s', + mandatory=True, + xor=['reg_file', 'reg_header', 'mni152reg'], ), - subjects_dir=dict(), - smooth_surf=dict(argstr='--surf-fwhm %.3f', + reg_header=dict(argstr='--regheader %s', + mandatory=True, + requires=['subject_id'], + xor=['reg_file', 'reg_header', 'mni152reg'], ), - float2int_method=dict(argstr='--float2int %s', + reshape=dict(argstr='--reshape', + xor=['no_reshape'], ), - hemi=dict(mandatory=True, - argstr='--hemi %s', + reshape_slices=dict(argstr='--rf %d', ), - surf_reg=dict(requires=['target_subject'], - argstr='--surfreg', + sampling_method=dict(argstr='%s', + mandatory=True, + requires=['sampling_range', 'sampling_units'], + xor=['projection_stem'], ), - out_file=dict(argstr='--o %s', - genfile=True, + sampling_range=dict(), + sampling_units=dict(), + scale_input=dict(argstr='--scale %.3f', ), - mask_label=dict(xor=['cortex_mask'], - argstr='--mask %s', + smooth_surf=dict(argstr='--surf-fwhm %.3f', ), - environ=dict(nohash=True, - usedefault=True, + smooth_vol=dict(argstr='--fwhm %.3f', ), - projection_stem=dict(xor=['sampling_method'], + source_file=dict(argstr='--mov %s', mandatory=True, ), - apply_rot=dict(argstr='--rot %.3f %.3f %.3f', + subject_id=dict(), + subjects_dir=dict(), + surf_reg=dict(argstr='--surfreg', + requires=['target_subject'], + ), + surface=dict(argstr='--surf %s', ), target_subject=dict(argstr='--trgsubject %s', ), - cortex_mask=dict(xor=['mask_label'], - argstr='--cortex', + terminal_output=dict(mandatory=True, + nohash=True, + ), + vox_file=dict(argstr='--nvox %s', ), ) inputs = SampleToSurface.input_spec() @@ -108,13 +109,15 @@ def test_SampleToSurface_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_SampleToSurface_outputs(): - output_map = dict(vox_file=dict(), - hits_file=dict(), + output_map = dict(hits_file=dict(), out_file=dict(), + vox_file=dict(), ) outputs = SampleToSurface.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SegStats.py b/nipype/interfaces/freesurfer/tests/test_auto_SegStats.py index c9f14e73a0..6b05f64641 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SegStats.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SegStats.py @@ -1,89 +1,90 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.freesurfer.model import SegStats + def test_SegStats_inputs(): - input_map = dict(exclude_ctx_gm_wm=dict(argstr='--excl-ctxgmwm', + input_map = dict(annot=dict(argstr='--annot %s %s %s', + mandatory=True, + xor=('segmentation_file', 'annot', 'surf_label'), ), - calc_snr=dict(argstr='--snr', + args=dict(argstr='%s', ), - frame=dict(argstr='--frame %d', + avgwf_file=dict(argstr='--avgwfvol %s', ), - cortex_vol_from_surf=dict(argstr='--surf-ctx-vol', + avgwf_txt_file=dict(argstr='--avgwf %s', ), - sf_avg_file=dict(argstr='--sfavg %s', + brain_vol=dict(), + calc_power=dict(argstr='--%s', ), - etiv=dict(argstr='--etiv', + calc_snr=dict(argstr='--snr', ), - exclude_id=dict(argstr='--excludeid %d', + color_table_file=dict(argstr='--ctab %s', + xor=('color_table_file', 'default_color_table', 'gca_color_table'), ), - etiv_only=dict(), - avgwf_txt_file=dict(argstr='--avgwf %s', + cortex_vol_from_surf=dict(argstr='--surf-ctx-vol', ), - default_color_table=dict(xor=('color_table_file', 'default_color_table', 'gca_color_table'), - argstr='--ctab-default', + default_color_table=dict(argstr='--ctab-default', + xor=('color_table_file', 'default_color_table', 'gca_color_table'), ), - mask_erode=dict(argstr='--maskerode %d', + environ=dict(nohash=True, + usedefault=True, ), - brain_vol=dict(), - in_file=dict(argstr='--i %s', + etiv=dict(argstr='--etiv', ), - gca_color_table=dict(xor=('color_table_file', 'default_color_table', 'gca_color_table'), - argstr='--ctab-gca %s', + etiv_only=dict(), + exclude_ctx_gm_wm=dict(argstr='--excl-ctxgmwm', ), - partial_volume_file=dict(argstr='--pv %f', + exclude_id=dict(argstr='--excludeid %d', ), - color_table_file=dict(xor=('color_table_file', 'default_color_table', 'gca_color_table'), - argstr='--ctab %s', + frame=dict(argstr='--frame %d', + ), + gca_color_table=dict(argstr='--ctab-gca %s', + xor=('color_table_file', 'default_color_table', 'gca_color_table'), ), ignore_exception=dict(nohash=True, usedefault=True, ), - surf_label=dict(mandatory=True, - xor=('segmentation_file', 'annot', 'surf_label'), - argstr='--slabel %s %s %s', - ), - segmentation_file=dict(xor=('segmentation_file', 'annot', 'surf_label'), - mandatory=True, - argstr='--seg %s', - ), - args=dict(argstr='%s', + in_file=dict(argstr='--i %s', ), - avgwf_file=dict(argstr='--avgwfvol %s', + mask_erode=dict(argstr='--maskerode %d', ), - terminal_output=dict(mandatory=True, - nohash=True, + mask_file=dict(argstr='--mask %s', ), - subjects_dir=dict(), - multiply=dict(argstr='--mul %f', + mask_frame=dict(requires=['mask_file'], ), mask_invert=dict(argstr='--maskinvert', ), mask_sign=dict(), - non_empty_only=dict(argstr='--nonempty', + mask_thresh=dict(argstr='--maskthresh %f', ), - calc_power=dict(argstr='--%s', + multiply=dict(argstr='--mul %f', ), - mask_frame=dict(requires=['mask_file'], + non_empty_only=dict(argstr='--nonempty', + ), + partial_volume_file=dict(argstr='--pv %f', ), segment_id=dict(argstr='--id %s...', ), - annot=dict(mandatory=True, + segmentation_file=dict(argstr='--seg %s', + mandatory=True, xor=('segmentation_file', 'annot', 'surf_label'), - argstr='--annot %s %s %s', ), - wm_vol_from_surf=dict(argstr='--surf-wm-vol', + sf_avg_file=dict(argstr='--sfavg %s', ), - environ=dict(nohash=True, - usedefault=True, + subjects_dir=dict(), + summary_file=dict(argstr='--sum %s', + genfile=True, ), - mask_thresh=dict(argstr='--maskthresh %f', + surf_label=dict(argstr='--slabel %s %s %s', + mandatory=True, + xor=('segmentation_file', 'annot', 'surf_label'), ), - mask_file=dict(argstr='--mask %s', + terminal_output=dict(mandatory=True, + nohash=True, ), vox=dict(argstr='--vox %s', ), - summary_file=dict(argstr='--sum %s', - genfile=True, + wm_vol_from_surf=dict(argstr='--surf-wm-vol', ), ) inputs = SegStats.input_spec() @@ -91,14 +92,16 @@ def test_SegStats_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_SegStats_outputs(): - output_map = dict(sf_avg_file=dict(), + output_map = dict(avgwf_file=dict(), avgwf_txt_file=dict(), + sf_avg_file=dict(), summary_file=dict(), - avgwf_file=dict(), ) outputs = SegStats.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Smooth.py b/nipype/interfaces/freesurfer/tests/test_auto_Smooth.py index 6fbf593c1c..e49046b6ab 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Smooth.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Smooth.py @@ -1,44 +1,45 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.freesurfer.preprocess import Smooth + def test_Smooth_inputs(): - input_map = dict(proj_frac_avg=dict(xor=['proj_frac'], - argstr='--projfrac-avg %.2f %.2f %.2f', + input_map = dict(args=dict(argstr='%s', + ), + environ=dict(nohash=True, + usedefault=True, ), ignore_exception=dict(nohash=True, usedefault=True, ), - reg_file=dict(mandatory=True, - argstr='--reg %s', + in_file=dict(argstr='--i %s', + mandatory=True, ), - num_iters=dict(mandatory=True, + num_iters=dict(argstr='--niters %d', + mandatory=True, xor=['surface_fwhm'], - argstr='--niters %d', ), - vol_fwhm=dict(argstr='--vol-fwhm %f', + proj_frac=dict(argstr='--projfrac %s', + xor=['proj_frac_avg'], ), - args=dict(argstr='%s', + proj_frac_avg=dict(argstr='--projfrac-avg %.2f %.2f %.2f', + xor=['proj_frac'], ), - terminal_output=dict(mandatory=True, - nohash=True, + reg_file=dict(argstr='--reg %s', + mandatory=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - in_file=dict(mandatory=True, - argstr='--i %s', + smoothed_file=dict(argstr='--o %s', + genfile=True, ), subjects_dir=dict(), - surface_fwhm=dict(mandatory=True, - xor=['num_iters'], - argstr='--fwhm %f', + surface_fwhm=dict(argstr='--fwhm %f', + mandatory=True, requires=['reg_file'], + xor=['num_iters'], ), - proj_frac=dict(xor=['proj_frac_avg'], - argstr='--projfrac %s', + terminal_output=dict(mandatory=True, + nohash=True, ), - smoothed_file=dict(genfile=True, - argstr='--o %s', + vol_fwhm=dict(argstr='--vol-fwhm %f', ), ) inputs = Smooth.input_spec() @@ -46,6 +47,7 @@ def test_Smooth_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Smooth_outputs(): output_map = dict(smoothed_file=dict(), ) @@ -54,3 +56,4 @@ def test_Smooth_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SmoothTessellation.py b/nipype/interfaces/freesurfer/tests/test_auto_SmoothTessellation.py index 2b56950a27..1931b56a73 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SmoothTessellation.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SmoothTessellation.py @@ -1,53 +1,54 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.freesurfer.utils import SmoothTessellation + def test_SmoothTessellation_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(args=dict(argstr='%s', ), - smoothing_iterations=dict(position=-2, - argstr='-n %d', + curvature_averaging_iterations=dict(argstr='-a %d', + position=-1, usedefault=True, ), - normalize_area=dict(argstr='-area', + disable_estimates=dict(argstr='-nw', ), - snapshot_writing_iterations=dict(argstr='-w %d', + environ=dict(nohash=True, + usedefault=True, ), - out_file=dict(position=2, - genfile=True, - argstr='%s', + gaussian_curvature_norm_steps=dict(argstr='%d ', + position=4, ), - disable_estimates=dict(argstr='-nw', + gaussian_curvature_smoothing_steps=dict(argstr='%d', + position=5, ), - out_area_file=dict(argstr='-b %s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - args=dict(argstr='%s', + in_file=dict(argstr='%s', + mandatory=True, + position=1, ), - use_gaussian_curvature_smoothing=dict(position=3, - argstr='-g', + normalize_area=dict(argstr='-area', ), - out_curvature_file=dict(argstr='-c %s', + out_area_file=dict(argstr='-b %s', ), - curvature_averaging_iterations=dict(position=-1, - argstr='-a %d', - usedefault=True, + out_curvature_file=dict(argstr='-c %s', ), - terminal_output=dict(mandatory=True, - nohash=True, + out_file=dict(argstr='%s', + genfile=True, + position=2, ), - environ=dict(nohash=True, + smoothing_iterations=dict(argstr='-n %d', + position=-2, usedefault=True, ), - in_file=dict(position=1, - mandatory=True, - argstr='%s', - ), - gaussian_curvature_smoothing_steps=dict(position=5, - argstr='%d', + snapshot_writing_iterations=dict(argstr='-w %d', ), subjects_dir=dict(), - gaussian_curvature_norm_steps=dict(position=4, - argstr='%d ', + terminal_output=dict(mandatory=True, + nohash=True, + ), + use_gaussian_curvature_smoothing=dict(argstr='-g', + position=3, ), use_momentum=dict(argstr='-m', ), @@ -57,6 +58,7 @@ def test_SmoothTessellation_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_SmoothTessellation_outputs(): output_map = dict(surface=dict(), ) @@ -65,3 +67,4 @@ def test_SmoothTessellation_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/freesurfer/tests/test_auto_Surface2VolTransform.py b/nipype/interfaces/freesurfer/tests/test_auto_Surface2VolTransform.py index 5a5846a930..6dd38f26ce 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_Surface2VolTransform.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_Surface2VolTransform.py @@ -1,58 +1,60 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.freesurfer.utils import Surface2VolTransform + def test_Surface2VolTransform_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, - ), - transformed_file=dict(name_source=['source_file'], - hash_files=False, - name_template='%s_asVol.nii', - argstr='--outvol %s', + input_map = dict(args=dict(argstr='%s', ), - hemi=dict(mandatory=True, - argstr='--hemi %s', - ), - template_file=dict(argstr='--template %s', + environ=dict(nohash=True, + usedefault=True, ), - subject_id=dict(xor=['reg_file'], - argstr='--identity %s', + hemi=dict(argstr='--hemi %s', + mandatory=True, ), - args=dict(argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - surf_name=dict(argstr='--surf %s', + mkmask=dict(argstr='--mkmask', ), - vertexvol_file=dict(name_source=['source_file'], - hash_files=False, - name_template='%s_asVol_vertex.nii', - argstr='--vtxvol %s', + projfrac=dict(argstr='--projfrac %s', ), - reg_file=dict(mandatory=True, - argstr='--volreg %s', + reg_file=dict(argstr='--volreg %s', + mandatory=True, xor=['subject_id'], ), - environ=dict(nohash=True, - usedefault=True, + source_file=dict(argstr='--surfval %s', + copyfile=False, + mandatory=True, ), - subjects_dir=dict(argstr='--sd %s', + subject_id=dict(argstr='--identity %s', + xor=['reg_file'], ), - source_file=dict(copyfile=False, - mandatory=True, - argstr='--surfval %s', + subjects_dir=dict(argstr='--sd %s', ), - projfrac=dict(argstr='--projfrac %s', + surf_name=dict(argstr='--surf %s', ), - mkmask=dict(argstr='--mkmask', + template_file=dict(argstr='--template %s', ), terminal_output=dict(mandatory=True, nohash=True, ), + transformed_file=dict(argstr='--outvol %s', + hash_files=False, + name_source=['source_file'], + name_template='%s_asVol.nii', + ), + vertexvol_file=dict(argstr='--vtxvol %s', + hash_files=False, + name_source=['source_file'], + name_template='%s_asVol_vertex.nii', + ), ) inputs = Surface2VolTransform.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Surface2VolTransform_outputs(): output_map = dict(transformed_file=dict(), vertexvol_file=dict(), @@ -62,3 +64,4 @@ def test_Surface2VolTransform_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSmooth.py b/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSmooth.py index 57fced4d4a..f4c44a8c34 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSmooth.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSmooth.py @@ -1,41 +1,42 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.freesurfer.utils import SurfaceSmooth + def test_SurfaceSmooth_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + cortex=dict(argstr='--cortex', usedefault=True, ), - hemi=dict(mandatory=True, - argstr='--hemi %s', + environ=dict(nohash=True, + usedefault=True, ), - out_file=dict(argstr='--tval %s', - genfile=True, + fwhm=dict(argstr='--fwhm %.4f', + xor=['smooth_iters'], ), - reshape=dict(argstr='--reshape', + hemi=dict(argstr='--hemi %s', + mandatory=True, ), - subject_id=dict(mandatory=True, - argstr='--s %s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - args=dict(argstr='%s', + in_file=dict(argstr='--sval %s', + mandatory=True, ), - terminal_output=dict(mandatory=True, - nohash=True, + out_file=dict(argstr='--tval %s', + genfile=True, ), - environ=dict(nohash=True, - usedefault=True, + reshape=dict(argstr='--reshape', ), - in_file=dict(mandatory=True, - argstr='--sval %s', + smooth_iters=dict(argstr='--smooth %d', + xor=['fwhm'], ), - smooth_iters=dict(xor=['fwhm'], - argstr='--smooth %d', + subject_id=dict(argstr='--s %s', + mandatory=True, ), subjects_dir=dict(), - fwhm=dict(xor=['smooth_iters'], - argstr='--fwhm %.4f', - ), - cortex=dict(argstr='--cortex', - usedefault=True, + terminal_output=dict(mandatory=True, + nohash=True, ), ) inputs = SurfaceSmooth.input_spec() @@ -43,6 +44,7 @@ def test_SurfaceSmooth_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_SurfaceSmooth_outputs(): output_map = dict(out_file=dict(), ) @@ -51,3 +53,4 @@ def test_SurfaceSmooth_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSnapshots.py b/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSnapshots.py index b6017f9bf6..f72a3bfc43 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSnapshots.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SurfaceSnapshots.py @@ -1,95 +1,96 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.freesurfer.utils import SurfaceSnapshots + def test_SurfaceSnapshots_inputs(): - input_map = dict(overlay_range=dict(argstr='%s', + input_map = dict(annot_file=dict(argstr='-annotation %s', + xor=['annot_name'], ), - show_color_scale=dict(argstr='-colscalebarflag 1', + annot_name=dict(argstr='-annotation %s', + xor=['annot_file'], ), - subjects_dir=dict(), - surface=dict(position=3, - mandatory=True, - argstr='%s', + args=dict(argstr='%s', ), - label_name=dict(xor=['label_file'], - argstr='-label %s', + colortable=dict(argstr='-colortable %s', ), - annot_name=dict(xor=['annot_file'], - argstr='-annotation %s', + demean_overlay=dict(argstr='-zm', ), - invert_overlay=dict(argstr='-invphaseflag 1', + environ=dict(nohash=True, + usedefault=True, ), - overlay=dict(requires=['overlay_range'], - argstr='-overlay %s', + hemi=dict(argstr='%s', + mandatory=True, + position=2, ), - overlay_range_offset=dict(argstr='-foffset %.3f', + identity_reg=dict(argstr='-overlay-reg-identity', + xor=['overlay_reg', 'identity_reg', 'mni152_reg'], ), - subject_id=dict(position=1, - mandatory=True, - argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - show_curv=dict(xor=['show_gray_curv'], - argstr='-curv', + invert_overlay=dict(argstr='-invphaseflag 1', ), - show_color_text=dict(argstr='-colscaletext 1', + label_file=dict(argstr='-label %s', + xor=['label_name'], ), - identity_reg=dict(xor=['overlay_reg', 'identity_reg', 'mni152_reg'], - argstr='-overlay-reg-identity', + label_name=dict(argstr='-label %s', + xor=['label_file'], + ), + label_outline=dict(argstr='-label-outline', ), label_under=dict(argstr='-labels-under', ), - environ=dict(nohash=True, - usedefault=True, + mni152_reg=dict(argstr='-mni152reg', + xor=['overlay_reg', 'identity_reg', 'mni152_reg'], ), - stem_template_args=dict(requires=['screenshot_stem'], + orig_suffix=dict(argstr='-orig %s', ), - screenshot_stem=dict(), - demean_overlay=dict(argstr='-zm', + overlay=dict(argstr='-overlay %s', + requires=['overlay_range'], ), - patch_file=dict(argstr='-patch %s', + overlay_range=dict(argstr='%s', ), - ignore_exception=dict(nohash=True, - usedefault=True, + overlay_range_offset=dict(argstr='-foffset %.3f', ), - hemi=dict(position=2, - mandatory=True, - argstr='%s', + overlay_reg=dict(argstr='-overlay-reg %s', + xor=['overlay_reg', 'identity_reg', 'mni152_reg'], ), - sphere_suffix=dict(argstr='-sphere %s', + patch_file=dict(argstr='-patch %s', ), - truncate_overlay=dict(argstr='-truncphaseflag 1', + reverse_overlay=dict(argstr='-revphaseflag 1', ), - args=dict(argstr='%s', + screenshot_stem=dict(), + show_color_scale=dict(argstr='-colscalebarflag 1', ), - orig_suffix=dict(argstr='-orig %s', + show_color_text=dict(argstr='-colscaletext 1', + ), + show_curv=dict(argstr='-curv', + xor=['show_gray_curv'], ), - show_gray_curv=dict(xor=['show_curv'], - argstr='-gray', + show_gray_curv=dict(argstr='-gray', + xor=['show_curv'], ), six_images=dict(), - mni152_reg=dict(xor=['overlay_reg', 'identity_reg', 'mni152_reg'], - argstr='-mni152reg', + sphere_suffix=dict(argstr='-sphere %s', ), - colortable=dict(argstr='-colortable %s', + stem_template_args=dict(requires=['screenshot_stem'], ), - label_outline=dict(argstr='-label-outline', + subject_id=dict(argstr='%s', + mandatory=True, + position=1, ), - annot_file=dict(xor=['annot_name'], - argstr='-annotation %s', + subjects_dir=dict(), + surface=dict(argstr='%s', + mandatory=True, + position=3, ), - reverse_overlay=dict(argstr='-revphaseflag 1', + tcl_script=dict(argstr='%s', + genfile=True, ), terminal_output=dict(mandatory=True, nohash=True, ), - overlay_reg=dict(xor=['overlay_reg', 'identity_reg', 'mni152_reg'], - argstr='-overlay-reg %s', - ), - label_file=dict(xor=['label_name'], - argstr='-label %s', - ), - tcl_script=dict(argstr='%s', - genfile=True, + truncate_overlay=dict(argstr='-truncphaseflag 1', ), ) inputs = SurfaceSnapshots.input_spec() @@ -97,6 +98,7 @@ def test_SurfaceSnapshots_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_SurfaceSnapshots_outputs(): output_map = dict(snapshots=dict(), ) @@ -105,3 +107,4 @@ def test_SurfaceSnapshots_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SurfaceTransform.py b/nipype/interfaces/freesurfer/tests/test_auto_SurfaceTransform.py index 946bc1bcc3..9a6c9ac64c 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SurfaceTransform.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SurfaceTransform.py @@ -1,49 +1,50 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.freesurfer.utils import SurfaceTransform + def test_SurfaceTransform_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + environ=dict(nohash=True, usedefault=True, ), - hemi=dict(mandatory=True, - argstr='--hemi %s', + hemi=dict(argstr='--hemi %s', + mandatory=True, + ), + ignore_exception=dict(nohash=True, + usedefault=True, ), out_file=dict(argstr='--tval %s', genfile=True, ), - source_subject=dict(mandatory=True, - argstr='--srcsubject %s', - ), reshape=dict(argstr='--reshape', ), - args=dict(argstr='%s', - ), - target_ico_order=dict(argstr='--trgicoorder %d', - ), - target_type=dict(argstr='--tfmt %s', - ), reshape_factor=dict(argstr='--reshape-factor', ), - source_type=dict(requires=['source_file'], - argstr='--sfmt %s', + source_annot_file=dict(argstr='--sval-annot %s', + mandatory=True, + xor=['source_file'], ), - terminal_output=dict(mandatory=True, - nohash=True, + source_file=dict(argstr='--sval %s', + mandatory=True, + xor=['source_annot_file'], ), - environ=dict(nohash=True, - usedefault=True, + source_subject=dict(argstr='--srcsubject %s', + mandatory=True, + ), + source_type=dict(argstr='--sfmt %s', + requires=['source_file'], ), subjects_dir=dict(), - source_file=dict(mandatory=True, - argstr='--sval %s', - xor=['source_annot_file'], + target_ico_order=dict(argstr='--trgicoorder %d', ), - target_subject=dict(mandatory=True, - argstr='--trgsubject %s', + target_subject=dict(argstr='--trgsubject %s', + mandatory=True, ), - source_annot_file=dict(mandatory=True, - argstr='--sval-annot %s', - xor=['source_file'], + target_type=dict(argstr='--tfmt %s', + ), + terminal_output=dict(mandatory=True, + nohash=True, ), ) inputs = SurfaceTransform.input_spec() @@ -51,6 +52,7 @@ def test_SurfaceTransform_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_SurfaceTransform_outputs(): output_map = dict(out_file=dict(), ) @@ -59,3 +61,4 @@ def test_SurfaceTransform_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/freesurfer/tests/test_auto_SynthesizeFLASH.py b/nipype/interfaces/freesurfer/tests/test_auto_SynthesizeFLASH.py index d9d2c792c6..7d10271668 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_SynthesizeFLASH.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_SynthesizeFLASH.py @@ -1,44 +1,45 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.freesurfer.preprocess import SynthesizeFLASH + def test_SynthesizeFLASH_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + environ=dict(nohash=True, usedefault=True, ), - out_file=dict(argstr='%s', - genfile=True, + fixed_weighting=dict(argstr='-w', + position=1, ), - flip_angle=dict(position=3, + flip_angle=dict(argstr='%.2f', mandatory=True, - argstr='%.2f', + position=3, ), - args=dict(argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - tr=dict(position=2, + out_file=dict(argstr='%s', + genfile=True, + ), + pd_image=dict(argstr='%s', mandatory=True, - argstr='%.2f', + position=6, ), - fixed_weighting=dict(position=1, - argstr='-w', + subjects_dir=dict(), + t1_image=dict(argstr='%s', + mandatory=True, + position=5, ), - pd_image=dict(position=6, + te=dict(argstr='%.3f', mandatory=True, - argstr='%s', + position=4, ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - subjects_dir=dict(), - te=dict(position=4, + tr=dict(argstr='%.2f', mandatory=True, - argstr='%.3f', - ), - t1_image=dict(position=5, - mandatory=True, - argstr='%s', + position=2, ), ) inputs = SynthesizeFLASH.input_spec() @@ -46,6 +47,7 @@ def test_SynthesizeFLASH_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_SynthesizeFLASH_outputs(): output_map = dict(out_file=dict(), ) @@ -54,3 +56,4 @@ def test_SynthesizeFLASH_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/freesurfer/tests/test_auto_UnpackSDICOMDir.py b/nipype/interfaces/freesurfer/tests/test_auto_UnpackSDICOMDir.py index 674a2ca88d..6de52d2765 100644 --- a/nipype/interfaces/freesurfer/tests/test_auto_UnpackSDICOMDir.py +++ b/nipype/interfaces/freesurfer/tests/test_auto_UnpackSDICOMDir.py @@ -1,47 +1,48 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.freesurfer.preprocess import UnpackSDICOMDir + def test_UnpackSDICOMDir_inputs(): - input_map = dict(seq_config=dict(mandatory=True, - argstr='-seqcfg %s', - xor=('run_info', 'config', 'seq_config'), + input_map = dict(args=dict(argstr='%s', ), - spm_zeropad=dict(argstr='-nspmzeropad %d', + config=dict(argstr='-cfg %s', + mandatory=True, + xor=('run_info', 'config', 'seq_config'), ), dir_structure=dict(argstr='-%s', ), + environ=dict(nohash=True, + usedefault=True, + ), ignore_exception=dict(nohash=True, usedefault=True, ), - args=dict(argstr='%s', + log_file=dict(argstr='-log %s', ), no_info_dump=dict(argstr='-noinfodump', ), - run_info=dict(xor=('run_info', 'config', 'seq_config'), - mandatory=True, - argstr='-run %d %s %s %s', - ), - terminal_output=dict(mandatory=True, - nohash=True, - ), - environ=dict(nohash=True, - usedefault=True, + no_unpack_err=dict(argstr='-no-unpackerr', ), output_dir=dict(argstr='-targ %s', ), - subjects_dir=dict(), - scan_only=dict(argstr='-scanonly %s', + run_info=dict(argstr='-run %d %s %s %s', + mandatory=True, + xor=('run_info', 'config', 'seq_config'), ), - log_file=dict(argstr='-log %s', + scan_only=dict(argstr='-scanonly %s', ), - config=dict(mandatory=True, - argstr='-cfg %s', + seq_config=dict(argstr='-seqcfg %s', + mandatory=True, xor=('run_info', 'config', 'seq_config'), ), - source_dir=dict(mandatory=True, - argstr='-src %s', + source_dir=dict(argstr='-src %s', + mandatory=True, ), - no_unpack_err=dict(argstr='-no-unpackerr', + spm_zeropad=dict(argstr='-nspmzeropad %d', + ), + subjects_dir=dict(), + terminal_output=dict(mandatory=True, + nohash=True, ), ) inputs = UnpackSDICOMDir.input_spec() @@ -49,3 +50,4 @@ def test_UnpackSDICOMDir_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_ApplyMask.py b/nipype/interfaces/fsl/tests/test_auto_ApplyMask.py index 4420cfb39f..536239933a 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ApplyMask.py +++ b/nipype/interfaces/fsl/tests/test_auto_ApplyMask.py @@ -1,40 +1,41 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.maths import ApplyMask + def test_ApplyMask_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + environ=dict(nohash=True, usedefault=True, ), - nan2zeros=dict(position=3, - argstr='-nan', + ignore_exception=dict(nohash=True, + usedefault=True, ), - out_file=dict(hash_files=False, - genfile=True, - position=-2, - argstr='%s', + in_file=dict(argstr='%s', + mandatory=True, + position=2, ), - args=dict(argstr='%s', + internal_datatype=dict(argstr='-dt %s', + position=1, ), - internal_datatype=dict(position=1, - argstr='-dt %s', + mask_file=dict(argstr='-mas %s', + mandatory=True, + position=4, ), - terminal_output=dict(mandatory=True, - nohash=True, + nan2zeros=dict(argstr='-nan', + position=3, ), - environ=dict(nohash=True, - usedefault=True, - ), - in_file=dict(position=2, - mandatory=True, - argstr='%s', + out_file=dict(argstr='%s', + genfile=True, + hash_files=False, + position=-2, ), - mask_file=dict(position=4, - mandatory=True, - argstr='-mas %s', + output_datatype=dict(argstr='-odt %s', + position=-1, ), output_type=dict(), - output_datatype=dict(position=-1, - argstr='-odt %s', + terminal_output=dict(mandatory=True, + nohash=True, ), ) inputs = ApplyMask.input_spec() @@ -42,6 +43,7 @@ def test_ApplyMask_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ApplyMask_outputs(): output_map = dict(out_file=dict(), ) @@ -50,3 +52,4 @@ def test_ApplyMask_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_ApplyTOPUP.py b/nipype/interfaces/fsl/tests/test_auto_ApplyTOPUP.py index 22c554fb99..700631023b 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ApplyTOPUP.py +++ b/nipype/interfaces/fsl/tests/test_auto_ApplyTOPUP.py @@ -1,38 +1,39 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.epi import ApplyTOPUP + def test_ApplyTOPUP_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(args=dict(argstr='%s', ), datatype=dict(argstr='-d=%s', ), - in_index=dict(mandatory=True, - argstr='%s', + encoding_file=dict(argstr='--datain=%s', + mandatory=True, ), - args=dict(argstr='%s', + environ=dict(nohash=True, + usedefault=True, ), - interp=dict(argstr='--interp=%s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - in_files=dict(mandatory=True, - argstr='%s', + in_files=dict(argstr='%s', + mandatory=True, ), - encoding_file=dict(mandatory=True, - argstr='--datain=%s', + in_index=dict(argstr='%s', + mandatory=True, ), - in_topup=dict(mandatory=True, - argstr='--topup=%s', + in_topup=dict(argstr='--topup=%s', + mandatory=True, ), - terminal_output=dict(mandatory=True, - nohash=True, + interp=dict(argstr='--interp=%s', ), - environ=dict(nohash=True, - usedefault=True, + method=dict(argstr='--method=%s', ), out_base=dict(argstr='--out=%s', ), output_type=dict(), - method=dict(argstr='--method=%s', + terminal_output=dict(mandatory=True, + nohash=True, ), ) inputs = ApplyTOPUP.input_spec() @@ -40,6 +41,7 @@ def test_ApplyTOPUP_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ApplyTOPUP_outputs(): output_map = dict(out_corrected=dict(), ) @@ -48,3 +50,4 @@ def test_ApplyTOPUP_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_ApplyWarp.py b/nipype/interfaces/fsl/tests/test_auto_ApplyWarp.py index 38aed0498d..ae3097937b 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ApplyWarp.py +++ b/nipype/interfaces/fsl/tests/test_auto_ApplyWarp.py @@ -1,50 +1,51 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.preprocess import ApplyWarp + def test_ApplyWarp_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, - ), - supersample=dict(argstr='--super', - ), - superlevel=dict(argstr='--superlevel=%s', + input_map = dict(abswarp=dict(argstr='--abs', + xor=['relwarp'], ), - out_file=dict(argstr='--out=%s', - hash_files=False, - genfile=True, + args=dict(argstr='%s', ), datatype=dict(argstr='--datatype=%s', ), - args=dict(argstr='%s', - ), - interp=dict(argstr='--interp=%s', + environ=dict(nohash=True, + usedefault=True, ), field_file=dict(argstr='--warp=%s', ), - ref_file=dict(mandatory=True, - argstr='--ref=%s', - ), - terminal_output=dict(mandatory=True, - nohash=True, - ), - environ=dict(nohash=True, + ignore_exception=dict(nohash=True, usedefault=True, ), - premat=dict(argstr='--premat=%s', + in_file=dict(argstr='--in=%s', + mandatory=True, + ), + interp=dict(argstr='--interp=%s', ), mask_file=dict(argstr='--mask=%s', ), + out_file=dict(argstr='--out=%s', + genfile=True, + hash_files=False, + ), output_type=dict(), postmat=dict(argstr='--postmat=%s', ), - relwarp=dict(xor=['abswarp'], - argstr='--rel', + premat=dict(argstr='--premat=%s', + ), + ref_file=dict(argstr='--ref=%s', + mandatory=True, ), - abswarp=dict(xor=['relwarp'], - argstr='--abs', + relwarp=dict(argstr='--rel', + xor=['abswarp'], ), - in_file=dict(mandatory=True, - argstr='--in=%s', + superlevel=dict(argstr='--superlevel=%s', + ), + supersample=dict(argstr='--super', + ), + terminal_output=dict(mandatory=True, + nohash=True, ), ) inputs = ApplyWarp.input_spec() @@ -52,6 +53,7 @@ def test_ApplyWarp_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ApplyWarp_outputs(): output_map = dict(out_file=dict(), ) @@ -60,3 +62,4 @@ def test_ApplyWarp_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_ApplyXfm.py b/nipype/interfaces/fsl/tests/test_auto_ApplyXfm.py index 4308799117..949fcf218b 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ApplyXfm.py +++ b/nipype/interfaces/fsl/tests/test_auto_ApplyXfm.py @@ -1,145 +1,146 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.preprocess import ApplyXfm + def test_ApplyXfm_inputs(): - input_map = dict(rigid2D=dict(argstr='-2D', + input_map = dict(angle_rep=dict(argstr='-anglerep %s', ), - in_matrix_file=dict(argstr='-init %s', + apply_isoxfm=dict(argstr='-applyisoxfm %f', + xor=['apply_xfm'], ), - verbose=dict(argstr='-verbose %d', + apply_xfm=dict(argstr='-applyxfm', + requires=['in_matrix_file'], + usedefault=True, ), - reference=dict(position=1, - mandatory=True, - argstr='-ref %s', + args=dict(argstr='%s', ), - padding_size=dict(units='voxels', - argstr='-paddingsize %d', + bbrslope=dict(argstr='-bbrslope %f', + min_ver='5.0.0', ), - sinc_window=dict(argstr='-sincwindow %s', + bbrtype=dict(argstr='-bbrtype %s', + min_ver='5.0.0', ), - interp=dict(argstr='-interp %s', + bins=dict(argstr='-bins %d', ), - wmnorms=dict(argstr='-wmnorms %s', - min_ver='5.0.0', + coarse_search=dict(argstr='-coarsesearch %d', + units='degrees', ), - coarse_search=dict(units='degrees', - argstr='-coarsesearch %d', + cost=dict(argstr='-cost %s', ), - no_resample=dict(argstr='-noresample', + cost_func=dict(argstr='-searchcost %s', ), - sinc_width=dict(units='voxels', - argstr='-sincwidth %d', + datatype=dict(argstr='-datatype %s', ), - in_weight=dict(argstr='-inweight %s', + display_init=dict(argstr='-displayinit', ), - fieldmap=dict(argstr='-fieldmap %s', - min_ver='5.0.0', + dof=dict(argstr='-dof %d', ), echospacing=dict(argstr='-echospacing %f', min_ver='5.0.0', ), - ref_weight=dict(argstr='-refweight %s', + environ=dict(nohash=True, + usedefault=True, ), - apply_isoxfm=dict(xor=['apply_xfm'], - argstr='-applyisoxfm %f', + fieldmap=dict(argstr='-fieldmap %s', + min_ver='5.0.0', ), fieldmapmask=dict(argstr='-fieldmapmask %s', min_ver='5.0.0', ), - in_file=dict(position=0, - mandatory=True, - argstr='-in %s', - ), - bbrtype=dict(min_ver='5.0.0', - argstr='-bbrtype %s', - ), - no_clamp=dict(argstr='-noclamp', + fine_search=dict(argstr='-finesearch %d', + units='degrees', ), force_scaling=dict(argstr='-forcescaling', ), - pedir=dict(argstr='-pedir %d', - min_ver='5.0.0', - ), ignore_exception=dict(nohash=True, usedefault=True, ), - display_init=dict(argstr='-displayinit', + in_file=dict(argstr='-in %s', + mandatory=True, + position=0, ), - schedule=dict(argstr='-schedule %s', + in_matrix_file=dict(argstr='-init %s', ), - args=dict(argstr='%s', + in_weight=dict(argstr='-inweight %s', ), - uses_qform=dict(argstr='-usesqform', + interp=dict(argstr='-interp %s', ), - wmcoords=dict(argstr='-wmcoords %s', - min_ver='5.0.0', + min_sampling=dict(argstr='-minsampling %f', + units='mm', ), - terminal_output=dict(mandatory=True, - nohash=True, + no_clamp=dict(argstr='-noclamp', ), - fine_search=dict(units='degrees', - argstr='-finesearch %d', + no_resample=dict(argstr='-noresample', ), - angle_rep=dict(argstr='-anglerep %s', + no_resample_blur=dict(argstr='-noresampblur', ), no_search=dict(argstr='-nosearch', ), - apply_xfm=dict(requires=['in_matrix_file'], - argstr='-applyxfm', - usedefault=True, - ), - wm_seg=dict(argstr='-wmseg %s', - min_ver='5.0.0', - ), - out_file=dict(name_source=['in_file'], + out_file=dict(argstr='-out %s', hash_files=False, + name_source=['in_file'], name_template='%s_flirt', position=2, - argstr='-out %s', ), - bbrslope=dict(argstr='-bbrslope %f', + out_log=dict(keep_extension=True, + name_source=['in_file'], + name_template='%s_flirt.log', + requires=['save_log'], + ), + out_matrix_file=dict(argstr='-omat %s', + hash_files=False, + keep_extension=True, + name_source=['in_file'], + name_template='%s_flirt.mat', + position=3, + ), + output_type=dict(), + padding_size=dict(argstr='-paddingsize %d', + units='voxels', + ), + pedir=dict(argstr='-pedir %d', min_ver='5.0.0', ), - datatype=dict(argstr='-datatype %s', + ref_weight=dict(argstr='-refweight %s', + ), + reference=dict(argstr='-ref %s', + mandatory=True, + position=1, + ), + rigid2D=dict(argstr='-2D', ), save_log=dict(), - dof=dict(argstr='-dof %d', + schedule=dict(argstr='-schedule %s', ), - out_matrix_file=dict(hash_files=False, - name_template='%s_flirt.mat', - name_source=['in_file'], - keep_extension=True, - position=3, - argstr='-omat %s', + searchr_x=dict(argstr='-searchrx %s', + units='degrees', ), - no_resample_blur=dict(argstr='-noresampblur', + searchr_y=dict(argstr='-searchry %s', + units='degrees', ), - min_sampling=dict(units='mm', - argstr='-minsampling %f', + searchr_z=dict(argstr='-searchrz %s', + units='degrees', ), - cost_func=dict(argstr='-searchcost %s', + sinc_width=dict(argstr='-sincwidth %d', + units='voxels', ), - cost=dict(argstr='-cost %s', + sinc_window=dict(argstr='-sincwindow %s', ), - environ=dict(nohash=True, - usedefault=True, + terminal_output=dict(mandatory=True, + nohash=True, ), - searchr_x=dict(units='degrees', - argstr='-searchrx %s', + uses_qform=dict(argstr='-usesqform', ), - out_log=dict(name_source=['in_file'], - keep_extension=True, - name_template='%s_flirt.log', - requires=['save_log'], + verbose=dict(argstr='-verbose %d', ), - output_type=dict(), - searchr_z=dict(units='degrees', - argstr='-searchrz %s', + wm_seg=dict(argstr='-wmseg %s', + min_ver='5.0.0', ), - bins=dict(argstr='-bins %d', + wmcoords=dict(argstr='-wmcoords %s', + min_ver='5.0.0', ), - searchr_y=dict(units='degrees', - argstr='-searchry %s', + wmnorms=dict(argstr='-wmnorms %s', + min_ver='5.0.0', ), ) inputs = ApplyXfm.input_spec() @@ -147,9 +148,10 @@ def test_ApplyXfm_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ApplyXfm_outputs(): - output_map = dict(out_log=dict(), - out_file=dict(), + output_map = dict(out_file=dict(), + out_log=dict(), out_matrix_file=dict(), ) outputs = ApplyXfm.output_spec() @@ -157,3 +159,4 @@ def test_ApplyXfm_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_AvScale.py b/nipype/interfaces/fsl/tests/test_auto_AvScale.py index 12e4017f99..a9480ad7d2 100644 --- a/nipype/interfaces/fsl/tests/test_auto_AvScale.py +++ b/nipype/interfaces/fsl/tests/test_auto_AvScale.py @@ -1,21 +1,22 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.utils import AvScale + def test_AvScale_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, - ), - args=dict(argstr='%s', - ), - terminal_output=dict(mandatory=True, - nohash=True, + input_map = dict(args=dict(argstr='%s', ), environ=dict(nohash=True, usedefault=True, ), + ignore_exception=dict(nohash=True, + usedefault=True, + ), + mat_file=dict(argstr='%s', + position=0, + ), output_type=dict(), - mat_file=dict(position=0, - argstr='%s', + terminal_output=dict(mandatory=True, + nohash=True, ), ) inputs = AvScale.input_spec() @@ -23,18 +24,20 @@ def test_AvScale_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_AvScale_outputs(): output_map = dict(average_scaling=dict(), - determinant=dict(), backward_half_transform=dict(), + determinant=dict(), forward_half_transform=dict(), - scales=dict(), left_right_orientation_preserved=dict(), - skews=dict(), rotation_translation_matrix=dict(), + scales=dict(), + skews=dict(), ) outputs = AvScale.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_BEDPOSTX.py b/nipype/interfaces/fsl/tests/test_auto_BEDPOSTX.py index 5ab1c43759..7b06b81137 100644 --- a/nipype/interfaces/fsl/tests/test_auto_BEDPOSTX.py +++ b/nipype/interfaces/fsl/tests/test_auto_BEDPOSTX.py @@ -1,39 +1,40 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.dti import BEDPOSTX + def test_BEDPOSTX_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + bpx_directory=dict(argstr='%s', usedefault=True, ), + burn_period=dict(argstr='-b %d', + ), + bvals=dict(mandatory=True, + ), bvecs=dict(mandatory=True, ), - bpx_directory=dict(argstr='%s', + dwi=dict(mandatory=True, + ), + environ=dict(nohash=True, usedefault=True, ), - bvals=dict(mandatory=True, + fibres=dict(argstr='-n %d', ), - weight=dict(argstr='-w %.2f', + ignore_exception=dict(nohash=True, + usedefault=True, ), jumps=dict(argstr='-j %d', ), - args=dict(argstr='%s', - ), mask=dict(mandatory=True, ), - burn_period=dict(argstr='-b %d', - ), + output_type=dict(), sampling=dict(argstr='-s %d', ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - output_type=dict(), - fibres=dict(argstr='-n %d', - ), - dwi=dict(mandatory=True, + weight=dict(argstr='-w %.2f', ), ) inputs = BEDPOSTX.input_spec() @@ -41,19 +42,21 @@ def test_BEDPOSTX_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_BEDPOSTX_outputs(): - output_map = dict(merged_phsamples=dict(), - bpx_out_directory=dict(), - xfms_directory=dict(), + output_map = dict(bpx_out_directory=dict(), dyads=dict(), - merged_fsamples=dict(), mean_fsamples=dict(), mean_phsamples=dict(), - merged_thsamples=dict(), mean_thsamples=dict(), + merged_fsamples=dict(), + merged_phsamples=dict(), + merged_thsamples=dict(), + xfms_directory=dict(), ) outputs = BEDPOSTX.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_BET.py b/nipype/interfaces/fsl/tests/test_auto_BET.py index e3772cde5e..6b6d9090ac 100644 --- a/nipype/interfaces/fsl/tests/test_auto_BET.py +++ b/nipype/interfaces/fsl/tests/test_auto_BET.py @@ -1,92 +1,95 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.preprocess import BET + def test_BET_inputs(): - input_map = dict(remove_eyes=dict(xor=('functional', 'reduce_bias', 'robust', 'padding', 'remove_eyes', 'surfaces', 't2_guided'), - argstr='-S', - ), - no_output=dict(argstr='-n', - ), - out_file=dict(hash_files=False, - genfile=True, - position=1, - argstr='%s', + input_map = dict(args=dict(argstr='%s', ), - functional=dict(xor=('functional', 'reduce_bias', 'robust', 'padding', 'remove_eyes', 'surfaces', 't2_guided'), - argstr='-F', + center=dict(argstr='-c %s', + units='voxels', ), - radius=dict(units='mm', - argstr='-r %d', + environ=dict(nohash=True, + usedefault=True, ), - threshold=dict(argstr='-t', + frac=dict(argstr='-f %.2f', ), - surfaces=dict(xor=('functional', 'reduce_bias', 'robust', 'padding', 'remove_eyes', 'surfaces', 't2_guided'), - argstr='-A', + functional=dict(argstr='-F', + xor=('functional', 'reduce_bias', 'robust', 'padding', 'remove_eyes', 'surfaces', 't2_guided'), ), - t2_guided=dict(xor=('functional', 'reduce_bias', 'robust', 'padding', 'remove_eyes', 'surfaces', 't2_guided'), - argstr='-A2 %s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - in_file=dict(position=0, + in_file=dict(argstr='%s', mandatory=True, - argstr='%s', + position=0, ), - ignore_exception=dict(nohash=True, - usedefault=True, + mask=dict(argstr='-m', ), - vertical_gradient=dict(argstr='-g %.2f', + mesh=dict(argstr='-e', ), - frac=dict(argstr='-f %.2f', + no_output=dict(argstr='-n', ), - reduce_bias=dict(xor=('functional', 'reduce_bias', 'robust', 'padding', 'remove_eyes', 'surfaces', 't2_guided'), - argstr='-B', + out_file=dict(argstr='%s', + genfile=True, + hash_files=False, + position=1, ), - args=dict(argstr='%s', + outline=dict(argstr='-o', ), - padding=dict(xor=('functional', 'reduce_bias', 'robust', 'padding', 'remove_eyes', 'surfaces', 't2_guided'), - argstr='-Z', + output_type=dict(), + padding=dict(argstr='-Z', + xor=('functional', 'reduce_bias', 'robust', 'padding', 'remove_eyes', 'surfaces', 't2_guided'), ), - mesh=dict(argstr='-e', + radius=dict(argstr='-r %d', + units='mm', ), - robust=dict(xor=('functional', 'reduce_bias', 'robust', 'padding', 'remove_eyes', 'surfaces', 't2_guided'), - argstr='-R', + reduce_bias=dict(argstr='-B', + xor=('functional', 'reduce_bias', 'robust', 'padding', 'remove_eyes', 'surfaces', 't2_guided'), ), - center=dict(units='voxels', - argstr='-c %s', + remove_eyes=dict(argstr='-S', + xor=('functional', 'reduce_bias', 'robust', 'padding', 'remove_eyes', 'surfaces', 't2_guided'), ), - outline=dict(argstr='-o', + robust=dict(argstr='-R', + xor=('functional', 'reduce_bias', 'robust', 'padding', 'remove_eyes', 'surfaces', 't2_guided'), ), skull=dict(argstr='-s', ), - mask=dict(argstr='-m', + surfaces=dict(argstr='-A', + xor=('functional', 'reduce_bias', 'robust', 'padding', 'remove_eyes', 'surfaces', 't2_guided'), + ), + t2_guided=dict(argstr='-A2 %s', + xor=('functional', 'reduce_bias', 'robust', 'padding', 'remove_eyes', 'surfaces', 't2_guided'), ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, + threshold=dict(argstr='-t', + ), + vertical_gradient=dict(argstr='-g %.2f', ), - output_type=dict(), ) inputs = BET.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_BET_outputs(): - output_map = dict(outline_file=dict(), - inskull_mask_file=dict(), - out_file=dict(), - meshfile=dict(), + output_map = dict(inskull_mask_file=dict(), inskull_mesh_file=dict(), - outskin_mask_file=dict(), - outskull_mesh_file=dict(), - skull_mask_file=dict(), mask_file=dict(), + meshfile=dict(), + out_file=dict(), + outline_file=dict(), + outskin_mask_file=dict(), outskin_mesh_file=dict(), outskull_mask_file=dict(), + outskull_mesh_file=dict(), + skull_mask_file=dict(), ) outputs = BET.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_BinaryMaths.py b/nipype/interfaces/fsl/tests/test_auto_BinaryMaths.py index a4e95710f1..699308f099 100644 --- a/nipype/interfaces/fsl/tests/test_auto_BinaryMaths.py +++ b/nipype/interfaces/fsl/tests/test_auto_BinaryMaths.py @@ -1,50 +1,51 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.maths import BinaryMaths + def test_BinaryMaths_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + environ=dict(nohash=True, usedefault=True, ), - nan2zeros=dict(position=3, - argstr='-nan', + ignore_exception=dict(nohash=True, + usedefault=True, ), - out_file=dict(hash_files=False, - genfile=True, - position=-2, - argstr='%s', + in_file=dict(argstr='%s', + mandatory=True, + position=2, ), - args=dict(argstr='%s', + internal_datatype=dict(argstr='-dt %s', + position=1, ), - operand_file=dict(xor=['operand_value'], - position=5, - mandatory=True, - argstr='%s', + nan2zeros=dict(argstr='-nan', + position=3, ), - internal_datatype=dict(position=1, - argstr='-dt %s', + operand_file=dict(argstr='%s', + mandatory=True, + position=5, + xor=['operand_value'], ), - operand_value=dict(mandatory=True, + operand_value=dict(argstr='%.8f', + mandatory=True, position=5, xor=['operand_file'], - argstr='%.8f', ), - terminal_output=dict(mandatory=True, - nohash=True, + operation=dict(argstr='-%s', + mandatory=True, + position=4, ), - environ=dict(nohash=True, - usedefault=True, + out_file=dict(argstr='%s', + genfile=True, + hash_files=False, + position=-2, ), - in_file=dict(position=2, - mandatory=True, - argstr='%s', + output_datatype=dict(argstr='-odt %s', + position=-1, ), output_type=dict(), - operation=dict(position=4, - mandatory=True, - argstr='-%s', - ), - output_datatype=dict(position=-1, - argstr='-odt %s', + terminal_output=dict(mandatory=True, + nohash=True, ), ) inputs = BinaryMaths.input_spec() @@ -52,6 +53,7 @@ def test_BinaryMaths_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_BinaryMaths_outputs(): output_map = dict(out_file=dict(), ) @@ -60,3 +62,4 @@ def test_BinaryMaths_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_ChangeDataType.py b/nipype/interfaces/fsl/tests/test_auto_ChangeDataType.py index a89deb45cf..2abe64953a 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ChangeDataType.py +++ b/nipype/interfaces/fsl/tests/test_auto_ChangeDataType.py @@ -1,37 +1,38 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.maths import ChangeDataType + def test_ChangeDataType_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(args=dict(argstr='%s', ), - nan2zeros=dict(position=3, - argstr='-nan', + environ=dict(nohash=True, + usedefault=True, ), - out_file=dict(hash_files=False, - genfile=True, - position=-2, - argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - args=dict(argstr='%s', + in_file=dict(argstr='%s', + mandatory=True, + position=2, ), - internal_datatype=dict(position=1, - argstr='-dt %s', + internal_datatype=dict(argstr='-dt %s', + position=1, ), - terminal_output=dict(mandatory=True, - nohash=True, + nan2zeros=dict(argstr='-nan', + position=3, ), - environ=dict(nohash=True, - usedefault=True, + out_file=dict(argstr='%s', + genfile=True, + hash_files=False, + position=-2, ), - in_file=dict(position=2, + output_datatype=dict(argstr='-odt %s', mandatory=True, - argstr='%s', + position=-1, ), output_type=dict(), - output_datatype=dict(position=-1, - mandatory=True, - argstr='-odt %s', + terminal_output=dict(mandatory=True, + nohash=True, ), ) inputs = ChangeDataType.input_spec() @@ -39,6 +40,7 @@ def test_ChangeDataType_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ChangeDataType_outputs(): output_map = dict(out_file=dict(), ) @@ -47,3 +49,4 @@ def test_ChangeDataType_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_Cluster.py b/nipype/interfaces/fsl/tests/test_auto_Cluster.py index cac3e2739f..1460f76254 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Cluster.py +++ b/nipype/interfaces/fsl/tests/test_auto_Cluster.py @@ -1,75 +1,76 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.model import Cluster + def test_Cluster_inputs(): - input_map = dict(dlh=dict(argstr='--dlh=%.10f', + input_map = dict(args=dict(argstr='%s', ), - num_maxima=dict(argstr='--num=%d', + connectivity=dict(argstr='--connectivity=%d', ), cope_file=dict(argstr='--cope=%s', ), - pthreshold=dict(requires=['dlh', 'volume'], - argstr='--pthresh=%.10f', + dlh=dict(argstr='--dlh=%.10f', ), - out_index_file=dict(hash_files=False, - argstr='--oindex=%s', - ), - threshold=dict(mandatory=True, - argstr='--thresh=%.10f', - ), - out_mean_file=dict(hash_files=False, - argstr='--omean=%s', + environ=dict(nohash=True, + usedefault=True, ), find_min=dict(), - std_space_file=dict(argstr='--stdvol=%s', - ), - out_localmax_txt_file=dict(hash_files=False, - argstr='--olmax=%s', - ), - out_localmax_vol_file=dict(hash_files=False, - argstr='--olmaxim=%s', - ), - in_file=dict(mandatory=True, - argstr='--in=%s', - ), fractional=dict(), - out_pval_file=dict(hash_files=False, - argstr='--opvals=%s', - ), ignore_exception=dict(nohash=True, usedefault=True, ), - use_mm=dict(), + in_file=dict(argstr='--in=%s', + mandatory=True, + ), minclustersize=dict(argstr='--minclustersize', ), no_table=dict(), - warpfield_file=dict(argstr='--warpvol=%s', + num_maxima=dict(argstr='--num=%d', ), - args=dict(argstr='%s', + out_index_file=dict(argstr='--oindex=%s', + hash_files=False, ), - volume=dict(argstr='--volume=%d', + out_localmax_txt_file=dict(argstr='--olmax=%s', + hash_files=False, ), - connectivity=dict(argstr='--connectivity=%d', + out_localmax_vol_file=dict(argstr='--olmaxim=%s', + hash_files=False, ), - terminal_output=dict(mandatory=True, - nohash=True, + out_max_file=dict(argstr='--omax=%s', + hash_files=False, ), - out_max_file=dict(hash_files=False, - argstr='--omax=%s', + out_mean_file=dict(argstr='--omean=%s', + hash_files=False, ), - output_type=dict(), - xfm_file=dict(argstr='--xfm=%s', + out_pval_file=dict(argstr='--opvals=%s', + hash_files=False, + ), + out_size_file=dict(argstr='--osize=%s', + hash_files=False, ), + out_threshold_file=dict(argstr='--othresh=%s', + hash_files=False, + ), + output_type=dict(), peak_distance=dict(argstr='--peakdist=%.10f', ), - out_threshold_file=dict(hash_files=False, - argstr='--othresh=%s', + pthreshold=dict(argstr='--pthresh=%.10f', + requires=['dlh', 'volume'], ), - environ=dict(nohash=True, - usedefault=True, + std_space_file=dict(argstr='--stdvol=%s', + ), + terminal_output=dict(mandatory=True, + nohash=True, + ), + threshold=dict(argstr='--thresh=%.10f', + mandatory=True, ), - out_size_file=dict(hash_files=False, - argstr='--osize=%s', + use_mm=dict(), + volume=dict(argstr='--volume=%d', + ), + warpfield_file=dict(argstr='--warpvol=%s', + ), + xfm_file=dict(argstr='--xfm=%s', ), ) inputs = Cluster.input_spec() @@ -77,18 +78,20 @@ def test_Cluster_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Cluster_outputs(): - output_map = dict(threshold_file=dict(), + output_map = dict(index_file=dict(), + localmax_txt_file=dict(), localmax_vol_file=dict(), - size_file=dict(), - mean_file=dict(), max_file=dict(), + mean_file=dict(), pval_file=dict(), - localmax_txt_file=dict(), - index_file=dict(), + size_file=dict(), + threshold_file=dict(), ) outputs = Cluster.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_Complex.py b/nipype/interfaces/fsl/tests/test_auto_Complex.py index 37f9a59167..d15df1d2e6 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Complex.py +++ b/nipype/interfaces/fsl/tests/test_auto_Complex.py @@ -1,107 +1,110 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.utils import Complex + def test_Complex_inputs(): - input_map = dict(real_cartesian=dict(position=1, + input_map = dict(args=dict(argstr='%s', + ), + complex_cartesian=dict(argstr='-complex', + position=1, xor=['real_polar', 'real_cartesian', 'complex_cartesian', 'complex_polar', 'complex_split', 'complex_merge'], - argstr='-realcartesian', ), - end_vol=dict(position=-1, - argstr='%d', + complex_in_file=dict(argstr='%s', + position=2, ), - complex_split=dict(position=1, - xor=['real_polar', 'real_cartesian', 'complex_cartesian', 'complex_polar', 'complex_split', 'complex_merge'], - argstr='-complexsplit', + complex_in_file2=dict(argstr='%s', + position=3, ), - start_vol=dict(position=-2, - argstr='%d', + complex_merge=dict(argstr='-complexmerge', + position=1, + xor=['real_polar', 'real_cartesian', 'complex_cartesian', 'complex_polar', 'complex_split', 'complex_merge', 'start_vol', 'end_vol'], ), - complex_cartesian=dict(position=1, - xor=['real_polar', 'real_cartesian', 'complex_cartesian', 'complex_polar', 'complex_split', 'complex_merge'], - argstr='-complex', + complex_out_file=dict(argstr='%s', + genfile=True, + position=-3, + xor=['complex_out_file', 'magnitude_out_file', 'phase_out_file', 'real_out_file', 'imaginary_out_file', 'real_polar', 'real_cartesian'], ), - real_polar=dict(position=1, + complex_polar=dict(argstr='-complexpolar', + position=1, xor=['real_polar', 'real_cartesian', 'complex_cartesian', 'complex_polar', 'complex_split', 'complex_merge'], - argstr='-realpolar', ), - imaginary_out_file=dict(position=-3, - genfile=True, - argstr='%s', - xor=['complex_out_file', 'magnitude_out_file', 'phase_out_file', 'real_polar', 'complex_cartesian', 'complex_polar', 'complex_split', 'complex_merge'], + complex_split=dict(argstr='-complexsplit', + position=1, + xor=['real_polar', 'real_cartesian', 'complex_cartesian', 'complex_polar', 'complex_split', 'complex_merge'], ), - phase_out_file=dict(position=-3, - genfile=True, - argstr='%s', - xor=['complex_out_file', 'real_out_file', 'imaginary_out_file', 'real_cartesian', 'complex_cartesian', 'complex_polar', 'complex_split', 'complex_merge'], + end_vol=dict(argstr='%d', + position=-1, ), - complex_merge=dict(position=1, - xor=['real_polar', 'real_cartesian', 'complex_cartesian', 'complex_polar', 'complex_split', 'complex_merge', 'start_vol', 'end_vol'], - argstr='-complexmerge', + environ=dict(nohash=True, + usedefault=True, ), ignore_exception=dict(nohash=True, usedefault=True, ), - magnitude_out_file=dict(position=-4, + imaginary_in_file=dict(argstr='%s', + position=3, + ), + imaginary_out_file=dict(argstr='%s', genfile=True, - argstr='%s', - xor=['complex_out_file', 'real_out_file', 'imaginary_out_file', 'real_cartesian', 'complex_cartesian', 'complex_polar', 'complex_split', 'complex_merge'], + position=-3, + xor=['complex_out_file', 'magnitude_out_file', 'phase_out_file', 'real_polar', 'complex_cartesian', 'complex_polar', 'complex_split', 'complex_merge'], ), - args=dict(argstr='%s', + magnitude_in_file=dict(argstr='%s', + position=2, ), - terminal_output=dict(mandatory=True, - nohash=True, - ), - complex_in_file=dict(position=2, - argstr='%s', + magnitude_out_file=dict(argstr='%s', + genfile=True, + position=-4, + xor=['complex_out_file', 'real_out_file', 'imaginary_out_file', 'real_cartesian', 'complex_cartesian', 'complex_polar', 'complex_split', 'complex_merge'], ), - magnitude_in_file=dict(position=2, - argstr='%s', + output_type=dict(), + phase_in_file=dict(argstr='%s', + position=3, ), - complex_out_file=dict(position=-3, + phase_out_file=dict(argstr='%s', genfile=True, - argstr='%s', - xor=['complex_out_file', 'magnitude_out_file', 'phase_out_file', 'real_out_file', 'imaginary_out_file', 'real_polar', 'real_cartesian'], - ), - real_in_file=dict(position=2, - argstr='%s', + position=-3, + xor=['complex_out_file', 'real_out_file', 'imaginary_out_file', 'real_cartesian', 'complex_cartesian', 'complex_polar', 'complex_split', 'complex_merge'], ), - complex_polar=dict(position=1, + real_cartesian=dict(argstr='-realcartesian', + position=1, xor=['real_polar', 'real_cartesian', 'complex_cartesian', 'complex_polar', 'complex_split', 'complex_merge'], - argstr='-complexpolar', ), - real_out_file=dict(position=-4, + real_in_file=dict(argstr='%s', + position=2, + ), + real_out_file=dict(argstr='%s', genfile=True, - argstr='%s', + position=-4, xor=['complex_out_file', 'magnitude_out_file', 'phase_out_file', 'real_polar', 'complex_cartesian', 'complex_polar', 'complex_split', 'complex_merge'], ), - imaginary_in_file=dict(position=3, - argstr='%s', + real_polar=dict(argstr='-realpolar', + position=1, + xor=['real_polar', 'real_cartesian', 'complex_cartesian', 'complex_polar', 'complex_split', 'complex_merge'], ), - complex_in_file2=dict(position=3, - argstr='%s', + start_vol=dict(argstr='%d', + position=-2, ), - environ=dict(nohash=True, - usedefault=True, - ), - phase_in_file=dict(position=3, - argstr='%s', + terminal_output=dict(mandatory=True, + nohash=True, ), - output_type=dict(), ) inputs = Complex.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Complex_outputs(): - output_map = dict(magnitude_out_file=dict(), + output_map = dict(complex_out_file=dict(), + imaginary_out_file=dict(), + magnitude_out_file=dict(), phase_out_file=dict(), real_out_file=dict(), - imaginary_out_file=dict(), - complex_out_file=dict(), ) outputs = Complex.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_ContrastMgr.py b/nipype/interfaces/fsl/tests/test_auto_ContrastMgr.py index adc9bbcdbf..7e342fa213 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ContrastMgr.py +++ b/nipype/interfaces/fsl/tests/test_auto_ContrastMgr.py @@ -1,44 +1,45 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.model import ContrastMgr + def test_ContrastMgr_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(args=dict(argstr='%s', ), - suffix=dict(argstr='-suffix %s', - ), - fcon_file=dict(argstr='-f %s', - ), - tcon_file=dict(position=-1, - mandatory=True, - argstr='%s', + contrast_num=dict(argstr='-cope', ), - param_estimates=dict(copyfile=False, + corrections=dict(copyfile=False, mandatory=True, - argstr='', ), - args=dict(argstr='%s', - ), - dof_file=dict(copyfile=False, + dof_file=dict(argstr='', + copyfile=False, mandatory=True, - argstr='', - ), - terminal_output=dict(mandatory=True, - nohash=True, ), environ=dict(nohash=True, usedefault=True, ), - corrections=dict(copyfile=False, - mandatory=True, + fcon_file=dict(argstr='-f %s', + ), + ignore_exception=dict(nohash=True, + usedefault=True, ), output_type=dict(), - contrast_num=dict(argstr='-cope', + param_estimates=dict(argstr='', + copyfile=False, + mandatory=True, ), - sigmasquareds=dict(copyfile=False, + sigmasquareds=dict(argstr='', + copyfile=False, mandatory=True, position=-2, - argstr='', + ), + suffix=dict(argstr='-suffix %s', + ), + tcon_file=dict(argstr='%s', + mandatory=True, + position=-1, + ), + terminal_output=dict(mandatory=True, + nohash=True, ), ) inputs = ContrastMgr.input_spec() @@ -46,17 +47,19 @@ def test_ContrastMgr_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ContrastMgr_outputs(): - output_map = dict(neffs=dict(), - varcopes=dict(), - tstats=dict(), - zstats=dict(), + output_map = dict(copes=dict(), fstats=dict(), + neffs=dict(), + tstats=dict(), + varcopes=dict(), zfstats=dict(), - copes=dict(), + zstats=dict(), ) outputs = ContrastMgr.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_ConvertXFM.py b/nipype/interfaces/fsl/tests/test_auto_ConvertXFM.py index c65e3b3b31..68cce822d9 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ConvertXFM.py +++ b/nipype/interfaces/fsl/tests/test_auto_ConvertXFM.py @@ -1,44 +1,45 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.utils import ConvertXFM + def test_ConvertXFM_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, - ), - out_file=dict(hash_files=False, - genfile=True, - position=1, - argstr='-omat %s', - ), - args=dict(argstr='%s', - ), - in_file2=dict(position=-2, - argstr='%s', + input_map = dict(args=dict(argstr='%s', ), - fix_scale_skew=dict(xor=['invert_xfm', 'concat_xfm', 'fix_scale_skew'], + concat_xfm=dict(argstr='-concat', position=-3, requires=['in_file2'], - argstr='-fixscaleskew', - ), - invert_xfm=dict(position=-3, xor=['invert_xfm', 'concat_xfm', 'fix_scale_skew'], - argstr='-inverse', ), - terminal_output=dict(mandatory=True, - nohash=True, + environ=dict(nohash=True, + usedefault=True, ), - concat_xfm=dict(xor=['invert_xfm', 'concat_xfm', 'fix_scale_skew'], + fix_scale_skew=dict(argstr='-fixscaleskew', position=-3, requires=['in_file2'], - argstr='-concat', + xor=['invert_xfm', 'concat_xfm', 'fix_scale_skew'], + ), + ignore_exception=dict(nohash=True, + usedefault=True, ), - in_file=dict(position=-1, + in_file=dict(argstr='%s', mandatory=True, - argstr='%s', + position=-1, + ), + in_file2=dict(argstr='%s', + position=-2, + ), + invert_xfm=dict(argstr='-inverse', + position=-3, + xor=['invert_xfm', 'concat_xfm', 'fix_scale_skew'], + ), + out_file=dict(argstr='-omat %s', + genfile=True, + hash_files=False, + position=1, ), output_type=dict(), - environ=dict(nohash=True, - usedefault=True, + terminal_output=dict(mandatory=True, + nohash=True, ), ) inputs = ConvertXFM.input_spec() @@ -46,6 +47,7 @@ def test_ConvertXFM_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ConvertXFM_outputs(): output_map = dict(out_file=dict(), ) @@ -54,3 +56,4 @@ def test_ConvertXFM_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_DTIFit.py b/nipype/interfaces/fsl/tests/test_auto_DTIFit.py index b62bc34027..4f74526f16 100644 --- a/nipype/interfaces/fsl/tests/test_auto_DTIFit.py +++ b/nipype/interfaces/fsl/tests/test_auto_DTIFit.py @@ -1,58 +1,59 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.dti import DTIFit + def test_DTIFit_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + base_name=dict(argstr='-o %s', + position=1, usedefault=True, ), - bvecs=dict(position=3, + bvals=dict(argstr='-b %s', mandatory=True, - argstr='-r %s', + position=4, ), - bvals=dict(position=4, + bvecs=dict(argstr='-r %s', mandatory=True, - argstr='-b %s', + position=3, ), - min_x=dict(argstr='-x %d', + cni=dict(argstr='-cni %s', ), - min_y=dict(argstr='-y %d', + dwi=dict(argstr='-k %s', + mandatory=True, + position=0, ), - min_z=dict(argstr='-z %d', + environ=dict(nohash=True, + usedefault=True, ), - base_name=dict(position=1, + ignore_exception=dict(nohash=True, usedefault=True, - argstr='-o %s', ), - args=dict(argstr='%s', + little_bit=dict(argstr='--littlebit', ), - mask=dict(position=2, + mask=dict(argstr='-m %s', mandatory=True, - argstr='-m %s', - ), - terminal_output=dict(mandatory=True, - nohash=True, - ), - environ=dict(nohash=True, - usedefault=True, + position=2, ), max_x=dict(argstr='-X %d', ), - little_bit=dict(argstr='--littlebit', + max_y=dict(argstr='-Y %d', ), - sse=dict(argstr='--sse', + max_z=dict(argstr='-Z %d', ), - output_type=dict(), - dwi=dict(position=0, - mandatory=True, - argstr='-k %s', + min_x=dict(argstr='-x %d', ), - max_z=dict(argstr='-Z %d', + min_y=dict(argstr='-y %d', ), - cni=dict(argstr='-cni %s', + min_z=dict(argstr='-z %d', ), + output_type=dict(), save_tensor=dict(argstr='--save_tensor', ), - max_y=dict(argstr='-Y %d', + sse=dict(argstr='--sse', + ), + terminal_output=dict(mandatory=True, + nohash=True, ), ) inputs = DTIFit.input_spec() @@ -60,21 +61,23 @@ def test_DTIFit_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_DTIFit_outputs(): - output_map = dict(MD=dict(), - tensor=dict(), - V1=dict(), + output_map = dict(FA=dict(), + L1=dict(), + L2=dict(), + L3=dict(), + MD=dict(), MO=dict(), S0=dict(), - FA=dict(), + V1=dict(), V2=dict(), V3=dict(), - L2=dict(), - L3=dict(), - L1=dict(), + tensor=dict(), ) outputs = DTIFit.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_DilateImage.py b/nipype/interfaces/fsl/tests/test_auto_DilateImage.py index 6e3ace5f2e..1f6d48a51c 100644 --- a/nipype/interfaces/fsl/tests/test_auto_DilateImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_DilateImage.py @@ -1,51 +1,52 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.maths import DilateImage + def test_DilateImage_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(args=dict(argstr='%s', ), - nan2zeros=dict(position=3, - argstr='-nan', + environ=dict(nohash=True, + usedefault=True, ), - kernel_file=dict(position=5, - xor=['kernel_size'], - argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - out_file=dict(hash_files=False, - genfile=True, - position=-2, - argstr='%s', + in_file=dict(argstr='%s', + mandatory=True, + position=2, ), - args=dict(argstr='%s', + internal_datatype=dict(argstr='-dt %s', + position=1, ), - internal_datatype=dict(position=1, - argstr='-dt %s', + kernel_file=dict(argstr='%s', + position=5, + xor=['kernel_size'], ), - terminal_output=dict(mandatory=True, - nohash=True, + kernel_shape=dict(argstr='-kernel %s', + position=4, ), - environ=dict(nohash=True, - usedefault=True, + kernel_size=dict(argstr='%.4f', + position=5, + xor=['kernel_file'], ), - kernel_shape=dict(position=4, - argstr='-kernel %s', + nan2zeros=dict(argstr='-nan', + position=3, ), - output_type=dict(), - operation=dict(position=6, + operation=dict(argstr='-dil%s', mandatory=True, - argstr='-dil%s', + position=6, ), - output_datatype=dict(position=-1, - argstr='-odt %s', + out_file=dict(argstr='%s', + genfile=True, + hash_files=False, + position=-2, ), - kernel_size=dict(position=5, - xor=['kernel_file'], - argstr='%.4f', + output_datatype=dict(argstr='-odt %s', + position=-1, ), - in_file=dict(position=2, - mandatory=True, - argstr='%s', + output_type=dict(), + terminal_output=dict(mandatory=True, + nohash=True, ), ) inputs = DilateImage.input_spec() @@ -53,6 +54,7 @@ def test_DilateImage_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_DilateImage_outputs(): output_map = dict(out_file=dict(), ) @@ -61,3 +63,4 @@ def test_DilateImage_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_DistanceMap.py b/nipype/interfaces/fsl/tests/test_auto_DistanceMap.py index a4a747a7bd..913cb1ca0f 100644 --- a/nipype/interfaces/fsl/tests/test_auto_DistanceMap.py +++ b/nipype/interfaces/fsl/tests/test_auto_DistanceMap.py @@ -1,32 +1,33 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.dti import DistanceMap + def test_DistanceMap_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, - ), - invert_input=dict(argstr='--invert', - ), - args=dict(argstr='%s', + input_map = dict(args=dict(argstr='%s', ), - terminal_output=dict(mandatory=True, - nohash=True, + distance_map=dict(argstr='--out=%s', + genfile=True, + hash_files=False, ), environ=dict(nohash=True, usedefault=True, ), - in_file=dict(mandatory=True, - argstr='--in=%s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - mask_file=dict(argstr='--mask=%s', + in_file=dict(argstr='--in=%s', + mandatory=True, ), - output_type=dict(), - distance_map=dict(argstr='--out=%s', + invert_input=dict(argstr='--invert', + ), + local_max_file=dict(argstr='--localmax=%s', hash_files=False, - genfile=True, ), - local_max_file=dict(hash_files=False, - argstr='--localmax=%s', + mask_file=dict(argstr='--mask=%s', + ), + output_type=dict(), + terminal_output=dict(mandatory=True, + nohash=True, ), ) inputs = DistanceMap.input_spec() @@ -34,6 +35,7 @@ def test_DistanceMap_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_DistanceMap_outputs(): output_map = dict(distance_map=dict(), local_max_file=dict(), @@ -43,3 +45,4 @@ def test_DistanceMap_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_EPIDeWarp.py b/nipype/interfaces/fsl/tests/test_auto_EPIDeWarp.py index b6f093b10f..a07999a965 100644 --- a/nipype/interfaces/fsl/tests/test_auto_EPIDeWarp.py +++ b/nipype/interfaces/fsl/tests/test_auto_EPIDeWarp.py @@ -1,55 +1,56 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.epi import EPIDeWarp + def test_EPIDeWarp_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, - ), - exf_file=dict(argstr='--exf %s', - ), - dph_file=dict(mandatory=True, - argstr='--dph %s', + input_map = dict(args=dict(argstr='%s', ), - esp=dict(usedefault=True, - argstr='--esp %s', + cleanup=dict(argstr='--cleanup', ), - mag_file=dict(position=0, + dph_file=dict(argstr='--dph %s', mandatory=True, - argstr='--mag %s', ), - nocleanup=dict(usedefault=True, - argstr='--nocleanup', - ), - args=dict(argstr='%s', + environ=dict(nohash=True, + usedefault=True, ), epi_file=dict(argstr='--epi %s', ), - tmpdir=dict(argstr='--tmpdir %s', - genfile=True, - ), - terminal_output=dict(mandatory=True, - nohash=True, + epidw=dict(argstr='--epidw %s', + genfile=False, ), - environ=dict(nohash=True, + esp=dict(argstr='--esp %s', usedefault=True, ), + exf_file=dict(argstr='--exf %s', + ), exfdw=dict(argstr='--exfdw %s', genfile=True, ), - output_type=dict(), - cleanup=dict(argstr='--cleanup', + ignore_exception=dict(nohash=True, + usedefault=True, ), - epidw=dict(argstr='--epidw %s', - genfile=False, + mag_file=dict(argstr='--mag %s', + mandatory=True, + position=0, + ), + nocleanup=dict(argstr='--nocleanup', + usedefault=True, ), + output_type=dict(), sigma=dict(argstr='--sigma %s', usedefault=True, ), - vsm=dict(argstr='--vsm %s', + tediff=dict(argstr='--tediff %s', + usedefault=True, + ), + terminal_output=dict(mandatory=True, + nohash=True, + ), + tmpdir=dict(argstr='--tmpdir %s', genfile=True, ), - tediff=dict(usedefault=True, - argstr='--tediff %s', + vsm=dict(argstr='--vsm %s', + genfile=True, ), ) inputs = EPIDeWarp.input_spec() @@ -57,14 +58,16 @@ def test_EPIDeWarp_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_EPIDeWarp_outputs(): - output_map = dict(unwarped_file=dict(), - vsm_file=dict(), + output_map = dict(exf_mask=dict(), exfdw=dict(), - exf_mask=dict(), + unwarped_file=dict(), + vsm_file=dict(), ) outputs = EPIDeWarp.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_Eddy.py b/nipype/interfaces/fsl/tests/test_auto_Eddy.py index 2ed933baca..20757beb05 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Eddy.py +++ b/nipype/interfaces/fsl/tests/test_auto_Eddy.py @@ -1,59 +1,61 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.epi import Eddy + def test_Eddy_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + environ=dict(nohash=True, usedefault=True, ), - niter=dict(argstr='--niter=%s', + flm=dict(argstr='--flm=%s', ), - in_acqp=dict(mandatory=True, - argstr='--acqp=%s', + fwhm=dict(argstr='--fwhm=%s', ), - out_base=dict(argstr='--out=%s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - args=dict(argstr='%s', + in_acqp=dict(argstr='--acqp=%s', + mandatory=True, ), - in_index=dict(mandatory=True, - argstr='--index=%s', + in_bval=dict(argstr='--bvals=%s', + mandatory=True, ), - in_mask=dict(mandatory=True, - argstr='--mask=%s', + in_bvec=dict(argstr='--bvecs=%s', + mandatory=True, ), - in_topup=dict(argstr='--topup=%s', + in_file=dict(argstr='--imain=%s', + mandatory=True, ), - session=dict(argstr='--session=%s', + in_index=dict(argstr='--index=%s', + mandatory=True, ), - environ=dict(nohash=True, - usedefault=True, + in_mask=dict(argstr='--mask=%s', + mandatory=True, ), - repol=dict(argstr='--repol', + in_topup=dict(argstr='--topup=%s', ), - output_type=dict(), - in_bval=dict(mandatory=True, - argstr='--bvals=%s', + method=dict(argstr='--resamp=%s', ), - flm=dict(argstr='--flm=%s', + niter=dict(argstr='--niter=%s', ), - in_bvec=dict(mandatory=True, - argstr='--bvecs=%s', + out_base=dict(argstr='--out=%s', ), - fwhm=dict(argstr='--fwhm=%s', + output_type=dict(), + repol=dict(argstr='--repol', ), - method=dict(argstr='--resamp=%s', + session=dict(argstr='--session=%s', ), terminal_output=dict(mandatory=True, nohash=True, ), - in_file=dict(mandatory=True, - argstr='--imain=%s', - ), ) inputs = Eddy.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Eddy_outputs(): output_map = dict(out_corrected=dict(), out_parameter=dict(), @@ -63,3 +65,4 @@ def test_Eddy_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_EddyCorrect.py b/nipype/interfaces/fsl/tests/test_auto_EddyCorrect.py index 4a178ce259..c8435e38d6 100644 --- a/nipype/interfaces/fsl/tests/test_auto_EddyCorrect.py +++ b/nipype/interfaces/fsl/tests/test_auto_EddyCorrect.py @@ -1,38 +1,40 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.epi import EddyCorrect + def test_EddyCorrect_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + environ=dict(nohash=True, + usedefault=True, + ), + ignore_exception=dict(nohash=True, usedefault=True, ), - out_file=dict(hash_files=False, + in_file=dict(argstr='%s', + mandatory=True, + position=0, + ), + out_file=dict(argstr='%s', genfile=True, + hash_files=False, position=1, - argstr='%s', ), - args=dict(argstr='%s', - ), - ref_num=dict(position=2, + output_type=dict(), + ref_num=dict(argstr='%d', mandatory=True, - argstr='%d', + position=2, ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - in_file=dict(position=0, - mandatory=True, - argstr='%s', - ), - output_type=dict(), ) inputs = EddyCorrect.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_EddyCorrect_outputs(): output_map = dict(eddy_corrected=dict(), ) @@ -41,3 +43,4 @@ def test_EddyCorrect_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_ErodeImage.py b/nipype/interfaces/fsl/tests/test_auto_ErodeImage.py index 53002605b4..77e4bcd3cc 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ErodeImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_ErodeImage.py @@ -1,51 +1,52 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.maths import ErodeImage + def test_ErodeImage_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + environ=dict(nohash=True, usedefault=True, ), - nan2zeros=dict(position=3, - argstr='-nan', + ignore_exception=dict(nohash=True, + usedefault=True, ), - kernel_file=dict(position=5, - xor=['kernel_size'], - argstr='%s', + in_file=dict(argstr='%s', + mandatory=True, + position=2, ), - out_file=dict(hash_files=False, - genfile=True, - position=-2, - argstr='%s', + internal_datatype=dict(argstr='-dt %s', + position=1, ), - args=dict(argstr='%s', + kernel_file=dict(argstr='%s', + position=5, + xor=['kernel_size'], ), - internal_datatype=dict(position=1, - argstr='-dt %s', + kernel_shape=dict(argstr='-kernel %s', + position=4, ), - terminal_output=dict(mandatory=True, - nohash=True, + kernel_size=dict(argstr='%.4f', + position=5, + xor=['kernel_file'], ), - environ=dict(nohash=True, + minimum_filter=dict(argstr='%s', + position=6, usedefault=True, ), - kernel_shape=dict(position=4, - argstr='-kernel %s', + nan2zeros=dict(argstr='-nan', + position=3, ), - minimum_filter=dict(position=6, - argstr='%s', - usedefault=True, - ), - output_type=dict(), - output_datatype=dict(position=-1, - argstr='-odt %s', + out_file=dict(argstr='%s', + genfile=True, + hash_files=False, + position=-2, ), - kernel_size=dict(position=5, - xor=['kernel_file'], - argstr='%.4f', + output_datatype=dict(argstr='-odt %s', + position=-1, ), - in_file=dict(position=2, - mandatory=True, - argstr='%s', + output_type=dict(), + terminal_output=dict(mandatory=True, + nohash=True, ), ) inputs = ErodeImage.input_spec() @@ -53,6 +54,7 @@ def test_ErodeImage_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ErodeImage_outputs(): output_map = dict(out_file=dict(), ) @@ -61,3 +63,4 @@ def test_ErodeImage_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_ExtractROI.py b/nipype/interfaces/fsl/tests/test_auto_ExtractROI.py index 8c31907de9..7961729175 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ExtractROI.py +++ b/nipype/interfaces/fsl/tests/test_auto_ExtractROI.py @@ -1,55 +1,56 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.utils import ExtractROI + def test_ExtractROI_inputs(): - input_map = dict(z_size=dict(position=7, - argstr='%d', - ), - ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(args=dict(argstr='%s', ), - t_min=dict(position=8, - argstr='%d', + crop_list=dict(argstr='%s', + position=2, + xor=['x_min', 'x_size', 'y_min', 'y_size', 'z_min', 'z_size', 't_min', 't_size'], ), - y_min=dict(position=4, - argstr='%d', + environ=dict(nohash=True, + usedefault=True, ), - y_size=dict(position=5, - argstr='%d', + ignore_exception=dict(nohash=True, + usedefault=True, ), - args=dict(argstr='%s', + in_file=dict(argstr='%s', + mandatory=True, + position=0, ), - z_min=dict(position=6, - argstr='%d', + output_type=dict(), + roi_file=dict(argstr='%s', + genfile=True, + hash_files=False, + position=1, ), - t_size=dict(position=9, - argstr='%d', + t_min=dict(argstr='%d', + position=8, ), - x_size=dict(position=3, - argstr='%d', + t_size=dict(argstr='%d', + position=9, ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, + x_min=dict(argstr='%d', + position=2, ), - in_file=dict(position=0, - mandatory=True, - argstr='%s', + x_size=dict(argstr='%d', + position=3, ), - x_min=dict(position=2, - argstr='%d', + y_min=dict(argstr='%d', + position=4, ), - output_type=dict(), - crop_list=dict(argstr='%s', - xor=['x_min', 'x_size', 'y_min', 'y_size', 'z_min', 'z_size', 't_min', 't_size'], - position=2, + y_size=dict(argstr='%d', + position=5, ), - roi_file=dict(hash_files=False, - genfile=True, - position=1, - argstr='%s', + z_min=dict(argstr='%d', + position=6, + ), + z_size=dict(argstr='%d', + position=7, ), ) inputs = ExtractROI.input_spec() @@ -57,6 +58,7 @@ def test_ExtractROI_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ExtractROI_outputs(): output_map = dict(roi_file=dict(), ) @@ -65,3 +67,4 @@ def test_ExtractROI_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_FAST.py b/nipype/interfaces/fsl/tests/test_auto_FAST.py index 53c30548d4..9cda0ade45 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FAST.py +++ b/nipype/interfaces/fsl/tests/test_auto_FAST.py @@ -1,66 +1,67 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.preprocess import FAST + def test_FAST_inputs(): - input_map = dict(number_classes=dict(argstr='-n %d', + input_map = dict(args=dict(argstr='%s', ), - out_basename=dict(argstr='-o %s', + bias_iters=dict(argstr='-I %d', + ), + bias_lowpass=dict(argstr='-l %d', + units='mm', + ), + environ=dict(nohash=True, + usedefault=True, ), hyper=dict(argstr='-H %.2f', ), - verbose=dict(argstr='-v', + ignore_exception=dict(nohash=True, + usedefault=True, ), - init_seg_smooth=dict(argstr='-f %.3f', + img_type=dict(argstr='-t %d', ), - in_files=dict(copyfile=False, + in_files=dict(argstr='%s', + copyfile=False, mandatory=True, position=-1, - argstr='%s', ), - no_pve=dict(argstr='--nopve', + init_seg_smooth=dict(argstr='-f %.3f', ), - output_biascorrected=dict(argstr='-B', + init_transform=dict(argstr='-a %s', + ), + iters_afterbias=dict(argstr='-O %d', + ), + manual_seg=dict(argstr='-s %s', ), mixel_smooth=dict(argstr='-R %.2f', ), - segments=dict(argstr='-g', + no_bias=dict(argstr='-N', ), - iters_afterbias=dict(argstr='-O %d', + no_pve=dict(argstr='--nopve', ), - bias_lowpass=dict(units='mm', - argstr='-l %d', + number_classes=dict(argstr='-n %d', ), other_priors=dict(argstr='-A %s', ), - ignore_exception=dict(nohash=True, - usedefault=True, + out_basename=dict(argstr='-o %s', ), - img_type=dict(argstr='-t %d', + output_biascorrected=dict(argstr='-B', ), - args=dict(argstr='%s', + output_biasfield=dict(argstr='-b', ), + output_type=dict(), probability_maps=dict(argstr='-p', ), - manual_seg=dict(argstr='-s %s', + segment_iters=dict(argstr='-W %d', + ), + segments=dict(argstr='-g', ), terminal_output=dict(mandatory=True, nohash=True, ), - output_biasfield=dict(argstr='-b', - ), - no_bias=dict(argstr='-N', - ), use_priors=dict(argstr='-P', ), - init_transform=dict(argstr='-a %s', - ), - segment_iters=dict(argstr='-W %d', - ), - environ=dict(nohash=True, - usedefault=True, - ), - output_type=dict(), - bias_iters=dict(argstr='-I %d', + verbose=dict(argstr='-v', ), ) inputs = FAST.input_spec() @@ -68,18 +69,20 @@ def test_FAST_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_FAST_outputs(): - output_map = dict(partial_volume_files=dict(), - tissue_class_files=dict(), + output_map = dict(bias_field=dict(), mixeltype=dict(), - restored_image=dict(), - tissue_class_map=dict(), + partial_volume_files=dict(), partial_volume_map=dict(), probability_maps=dict(), - bias_field=dict(), + restored_image=dict(), + tissue_class_files=dict(), + tissue_class_map=dict(), ) outputs = FAST.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_FEAT.py b/nipype/interfaces/fsl/tests/test_auto_FEAT.py index 727bbb06c7..1c5689b51d 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FEAT.py +++ b/nipype/interfaces/fsl/tests/test_auto_FEAT.py @@ -1,29 +1,31 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.model import FEAT + def test_FEAT_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + environ=dict(nohash=True, usedefault=True, ), - fsf_file=dict(position=0, + fsf_file=dict(argstr='%s', mandatory=True, - argstr='%s', + position=0, ), - args=dict(argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, ), + output_type=dict(), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - output_type=dict(), ) inputs = FEAT.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_FEAT_outputs(): output_map = dict(feat_dir=dict(), ) @@ -32,3 +34,4 @@ def test_FEAT_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_FEATModel.py b/nipype/interfaces/fsl/tests/test_auto_FEATModel.py index a04f4fedcf..5a3d0f08ca 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FEATModel.py +++ b/nipype/interfaces/fsl/tests/test_auto_FEATModel.py @@ -1,40 +1,42 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.model import FEATModel + def test_FEATModel_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, - ), - fsf_file=dict(copyfile=False, - mandatory=True, - position=0, - argstr='%s', + input_map = dict(args=dict(argstr='%s', ), - args=dict(argstr='%s', + environ=dict(nohash=True, + usedefault=True, ), - ev_files=dict(copyfile=False, + ev_files=dict(argstr='%s', + copyfile=False, mandatory=True, position=1, - argstr='%s', ), - terminal_output=dict(mandatory=True, - nohash=True, + fsf_file=dict(argstr='%s', + copyfile=False, + mandatory=True, + position=0, ), - environ=dict(nohash=True, + ignore_exception=dict(nohash=True, usedefault=True, ), output_type=dict(), + terminal_output=dict(mandatory=True, + nohash=True, + ), ) inputs = FEATModel.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_FEATModel_outputs(): - output_map = dict(design_cov=dict(), + output_map = dict(con_file=dict(), + design_cov=dict(), design_file=dict(), design_image=dict(), - con_file=dict(), fcon_file=dict(), ) outputs = FEATModel.output_spec() @@ -42,3 +44,4 @@ def test_FEATModel_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_FEATRegister.py b/nipype/interfaces/fsl/tests/test_auto_FEATRegister.py index b77d098f6e..3320d83eb1 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FEATRegister.py +++ b/nipype/interfaces/fsl/tests/test_auto_FEATRegister.py @@ -1,22 +1,24 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.model import FEATRegister + def test_FEATRegister_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(feat_dirs=dict(mandatory=True, + ), + ignore_exception=dict(nohash=True, usedefault=True, ), reg_dof=dict(usedefault=True, ), reg_image=dict(mandatory=True, ), - feat_dirs=dict(mandatory=True, - ), ) inputs = FEATRegister.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_FEATRegister_outputs(): output_map = dict(fsf_file=dict(), ) @@ -25,3 +27,4 @@ def test_FEATRegister_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_FIRST.py b/nipype/interfaces/fsl/tests/test_auto_FIRST.py index d88b9ec2b8..c866ba8874 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FIRST.py +++ b/nipype/interfaces/fsl/tests/test_auto_FIRST.py @@ -1,51 +1,52 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.preprocess import FIRST + def test_FIRST_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(affine_file=dict(argstr='-a %s', + position=6, + ), + args=dict(argstr='%s', + ), + brain_extracted=dict(argstr='-b', + position=2, + ), + environ=dict(nohash=True, + usedefault=True, + ), + ignore_exception=dict(nohash=True, usedefault=True, ), - affine_file=dict(position=6, - argstr='-a %s', + in_file=dict(argstr='-i %s', + mandatory=True, + position=-2, ), list_of_specific_structures=dict(argstr='-s %s', - sep=',', position=5, + sep=',', ), - verbose=dict(position=1, - argstr='-v', + method=dict(argstr='-m', + position=4, + xor=['method_as_numerical_threshold'], ), - args=dict(argstr='%s', + method_as_numerical_threshold=dict(argstr='-m', + position=4, ), - brain_extracted=dict(position=2, - argstr='-b', + no_cleanup=dict(argstr='-d', + position=3, ), - in_file=dict(position=-2, + out_file=dict(argstr='-o %s', + hash_files=False, mandatory=True, - argstr='-i %s', - ), - terminal_output=dict(mandatory=True, - nohash=True, - ), - environ=dict(nohash=True, + position=-1, usedefault=True, ), - no_cleanup=dict(position=3, - argstr='-d', - ), - method_as_numerical_threshold=dict(position=4, - argstr='-m', - ), output_type=dict(), - method=dict(position=4, - xor=['method_as_numerical_threshold'], - argstr='-m', + terminal_output=dict(mandatory=True, + nohash=True, ), - out_file=dict(hash_files=False, - mandatory=True, - usedefault=True, - position=-1, - argstr='-o %s', + verbose=dict(argstr='-v', + position=1, ), ) inputs = FIRST.input_spec() @@ -53,14 +54,16 @@ def test_FIRST_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_FIRST_outputs(): - output_map = dict(vtk_surfaces=dict(), - segmentation_file=dict(), - bvars=dict(), + output_map = dict(bvars=dict(), original_segmentations=dict(), + segmentation_file=dict(), + vtk_surfaces=dict(), ) outputs = FIRST.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_FLAMEO.py b/nipype/interfaces/fsl/tests/test_auto_FLAMEO.py index 12066c34c5..7ac19140d8 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FLAMEO.py +++ b/nipype/interfaces/fsl/tests/test_auto_FLAMEO.py @@ -1,61 +1,62 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.model import FLAMEO + def test_FLAMEO_inputs(): - input_map = dict(sample_every=dict(argstr='--sampleevery=%d', + input_map = dict(args=dict(argstr='%s', ), - cope_file=dict(mandatory=True, - argstr='--copefile=%s', + burnin=dict(argstr='--burnin=%d', ), - cov_split_file=dict(mandatory=True, - argstr='--covsplitfile=%s', + cope_file=dict(argstr='--copefile=%s', + mandatory=True, ), - n_jumps=dict(argstr='--njumps=%d', + cov_split_file=dict(argstr='--covsplitfile=%s', + mandatory=True, ), - burnin=dict(argstr='--burnin=%d', + design_file=dict(argstr='--designfile=%s', + mandatory=True, ), - design_file=dict(mandatory=True, - argstr='--designfile=%s', + dof_var_cope_file=dict(argstr='--dofvarcopefile=%s', ), - no_pe_outputs=dict(argstr='--nopeoutput', + environ=dict(nohash=True, + usedefault=True, ), - log_dir=dict(usedefault=True, - argstr='--ld=%s', + f_con_file=dict(argstr='--fcontrastsfile=%s', ), - run_mode=dict(mandatory=True, - argstr='--runmode=%s', + fix_mean=dict(argstr='--fixmean', ), ignore_exception=dict(nohash=True, usedefault=True, ), - f_con_file=dict(argstr='--fcontrastsfile=%s', + infer_outliers=dict(argstr='--inferoutliers', ), - args=dict(argstr='%s', + log_dir=dict(argstr='--ld=%s', + usedefault=True, ), - t_con_file=dict(mandatory=True, - argstr='--tcontrastsfile=%s', + mask_file=dict(argstr='--maskfile=%s', + mandatory=True, ), - dof_var_cope_file=dict(argstr='--dofvarcopefile=%s', + n_jumps=dict(argstr='--njumps=%d', ), - terminal_output=dict(mandatory=True, - nohash=True, + no_pe_outputs=dict(argstr='--nopeoutput', ), - var_cope_file=dict(argstr='--varcopefile=%s', + outlier_iter=dict(argstr='--ioni=%d', ), - fix_mean=dict(argstr='--fixmean', + output_type=dict(), + run_mode=dict(argstr='--runmode=%s', + mandatory=True, ), - sigma_dofs=dict(argstr='--sigma_dofs=%d', + sample_every=dict(argstr='--sampleevery=%d', ), - outlier_iter=dict(argstr='--ioni=%d', + sigma_dofs=dict(argstr='--sigma_dofs=%d', ), - environ=dict(nohash=True, - usedefault=True, + t_con_file=dict(argstr='--tcontrastsfile=%s', + mandatory=True, ), - mask_file=dict(mandatory=True, - argstr='--maskfile=%s', + terminal_output=dict(mandatory=True, + nohash=True, ), - output_type=dict(), - infer_outliers=dict(argstr='--inferoutliers', + var_cope_file=dict(argstr='--varcopefile=%s', ), ) inputs = FLAMEO.input_spec() @@ -63,22 +64,24 @@ def test_FLAMEO_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_FLAMEO_outputs(): - output_map = dict(mrefvars=dict(), - tstats=dict(), + output_map = dict(copes=dict(), + fstats=dict(), + mrefvars=dict(), pes=dict(), + res4d=dict(), stats_dir=dict(), - zstats=dict(), - weights=dict(), tdof=dict(), + tstats=dict(), var_copes=dict(), - copes=dict(), - fstats=dict(), + weights=dict(), zfstats=dict(), - res4d=dict(), + zstats=dict(), ) outputs = FLAMEO.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_FLIRT.py b/nipype/interfaces/fsl/tests/test_auto_FLIRT.py index 3f3ad8fef0..198afa62f2 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FLIRT.py +++ b/nipype/interfaces/fsl/tests/test_auto_FLIRT.py @@ -1,144 +1,145 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.preprocess import FLIRT + def test_FLIRT_inputs(): - input_map = dict(rigid2D=dict(argstr='-2D', + input_map = dict(angle_rep=dict(argstr='-anglerep %s', ), - in_matrix_file=dict(argstr='-init %s', + apply_isoxfm=dict(argstr='-applyisoxfm %f', + xor=['apply_xfm'], ), - verbose=dict(argstr='-verbose %d', + apply_xfm=dict(argstr='-applyxfm', + requires=['in_matrix_file'], ), - reference=dict(position=1, - mandatory=True, - argstr='-ref %s', + args=dict(argstr='%s', ), - padding_size=dict(units='voxels', - argstr='-paddingsize %d', + bbrslope=dict(argstr='-bbrslope %f', + min_ver='5.0.0', ), - sinc_window=dict(argstr='-sincwindow %s', + bbrtype=dict(argstr='-bbrtype %s', + min_ver='5.0.0', ), - interp=dict(argstr='-interp %s', + bins=dict(argstr='-bins %d', ), - wmnorms=dict(argstr='-wmnorms %s', - min_ver='5.0.0', + coarse_search=dict(argstr='-coarsesearch %d', + units='degrees', ), - display_init=dict(argstr='-displayinit', + cost=dict(argstr='-cost %s', ), - no_resample=dict(argstr='-noresample', + cost_func=dict(argstr='-searchcost %s', ), - sinc_width=dict(units='voxels', - argstr='-sincwidth %d', + datatype=dict(argstr='-datatype %s', ), - in_weight=dict(argstr='-inweight %s', + display_init=dict(argstr='-displayinit', ), - fieldmap=dict(argstr='-fieldmap %s', - min_ver='5.0.0', + dof=dict(argstr='-dof %d', ), - no_search=dict(argstr='-nosearch', + echospacing=dict(argstr='-echospacing %f', + min_ver='5.0.0', ), - ref_weight=dict(argstr='-refweight %s', + environ=dict(nohash=True, + usedefault=True, ), - apply_isoxfm=dict(xor=['apply_xfm'], - argstr='-applyisoxfm %f', + fieldmap=dict(argstr='-fieldmap %s', + min_ver='5.0.0', ), fieldmapmask=dict(argstr='-fieldmapmask %s', min_ver='5.0.0', ), - in_file=dict(position=0, - mandatory=True, - argstr='-in %s', - ), - bbrtype=dict(min_ver='5.0.0', - argstr='-bbrtype %s', - ), - no_clamp=dict(argstr='-noclamp', + fine_search=dict(argstr='-finesearch %d', + units='degrees', ), force_scaling=dict(argstr='-forcescaling', ), - pedir=dict(argstr='-pedir %d', - min_ver='5.0.0', - ), ignore_exception=dict(nohash=True, usedefault=True, ), - coarse_search=dict(units='degrees', - argstr='-coarsesearch %d', - ), - schedule=dict(argstr='-schedule %s', - ), - args=dict(argstr='%s', + in_file=dict(argstr='-in %s', + mandatory=True, + position=0, ), - uses_qform=dict(argstr='-usesqform', + in_matrix_file=dict(argstr='-init %s', ), - wmcoords=dict(argstr='-wmcoords %s', - min_ver='5.0.0', + in_weight=dict(argstr='-inweight %s', ), - terminal_output=dict(mandatory=True, - nohash=True, + interp=dict(argstr='-interp %s', ), - fine_search=dict(units='degrees', - argstr='-finesearch %d', + min_sampling=dict(argstr='-minsampling %f', + units='mm', ), - angle_rep=dict(argstr='-anglerep %s', + no_clamp=dict(argstr='-noclamp', ), - echospacing=dict(argstr='-echospacing %f', - min_ver='5.0.0', + no_resample=dict(argstr='-noresample', ), - apply_xfm=dict(requires=['in_matrix_file'], - argstr='-applyxfm', + no_resample_blur=dict(argstr='-noresampblur', ), - wm_seg=dict(argstr='-wmseg %s', - min_ver='5.0.0', + no_search=dict(argstr='-nosearch', ), - out_file=dict(name_source=['in_file'], + out_file=dict(argstr='-out %s', hash_files=False, + name_source=['in_file'], name_template='%s_flirt', position=2, - argstr='-out %s', ), - bbrslope=dict(argstr='-bbrslope %f', + out_log=dict(keep_extension=True, + name_source=['in_file'], + name_template='%s_flirt.log', + requires=['save_log'], + ), + out_matrix_file=dict(argstr='-omat %s', + hash_files=False, + keep_extension=True, + name_source=['in_file'], + name_template='%s_flirt.mat', + position=3, + ), + output_type=dict(), + padding_size=dict(argstr='-paddingsize %d', + units='voxels', + ), + pedir=dict(argstr='-pedir %d', min_ver='5.0.0', ), - datatype=dict(argstr='-datatype %s', + ref_weight=dict(argstr='-refweight %s', ), - searchr_z=dict(units='degrees', - argstr='-searchrz %s', + reference=dict(argstr='-ref %s', + mandatory=True, + position=1, ), - dof=dict(argstr='-dof %d', + rigid2D=dict(argstr='-2D', ), - out_matrix_file=dict(hash_files=False, - name_template='%s_flirt.mat', - name_source=['in_file'], - keep_extension=True, - position=3, - argstr='-omat %s', + save_log=dict(), + schedule=dict(argstr='-schedule %s', ), - no_resample_blur=dict(argstr='-noresampblur', + searchr_x=dict(argstr='-searchrx %s', + units='degrees', ), - min_sampling=dict(units='mm', - argstr='-minsampling %f', + searchr_y=dict(argstr='-searchry %s', + units='degrees', ), - cost_func=dict(argstr='-searchcost %s', + searchr_z=dict(argstr='-searchrz %s', + units='degrees', ), - cost=dict(argstr='-cost %s', + sinc_width=dict(argstr='-sincwidth %d', + units='voxels', ), - environ=dict(nohash=True, - usedefault=True, + sinc_window=dict(argstr='-sincwindow %s', ), - bins=dict(argstr='-bins %d', + terminal_output=dict(mandatory=True, + nohash=True, ), - out_log=dict(name_source=['in_file'], - keep_extension=True, - name_template='%s_flirt.log', - requires=['save_log'], + uses_qform=dict(argstr='-usesqform', ), - output_type=dict(), - save_log=dict(), - searchr_x=dict(units='degrees', - argstr='-searchrx %s', + verbose=dict(argstr='-verbose %d', ), - searchr_y=dict(units='degrees', - argstr='-searchry %s', + wm_seg=dict(argstr='-wmseg %s', + min_ver='5.0.0', + ), + wmcoords=dict(argstr='-wmcoords %s', + min_ver='5.0.0', + ), + wmnorms=dict(argstr='-wmnorms %s', + min_ver='5.0.0', ), ) inputs = FLIRT.input_spec() @@ -146,9 +147,10 @@ def test_FLIRT_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_FLIRT_outputs(): - output_map = dict(out_log=dict(), - out_file=dict(), + output_map = dict(out_file=dict(), + out_log=dict(), out_matrix_file=dict(), ) outputs = FLIRT.output_spec() @@ -156,3 +158,4 @@ def test_FLIRT_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_FNIRT.py b/nipype/interfaces/fsl/tests/test_auto_FNIRT.py index cf98fe15ac..09159a3549 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FNIRT.py +++ b/nipype/interfaces/fsl/tests/test_auto_FNIRT.py @@ -1,124 +1,125 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.preprocess import FNIRT + def test_FNIRT_inputs(): - input_map = dict(derive_from_ref=dict(argstr='--refderiv', - ), - in_intensitymap_file=dict(argstr='--intin=%s', - ), - modulatedref_file=dict(hash_files=False, - argstr='--refout=%s', + input_map = dict(affine_file=dict(argstr='--aff=%s', ), - refmask_val=dict(argstr='--imprefval=%f', - ), - hessian_precision=dict(argstr='--numprec=%s', - ), - skip_implicit_in_masking=dict(argstr='--impinm=0', - ), - inmask_file=dict(argstr='--inmask=%s', + apply_inmask=dict(argstr='--applyinmask=%s', + sep=',', + xor=['skip_inmask'], ), - refmask_file=dict(argstr='--refmask=%s', + apply_intensity_mapping=dict(argstr='--estint=%s', + sep=',', + xor=['skip_intensity_mapping'], ), apply_refmask=dict(argstr='--applyrefmask=%s', - xor=['skip_refmask'], sep=',', + xor=['skip_refmask'], ), - skip_lambda_ssq=dict(argstr='--ssqlambda=0', - ), - intensity_mapping_model=dict(argstr='--intmod=%s', - ), - affine_file=dict(argstr='--aff=%s', + args=dict(argstr='%s', ), - apply_inmask=dict(argstr='--applyinmask=%s', - xor=['skip_inmask'], - sep=',', + bias_regularization_lambda=dict(argstr='--biaslambda=%f', ), - spline_order=dict(argstr='--splineorder=%d', + biasfield_resolution=dict(argstr='--biasres=%d,%d,%d', ), - inwarp_file=dict(argstr='--inwarp=%s', + config_file=dict(argstr='--config=%s', ), - subsampling_scheme=dict(sep=',', - argstr='--subsamp=%s', + derive_from_ref=dict(argstr='--refderiv', ), - in_file=dict(mandatory=True, - argstr='--in=%s', + environ=dict(nohash=True, + usedefault=True, ), - warped_file=dict(argstr='--iout=%s', + field_file=dict(argstr='--fout=%s', hash_files=False, - genfile=True, ), - skip_refmask=dict(xor=['apply_refmask'], - argstr='--applyrefmask=0', + fieldcoeff_file=dict(argstr='--cout=%s', + ), + hessian_precision=dict(argstr='--numprec=%s', ), ignore_exception=dict(nohash=True, usedefault=True, ), - ref_fwhm=dict(sep=',', - argstr='--reffwhm=%s', - ), - args=dict(argstr='%s', + in_file=dict(argstr='--in=%s', + mandatory=True, ), - config_file=dict(argstr='--config=%s', + in_fwhm=dict(argstr='--infwhm=%s', + sep=',', ), - skip_inmask=dict(xor=['apply_inmask'], - argstr='--applyinmask=0', + in_intensitymap_file=dict(argstr='--intin=%s', ), - field_file=dict(hash_files=False, - argstr='--fout=%s', + inmask_file=dict(argstr='--inmask=%s', ), inmask_val=dict(argstr='--impinval=%f', ), - apply_intensity_mapping=dict(argstr='--estint=%s', - xor=['skip_intensity_mapping'], - sep=',', + intensity_mapping_model=dict(argstr='--intmod=%s', ), - regularization_lambda=dict(sep=',', - argstr='--lambda=%s', + intensity_mapping_order=dict(argstr='--intorder=%d', ), - terminal_output=dict(mandatory=True, - nohash=True, + inwarp_file=dict(argstr='--inwarp=%s', ), - regularization_model=dict(argstr='--regmod=%s', + jacobian_file=dict(argstr='--jout=%s', + hash_files=False, ), jacobian_range=dict(argstr='--jacrange=%f,%f', ), - out_intensitymap_file=dict(hash_files=False, - argstr='--intout=%s', + log_file=dict(argstr='--logout=%s', + genfile=True, + hash_files=False, ), - skip_implicit_ref_masking=dict(argstr='--imprefm=0', + max_nonlin_iter=dict(argstr='--miter=%s', + sep=',', ), - log_file=dict(argstr='--logout=%s', + modulatedref_file=dict(argstr='--refout=%s', hash_files=False, - genfile=True, ), - ref_file=dict(mandatory=True, - argstr='--ref=%s', + out_intensitymap_file=dict(argstr='--intout=%s', + hash_files=False, ), - biasfield_resolution=dict(argstr='--biasres=%d,%d,%d', + output_type=dict(), + ref_file=dict(argstr='--ref=%s', + mandatory=True, ), - fieldcoeff_file=dict(argstr='--cout=%s', + ref_fwhm=dict(argstr='--reffwhm=%s', + sep=',', ), - warp_resolution=dict(argstr='--warpres=%d,%d,%d', + refmask_file=dict(argstr='--refmask=%s', ), - jacobian_file=dict(hash_files=False, - argstr='--jout=%s', + refmask_val=dict(argstr='--imprefval=%f', ), - environ=dict(nohash=True, - usedefault=True, + regularization_lambda=dict(argstr='--lambda=%s', + sep=',', ), - output_type=dict(), - skip_intensity_mapping=dict(xor=['apply_intensity_mapping'], - argstr='--estint=0', + regularization_model=dict(argstr='--regmod=%s', ), - in_fwhm=dict(sep=',', - argstr='--infwhm=%s', + skip_implicit_in_masking=dict(argstr='--impinm=0', ), - bias_regularization_lambda=dict(argstr='--biaslambda=%f', + skip_implicit_ref_masking=dict(argstr='--imprefm=0', ), - intensity_mapping_order=dict(argstr='--intorder=%d', + skip_inmask=dict(argstr='--applyinmask=0', + xor=['apply_inmask'], + ), + skip_intensity_mapping=dict(argstr='--estint=0', + xor=['apply_intensity_mapping'], ), - max_nonlin_iter=dict(sep=',', - argstr='--miter=%s', + skip_lambda_ssq=dict(argstr='--ssqlambda=0', + ), + skip_refmask=dict(argstr='--applyrefmask=0', + xor=['apply_refmask'], + ), + spline_order=dict(argstr='--splineorder=%d', + ), + subsampling_scheme=dict(argstr='--subsamp=%s', + sep=',', + ), + terminal_output=dict(mandatory=True, + nohash=True, + ), + warp_resolution=dict(argstr='--warpres=%d,%d,%d', + ), + warped_file=dict(argstr='--iout=%s', + genfile=True, + hash_files=False, ), ) inputs = FNIRT.input_spec() @@ -126,17 +127,19 @@ def test_FNIRT_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_FNIRT_outputs(): - output_map = dict(modulatedref_file=dict(), + output_map = dict(field_file=dict(), fieldcoeff_file=dict(), jacobian_file=dict(), - field_file=dict(), - warped_file=dict(), log_file=dict(), + modulatedref_file=dict(), out_intensitymap_file=dict(), + warped_file=dict(), ) outputs = FNIRT.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_FSLCommand.py b/nipype/interfaces/fsl/tests/test_auto_FSLCommand.py index 3c754b4445..066b10102f 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FSLCommand.py +++ b/nipype/interfaces/fsl/tests/test_auto_FSLCommand.py @@ -1,22 +1,24 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.base import FSLCommand + def test_FSLCommand_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + environ=dict(nohash=True, + usedefault=True, + ), + ignore_exception=dict(nohash=True, usedefault=True, ), output_type=dict(), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - args=dict(argstr='%s', - ), ) inputs = FSLCommand.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_FUGUE.py b/nipype/interfaces/fsl/tests/test_auto_FUGUE.py index c93ed81922..d27a0f9d27 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FUGUE.py +++ b/nipype/interfaces/fsl/tests/test_auto_FUGUE.py @@ -1,88 +1,89 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.preprocess import FUGUE + def test_FUGUE_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, - ), - dwell_time=dict(argstr='--dwell=%.10f', + input_map = dict(args=dict(argstr='%s', ), asym_se_time=dict(argstr='--asym=%.10f', ), - smooth3d=dict(argstr='--smooth3=%.2f', + despike_2dfilter=dict(argstr='--despike', ), - no_gap_fill=dict(argstr='--nofill', + despike_threshold=dict(argstr='--despikethreshold=%s', ), - forward_warping=dict(usedefault=True, + dwell_time=dict(argstr='--dwell=%.10f', ), - phasemap_file=dict(argstr='--phasemap=%s', + dwell_to_asym_ratio=dict(argstr='--dwelltoasym=%.10f', ), - save_shift=dict(), - poly_order=dict(argstr='--poly=%d', + environ=dict(nohash=True, + usedefault=True, ), - shift_in_file=dict(argstr='--loadshift=%s', + fmap_in_file=dict(argstr='--loadfmap=%s', ), - shift_out_file=dict(hash_files=False, - argstr='--saveshift=%s', + fmap_out_file=dict(argstr='--savefmap=%s', + hash_files=False, ), - median_2dfilter=dict(argstr='--median', + forward_warping=dict(usedefault=True, ), - save_unmasked_shift=dict(requires=['shift_out_file'], - argstr='--unmaskshift', + fourier_order=dict(argstr='--fourier=%d', ), - despike_2dfilter=dict(argstr='--despike', + icorr=dict(argstr='--icorr', + requires=['shift_in_file'], ), - save_unmasked_fmap=dict(requires=['fmap_out_file'], - argstr='--unmaskfmap', + icorr_only=dict(argstr='--icorronly', + requires=['unwarped_file'], ), - in_file=dict(argstr='--in=%s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - warped_file=dict(hash_files=False, - argstr='--warp=%s', + in_file=dict(argstr='--in=%s', ), - dwell_to_asym_ratio=dict(argstr='--dwelltoasym=%.10f', + mask_file=dict(argstr='--mask=%s', ), - unwarped_file=dict(argstr='--unwarp=%s', - hash_files=False, - genfile=True, + median_2dfilter=dict(argstr='--median', ), - icorr_only=dict(requires=['unwarped_file'], - argstr='--icorronly', + no_extend=dict(argstr='--noextend', ), - smooth2d=dict(argstr='--smooth2=%.2f', + no_gap_fill=dict(argstr='--nofill', ), - phase_conjugate=dict(argstr='--phaseconj', + nokspace=dict(argstr='--nokspace', ), + output_type=dict(), pava=dict(argstr='--pava', ), - args=dict(argstr='%s', + phase_conjugate=dict(argstr='--phaseconj', ), - terminal_output=dict(mandatory=True, - nohash=True, + phasemap_file=dict(argstr='--phasemap=%s', ), - output_type=dict(), - icorr=dict(requires=['shift_in_file'], - argstr='--icorr', + poly_order=dict(argstr='--poly=%d', ), - fmap_in_file=dict(argstr='--loadfmap=%s', + save_shift=dict(), + save_unmasked_fmap=dict(argstr='--unmaskfmap', + requires=['fmap_out_file'], ), - despike_threshold=dict(argstr='--despikethreshold=%s', + save_unmasked_shift=dict(argstr='--unmaskshift', + requires=['shift_out_file'], ), - unwarp_direction=dict(argstr='--unwarpdir=%s', + shift_in_file=dict(argstr='--loadshift=%s', ), - fmap_out_file=dict(hash_files=False, - argstr='--savefmap=%s', + shift_out_file=dict(argstr='--saveshift=%s', + hash_files=False, ), - environ=dict(nohash=True, - usedefault=True, + smooth2d=dict(argstr='--smooth2=%.2f', ), - mask_file=dict(argstr='--mask=%s', + smooth3d=dict(argstr='--smooth3=%.2f', ), - no_extend=dict(argstr='--noextend', + terminal_output=dict(mandatory=True, + nohash=True, ), - fourier_order=dict(argstr='--fourier=%d', + unwarp_direction=dict(argstr='--unwarpdir=%s', ), - nokspace=dict(argstr='--nokspace', + unwarped_file=dict(argstr='--unwarp=%s', + genfile=True, + hash_files=False, + ), + warped_file=dict(argstr='--warp=%s', + hash_files=False, ), ) inputs = FUGUE.input_spec() @@ -90,10 +91,11 @@ def test_FUGUE_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_FUGUE_outputs(): - output_map = dict(unwarped_file=dict(), + output_map = dict(fmap_out_file=dict(), shift_out_file=dict(), - fmap_out_file=dict(), + unwarped_file=dict(), warped_file=dict(), ) outputs = FUGUE.output_spec() @@ -101,3 +103,4 @@ def test_FUGUE_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_FilterRegressor.py b/nipype/interfaces/fsl/tests/test_auto_FilterRegressor.py index 37a6672a95..d32173886d 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FilterRegressor.py +++ b/nipype/interfaces/fsl/tests/test_auto_FilterRegressor.py @@ -1,54 +1,56 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.utils import FilterRegressor + def test_FilterRegressor_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(args=dict(argstr='%s', ), - out_file=dict(hash_files=False, - genfile=True, - position=2, - argstr='-o %s', + design_file=dict(argstr='-d %s', + mandatory=True, + position=3, + ), + environ=dict(nohash=True, + usedefault=True, ), - filter_all=dict(mandatory=True, + filter_all=dict(argstr="-f '%s'", + mandatory=True, position=4, xor=['filter_columns'], - argstr="-f '%s'", ), - out_vnscales=dict(argstr='--out_vnscales', + filter_columns=dict(argstr="-f '%s'", + mandatory=True, + position=4, + xor=['filter_all'], ), - args=dict(argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - mask=dict(argstr='-m %s', + in_file=dict(argstr='-i %s', + mandatory=True, + position=1, ), - terminal_output=dict(mandatory=True, - nohash=True, + mask=dict(argstr='-m %s', ), - environ=dict(nohash=True, - usedefault=True, + out_file=dict(argstr='-o %s', + genfile=True, + hash_files=False, + position=2, ), - in_file=dict(position=1, - mandatory=True, - argstr='-i %s', + out_vnscales=dict(argstr='--out_vnscales', ), output_type=dict(), - filter_columns=dict(xor=['filter_all'], - position=4, - mandatory=True, - argstr="-f '%s'", + terminal_output=dict(mandatory=True, + nohash=True, ), var_norm=dict(argstr='--vn', ), - design_file=dict(position=3, - mandatory=True, - argstr='-d %s', - ), ) inputs = FilterRegressor.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_FilterRegressor_outputs(): output_map = dict(out_file=dict(), ) @@ -57,3 +59,4 @@ def test_FilterRegressor_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_FindTheBiggest.py b/nipype/interfaces/fsl/tests/test_auto_FindTheBiggest.py index e02cf782ce..8a9570f31e 100644 --- a/nipype/interfaces/fsl/tests/test_auto_FindTheBiggest.py +++ b/nipype/interfaces/fsl/tests/test_auto_FindTheBiggest.py @@ -1,34 +1,36 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.dti import FindTheBiggest + def test_FindTheBiggest_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(args=dict(argstr='%s', ), - out_file=dict(hash_files=False, - genfile=True, - position=2, - argstr='%s', + environ=dict(nohash=True, + usedefault=True, ), - args=dict(argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, ), in_files=dict(argstr='%s', mandatory=True, position=0, ), + out_file=dict(argstr='%s', + genfile=True, + hash_files=False, + position=2, + ), + output_type=dict(), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - output_type=dict(), ) inputs = FindTheBiggest.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_FindTheBiggest_outputs(): output_map = dict(out_file=dict(argstr='%s', ), @@ -38,3 +40,4 @@ def test_FindTheBiggest_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_GLM.py b/nipype/interfaces/fsl/tests/test_auto_GLM.py index 5e8d1fc5bb..85dce3e1cf 100644 --- a/nipype/interfaces/fsl/tests/test_auto_GLM.py +++ b/nipype/interfaces/fsl/tests/test_auto_GLM.py @@ -1,68 +1,69 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.model import GLM + def test_GLM_inputs(): - input_map = dict(out_sigsq_name=dict(argstr='--out_sigsq=%s', + input_map = dict(args=dict(argstr='%s', ), - dof=dict(argstr='--dof=%d', + contrasts=dict(argstr='-c %s', ), - out_pf_name=dict(argstr='--out_pf=%s', + dat_norm=dict(argstr='--dat_norm', ), - out_t_name=dict(argstr='--out_t=%s', + demean=dict(argstr='--demean', ), - out_cope=dict(argstr='--out_cope=%s', + des_norm=dict(argstr='--des_norm', ), - design=dict(position=2, + design=dict(argstr='-d %s', mandatory=True, - argstr='-d %s', + position=2, ), - mask=dict(argstr='-m %s', - ), - out_res_name=dict(argstr='--out_res=%s', - ), - in_file=dict(position=1, - mandatory=True, - argstr='-i %s', + dof=dict(argstr='--dof=%d', ), environ=dict(nohash=True, usedefault=True, ), - out_vnscales_name=dict(argstr='--out_vnscales=%s', - ), ignore_exception=dict(nohash=True, usedefault=True, ), - out_varcb_name=dict(argstr='--out_varcb=%s', - ), - args=dict(argstr='%s', - ), - out_z_name=dict(argstr='--out_z=%s', - ), - terminal_output=dict(mandatory=True, - nohash=True, + in_file=dict(argstr='-i %s', + mandatory=True, + position=1, ), - var_norm=dict(argstr='--vn', + mask=dict(argstr='-m %s', ), - out_f_name=dict(argstr='--out_f=%s', + out_cope=dict(argstr='--out_cope=%s', ), out_data_name=dict(argstr='--out_data=%s', ), - contrasts=dict(argstr='-c %s', + out_f_name=dict(argstr='--out_f=%s', ), - out_file=dict(name_source='in_file', + out_file=dict(argstr='-o %s', keep_extension=True, - position=3, + name_source='in_file', name_template='%s_glm', - argstr='-o %s', + position=3, ), - dat_norm=dict(argstr='--dat_norm', + out_p_name=dict(argstr='--out_p=%s', ), - demean=dict(argstr='--demean', + out_pf_name=dict(argstr='--out_pf=%s', + ), + out_res_name=dict(argstr='--out_res=%s', + ), + out_sigsq_name=dict(argstr='--out_sigsq=%s', + ), + out_t_name=dict(argstr='--out_t=%s', + ), + out_varcb_name=dict(argstr='--out_varcb=%s', + ), + out_vnscales_name=dict(argstr='--out_vnscales=%s', + ), + out_z_name=dict(argstr='--out_z=%s', ), output_type=dict(), - des_norm=dict(argstr='--des_norm', + terminal_output=dict(mandatory=True, + nohash=True, ), - out_p_name=dict(argstr='--out_p=%s', + var_norm=dict(argstr='--vn', ), ) inputs = GLM.input_spec() @@ -70,18 +71,19 @@ def test_GLM_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_GLM_outputs(): - output_map = dict(out_res=dict(), - out_varcb=dict(), + output_map = dict(out_cope=dict(), + out_data=dict(), out_f=dict(), out_file=dict(), - out_vnscales=dict(), - out_cope=dict(), + out_p=dict(), + out_pf=dict(), + out_res=dict(), out_sigsq=dict(), out_t=dict(), - out_pf=dict(), - out_p=dict(), - out_data=dict(), + out_varcb=dict(), + out_vnscales=dict(), out_z=dict(), ) outputs = GLM.output_spec() @@ -89,3 +91,4 @@ def test_GLM_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_ImageMaths.py b/nipype/interfaces/fsl/tests/test_auto_ImageMaths.py index ea1932a123..1e076808cb 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ImageMaths.py +++ b/nipype/interfaces/fsl/tests/test_auto_ImageMaths.py @@ -1,44 +1,46 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.utils import ImageMaths + def test_ImageMaths_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(args=dict(argstr='%s', ), - op_string=dict(position=2, - argstr='%s', + environ=dict(nohash=True, + usedefault=True, ), - out_data_type=dict(position=5, - argstr='-odt %s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - out_file=dict(position=4, - hash_files=False, - genfile=True, - argstr='%s', + in_file=dict(argstr='%s', + mandatory=True, + position=1, ), - args=dict(argstr='%s', + in_file2=dict(argstr='%s', + position=3, ), - in_file2=dict(position=3, - argstr='%s', + op_string=dict(argstr='%s', + position=2, ), - terminal_output=dict(mandatory=True, - nohash=True, + out_data_type=dict(argstr='-odt %s', + position=5, ), - environ=dict(nohash=True, - usedefault=True, - ), - in_file=dict(position=1, - mandatory=True, - argstr='%s', + out_file=dict(argstr='%s', + genfile=True, + hash_files=False, + position=4, ), output_type=dict(), suffix=dict(), + terminal_output=dict(mandatory=True, + nohash=True, + ), ) inputs = ImageMaths.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ImageMaths_outputs(): output_map = dict(out_file=dict(), ) @@ -47,3 +49,4 @@ def test_ImageMaths_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_ImageMeants.py b/nipype/interfaces/fsl/tests/test_auto_ImageMeants.py index 6f16a57b33..0cf60abdf3 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ImageMeants.py +++ b/nipype/interfaces/fsl/tests/test_auto_ImageMeants.py @@ -1,50 +1,52 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.utils import ImageMeants + def test_ImageMeants_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + eig=dict(argstr='--eig', + ), + environ=dict(nohash=True, + usedefault=True, + ), + ignore_exception=dict(nohash=True, usedefault=True, ), + in_file=dict(argstr='-i %s', + mandatory=True, + position=0, + ), + mask=dict(argstr='-m %s', + ), nobin=dict(argstr='--no_bin', ), - show_all=dict(argstr='--showall', + order=dict(argstr='--order=%d', + usedefault=True, ), - out_file=dict(hash_files=False, + out_file=dict(argstr='-o %s', genfile=True, - argstr='-o %s', - ), - mask=dict(argstr='-m %s', + hash_files=False, ), - args=dict(argstr='%s', + output_type=dict(), + show_all=dict(argstr='--showall', ), - transpose=dict(argstr='--transpose', + spatial_coord=dict(argstr='-c %s', ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - in_file=dict(position=0, - mandatory=True, - argstr='-i %s', - ), - eig=dict(argstr='--eig', + transpose=dict(argstr='--transpose', ), - output_type=dict(), use_mm=dict(argstr='--usemm', ), - order=dict(usedefault=True, - argstr='--order=%d', - ), - spatial_coord=dict(argstr='-c %s', - ), ) inputs = ImageMeants.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ImageMeants_outputs(): output_map = dict(out_file=dict(), ) @@ -53,3 +55,4 @@ def test_ImageMeants_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_ImageStats.py b/nipype/interfaces/fsl/tests/test_auto_ImageStats.py index ed685e3708..bc61a49004 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ImageStats.py +++ b/nipype/interfaces/fsl/tests/test_auto_ImageStats.py @@ -1,38 +1,40 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.utils import ImageStats + def test_ImageStats_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, - ), - op_string=dict(position=3, - mandatory=True, - argstr='%s', - ), - split_4d=dict(position=1, - argstr='-t', - ), - args=dict(argstr='%s', - ), - terminal_output=dict(mandatory=True, - nohash=True, + input_map = dict(args=dict(argstr='%s', ), environ=dict(nohash=True, usedefault=True, ), - in_file=dict(position=2, + ignore_exception=dict(nohash=True, + usedefault=True, + ), + in_file=dict(argstr='%s', mandatory=True, - argstr='%s', + position=2, ), mask_file=dict(argstr='', ), + op_string=dict(argstr='%s', + mandatory=True, + position=3, + ), output_type=dict(), + split_4d=dict(argstr='-t', + position=1, + ), + terminal_output=dict(mandatory=True, + nohash=True, + ), ) inputs = ImageStats.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ImageStats_outputs(): output_map = dict(out_stat=dict(), ) @@ -41,3 +43,4 @@ def test_ImageStats_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_InvWarp.py b/nipype/interfaces/fsl/tests/test_auto_InvWarp.py index 5bc39724b1..412cdaa912 100644 --- a/nipype/interfaces/fsl/tests/test_auto_InvWarp.py +++ b/nipype/interfaces/fsl/tests/test_auto_InvWarp.py @@ -1,45 +1,46 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.utils import InvWarp + def test_InvWarp_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(absolute=dict(argstr='--abs', + xor=['relative'], ), - niter=dict(argstr='--niter=%d', + args=dict(argstr='%s', ), - regularise=dict(argstr='--regularise=%f', + environ=dict(nohash=True, + usedefault=True, ), - inverse_warp=dict(name_source=['warp'], + ignore_exception=dict(nohash=True, + usedefault=True, + ), + inverse_warp=dict(argstr='--out=%s', hash_files=False, + name_source=['warp'], name_template='%s_inverse', - argstr='--out=%s', - ), - reference=dict(mandatory=True, - argstr='--ref=%s', - ), - args=dict(argstr='%s', ), - warp=dict(mandatory=True, - argstr='--warp=%s', - ), - relative=dict(xor=['absolute'], - argstr='--rel', + jacobian_max=dict(argstr='--jmax=%f', ), - terminal_output=dict(mandatory=True, - nohash=True, + jacobian_min=dict(argstr='--jmin=%f', ), - environ=dict(nohash=True, - usedefault=True, + niter=dict(argstr='--niter=%d', ), noconstraint=dict(argstr='--noconstraint', ), output_type=dict(), - jacobian_max=dict(argstr='--jmax=%f', + reference=dict(argstr='--ref=%s', + mandatory=True, ), - jacobian_min=dict(argstr='--jmin=%f', + regularise=dict(argstr='--regularise=%f', + ), + relative=dict(argstr='--rel', + xor=['absolute'], ), - absolute=dict(xor=['relative'], - argstr='--abs', + terminal_output=dict(mandatory=True, + nohash=True, + ), + warp=dict(argstr='--warp=%s', + mandatory=True, ), ) inputs = InvWarp.input_spec() @@ -47,6 +48,7 @@ def test_InvWarp_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_InvWarp_outputs(): output_map = dict(inverse_warp=dict(), ) @@ -55,3 +57,4 @@ def test_InvWarp_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_IsotropicSmooth.py b/nipype/interfaces/fsl/tests/test_auto_IsotropicSmooth.py index 995e4867d5..094142b0f6 100644 --- a/nipype/interfaces/fsl/tests/test_auto_IsotropicSmooth.py +++ b/nipype/interfaces/fsl/tests/test_auto_IsotropicSmooth.py @@ -1,46 +1,47 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.maths import IsotropicSmooth + def test_IsotropicSmooth_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(args=dict(argstr='%s', ), - nan2zeros=dict(position=3, - argstr='-nan', - ), - out_file=dict(hash_files=False, - genfile=True, - position=-2, - argstr='%s', + environ=dict(nohash=True, + usedefault=True, ), - sigma=dict(mandatory=True, + fwhm=dict(argstr='-s %.5f', + mandatory=True, position=4, - xor=['fwhm'], - argstr='-s %.5f', + xor=['sigma'], ), - args=dict(argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - internal_datatype=dict(position=1, - argstr='-dt %s', + in_file=dict(argstr='%s', + mandatory=True, + position=2, ), - terminal_output=dict(mandatory=True, - nohash=True, + internal_datatype=dict(argstr='-dt %s', + position=1, ), - environ=dict(nohash=True, - usedefault=True, + nan2zeros=dict(argstr='-nan', + position=3, ), - in_file=dict(position=2, - mandatory=True, - argstr='%s', + out_file=dict(argstr='%s', + genfile=True, + hash_files=False, + position=-2, + ), + output_datatype=dict(argstr='-odt %s', + position=-1, ), output_type=dict(), - fwhm=dict(mandatory=True, + sigma=dict(argstr='-s %.5f', + mandatory=True, position=4, - xor=['sigma'], - argstr='-s %.5f', + xor=['fwhm'], ), - output_datatype=dict(position=-1, - argstr='-odt %s', + terminal_output=dict(mandatory=True, + nohash=True, ), ) inputs = IsotropicSmooth.input_spec() @@ -48,6 +49,7 @@ def test_IsotropicSmooth_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_IsotropicSmooth_outputs(): output_map = dict(out_file=dict(), ) @@ -56,3 +58,4 @@ def test_IsotropicSmooth_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_L2Model.py b/nipype/interfaces/fsl/tests/test_auto_L2Model.py index 4a3a20e914..7e8f957a68 100644 --- a/nipype/interfaces/fsl/tests/test_auto_L2Model.py +++ b/nipype/interfaces/fsl/tests/test_auto_L2Model.py @@ -1,6 +1,7 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.model import L2Model + def test_L2Model_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, @@ -13,9 +14,10 @@ def test_L2Model_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_L2Model_outputs(): - output_map = dict(design_grp=dict(), - design_con=dict(), + output_map = dict(design_con=dict(), + design_grp=dict(), design_mat=dict(), ) outputs = L2Model.output_spec() @@ -23,3 +25,4 @@ def test_L2Model_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_Level1Design.py b/nipype/interfaces/fsl/tests/test_auto_Level1Design.py index 0b95269b0d..3dd68b4041 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Level1Design.py +++ b/nipype/interfaces/fsl/tests/test_auto_Level1Design.py @@ -1,25 +1,27 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.model import Level1Design + def test_Level1Design_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(bases=dict(mandatory=True, ), - session_info=dict(mandatory=True, + contrasts=dict(), + ignore_exception=dict(nohash=True, + usedefault=True, ), interscan_interval=dict(mandatory=True, ), - bases=dict(mandatory=True, - ), model_serial_correlations=dict(mandatory=True, ), - contrasts=dict(), + session_info=dict(mandatory=True, + ), ) inputs = Level1Design.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Level1Design_outputs(): output_map = dict(ev_files=dict(), fsf_files=dict(), @@ -29,3 +31,4 @@ def test_Level1Design_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_MCFLIRT.py b/nipype/interfaces/fsl/tests/test_auto_MCFLIRT.py index 26bc9be242..f31d503e4a 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MCFLIRT.py +++ b/nipype/interfaces/fsl/tests/test_auto_MCFLIRT.py @@ -1,62 +1,63 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.preprocess import MCFLIRT + def test_MCFLIRT_inputs(): - input_map = dict(use_gradient=dict(argstr='-gdt', + input_map = dict(args=dict(argstr='%s', ), - smooth=dict(argstr='-smooth %.2f', + bins=dict(argstr='-bins %d', ), cost=dict(argstr='-cost %s', ), - stats_imgs=dict(argstr='-stats', - ), - save_mats=dict(argstr='-mats', + dof=dict(argstr='-dof %d', ), - use_contour=dict(argstr='-edge', + environ=dict(nohash=True, + usedefault=True, ), - init=dict(argstr='-init %s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - in_file=dict(position=0, + in_file=dict(argstr='-in %s', mandatory=True, - argstr='-in %s', + position=0, ), - ref_vol=dict(argstr='-refvol %d', + init=dict(argstr='-init %s', ), interpolation=dict(argstr='-%s_final', ), - ignore_exception=dict(nohash=True, - usedefault=True, - ), - save_rms=dict(argstr='-rmsabs -rmsrel', + mean_vol=dict(argstr='-meanvol', ), - args=dict(argstr='%s', + out_file=dict(argstr='-out %s', + genfile=True, + hash_files=False, ), - scaling=dict(argstr='-scaling %.2f', + output_type=dict(), + ref_file=dict(argstr='-reffile %s', ), - terminal_output=dict(mandatory=True, - nohash=True, + ref_vol=dict(argstr='-refvol %d', ), rotation=dict(argstr='-rotation %d', ), - mean_vol=dict(argstr='-meanvol', - ), - out_file=dict(argstr='-out %s', - hash_files=False, - genfile=True, + save_mats=dict(argstr='-mats', ), save_plots=dict(argstr='-plots', ), - dof=dict(argstr='-dof %d', + save_rms=dict(argstr='-rmsabs -rmsrel', ), - ref_file=dict(argstr='-reffile %s', + scaling=dict(argstr='-scaling %.2f', ), - environ=dict(nohash=True, - usedefault=True, + smooth=dict(argstr='-smooth %.2f', ), - output_type=dict(), stages=dict(argstr='-stages %d', ), - bins=dict(argstr='-bins %d', + stats_imgs=dict(argstr='-stats', + ), + terminal_output=dict(mandatory=True, + nohash=True, + ), + use_contour=dict(argstr='-edge', + ), + use_gradient=dict(argstr='-gdt', ), ) inputs = MCFLIRT.input_spec() @@ -64,17 +65,19 @@ def test_MCFLIRT_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MCFLIRT_outputs(): - output_map = dict(mean_img=dict(), - std_img=dict(), + output_map = dict(mat_file=dict(), + mean_img=dict(), out_file=dict(), - variance_img=dict(), - mat_file=dict(), par_file=dict(), rms_files=dict(), + std_img=dict(), + variance_img=dict(), ) outputs = MCFLIRT.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_MELODIC.py b/nipype/interfaces/fsl/tests/test_auto_MELODIC.py index c6a46c0eb6..ba2030bb03 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MELODIC.py +++ b/nipype/interfaces/fsl/tests/test_auto_MELODIC.py @@ -1,109 +1,110 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.model import MELODIC + def test_MELODIC_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(ICs=dict(argstr='--ICs=%s', ), - dim_est=dict(argstr='--dimest=%s', + approach=dict(argstr='-a %s', ), - out_dir=dict(argstr='-o %s', - genfile=True, + args=dict(argstr='%s', ), - pbsc=dict(argstr='--pbsc', + bg_image=dict(argstr='--bgimage=%s', ), - smode=dict(argstr='--smode=%s', + bg_threshold=dict(argstr='--bgthreshold=%f', ), - out_orig=dict(argstr='--Oorig', + cov_weight=dict(argstr='--covarweight=%f', ), - sep_whiten=dict(argstr='--sep_whiten', + dim=dict(argstr='-d %d', ), - t_des=dict(argstr='--Tdes=%s', + dim_est=dict(argstr='--dimest=%s', ), - maxit=dict(argstr='--maxit=%d', + environ=dict(nohash=True, + usedefault=True, ), - report_maps=dict(argstr='--report_maps=%s', + epsilon=dict(argstr='--eps=%f', ), - t_con=dict(argstr='--Tcon=%s', + epsilonS=dict(argstr='--epsS=%f', ), - num_ICs=dict(argstr='-n %d', + ignore_exception=dict(nohash=True, + usedefault=True, ), - no_mm=dict(argstr='--no_mm', + in_files=dict(argstr='-i %s', + mandatory=True, + position=0, ), log_power=dict(argstr='--logPower', ), - var_norm=dict(argstr='--vn', + mask=dict(argstr='-m %s', ), - cov_weight=dict(argstr='--covarweight=%f', + max_restart=dict(argstr='--maxrestart=%d', ), - tr_sec=dict(argstr='--tr=%f', + maxit=dict(argstr='--maxit=%d', ), mix=dict(argstr='--mix=%s', ), - out_all=dict(argstr='--Oall', - ), - epsilonS=dict(argstr='--epsS=%f', - ), - approach=dict(argstr='-a %s', + mm_thresh=dict(argstr='--mmthresh=%f', ), - update_mask=dict(argstr='--update_mask', + no_bet=dict(argstr='--nobet', ), no_mask=dict(argstr='--nomask', ), - out_mean=dict(argstr='--Omean', + no_mm=dict(argstr='--no_mm', ), - bg_threshold=dict(argstr='--bgthreshold=%f', + non_linearity=dict(argstr='--nl=%s', ), - out_unmix=dict(argstr='--Ounmix', + num_ICs=dict(argstr='-n %d', ), - sep_vn=dict(argstr='--sep_vn', + out_all=dict(argstr='--Oall', ), - epsilon=dict(argstr='--eps=%f', + out_dir=dict(argstr='-o %s', + genfile=True, ), - args=dict(argstr='%s', + out_mean=dict(argstr='--Omean', ), - rem_cmp=dict(argstr='-f %d', + out_orig=dict(argstr='--Oorig', ), - remove_deriv=dict(argstr='--remove_deriv', + out_pca=dict(argstr='--Opca', ), - bg_image=dict(argstr='--bgimage=%s', + out_stats=dict(argstr='--Ostats', ), - non_linearity=dict(argstr='--nl=%s', + out_unmix=dict(argstr='--Ounmix', ), - out_pca=dict(argstr='--Opca', + out_white=dict(argstr='--Owhite', ), output_type=dict(), + pbsc=dict(argstr='--pbsc', + ), + rem_cmp=dict(argstr='-f %d', + ), + remove_deriv=dict(argstr='--remove_deriv', + ), report=dict(argstr='--report', ), - s_con=dict(argstr='--Scon=%s', + report_maps=dict(argstr='--report_maps=%s', ), - dim=dict(argstr='-d %d', + s_con=dict(argstr='--Scon=%s', ), s_des=dict(argstr='--Sdes=%s', ), - no_bet=dict(argstr='--nobet', - ), - mask=dict(argstr='-m %s', + sep_vn=dict(argstr='--sep_vn', ), - in_files=dict(argstr='-i %s', - mandatory=True, - position=0, + sep_whiten=dict(argstr='--sep_whiten', ), - terminal_output=dict(mandatory=True, - nohash=True, + smode=dict(argstr='--smode=%s', ), - environ=dict(nohash=True, - usedefault=True, + t_con=dict(argstr='--Tcon=%s', ), - max_restart=dict(argstr='--maxrestart=%d', + t_des=dict(argstr='--Tdes=%s', ), - mm_thresh=dict(argstr='--mmthresh=%f', + terminal_output=dict(mandatory=True, + nohash=True, ), - ICs=dict(argstr='--ICs=%s', + tr_sec=dict(argstr='--tr=%f', ), - out_stats=dict(argstr='--Ostats', + update_mask=dict(argstr='--update_mask', ), - out_white=dict(argstr='--Owhite', + var_norm=dict(argstr='--vn', ), ) inputs = MELODIC.input_spec() @@ -111,12 +112,14 @@ def test_MELODIC_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MELODIC_outputs(): - output_map = dict(report_dir=dict(), - out_dir=dict(), + output_map = dict(out_dir=dict(), + report_dir=dict(), ) outputs = MELODIC.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_MakeDyadicVectors.py b/nipype/interfaces/fsl/tests/test_auto_MakeDyadicVectors.py index 936fcb7ea0..2fae373b2b 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MakeDyadicVectors.py +++ b/nipype/interfaces/fsl/tests/test_auto_MakeDyadicVectors.py @@ -1,37 +1,38 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.dti import MakeDyadicVectors + def test_MakeDyadicVectors_inputs(): - input_map = dict(perc=dict(position=4, - argstr='%f', + input_map = dict(args=dict(argstr='%s', + ), + environ=dict(nohash=True, + usedefault=True, ), ignore_exception=dict(nohash=True, usedefault=True, ), - args=dict(argstr='%s', + mask=dict(argstr='%s', + position=2, ), - mask=dict(position=2, - argstr='%s', + output=dict(argstr='%s', + hash_files=False, + position=3, + usedefault=True, + ), + output_type=dict(), + perc=dict(argstr='%f', + position=4, ), - phi_vol=dict(position=1, + phi_vol=dict(argstr='%s', mandatory=True, - argstr='%s', + position=1, ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - output_type=dict(), - output=dict(position=3, - hash_files=False, - usedefault=True, - argstr='%s', - ), - theta_vol=dict(position=0, + theta_vol=dict(argstr='%s', mandatory=True, - argstr='%s', + position=0, ), ) inputs = MakeDyadicVectors.input_spec() @@ -39,6 +40,7 @@ def test_MakeDyadicVectors_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MakeDyadicVectors_outputs(): output_map = dict(dispersion=dict(), dyads=dict(), @@ -48,3 +50,4 @@ def test_MakeDyadicVectors_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_MathsCommand.py b/nipype/interfaces/fsl/tests/test_auto_MathsCommand.py index ac6d8166c7..fcd1f0d772 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MathsCommand.py +++ b/nipype/interfaces/fsl/tests/test_auto_MathsCommand.py @@ -1,36 +1,37 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.maths import MathsCommand + def test_MathsCommand_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(args=dict(argstr='%s', ), - nan2zeros=dict(position=3, - argstr='-nan', + environ=dict(nohash=True, + usedefault=True, ), - out_file=dict(hash_files=False, - genfile=True, - position=-2, - argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - args=dict(argstr='%s', + in_file=dict(argstr='%s', + mandatory=True, + position=2, ), - internal_datatype=dict(position=1, - argstr='-dt %s', + internal_datatype=dict(argstr='-dt %s', + position=1, ), - terminal_output=dict(mandatory=True, - nohash=True, + nan2zeros=dict(argstr='-nan', + position=3, ), - environ=dict(nohash=True, - usedefault=True, + out_file=dict(argstr='%s', + genfile=True, + hash_files=False, + position=-2, ), - in_file=dict(position=2, - mandatory=True, - argstr='%s', + output_datatype=dict(argstr='-odt %s', + position=-1, ), output_type=dict(), - output_datatype=dict(position=-1, - argstr='-odt %s', + terminal_output=dict(mandatory=True, + nohash=True, ), ) inputs = MathsCommand.input_spec() @@ -38,6 +39,7 @@ def test_MathsCommand_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MathsCommand_outputs(): output_map = dict(out_file=dict(), ) @@ -46,3 +48,4 @@ def test_MathsCommand_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_MaxImage.py b/nipype/interfaces/fsl/tests/test_auto_MaxImage.py index 457b017542..9f4921614a 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MaxImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_MaxImage.py @@ -1,40 +1,41 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.maths import MaxImage + def test_MaxImage_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + dimension=dict(argstr='-%smax', + position=4, usedefault=True, ), - nan2zeros=dict(position=3, - argstr='-nan', + environ=dict(nohash=True, + usedefault=True, ), - out_file=dict(hash_files=False, - genfile=True, - position=-2, - argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - args=dict(argstr='%s', + in_file=dict(argstr='%s', + mandatory=True, + position=2, ), - internal_datatype=dict(position=1, - argstr='-dt %s', + internal_datatype=dict(argstr='-dt %s', + position=1, ), - terminal_output=dict(mandatory=True, - nohash=True, + nan2zeros=dict(argstr='-nan', + position=3, ), - environ=dict(nohash=True, - usedefault=True, - ), - in_file=dict(position=2, - mandatory=True, - argstr='%s', + out_file=dict(argstr='%s', + genfile=True, + hash_files=False, + position=-2, ), - output_datatype=dict(position=-1, - argstr='-odt %s', + output_datatype=dict(argstr='-odt %s', + position=-1, ), output_type=dict(), - dimension=dict(position=4, - usedefault=True, - argstr='-%smax', + terminal_output=dict(mandatory=True, + nohash=True, ), ) inputs = MaxImage.input_spec() @@ -42,6 +43,7 @@ def test_MaxImage_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MaxImage_outputs(): output_map = dict(out_file=dict(), ) @@ -50,3 +52,4 @@ def test_MaxImage_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_MeanImage.py b/nipype/interfaces/fsl/tests/test_auto_MeanImage.py index 28eb585ddc..f297cdcc55 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MeanImage.py +++ b/nipype/interfaces/fsl/tests/test_auto_MeanImage.py @@ -1,40 +1,41 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.maths import MeanImage + def test_MeanImage_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + dimension=dict(argstr='-%smean', + position=4, usedefault=True, ), - nan2zeros=dict(position=3, - argstr='-nan', + environ=dict(nohash=True, + usedefault=True, ), - out_file=dict(hash_files=False, - genfile=True, - position=-2, - argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - args=dict(argstr='%s', + in_file=dict(argstr='%s', + mandatory=True, + position=2, ), - internal_datatype=dict(position=1, - argstr='-dt %s', + internal_datatype=dict(argstr='-dt %s', + position=1, ), - terminal_output=dict(mandatory=True, - nohash=True, + nan2zeros=dict(argstr='-nan', + position=3, ), - environ=dict(nohash=True, - usedefault=True, - ), - in_file=dict(position=2, - mandatory=True, - argstr='%s', + out_file=dict(argstr='%s', + genfile=True, + hash_files=False, + position=-2, ), - output_datatype=dict(position=-1, - argstr='-odt %s', + output_datatype=dict(argstr='-odt %s', + position=-1, ), output_type=dict(), - dimension=dict(position=4, - usedefault=True, - argstr='-%smean', + terminal_output=dict(mandatory=True, + nohash=True, ), ) inputs = MeanImage.input_spec() @@ -42,6 +43,7 @@ def test_MeanImage_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MeanImage_outputs(): output_map = dict(out_file=dict(), ) @@ -50,3 +52,4 @@ def test_MeanImage_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_Merge.py b/nipype/interfaces/fsl/tests/test_auto_Merge.py index 5a64e7c70c..dff840a2c2 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Merge.py +++ b/nipype/interfaces/fsl/tests/test_auto_Merge.py @@ -1,35 +1,36 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.utils import Merge + def test_Merge_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(args=dict(argstr='%s', ), - merged_file=dict(name_source='in_files', - hash_files=False, - name_template='%s_merged', - position=1, - argstr='%s', + dimension=dict(argstr='-%s', + mandatory=True, + position=0, ), - args=dict(argstr='%s', + environ=dict(nohash=True, + usedefault=True, ), - tr=dict(position=-1, - argstr='%.2f', + ignore_exception=dict(nohash=True, + usedefault=True, ), - in_files=dict(position=2, + in_files=dict(argstr='%s', mandatory=True, - argstr='%s', + position=2, ), + merged_file=dict(argstr='%s', + hash_files=False, + name_source='in_files', + name_template='%s_merged', + position=1, + ), + output_type=dict(), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - output_type=dict(), - dimension=dict(position=0, - mandatory=True, - argstr='-%s', + tr=dict(argstr='%.2f', + position=-1, ), ) inputs = Merge.input_spec() @@ -37,6 +38,7 @@ def test_Merge_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Merge_outputs(): output_map = dict(merged_file=dict(), ) @@ -45,3 +47,4 @@ def test_Merge_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_MultiImageMaths.py b/nipype/interfaces/fsl/tests/test_auto_MultiImageMaths.py index 0164389ceb..c5ed943387 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MultiImageMaths.py +++ b/nipype/interfaces/fsl/tests/test_auto_MultiImageMaths.py @@ -1,42 +1,43 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.maths import MultiImageMaths + def test_MultiImageMaths_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + environ=dict(nohash=True, usedefault=True, ), - nan2zeros=dict(position=3, - argstr='-nan', + ignore_exception=dict(nohash=True, + usedefault=True, ), - op_string=dict(position=4, + in_file=dict(argstr='%s', mandatory=True, - argstr='%s', + position=2, ), - out_file=dict(hash_files=False, - genfile=True, - position=-2, - argstr='%s', + internal_datatype=dict(argstr='-dt %s', + position=1, ), - args=dict(argstr='%s', + nan2zeros=dict(argstr='-nan', + position=3, ), - internal_datatype=dict(position=1, - argstr='-dt %s', + op_string=dict(argstr='%s', + mandatory=True, + position=4, ), - terminal_output=dict(mandatory=True, - nohash=True, + operand_files=dict(mandatory=True, ), - environ=dict(nohash=True, - usedefault=True, + out_file=dict(argstr='%s', + genfile=True, + hash_files=False, + position=-2, ), - in_file=dict(position=2, - mandatory=True, - argstr='%s', + output_datatype=dict(argstr='-odt %s', + position=-1, ), output_type=dict(), - output_datatype=dict(position=-1, - argstr='-odt %s', - ), - operand_files=dict(mandatory=True, + terminal_output=dict(mandatory=True, + nohash=True, ), ) inputs = MultiImageMaths.input_spec() @@ -44,6 +45,7 @@ def test_MultiImageMaths_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MultiImageMaths_outputs(): output_map = dict(out_file=dict(), ) @@ -52,3 +54,4 @@ def test_MultiImageMaths_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_MultipleRegressDesign.py b/nipype/interfaces/fsl/tests/test_auto_MultipleRegressDesign.py index 64158ab380..93002e6500 100644 --- a/nipype/interfaces/fsl/tests/test_auto_MultipleRegressDesign.py +++ b/nipype/interfaces/fsl/tests/test_auto_MultipleRegressDesign.py @@ -1,29 +1,32 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.model import MultipleRegressDesign + def test_MultipleRegressDesign_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(contrasts=dict(mandatory=True, ), - contrasts=dict(mandatory=True, + groups=dict(), + ignore_exception=dict(nohash=True, + usedefault=True, ), regressors=dict(mandatory=True, ), - groups=dict(), ) inputs = MultipleRegressDesign.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MultipleRegressDesign_outputs(): - output_map = dict(design_fts=dict(), + output_map = dict(design_con=dict(), + design_fts=dict(), design_grp=dict(), design_mat=dict(), - design_con=dict(), ) outputs = MultipleRegressDesign.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_Overlay.py b/nipype/interfaces/fsl/tests/test_auto_Overlay.py index f8ba5da347..b0c1961776 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Overlay.py +++ b/nipype/interfaces/fsl/tests/test_auto_Overlay.py @@ -1,72 +1,73 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.utils import Overlay + def test_Overlay_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(args=dict(argstr='%s', ), - stat_thresh=dict(position=7, + auto_thresh_bg=dict(argstr='-a', mandatory=True, - argstr='%.2f %.2f', - ), - background_image=dict(position=4, - mandatory=True, - argstr='%s', - ), - args=dict(argstr='%s', - ), - show_negative_stats=dict(position=8, - xor=['stat_image2'], - argstr='%s', - ), - stat_image2=dict(position=9, - xor=['show_negative_stats'], - argstr='%s', - ), - bg_thresh=dict(mandatory=True, position=5, xor=('auto_thresh_bg', 'full_bg_range', 'bg_thresh'), - argstr='%.3f %.3f', ), - full_bg_range=dict(xor=('auto_thresh_bg', 'full_bg_range', 'bg_thresh'), - position=5, + background_image=dict(argstr='%s', mandatory=True, - argstr='-A', + position=4, ), - auto_thresh_bg=dict(xor=('auto_thresh_bg', 'full_bg_range', 'bg_thresh'), - position=5, + bg_thresh=dict(argstr='%.3f %.3f', mandatory=True, - argstr='-a', + position=5, + xor=('auto_thresh_bg', 'full_bg_range', 'bg_thresh'), ), - use_checkerboard=dict(position=3, - argstr='-c', + environ=dict(nohash=True, + usedefault=True, ), - terminal_output=dict(mandatory=True, - nohash=True, + full_bg_range=dict(argstr='-A', + mandatory=True, + position=5, + xor=('auto_thresh_bg', 'full_bg_range', 'bg_thresh'), ), - environ=dict(nohash=True, + ignore_exception=dict(nohash=True, usedefault=True, ), - transparency=dict(position=1, + out_file=dict(argstr='%s', + genfile=True, + hash_files=False, + position=-1, + ), + out_type=dict(argstr='%s', + position=2, usedefault=True, - argstr='%s', ), output_type=dict(), - out_type=dict(position=2, - usedefault=True, - argstr='%s', + show_negative_stats=dict(argstr='%s', + position=8, + xor=['stat_image2'], ), - stat_thresh2=dict(position=10, - argstr='%.2f %.2f', + stat_image=dict(argstr='%s', + mandatory=True, + position=6, + ), + stat_image2=dict(argstr='%s', + position=9, + xor=['show_negative_stats'], ), - stat_image=dict(position=6, + stat_thresh=dict(argstr='%.2f %.2f', mandatory=True, - argstr='%s', + position=7, ), - out_file=dict(hash_files=False, - genfile=True, - position=-1, - argstr='%s', + stat_thresh2=dict(argstr='%.2f %.2f', + position=10, + ), + terminal_output=dict(mandatory=True, + nohash=True, + ), + transparency=dict(argstr='%s', + position=1, + usedefault=True, + ), + use_checkerboard=dict(argstr='-c', + position=3, ), ) inputs = Overlay.input_spec() @@ -74,6 +75,7 @@ def test_Overlay_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Overlay_outputs(): output_map = dict(out_file=dict(), ) @@ -82,3 +84,4 @@ def test_Overlay_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_PRELUDE.py b/nipype/interfaces/fsl/tests/test_auto_PRELUDE.py index 1f4e56e713..358571584e 100644 --- a/nipype/interfaces/fsl/tests/test_auto_PRELUDE.py +++ b/nipype/interfaces/fsl/tests/test_auto_PRELUDE.py @@ -1,63 +1,64 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.preprocess import PRELUDE + def test_PRELUDE_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, - ), - magnitude_file=dict(mandatory=True, - argstr='--abs=%s', - xor=['complex_phase_file'], + input_map = dict(args=dict(argstr='%s', ), - removeramps=dict(argstr='--removeramps', + complex_phase_file=dict(argstr='--complex=%s', + mandatory=True, + xor=['magnitude_file', 'phase_file'], ), end=dict(argstr='--end=%d', ), - process3d=dict(xor=['labelprocess2d', 'process2d'], - argstr='--force3D', + environ=dict(nohash=True, + usedefault=True, ), - complex_phase_file=dict(mandatory=True, - argstr='--complex=%s', - xor=['magnitude_file', 'phase_file'], + ignore_exception=dict(nohash=True, + usedefault=True, ), - process2d=dict(xor=['labelprocess2d'], - argstr='--slices', + label_file=dict(argstr='--labels=%s', + hash_files=False, ), - args=dict(argstr='%s', + labelprocess2d=dict(argstr='--labelslices', ), - num_partitions=dict(argstr='--numphasesplit=%d', + magnitude_file=dict(argstr='--abs=%s', + mandatory=True, + xor=['complex_phase_file'], ), - unwrapped_phase_file=dict(argstr='--unwrap=%s', - hash_files=False, - genfile=True, + mask_file=dict(argstr='--mask=%s', ), - rawphase_file=dict(hash_files=False, - argstr='--rawphase=%s', + num_partitions=dict(argstr='--numphasesplit=%d', ), - phase_file=dict(mandatory=True, - argstr='--phase=%s', + output_type=dict(), + phase_file=dict(argstr='--phase=%s', + mandatory=True, xor=['complex_phase_file'], ), - threshold=dict(argstr='--thresh=%.10f', + process2d=dict(argstr='--slices', + xor=['labelprocess2d'], ), - terminal_output=dict(mandatory=True, - nohash=True, + process3d=dict(argstr='--force3D', + xor=['labelprocess2d', 'process2d'], ), - environ=dict(nohash=True, - usedefault=True, + rawphase_file=dict(argstr='--rawphase=%s', + hash_files=False, ), - label_file=dict(hash_files=False, - argstr='--labels=%s', + removeramps=dict(argstr='--removeramps', ), - savemask_file=dict(hash_files=False, - argstr='--savemask=%s', + savemask_file=dict(argstr='--savemask=%s', + hash_files=False, ), - mask_file=dict(argstr='--mask=%s', + start=dict(argstr='--start=%d', ), - labelprocess2d=dict(argstr='--labelslices', + terminal_output=dict(mandatory=True, + nohash=True, ), - output_type=dict(), - start=dict(argstr='--start=%d', + threshold=dict(argstr='--thresh=%.10f', + ), + unwrapped_phase_file=dict(argstr='--unwrap=%s', + genfile=True, + hash_files=False, ), ) inputs = PRELUDE.input_spec() @@ -65,6 +66,7 @@ def test_PRELUDE_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_PRELUDE_outputs(): output_map = dict(unwrapped_phase_file=dict(), ) @@ -73,3 +75,4 @@ def test_PRELUDE_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_PlotMotionParams.py b/nipype/interfaces/fsl/tests/test_auto_PlotMotionParams.py index f09bfb7907..0b4dd5d10f 100644 --- a/nipype/interfaces/fsl/tests/test_auto_PlotMotionParams.py +++ b/nipype/interfaces/fsl/tests/test_auto_PlotMotionParams.py @@ -1,33 +1,34 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.utils import PlotMotionParams + def test_PlotMotionParams_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + environ=dict(nohash=True, usedefault=True, ), - plot_type=dict(mandatory=True, - argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - plot_size=dict(argstr='%s', + in_file=dict(argstr='%s', + mandatory=True, + position=1, + ), + in_source=dict(mandatory=True, ), out_file=dict(argstr='-o %s', - hash_files=False, genfile=True, + hash_files=False, ), - args=dict(argstr='%s', - ), - terminal_output=dict(mandatory=True, - nohash=True, - ), - environ=dict(nohash=True, - usedefault=True, + output_type=dict(), + plot_size=dict(argstr='%s', ), - in_file=dict(position=1, + plot_type=dict(argstr='%s', mandatory=True, - argstr='%s', ), - output_type=dict(), - in_source=dict(mandatory=True, + terminal_output=dict(mandatory=True, + nohash=True, ), ) inputs = PlotMotionParams.input_spec() @@ -35,6 +36,7 @@ def test_PlotMotionParams_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_PlotMotionParams_outputs(): output_map = dict(out_file=dict(), ) @@ -43,3 +45,4 @@ def test_PlotMotionParams_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_PlotTimeSeries.py b/nipype/interfaces/fsl/tests/test_auto_PlotTimeSeries.py index 13fdfda494..48b2fa511b 100644 --- a/nipype/interfaces/fsl/tests/test_auto_PlotTimeSeries.py +++ b/nipype/interfaces/fsl/tests/test_auto_PlotTimeSeries.py @@ -1,59 +1,60 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.utils import PlotTimeSeries + def test_PlotTimeSeries_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + environ=dict(nohash=True, usedefault=True, ), - plot_size=dict(argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - labels=dict(argstr='%s', + in_file=dict(argstr='%s', + mandatory=True, + position=1, ), - y_min=dict(xor=('y_range',), - argstr='--ymin=%.2f', + labels=dict(argstr='%s', ), - title=dict(argstr='%s', + legend_file=dict(argstr='--legend=%s', ), - args=dict(argstr='%s', + out_file=dict(argstr='-o %s', + genfile=True, + hash_files=False, ), - sci_notation=dict(argstr='--sci', + output_type=dict(), + plot_finish=dict(argstr='--finish=%d', + xor=('plot_range',), ), - plot_range=dict(xor=('plot_start', 'plot_finish'), - argstr='%s', + plot_range=dict(argstr='%s', + xor=('plot_start', 'plot_finish'), ), - plot_start=dict(xor=('plot_range',), - argstr='--start=%d', + plot_size=dict(argstr='%s', ), - legend_file=dict(argstr='--legend=%s', + plot_start=dict(argstr='--start=%d', + xor=('plot_range',), ), - in_file=dict(position=1, - mandatory=True, - argstr='%s', + sci_notation=dict(argstr='--sci', ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - x_units=dict(argstr='-u %d', - usedefault=True, + title=dict(argstr='%s', ), x_precision=dict(argstr='--precision=%d', ), - y_max=dict(xor=('y_range',), - argstr='--ymax=%.2f', + x_units=dict(argstr='-u %d', + usedefault=True, ), - output_type=dict(), - y_range=dict(xor=('y_min', 'y_max'), - argstr='%s', + y_max=dict(argstr='--ymax=%.2f', + xor=('y_range',), ), - plot_finish=dict(xor=('plot_range',), - argstr='--finish=%d', + y_min=dict(argstr='--ymin=%.2f', + xor=('y_range',), ), - out_file=dict(argstr='-o %s', - hash_files=False, - genfile=True, + y_range=dict(argstr='%s', + xor=('y_min', 'y_max'), ), ) inputs = PlotTimeSeries.input_spec() @@ -61,6 +62,7 @@ def test_PlotTimeSeries_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_PlotTimeSeries_outputs(): output_map = dict(out_file=dict(), ) @@ -69,3 +71,4 @@ def test_PlotTimeSeries_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_PowerSpectrum.py b/nipype/interfaces/fsl/tests/test_auto_PowerSpectrum.py index 36fe800846..42e5fbd33e 100644 --- a/nipype/interfaces/fsl/tests/test_auto_PowerSpectrum.py +++ b/nipype/interfaces/fsl/tests/test_auto_PowerSpectrum.py @@ -1,34 +1,36 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.utils import PowerSpectrum + def test_PowerSpectrum_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + environ=dict(nohash=True, + usedefault=True, + ), + ignore_exception=dict(nohash=True, usedefault=True, ), - out_file=dict(hash_files=False, + in_file=dict(argstr='%s', + mandatory=True, + position=0, + ), + out_file=dict(argstr='%s', genfile=True, + hash_files=False, position=1, - argstr='%s', - ), - args=dict(argstr='%s', ), + output_type=dict(), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - in_file=dict(position=0, - mandatory=True, - argstr='%s', - ), - output_type=dict(), ) inputs = PowerSpectrum.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_PowerSpectrum_outputs(): output_map = dict(out_file=dict(), ) @@ -37,3 +39,4 @@ def test_PowerSpectrum_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_PrepareFieldmap.py b/nipype/interfaces/fsl/tests/test_auto_PrepareFieldmap.py index db7ad06603..88a1a65e7d 100644 --- a/nipype/interfaces/fsl/tests/test_auto_PrepareFieldmap.py +++ b/nipype/interfaces/fsl/tests/test_auto_PrepareFieldmap.py @@ -1,42 +1,43 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.epi import PrepareFieldmap + def test_PrepareFieldmap_inputs(): - input_map = dict(delta_TE=dict(mandatory=True, - usedefault=True, - position=-2, - argstr='%f', + input_map = dict(args=dict(argstr='%s', ), - ignore_exception=dict(nohash=True, + delta_TE=dict(argstr='%f', + mandatory=True, + position=-2, usedefault=True, ), - out_fieldmap=dict(position=5, - argstr='%s', - ), - args=dict(argstr='%s', - ), - nocheck=dict(position=-1, - argstr='--nocheck', + environ=dict(nohash=True, usedefault=True, ), - terminal_output=dict(mandatory=True, - nohash=True, - ), - environ=dict(nohash=True, + ignore_exception=dict(nohash=True, usedefault=True, ), - in_phase=dict(position=2, + in_magnitude=dict(argstr='%s', mandatory=True, - argstr='%s', + position=3, ), - in_magnitude=dict(position=3, + in_phase=dict(argstr='%s', mandatory=True, - argstr='%s', + position=2, + ), + nocheck=dict(argstr='--nocheck', + position=-1, + usedefault=True, + ), + out_fieldmap=dict(argstr='%s', + position=5, ), output_type=dict(), - scanner=dict(position=1, + scanner=dict(argstr='%s', + position=1, usedefault=True, - argstr='%s', + ), + terminal_output=dict(mandatory=True, + nohash=True, ), ) inputs = PrepareFieldmap.input_spec() @@ -44,6 +45,7 @@ def test_PrepareFieldmap_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_PrepareFieldmap_outputs(): output_map = dict(out_fieldmap=dict(), ) @@ -52,3 +54,4 @@ def test_PrepareFieldmap_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_ProbTrackX.py b/nipype/interfaces/fsl/tests/test_auto_ProbTrackX.py index 91335ff048..79a892c20e 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ProbTrackX.py +++ b/nipype/interfaces/fsl/tests/test_auto_ProbTrackX.py @@ -1,98 +1,99 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.dti import ProbTrackX + def test_ProbTrackX_inputs(): - input_map = dict(rand_fib=dict(argstr='--randfib=%d', + input_map = dict(args=dict(argstr='%s', ), - verbose=dict(argstr='--verbose=%d', + avoid_mp=dict(argstr='--avoid=%s', ), - out_dir=dict(argstr='--dir=%s', - genfile=True, + c_thresh=dict(argstr='--cthr=%.3f', ), - waypoints=dict(argstr='--waypoints=%s', + correct_path_distribution=dict(argstr='--pd', ), - mask2=dict(argstr='--mask2=%s', + dist_thresh=dict(argstr='--distthresh=%.3f', ), - phsamples=dict(mandatory=True, + environ=dict(nohash=True, + usedefault=True, ), - seed=dict(mandatory=True, - argstr='--seed=%s', + fibst=dict(argstr='--fibst=%d', ), - n_steps=dict(argstr='--nsteps=%d', + force_dir=dict(argstr='--forcedir', + usedefault=True, ), - seed_ref=dict(argstr='--seedref=%s', + fsamples=dict(mandatory=True, ), - dist_thresh=dict(argstr='--distthresh=%.3f', + ignore_exception=dict(nohash=True, + usedefault=True, ), - use_anisotropy=dict(argstr='--usef', + inv_xfm=dict(argstr='--invxfm=%s', ), - network=dict(argstr='--network', + loop_check=dict(argstr='--loopcheck', ), - sample_random_points=dict(argstr='--sampvox', + mask=dict(argstr='-m %s', + mandatory=True, ), - os2t=dict(argstr='--os2t', + mask2=dict(argstr='--mask2=%s', ), - avoid_mp=dict(argstr='--avoid=%s', + mesh=dict(argstr='--mesh=%s', ), - target_masks=dict(argstr='--targetmasks=%s', + mod_euler=dict(argstr='--modeuler', ), - step_length=dict(argstr='--steplength=%.3f', + mode=dict(argstr='--mode=%s', + genfile=True, ), n_samples=dict(argstr='--nsamples=%d', usedefault=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - thsamples=dict(mandatory=True, + n_steps=dict(argstr='--nsteps=%d', ), - s2tastext=dict(argstr='--s2tastext', + network=dict(argstr='--network', ), - ignore_exception=dict(nohash=True, + opd=dict(argstr='--opd', usedefault=True, ), - xfm=dict(argstr='--xfm=%s', + os2t=dict(argstr='--os2t', ), - samples_base_name=dict(usedefault=True, - argstr='--samples=%s', + out_dir=dict(argstr='--dir=%s', + genfile=True, ), - args=dict(argstr='%s', + output_type=dict(), + phsamples=dict(mandatory=True, ), - inv_xfm=dict(argstr='--invxfm=%s', + rand_fib=dict(argstr='--randfib=%d', ), - force_dir=dict(usedefault=True, - argstr='--forcedir', + random_seed=dict(argstr='--rseed', ), - mesh=dict(argstr='--mesh=%s', + s2tastext=dict(argstr='--s2tastext', ), - stop_mask=dict(argstr='--stop=%s', + sample_random_points=dict(argstr='--sampvox', ), - fibst=dict(argstr='--fibst=%d', + samples_base_name=dict(argstr='--samples=%s', + usedefault=True, ), - random_seed=dict(argstr='--rseed', + seed=dict(argstr='--seed=%s', + mandatory=True, ), - opd=dict(usedefault=True, - argstr='--opd', + seed_ref=dict(argstr='--seedref=%s', ), - mod_euler=dict(argstr='--modeuler', + step_length=dict(argstr='--steplength=%.3f', ), - mask=dict(mandatory=True, - argstr='-m %s', + stop_mask=dict(argstr='--stop=%s', ), - loop_check=dict(argstr='--loopcheck', + target_masks=dict(argstr='--targetmasks=%s', ), - c_thresh=dict(argstr='--cthr=%.3f', + terminal_output=dict(mandatory=True, + nohash=True, ), - fsamples=dict(mandatory=True, + thsamples=dict(mandatory=True, ), - correct_path_distribution=dict(argstr='--pd', + use_anisotropy=dict(argstr='--usef', ), - mode=dict(argstr='--mode=%s', - genfile=True, + verbose=dict(argstr='--verbose=%d', ), - output_type=dict(), - terminal_output=dict(mandatory=True, - nohash=True, + waypoints=dict(argstr='--waypoints=%s', + ), + xfm=dict(argstr='--xfm=%s', ), ) inputs = ProbTrackX.input_spec() @@ -100,11 +101,12 @@ def test_ProbTrackX_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ProbTrackX_outputs(): - output_map = dict(targets=dict(), - fdt_paths=dict(), - particle_files=dict(), + output_map = dict(fdt_paths=dict(), log=dict(), + particle_files=dict(), + targets=dict(), way_total=dict(), ) outputs = ProbTrackX.output_spec() @@ -112,3 +114,4 @@ def test_ProbTrackX_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_ProjThresh.py b/nipype/interfaces/fsl/tests/test_auto_ProjThresh.py index 23b88d81a1..f14eb8b2a5 100644 --- a/nipype/interfaces/fsl/tests/test_auto_ProjThresh.py +++ b/nipype/interfaces/fsl/tests/test_auto_ProjThresh.py @@ -1,33 +1,35 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.dti import ProjThresh + def test_ProjThresh_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + environ=dict(nohash=True, usedefault=True, ), - args=dict(argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, ), in_files=dict(argstr='%s', mandatory=True, position=0, ), + output_type=dict(), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - threshold=dict(position=1, + threshold=dict(argstr='%d', mandatory=True, - argstr='%d', + position=1, ), - output_type=dict(), ) inputs = ProjThresh.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ProjThresh_outputs(): output_map = dict(out_files=dict(), ) @@ -36,3 +38,4 @@ def test_ProjThresh_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_Randomise.py b/nipype/interfaces/fsl/tests/test_auto_Randomise.py index 03926fefa0..e12967f438 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Randomise.py +++ b/nipype/interfaces/fsl/tests/test_auto_Randomise.py @@ -1,78 +1,79 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.model import Randomise + def test_Randomise_inputs(): - input_map = dict(one_sample_group_mean=dict(argstr='-1', - ), - vox_p_values=dict(argstr='-x', - ), - show_total_perms=dict(argstr='-q', + input_map = dict(args=dict(argstr='%s', ), - tfce2D=dict(argstr='--T2', - ), - tfce_H=dict(argstr='--tfce_H=%.2f', + base_name=dict(argstr='-o "%s"', + position=1, + usedefault=True, ), - p_vec_n_dist_files=dict(argstr='-P', + c_thresh=dict(argstr='-c %.2f', ), cm_thresh=dict(argstr='-C %.2f', ), - f_only=dict(argstr='--f_only', + demean=dict(argstr='-D', + ), + design_mat=dict(argstr='-d %s', + position=2, ), environ=dict(nohash=True, usedefault=True, ), - in_file=dict(position=0, - mandatory=True, - argstr='-i %s', + f_c_thresh=dict(argstr='-F %.2f', + ), + f_cm_thresh=dict(argstr='-S %.2f', + ), + f_only=dict(argstr='--f_only', + ), + fcon=dict(argstr='-f %s', ), ignore_exception=dict(nohash=True, usedefault=True, ), - f_cm_thresh=dict(argstr='-S %.2f', + in_file=dict(argstr='-i %s', + mandatory=True, + position=0, ), - tfce=dict(argstr='-T', + mask=dict(argstr='-m %s', ), - tfce_E=dict(argstr='--tfce_E=%.2f', + num_perm=dict(argstr='-n %d', ), - args=dict(argstr='%s', + one_sample_group_mean=dict(argstr='-1', ), - tfce_C=dict(argstr='--tfce_C=%.2f', + output_type=dict(), + p_vec_n_dist_files=dict(argstr='-P', ), raw_stats_imgs=dict(argstr='-R', ), - terminal_output=dict(mandatory=True, - nohash=True, - ), - var_smooth=dict(argstr='-v %d', + seed=dict(argstr='--seed=%d', ), - design_mat=dict(position=2, - argstr='-d %s', + show_info_parallel_mode=dict(argstr='-Q', ), - tcon=dict(position=3, - argstr='-t %s', + show_total_perms=dict(argstr='-q', ), - show_info_parallel_mode=dict(argstr='-Q', + tcon=dict(argstr='-t %s', + position=3, ), - base_name=dict(position=1, - usedefault=True, - argstr='-o "%s"', + terminal_output=dict(mandatory=True, + nohash=True, ), - f_c_thresh=dict(argstr='-F %.2f', + tfce=dict(argstr='-T', ), - num_perm=dict(argstr='-n %d', + tfce2D=dict(argstr='--T2', ), - mask=dict(argstr='-m %s', + tfce_C=dict(argstr='--tfce_C=%.2f', ), - c_thresh=dict(argstr='-c %.2f', + tfce_E=dict(argstr='--tfce_E=%.2f', ), - x_block_labels=dict(argstr='-e %s', + tfce_H=dict(argstr='--tfce_H=%.2f', ), - seed=dict(argstr='--seed=%d', + var_smooth=dict(argstr='-v %d', ), - demean=dict(argstr='-D', + vox_p_values=dict(argstr='-x', ), - output_type=dict(), - fcon=dict(argstr='-f %s', + x_block_labels=dict(argstr='-e %s', ), ) inputs = Randomise.input_spec() @@ -80,16 +81,18 @@ def test_Randomise_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Randomise_outputs(): - output_map = dict(tstat_files=dict(), - t_p_files=dict(), + output_map = dict(f_corrected_p_files=dict(), f_p_files=dict(), - f_corrected_p_files=dict(), - t_corrected_p_files=dict(), fstat_files=dict(), + t_corrected_p_files=dict(), + t_p_files=dict(), + tstat_files=dict(), ) outputs = Randomise.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_Reorient2Std.py b/nipype/interfaces/fsl/tests/test_auto_Reorient2Std.py index 8d9f507ef0..6444a57206 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Reorient2Std.py +++ b/nipype/interfaces/fsl/tests/test_auto_Reorient2Std.py @@ -1,32 +1,34 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.utils import Reorient2Std + def test_Reorient2Std_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + environ=dict(nohash=True, usedefault=True, ), - out_file=dict(hash_files=False, - genfile=True, - argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, + ), + in_file=dict(argstr='%s', + mandatory=True, ), - args=dict(argstr='%s', + out_file=dict(argstr='%s', + genfile=True, + hash_files=False, ), + output_type=dict(), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - in_file=dict(mandatory=True, - argstr='%s', - ), - output_type=dict(), ) inputs = Reorient2Std.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Reorient2Std_outputs(): output_map = dict(out_file=dict(), ) @@ -35,3 +37,4 @@ def test_Reorient2Std_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_SMM.py b/nipype/interfaces/fsl/tests/test_auto_SMM.py index deb645b788..3af66f58d4 100644 --- a/nipype/interfaces/fsl/tests/test_auto_SMM.py +++ b/nipype/interfaces/fsl/tests/test_auto_SMM.py @@ -1,38 +1,40 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.model import SMM + def test_SMM_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + environ=dict(nohash=True, usedefault=True, ), - spatial_data_file=dict(copyfile=False, - mandatory=True, - position=0, - argstr='--sdf="%s"', + ignore_exception=dict(nohash=True, + usedefault=True, ), - no_deactivation_class=dict(position=2, - argstr='--zfstatmode', + mask=dict(argstr='--mask="%s"', + copyfile=False, + mandatory=True, + position=1, ), - args=dict(argstr='%s', + no_deactivation_class=dict(argstr='--zfstatmode', + position=2, ), - mask=dict(copyfile=False, + output_type=dict(), + spatial_data_file=dict(argstr='--sdf="%s"', + copyfile=False, mandatory=True, - position=1, - argstr='--mask="%s"', + position=0, ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - output_type=dict(), ) inputs = SMM.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_SMM_outputs(): output_map = dict(activation_p_map=dict(), deactivation_p_map=dict(), @@ -43,3 +45,4 @@ def test_SMM_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_SUSAN.py b/nipype/interfaces/fsl/tests/test_auto_SUSAN.py index 0a474feff4..320bb5d763 100644 --- a/nipype/interfaces/fsl/tests/test_auto_SUSAN.py +++ b/nipype/interfaces/fsl/tests/test_auto_SUSAN.py @@ -1,47 +1,48 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.preprocess import SUSAN + def test_SUSAN_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(args=dict(argstr='%s', ), - out_file=dict(hash_files=False, - genfile=True, - position=-1, - argstr='%s', - ), - fwhm=dict(position=3, + brightness_threshold=dict(argstr='%.10f', mandatory=True, - argstr='%.10f', + position=2, ), - args=dict(argstr='%s', + dimension=dict(argstr='%d', + position=4, + usedefault=True, ), - brightness_threshold=dict(position=2, - mandatory=True, - argstr='%.10f', + environ=dict(nohash=True, + usedefault=True, ), - terminal_output=dict(mandatory=True, - nohash=True, + fwhm=dict(argstr='%.10f', + mandatory=True, + position=3, ), - environ=dict(nohash=True, + ignore_exception=dict(nohash=True, usedefault=True, ), - in_file=dict(position=1, + in_file=dict(argstr='%s', mandatory=True, - argstr='%s', + position=1, + ), + out_file=dict(argstr='%s', + genfile=True, + hash_files=False, + position=-1, ), output_type=dict(), - use_median=dict(position=5, - usedefault=True, - argstr='%d', + terminal_output=dict(mandatory=True, + nohash=True, ), - dimension=dict(position=4, + usans=dict(argstr='', + position=6, usedefault=True, - argstr='%d', ), - usans=dict(argstr='', + use_median=dict(argstr='%d', + position=5, usedefault=True, - position=6, ), ) inputs = SUSAN.input_spec() @@ -49,6 +50,7 @@ def test_SUSAN_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_SUSAN_outputs(): output_map = dict(smoothed_file=dict(), ) @@ -57,3 +59,4 @@ def test_SUSAN_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_SigLoss.py b/nipype/interfaces/fsl/tests/test_auto_SigLoss.py index bda4bb1a6d..1c6383ff36 100644 --- a/nipype/interfaces/fsl/tests/test_auto_SigLoss.py +++ b/nipype/interfaces/fsl/tests/test_auto_SigLoss.py @@ -1,37 +1,39 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.utils import SigLoss + def test_SigLoss_inputs(): - input_map = dict(echo_time=dict(argstr='--te=%f', + input_map = dict(args=dict(argstr='%s', + ), + echo_time=dict(argstr='--te=%f', + ), + environ=dict(nohash=True, + usedefault=True, ), ignore_exception=dict(nohash=True, usedefault=True, ), + in_file=dict(argstr='-i %s', + mandatory=True, + ), + mask_file=dict(argstr='-m %s', + ), out_file=dict(argstr='-s %s', genfile=True, ), - args=dict(argstr='%s', - ), + output_type=dict(), slice_direction=dict(argstr='-d %s', ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - in_file=dict(mandatory=True, - argstr='-i %s', - ), - mask_file=dict(argstr='-m %s', - ), - output_type=dict(), ) inputs = SigLoss.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_SigLoss_outputs(): output_map = dict(out_file=dict(), ) @@ -40,3 +42,4 @@ def test_SigLoss_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_SliceTimer.py b/nipype/interfaces/fsl/tests/test_auto_SliceTimer.py index 19d2fb8c57..88fade8e3a 100644 --- a/nipype/interfaces/fsl/tests/test_auto_SliceTimer.py +++ b/nipype/interfaces/fsl/tests/test_auto_SliceTimer.py @@ -1,40 +1,41 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.preprocess import SliceTimer + def test_SliceTimer_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + custom_order=dict(argstr='--ocustom=%s', + ), + custom_timings=dict(argstr='--tcustom=%s', + ), + environ=dict(nohash=True, + usedefault=True, + ), + global_shift=dict(argstr='--tglobal', + ), + ignore_exception=dict(nohash=True, usedefault=True, ), + in_file=dict(argstr='--in=%s', + mandatory=True, + position=0, + ), index_dir=dict(argstr='--down', ), - args=dict(argstr='%s', + interleaved=dict(argstr='--odd', ), out_file=dict(argstr='--out=%s', - hash_files=False, genfile=True, + hash_files=False, ), - custom_timings=dict(argstr='--tcustom=%s', - ), - time_repetition=dict(argstr='--repeat=%f', - ), + output_type=dict(), slice_direction=dict(argstr='--direction=%d', ), - custom_order=dict(argstr='--ocustom=%s', - ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - in_file=dict(position=0, - mandatory=True, - argstr='--in=%s', - ), - global_shift=dict(argstr='--tglobal', - ), - output_type=dict(), - interleaved=dict(argstr='--odd', + time_repetition=dict(argstr='--repeat=%f', ), ) inputs = SliceTimer.input_spec() @@ -42,6 +43,7 @@ def test_SliceTimer_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_SliceTimer_outputs(): output_map = dict(slice_time_corrected_file=dict(), ) @@ -50,3 +52,4 @@ def test_SliceTimer_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_Slicer.py b/nipype/interfaces/fsl/tests/test_auto_Slicer.py index 5a11784ba4..43e40ae8e8 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Slicer.py +++ b/nipype/interfaces/fsl/tests/test_auto_Slicer.py @@ -1,81 +1,82 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.utils import Slicer + def test_Slicer_inputs(): - input_map = dict(colour_map=dict(position=4, - argstr='-l %s', - ), - image_edges=dict(position=2, - argstr='%s', - ), - sample_axial=dict(xor=('single_slice', 'middle_slices', 'all_axial', 'sample_axial'), + input_map = dict(all_axial=dict(argstr='-A', position=10, requires=['image_width'], - argstr='-S %d', + xor=('single_slice', 'middle_slices', 'all_axial', 'sample_axial'), ), - image_width=dict(position=-2, - argstr='%d', + args=dict(argstr='%s', ), - middle_slices=dict(position=10, - xor=('single_slice', 'middle_slices', 'all_axial', 'sample_axial'), - argstr='-a', + colour_map=dict(argstr='-l %s', + position=4, ), - dither_edges=dict(position=7, - argstr='-t', + dither_edges=dict(argstr='-t', + position=7, ), - label_slices=dict(position=3, - argstr='-L', + environ=dict(nohash=True, usedefault=True, ), - in_file=dict(position=1, - mandatory=True, - argstr='%s', - ), ignore_exception=dict(nohash=True, usedefault=True, ), - single_slice=dict(xor=('single_slice', 'middle_slices', 'all_axial', 'sample_axial'), - position=10, - argstr='-%s', - requires=['slice_number'], - ), - args=dict(argstr='%s', + image_edges=dict(argstr='%s', + position=2, ), - scaling=dict(position=0, - argstr='-s %f', + image_width=dict(argstr='%d', + position=-2, ), - terminal_output=dict(mandatory=True, - nohash=True, + in_file=dict(argstr='%s', + mandatory=True, + position=1, ), - out_file=dict(hash_files=False, - genfile=True, - position=-1, - argstr='%s', + intensity_range=dict(argstr='-i %.3f %.3f', + position=5, ), - intensity_range=dict(position=5, - argstr='-i %.3f %.3f', + label_slices=dict(argstr='-L', + position=3, + usedefault=True, ), - threshold_edges=dict(position=6, - argstr='-e %.3f', + middle_slices=dict(argstr='-a', + position=10, + xor=('single_slice', 'middle_slices', 'all_axial', 'sample_axial'), ), - nearest_neighbour=dict(position=8, - argstr='-n', + nearest_neighbour=dict(argstr='-n', + position=8, ), - environ=dict(nohash=True, - usedefault=True, + out_file=dict(argstr='%s', + genfile=True, + hash_files=False, + position=-1, ), output_type=dict(), - all_axial=dict(xor=('single_slice', 'middle_slices', 'all_axial', 'sample_axial'), + sample_axial=dict(argstr='-S %d', position=10, requires=['image_width'], - argstr='-A', + xor=('single_slice', 'middle_slices', 'all_axial', 'sample_axial'), ), - show_orientation=dict(position=9, - argstr='%s', + scaling=dict(argstr='-s %f', + position=0, + ), + show_orientation=dict(argstr='%s', + position=9, usedefault=True, ), - slice_number=dict(position=11, - argstr='-%d', + single_slice=dict(argstr='-%s', + position=10, + requires=['slice_number'], + xor=('single_slice', 'middle_slices', 'all_axial', 'sample_axial'), + ), + slice_number=dict(argstr='-%d', + position=11, + ), + terminal_output=dict(mandatory=True, + nohash=True, + ), + threshold_edges=dict(argstr='-e %.3f', + position=6, ), ) inputs = Slicer.input_spec() @@ -83,6 +84,7 @@ def test_Slicer_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Slicer_outputs(): output_map = dict(out_file=dict(), ) @@ -91,3 +93,4 @@ def test_Slicer_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_Smooth.py b/nipype/interfaces/fsl/tests/test_auto_Smooth.py index cd4be55087..30c47447d3 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Smooth.py +++ b/nipype/interfaces/fsl/tests/test_auto_Smooth.py @@ -1,31 +1,32 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.utils import Smooth + def test_Smooth_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, - ), - args=dict(argstr='%s', - ), - terminal_output=dict(mandatory=True, - nohash=True, + input_map = dict(args=dict(argstr='%s', ), environ=dict(nohash=True, usedefault=True, ), - in_file=dict(position=0, + fwhm=dict(argstr='-kernel gauss %f -fmean', mandatory=True, - argstr='%s', + position=1, ), - output_type=dict(), - fwhm=dict(position=1, + ignore_exception=dict(nohash=True, + usedefault=True, + ), + in_file=dict(argstr='%s', mandatory=True, - argstr='-kernel gauss %f -fmean', + position=0, ), - smoothed_file=dict(position=2, - hash_files=False, + output_type=dict(), + smoothed_file=dict(argstr='%s', genfile=True, - argstr='%s', + hash_files=False, + position=2, + ), + terminal_output=dict(mandatory=True, + nohash=True, ), ) inputs = Smooth.input_spec() @@ -33,6 +34,7 @@ def test_Smooth_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Smooth_outputs(): output_map = dict(smoothed_file=dict(), ) @@ -41,3 +43,4 @@ def test_Smooth_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_SmoothEstimate.py b/nipype/interfaces/fsl/tests/test_auto_SmoothEstimate.py index fe0f715fd5..4c68ad5cc6 100644 --- a/nipype/interfaces/fsl/tests/test_auto_SmoothEstimate.py +++ b/nipype/interfaces/fsl/tests/test_auto_SmoothEstimate.py @@ -1,45 +1,48 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.model import SmoothEstimate + def test_SmoothEstimate_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, - ), - residual_fit_file=dict(requires=['dof'], - argstr='--res=%s', - ), - args=dict(argstr='%s', + input_map = dict(args=dict(argstr='%s', ), - dof=dict(mandatory=True, - argstr='--dof=%d', + dof=dict(argstr='--dof=%d', + mandatory=True, xor=['zstat_file'], ), - terminal_output=dict(mandatory=True, - nohash=True, - ), environ=dict(nohash=True, usedefault=True, ), - zstat_file=dict(xor=['dof'], - argstr='--zstat=%s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - mask_file=dict(mandatory=True, - argstr='--mask=%s', + mask_file=dict(argstr='--mask=%s', + mandatory=True, ), output_type=dict(), + residual_fit_file=dict(argstr='--res=%s', + requires=['dof'], + ), + terminal_output=dict(mandatory=True, + nohash=True, + ), + zstat_file=dict(argstr='--zstat=%s', + xor=['dof'], + ), ) inputs = SmoothEstimate.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_SmoothEstimate_outputs(): - output_map = dict(volume=dict(), + output_map = dict(dlh=dict(), resels=dict(), - dlh=dict(), + volume=dict(), ) outputs = SmoothEstimate.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_SpatialFilter.py b/nipype/interfaces/fsl/tests/test_auto_SpatialFilter.py index 6ac55239c1..9d5f022ca4 100644 --- a/nipype/interfaces/fsl/tests/test_auto_SpatialFilter.py +++ b/nipype/interfaces/fsl/tests/test_auto_SpatialFilter.py @@ -1,51 +1,52 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.maths import SpatialFilter + def test_SpatialFilter_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(args=dict(argstr='%s', ), - nan2zeros=dict(position=3, - argstr='-nan', + environ=dict(nohash=True, + usedefault=True, ), - kernel_file=dict(position=5, - xor=['kernel_size'], - argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - out_file=dict(hash_files=False, - genfile=True, - position=-2, - argstr='%s', + in_file=dict(argstr='%s', + mandatory=True, + position=2, ), - args=dict(argstr='%s', + internal_datatype=dict(argstr='-dt %s', + position=1, ), - internal_datatype=dict(position=1, - argstr='-dt %s', + kernel_file=dict(argstr='%s', + position=5, + xor=['kernel_size'], ), - terminal_output=dict(mandatory=True, - nohash=True, + kernel_shape=dict(argstr='-kernel %s', + position=4, ), - environ=dict(nohash=True, - usedefault=True, + kernel_size=dict(argstr='%.4f', + position=5, + xor=['kernel_file'], ), - kernel_shape=dict(position=4, - argstr='-kernel %s', + nan2zeros=dict(argstr='-nan', + position=3, ), - output_type=dict(), - operation=dict(position=6, + operation=dict(argstr='-f%s', mandatory=True, - argstr='-f%s', + position=6, ), - output_datatype=dict(position=-1, - argstr='-odt %s', + out_file=dict(argstr='%s', + genfile=True, + hash_files=False, + position=-2, ), - kernel_size=dict(position=5, - xor=['kernel_file'], - argstr='%.4f', + output_datatype=dict(argstr='-odt %s', + position=-1, ), - in_file=dict(position=2, - mandatory=True, - argstr='%s', + output_type=dict(), + terminal_output=dict(mandatory=True, + nohash=True, ), ) inputs = SpatialFilter.input_spec() @@ -53,6 +54,7 @@ def test_SpatialFilter_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_SpatialFilter_outputs(): output_map = dict(out_file=dict(), ) @@ -61,3 +63,4 @@ def test_SpatialFilter_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_Split.py b/nipype/interfaces/fsl/tests/test_auto_Split.py index abfb4079ac..ac96e0dba2 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Split.py +++ b/nipype/interfaces/fsl/tests/test_auto_Split.py @@ -1,29 +1,30 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.utils import Split + def test_Split_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, - ), - args=dict(argstr='%s', - ), - out_base_name=dict(position=1, - argstr='%s', + input_map = dict(args=dict(argstr='%s', ), - terminal_output=dict(mandatory=True, - nohash=True, + dimension=dict(argstr='-%s', + mandatory=True, + position=2, ), environ=dict(nohash=True, usedefault=True, ), - in_file=dict(position=0, + ignore_exception=dict(nohash=True, + usedefault=True, + ), + in_file=dict(argstr='%s', mandatory=True, - argstr='%s', + position=0, + ), + out_base_name=dict(argstr='%s', + position=1, ), output_type=dict(), - dimension=dict(position=2, - mandatory=True, - argstr='-%s', + terminal_output=dict(mandatory=True, + nohash=True, ), ) inputs = Split.input_spec() @@ -31,6 +32,7 @@ def test_Split_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Split_outputs(): output_map = dict(out_files=dict(), ) @@ -39,3 +41,4 @@ def test_Split_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_SwapDimensions.py b/nipype/interfaces/fsl/tests/test_auto_SwapDimensions.py index ee1c6fc9b5..fa1dabe145 100644 --- a/nipype/interfaces/fsl/tests/test_auto_SwapDimensions.py +++ b/nipype/interfaces/fsl/tests/test_auto_SwapDimensions.py @@ -1,36 +1,38 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.utils import SwapDimensions + def test_SwapDimensions_inputs(): - input_map = dict(new_dims=dict(mandatory=True, - argstr='%s %s %s', + input_map = dict(args=dict(argstr='%s', + ), + environ=dict(nohash=True, + usedefault=True, ), ignore_exception=dict(nohash=True, usedefault=True, ), + in_file=dict(argstr='%s', + mandatory=True, + position='1', + ), + new_dims=dict(argstr='%s %s %s', + mandatory=True, + ), out_file=dict(argstr='%s', - hash_files=False, genfile=True, + hash_files=False, ), - args=dict(argstr='%s', - ), + output_type=dict(), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - in_file=dict(position='1', - mandatory=True, - argstr='%s', - ), - output_type=dict(), ) inputs = SwapDimensions.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_SwapDimensions_outputs(): output_map = dict(out_file=dict(), ) @@ -39,3 +41,4 @@ def test_SwapDimensions_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_TOPUP.py b/nipype/interfaces/fsl/tests/test_auto_TOPUP.py index b60d7cf7e1..dd9f821ca3 100644 --- a/nipype/interfaces/fsl/tests/test_auto_TOPUP.py +++ b/nipype/interfaces/fsl/tests/test_auto_TOPUP.py @@ -1,58 +1,59 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.epi import TOPUP + def test_TOPUP_inputs(): - input_map = dict(minmet=dict(argstr='--minmet=%d', + input_map = dict(args=dict(argstr='%s', ), - splineorder=dict(argstr='--splineorder=%d', + config=dict(argstr='--config=%s', + usedefault=True, ), - out_base=dict(argstr='--out=%s', + encoding_direction=dict(), + encoding_file=dict(argstr='--datain=%s', ), - subsamp=dict(argstr='--subsamp=%d', + environ=dict(nohash=True, + usedefault=True, ), - fwhm=dict(argstr='--fwhm=%f', + estmov=dict(argstr='--estmov=%d', ), - out_logfile=dict(argstr='--logout=%s', + fwhm=dict(argstr='--fwhm=%f', ), - scale=dict(argstr='--scale=%d', + ignore_exception=dict(nohash=True, + usedefault=True, ), - encoding_direction=dict(), - out_field=dict(argstr='--fout=%s', + in_file=dict(argstr='--imain=%s', + mandatory=True, ), - regrid=dict(argstr='--regrid=%d', + interp=dict(argstr='--interp=%s', ), - in_file=dict(mandatory=True, - argstr='--imain=%s', + max_iter=dict(argstr='--miter=%d', ), - config=dict(argstr='--config=%s', - usedefault=True, + minmet=dict(argstr='--minmet=%d', ), - encoding_file=dict(argstr='--datain=%s', + numprec=dict(argstr='--numprec=%s', ), - ignore_exception=dict(nohash=True, - usedefault=True, + out_base=dict(argstr='--out=%s', ), out_corrected=dict(argstr='--iout=%s', ), - max_iter=dict(argstr='--miter=%d', + out_field=dict(argstr='--fout=%s', ), - interp=dict(argstr='--interp=%s', + out_logfile=dict(argstr='--logout=%s', ), + output_type=dict(), readout_times=dict(), - args=dict(argstr='%s', + regrid=dict(argstr='--regrid=%d', ), - terminal_output=dict(mandatory=True, - nohash=True, + scale=dict(argstr='--scale=%d', ), - warp_res=dict(argstr='--warpres=%f', + splineorder=dict(argstr='--splineorder=%d', ), - estmov=dict(argstr='--estmov=%d', + subsamp=dict(argstr='--subsamp=%d', ), - environ=dict(nohash=True, - usedefault=True, + terminal_output=dict(mandatory=True, + nohash=True, ), - output_type=dict(), - numprec=dict(argstr='--numprec=%s', + warp_res=dict(argstr='--warpres=%f', ), ) inputs = TOPUP.input_spec() @@ -60,17 +61,19 @@ def test_TOPUP_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_TOPUP_outputs(): output_map = dict(out_corrected=dict(), - out_logfile=dict(), - out_topup=dict(), - out_fieldcoef=dict(), - out_movpar=dict(), out_enc_file=dict(), out_field=dict(), + out_fieldcoef=dict(), + out_logfile=dict(), + out_movpar=dict(), + out_topup=dict(), ) outputs = TOPUP.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_TemporalFilter.py b/nipype/interfaces/fsl/tests/test_auto_TemporalFilter.py index ff77f71125..eb5ab790c9 100644 --- a/nipype/interfaces/fsl/tests/test_auto_TemporalFilter.py +++ b/nipype/interfaces/fsl/tests/test_auto_TemporalFilter.py @@ -1,44 +1,45 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.maths import TemporalFilter + def test_TemporalFilter_inputs(): - input_map = dict(lowpass_sigma=dict(position=5, - argstr='%.6f', - usedefault=True, + input_map = dict(args=dict(argstr='%s', ), - ignore_exception=dict(nohash=True, + environ=dict(nohash=True, usedefault=True, ), - out_file=dict(hash_files=False, - genfile=True, - position=-2, - argstr='%s', + highpass_sigma=dict(argstr='-bptf %.6f', + position=4, + usedefault=True, ), - nan2zeros=dict(position=3, - argstr='-nan', + ignore_exception=dict(nohash=True, + usedefault=True, ), - args=dict(argstr='%s', + in_file=dict(argstr='%s', + mandatory=True, + position=2, ), - internal_datatype=dict(position=1, - argstr='-dt %s', + internal_datatype=dict(argstr='-dt %s', + position=1, ), - highpass_sigma=dict(position=4, - argstr='-bptf %.6f', + lowpass_sigma=dict(argstr='%.6f', + position=5, usedefault=True, ), - terminal_output=dict(mandatory=True, - nohash=True, + nan2zeros=dict(argstr='-nan', + position=3, ), - environ=dict(nohash=True, - usedefault=True, + out_file=dict(argstr='%s', + genfile=True, + hash_files=False, + position=-2, ), - in_file=dict(position=2, - mandatory=True, - argstr='%s', + output_datatype=dict(argstr='-odt %s', + position=-1, ), output_type=dict(), - output_datatype=dict(position=-1, - argstr='-odt %s', + terminal_output=dict(mandatory=True, + nohash=True, ), ) inputs = TemporalFilter.input_spec() @@ -46,6 +47,7 @@ def test_TemporalFilter_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_TemporalFilter_outputs(): output_map = dict(out_file=dict(), ) @@ -54,3 +56,4 @@ def test_TemporalFilter_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_Threshold.py b/nipype/interfaces/fsl/tests/test_auto_Threshold.py index 6f88592221..78633dd902 100644 --- a/nipype/interfaces/fsl/tests/test_auto_Threshold.py +++ b/nipype/interfaces/fsl/tests/test_auto_Threshold.py @@ -1,52 +1,54 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.maths import Threshold + def test_Threshold_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + direction=dict(usedefault=True, + ), + environ=dict(nohash=True, + usedefault=True, + ), + ignore_exception=dict(nohash=True, usedefault=True, ), - nan2zeros=dict(position=3, - argstr='-nan', + in_file=dict(argstr='%s', + mandatory=True, + position=2, ), - direction=dict(usedefault=True, + internal_datatype=dict(argstr='-dt %s', + position=1, ), - out_file=dict(hash_files=False, + nan2zeros=dict(argstr='-nan', + position=3, + ), + out_file=dict(argstr='%s', genfile=True, + hash_files=False, position=-2, - argstr='%s', - ), - args=dict(argstr='%s', ), - internal_datatype=dict(position=1, - argstr='-dt %s', + output_datatype=dict(argstr='-odt %s', + position=-1, ), + output_type=dict(), terminal_output=dict(mandatory=True, nohash=True, ), - thresh=dict(position=4, + thresh=dict(argstr='%s', mandatory=True, - argstr='%s', - ), - use_robust_range=dict(), - output_type=dict(), - environ=dict(nohash=True, - usedefault=True, + position=4, ), use_nonzero_voxels=dict(requires=['use_robust_range'], ), - output_datatype=dict(position=-1, - argstr='-odt %s', - ), - in_file=dict(position=2, - mandatory=True, - argstr='%s', - ), + use_robust_range=dict(), ) inputs = Threshold.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Threshold_outputs(): output_map = dict(out_file=dict(), ) @@ -55,3 +57,4 @@ def test_Threshold_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_TractSkeleton.py b/nipype/interfaces/fsl/tests/test_auto_TractSkeleton.py index 0f7ece2678..4ce433c7f9 100644 --- a/nipype/interfaces/fsl/tests/test_auto_TractSkeleton.py +++ b/nipype/interfaces/fsl/tests/test_auto_TractSkeleton.py @@ -1,46 +1,48 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.dti import TractSkeleton + def test_TractSkeleton_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(alt_data_file=dict(argstr='-a %s', + ), + alt_skeleton=dict(argstr='-s %s', + ), + args=dict(argstr='%s', + ), + data_file=dict(), + distance_map=dict(), + environ=dict(nohash=True, usedefault=True, ), - use_cingulum_mask=dict(xor=['search_mask_file'], + ignore_exception=dict(nohash=True, usedefault=True, ), - skeleton_file=dict(argstr='-o %s', + in_file=dict(argstr='-i %s', + mandatory=True, ), - data_file=dict(), - args=dict(argstr='%s', + output_type=dict(), + project_data=dict(argstr='-p %.3f %s %s %s %s', + requires=['threshold', 'distance_map', 'data_file'], ), projected_data=dict(), - alt_skeleton=dict(argstr='-s %s', + search_mask_file=dict(xor=['use_cingulum_mask'], ), - alt_data_file=dict(argstr='-a %s', + skeleton_file=dict(argstr='-o %s', ), - threshold=dict(), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - in_file=dict(mandatory=True, - argstr='-i %s', - ), - project_data=dict(requires=['threshold', 'distance_map', 'data_file'], - argstr='-p %.3f %s %s %s %s', - ), - search_mask_file=dict(xor=['use_cingulum_mask'], + threshold=dict(), + use_cingulum_mask=dict(usedefault=True, + xor=['search_mask_file'], ), - output_type=dict(), - distance_map=dict(), ) inputs = TractSkeleton.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_TractSkeleton_outputs(): output_map = dict(projected_data=dict(), skeleton_file=dict(), @@ -50,3 +52,4 @@ def test_TractSkeleton_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_UnaryMaths.py b/nipype/interfaces/fsl/tests/test_auto_UnaryMaths.py index 98a8d208cb..540decac1c 100644 --- a/nipype/interfaces/fsl/tests/test_auto_UnaryMaths.py +++ b/nipype/interfaces/fsl/tests/test_auto_UnaryMaths.py @@ -1,40 +1,41 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.maths import UnaryMaths + def test_UnaryMaths_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + environ=dict(nohash=True, usedefault=True, ), - nan2zeros=dict(position=3, - argstr='-nan', + ignore_exception=dict(nohash=True, + usedefault=True, ), - out_file=dict(hash_files=False, - genfile=True, - position=-2, - argstr='%s', + in_file=dict(argstr='%s', + mandatory=True, + position=2, ), - args=dict(argstr='%s', + internal_datatype=dict(argstr='-dt %s', + position=1, ), - internal_datatype=dict(position=1, - argstr='-dt %s', + nan2zeros=dict(argstr='-nan', + position=3, ), - terminal_output=dict(mandatory=True, - nohash=True, + operation=dict(argstr='-%s', + mandatory=True, + position=4, ), - environ=dict(nohash=True, - usedefault=True, + out_file=dict(argstr='%s', + genfile=True, + hash_files=False, + position=-2, ), - in_file=dict(position=2, - mandatory=True, - argstr='%s', + output_datatype=dict(argstr='-odt %s', + position=-1, ), output_type=dict(), - operation=dict(position=4, - mandatory=True, - argstr='-%s', - ), - output_datatype=dict(position=-1, - argstr='-odt %s', + terminal_output=dict(mandatory=True, + nohash=True, ), ) inputs = UnaryMaths.input_spec() @@ -42,6 +43,7 @@ def test_UnaryMaths_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_UnaryMaths_outputs(): output_map = dict(out_file=dict(), ) @@ -50,3 +52,4 @@ def test_UnaryMaths_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_VecReg.py b/nipype/interfaces/fsl/tests/test_auto_VecReg.py index 56c224936f..5fad4061f1 100644 --- a/nipype/interfaces/fsl/tests/test_auto_VecReg.py +++ b/nipype/interfaces/fsl/tests/test_auto_VecReg.py @@ -1,42 +1,43 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.dti import VecReg + def test_VecReg_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(affine_mat=dict(argstr='-t %s', ), - warp_field=dict(argstr='-w %s', + args=dict(argstr='%s', ), - affine_mat=dict(argstr='-t %s', + environ=dict(nohash=True, + usedefault=True, ), - out_file=dict(argstr='-o %s', - hash_files=False, - genfile=True, + ignore_exception=dict(nohash=True, + usedefault=True, ), - rotation_warp=dict(argstr='--rotwarp=%s', + in_file=dict(argstr='-i %s', + mandatory=True, ), - args=dict(argstr='%s', + interpolation=dict(argstr='--interp=%s', ), mask=dict(argstr='-m %s', ), - rotation_mat=dict(argstr='--rotmat=%s', + out_file=dict(argstr='-o %s', + genfile=True, + hash_files=False, ), - terminal_output=dict(mandatory=True, - nohash=True, + output_type=dict(), + ref_mask=dict(argstr='--refmask=%s', ), - environ=dict(nohash=True, - usedefault=True, + ref_vol=dict(argstr='-r %s', + mandatory=True, ), - in_file=dict(mandatory=True, - argstr='-i %s', + rotation_mat=dict(argstr='--rotmat=%s', ), - ref_vol=dict(mandatory=True, - argstr='-r %s', + rotation_warp=dict(argstr='--rotwarp=%s', ), - output_type=dict(), - ref_mask=dict(argstr='--refmask=%s', + terminal_output=dict(mandatory=True, + nohash=True, ), - interpolation=dict(argstr='--interp=%s', + warp_field=dict(argstr='-w %s', ), ) inputs = VecReg.input_spec() @@ -44,6 +45,7 @@ def test_VecReg_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_VecReg_outputs(): output_map = dict(out_file=dict(), ) @@ -52,3 +54,4 @@ def test_VecReg_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/fsl/tests/test_auto_XFibres.py b/nipype/interfaces/fsl/tests/test_auto_XFibres.py index 6b83581ae5..f5c3746085 100644 --- a/nipype/interfaces/fsl/tests/test_auto_XFibres.py +++ b/nipype/interfaces/fsl/tests/test_auto_XFibres.py @@ -1,66 +1,67 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.fsl.dti import XFibres + def test_XFibres_inputs(): - input_map = dict(sample_every=dict(argstr='--sampleevery=%d', - ), - no_spat=dict(xor=('no_spat', 'non_linear'), - argstr='--nospat', + input_map = dict(all_ard=dict(argstr='--allard', + xor=('no_ard', 'all_ard'), ), - n_jumps=dict(argstr='--njumps=%d', - ), - seed=dict(argstr='--seed=%d', + args=dict(argstr='%s', ), burn_in=dict(argstr='--burnin=%d', ), - bvecs=dict(mandatory=True, - argstr='--bvecs=%s', + burn_in_no_ard=dict(argstr='--burninnoard=%d', ), - all_ard=dict(xor=('no_ard', 'all_ard'), - argstr='--allard', + bvals=dict(argstr='--bvals=%s', + mandatory=True, ), - n_fibres=dict(argstr='--nfibres=%d', + bvecs=dict(argstr='--bvecs=%s', + mandatory=True, ), - non_linear=dict(xor=('no_spat', 'non_linear'), - argstr='--nonlinear', + dwi=dict(argstr='--data=%s', + mandatory=True, ), - logdir=dict(usedefault=True, - argstr='--logdir=%s', + environ=dict(nohash=True, + usedefault=True, ), - dwi=dict(mandatory=True, - argstr='--data=%s', + force_dir=dict(argstr='--forcedir', + usedefault=True, ), fudge=dict(argstr='--fudge=%d', ), ignore_exception=dict(nohash=True, usedefault=True, ), - no_ard=dict(xor=('no_ard', 'all_ard'), - argstr='--noard', - ), - args=dict(argstr='%s', + logdir=dict(argstr='--logdir=%s', + usedefault=True, ), - force_dir=dict(usedefault=True, - argstr='--forcedir', + mask=dict(argstr='--mask=%s', + mandatory=True, ), - update_proposal_every=dict(argstr='--updateproposalevery=%d', + model=dict(argstr='--model=%d', ), - terminal_output=dict(mandatory=True, - nohash=True, + n_fibres=dict(argstr='--nfibres=%d', ), - bvals=dict(mandatory=True, - argstr='--bvals=%s', + n_jumps=dict(argstr='--njumps=%d', ), - mask=dict(mandatory=True, - argstr='--mask=%s', + no_ard=dict(argstr='--noard', + xor=('no_ard', 'all_ard'), ), - burn_in_no_ard=dict(argstr='--burninnoard=%d', + no_spat=dict(argstr='--nospat', + xor=('no_spat', 'non_linear'), ), - environ=dict(nohash=True, - usedefault=True, + non_linear=dict(argstr='--nonlinear', + xor=('no_spat', 'non_linear'), ), output_type=dict(), - model=dict(argstr='--model=%d', + sample_every=dict(argstr='--sampleevery=%d', + ), + seed=dict(argstr='--seed=%d', + ), + terminal_output=dict(mandatory=True, + nohash=True, + ), + update_proposal_every=dict(argstr='--updateproposalevery=%d', ), ) inputs = XFibres.input_spec() @@ -68,17 +69,19 @@ def test_XFibres_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_XFibres_outputs(): - output_map = dict(mean_fsamples=dict(), + output_map = dict(dyads=dict(), + fsamples=dict(), mean_S0samples=dict(), - dyads=dict(), + mean_dsamples=dict(), + mean_fsamples=dict(), phsamples=dict(), - fsamples=dict(), thsamples=dict(), - mean_dsamples=dict(), ) outputs = XFibres.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/mne/tests/test_auto_WatershedBEM.py b/nipype/interfaces/mne/tests/test_auto_WatershedBEM.py index 748834e235..3a26504fcd 100644 --- a/nipype/interfaces/mne/tests/test_auto_WatershedBEM.py +++ b/nipype/interfaces/mne/tests/test_auto_WatershedBEM.py @@ -1,30 +1,31 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.mne.base import WatershedBEM + def test_WatershedBEM_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, - ), - subject_id=dict(mandatory=True, - argstr='--subject %s', - ), - args=dict(argstr='%s', + input_map = dict(args=dict(argstr='%s', ), atlas_mode=dict(argstr='--atlas', ), - volume=dict(usedefault=True, - argstr='--volume %s', + environ=dict(nohash=True, + usedefault=True, ), - terminal_output=dict(mandatory=True, - nohash=True, + ignore_exception=dict(nohash=True, + usedefault=True, ), - environ=dict(nohash=True, + overwrite=dict(argstr='--overwrite', usedefault=True, ), + subject_id=dict(argstr='--subject %s', + mandatory=True, + ), subjects_dir=dict(mandatory=True, usedefault=True, ), - overwrite=dict(argstr='--overwrite', + terminal_output=dict(mandatory=True, + nohash=True, + ), + volume=dict(argstr='--volume %s', usedefault=True, ), ) @@ -33,21 +34,22 @@ def test_WatershedBEM_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_WatershedBEM_outputs(): - output_map = dict(cor_files=dict(altkey='COR', + output_map = dict(brain_surface=dict(loc='bem/watershed', + ), + cor_files=dict(altkey='COR', loc='bem/watershed/ws', ), - outer_skull_surface=dict(loc='bem/watershed', + fif_file=dict(altkey='fif', + loc='bem', ), inner_skull_surface=dict(loc='bem/watershed', ), + mesh_files=dict(), outer_skin_surface=dict(loc='bem/watershed', ), - fif_file=dict(altkey='fif', - loc='bem', - ), - mesh_files=dict(), - brain_surface=dict(loc='bem/watershed', + outer_skull_surface=dict(loc='bem/watershed', ), ) outputs = WatershedBEM.output_spec() @@ -55,3 +57,4 @@ def test_WatershedBEM_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/mrtrix/tests/test_auto_ConstrainedSphericalDeconvolution.py b/nipype/interfaces/mrtrix/tests/test_auto_ConstrainedSphericalDeconvolution.py index 9c94ab7b34..a394942814 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_ConstrainedSphericalDeconvolution.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_ConstrainedSphericalDeconvolution.py @@ -1,54 +1,55 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.mrtrix.tensors import ConstrainedSphericalDeconvolution + def test_ConstrainedSphericalDeconvolution_inputs(): - input_map = dict(out_filename=dict(position=-1, - genfile=True, - argstr='%s', - ), - ignore_exception=dict(nohash=True, - usedefault=True, - ), - args=dict(argstr='%s', + input_map = dict(args=dict(argstr='%s', ), - mask_image=dict(position=2, - argstr='-mask %s', - ), - maximum_harmonic_order=dict(argstr='-lmax %s', + debug=dict(argstr='-debug', ), - filter_file=dict(position=-2, - argstr='-filter %s', + directions_file=dict(argstr='-directions %s', + position=-2, ), - normalise=dict(position=3, - argstr='-normalise', + encoding_file=dict(argstr='-grad %s', + position=1, ), - directions_file=dict(position=-2, - argstr='-directions %s', + environ=dict(nohash=True, + usedefault=True, ), - terminal_output=dict(mandatory=True, - nohash=True, + filter_file=dict(argstr='-filter %s', + position=-2, ), - environ=dict(nohash=True, + ignore_exception=dict(nohash=True, usedefault=True, ), - in_file=dict(position=-3, + in_file=dict(argstr='%s', mandatory=True, - argstr='%s', + position=-3, ), iterations=dict(argstr='-niter %s', ), - debug=dict(argstr='-debug', + lambda_value=dict(argstr='-lambda %s', ), - threshold_value=dict(argstr='-threshold %s', + mask_image=dict(argstr='-mask %s', + position=2, ), - lambda_value=dict(argstr='-lambda %s', + maximum_harmonic_order=dict(argstr='-lmax %s', + ), + normalise=dict(argstr='-normalise', + position=3, ), - encoding_file=dict(position=1, - argstr='-grad %s', + out_filename=dict(argstr='%s', + genfile=True, + position=-1, ), - response_file=dict(position=-2, + response_file=dict(argstr='%s', mandatory=True, - argstr='%s', + position=-2, + ), + terminal_output=dict(mandatory=True, + nohash=True, + ), + threshold_value=dict(argstr='-threshold %s', ), ) inputs = ConstrainedSphericalDeconvolution.input_spec() @@ -56,6 +57,7 @@ def test_ConstrainedSphericalDeconvolution_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ConstrainedSphericalDeconvolution_outputs(): output_map = dict(spherical_harmonics_image=dict(), ) @@ -64,3 +66,4 @@ def test_ConstrainedSphericalDeconvolution_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/mrtrix/tests/test_auto_DWI2SphericalHarmonicsImage.py b/nipype/interfaces/mrtrix/tests/test_auto_DWI2SphericalHarmonicsImage.py index 6e6003969d..502d588fb7 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_DWI2SphericalHarmonicsImage.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_DWI2SphericalHarmonicsImage.py @@ -1,41 +1,43 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.mrtrix.tensors import DWI2SphericalHarmonicsImage + def test_DWI2SphericalHarmonicsImage_inputs(): - input_map = dict(out_filename=dict(position=-1, - genfile=True, - argstr='%s', + input_map = dict(args=dict(argstr='%s', + ), + encoding_file=dict(argstr='-grad %s', + mandatory=True, + position=1, + ), + environ=dict(nohash=True, + usedefault=True, ), ignore_exception=dict(nohash=True, usedefault=True, ), - args=dict(argstr='%s', + in_file=dict(argstr='%s', + mandatory=True, + position=-2, ), maximum_harmonic_order=dict(argstr='-lmax %s', ), - normalise=dict(position=3, - argstr='-normalise', + normalise=dict(argstr='-normalise', + position=3, + ), + out_filename=dict(argstr='%s', + genfile=True, + position=-1, ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - in_file=dict(position=-2, - mandatory=True, - argstr='%s', - ), - encoding_file=dict(position=1, - mandatory=True, - argstr='-grad %s', - ), ) inputs = DWI2SphericalHarmonicsImage.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_DWI2SphericalHarmonicsImage_outputs(): output_map = dict(spherical_harmonics_image=dict(), ) @@ -44,3 +46,4 @@ def test_DWI2SphericalHarmonicsImage_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/mrtrix/tests/test_auto_DWI2Tensor.py b/nipype/interfaces/mrtrix/tests/test_auto_DWI2Tensor.py index d527d9152b..2c121da52d 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_DWI2Tensor.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_DWI2Tensor.py @@ -1,44 +1,45 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.mrtrix.preprocess import DWI2Tensor + def test_DWI2Tensor_inputs(): - input_map = dict(out_filename=dict(name_source='in_file', - output_name='tensor', - name_template='%s_tensor.mif', - position=-1, - argstr='%s', + input_map = dict(args=dict(argstr='%s', + ), + debug=dict(argstr='-debug', + position=1, + ), + encoding_file=dict(argstr='-grad %s', + position=2, + ), + environ=dict(nohash=True, + usedefault=True, ), ignore_exception=dict(nohash=True, usedefault=True, ), ignore_slice_by_volume=dict(argstr='-ignoreslices %s', - sep=' ', position=2, - ), - args=dict(argstr='%s', + sep=' ', ), ignore_volumes=dict(argstr='-ignorevolumes %s', - sep=' ', position=2, - ), - quiet=dict(position=1, - argstr='-quiet', - ), - terminal_output=dict(mandatory=True, - nohash=True, - ), - environ=dict(nohash=True, - usedefault=True, + sep=' ', ), in_file=dict(argstr='%s', mandatory=True, position=-2, ), - debug=dict(position=1, - argstr='-debug', + out_filename=dict(argstr='%s', + name_source='in_file', + name_template='%s_tensor.mif', + output_name='tensor', + position=-1, ), - encoding_file=dict(position=2, - argstr='-grad %s', + quiet=dict(argstr='-quiet', + position=1, + ), + terminal_output=dict(mandatory=True, + nohash=True, ), ) inputs = DWI2Tensor.input_spec() @@ -46,6 +47,7 @@ def test_DWI2Tensor_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_DWI2Tensor_outputs(): output_map = dict(tensor=dict(), ) @@ -54,3 +56,4 @@ def test_DWI2Tensor_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/mrtrix/tests/test_auto_DiffusionTensorStreamlineTrack.py b/nipype/interfaces/mrtrix/tests/test_auto_DiffusionTensorStreamlineTrack.py index 8e231bf345..111260c571 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_DiffusionTensorStreamlineTrack.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_DiffusionTensorStreamlineTrack.py @@ -1,98 +1,99 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.mrtrix.tracking import DiffusionTensorStreamlineTrack + def test_DiffusionTensorStreamlineTrack_inputs(): - input_map = dict(do_not_precompute=dict(argstr='-noprecomputed', - ), - maximum_number_of_tracks=dict(argstr='-maxnum %d', + input_map = dict(args=dict(argstr='%s', ), - exclude_file=dict(position=2, - argstr='-exclude %s', + cutoff_value=dict(argstr='-cutoff %s', + units='NA', ), - cutoff_value=dict(units='NA', - argstr='-cutoff %s', + desired_number_of_tracks=dict(argstr='-number %d', ), - seed_file=dict(position=2, - argstr='-seed %s', + do_not_precompute=dict(argstr='-noprecomputed', ), - step_size=dict(units='mm', - argstr='-step %s', + environ=dict(nohash=True, + usedefault=True, ), - in_file=dict(position=-2, - mandatory=True, - argstr='%s', + exclude_file=dict(argstr='-exclude %s', + position=2, ), - unidirectional=dict(argstr='-unidirectional', + exclude_spec=dict(argstr='-seed %s', + position=2, + sep=',', + units='mm', ), - no_mask_interpolation=dict(argstr='-nomaskinterp', + gradient_encoding_file=dict(argstr='-grad %s', + mandatory=True, + position=-2, ), ignore_exception=dict(nohash=True, usedefault=True, ), - include_file=dict(position=2, - argstr='-include %s', + in_file=dict(argstr='%s', + mandatory=True, + position=-2, ), - maximum_tract_length=dict(units='mm', - argstr='-length %s', + include_file=dict(argstr='-include %s', + position=2, ), - args=dict(argstr='%s', + include_spec=dict(argstr='-seed %s', + position=2, + sep=',', + units='mm', ), - stop=dict(argstr='-gzip', + initial_cutoff_value=dict(argstr='-initcutoff %s', + units='NA', ), - minimum_tract_length=dict(units='mm', - argstr='-minlength %s', + initial_direction=dict(argstr='-initdirection %s', + units='voxels', ), - inputmodel=dict(position=-3, + inputmodel=dict(argstr='%s', + position=-3, usedefault=True, - argstr='%s', ), - initial_direction=dict(units='voxels', - argstr='-initdirection %s', + mask_file=dict(argstr='-exclude %s', + position=2, ), - exclude_spec=dict(sep=',', - units='mm', + mask_spec=dict(argstr='-seed %s', position=2, - argstr='-seed %s', + sep=',', + units='mm', ), - desired_number_of_tracks=dict(argstr='-number %d', + maximum_number_of_tracks=dict(argstr='-maxnum %d', ), - seed_spec=dict(sep=',', + maximum_tract_length=dict(argstr='-length %s', units='mm', - position=2, - argstr='-seed %s', - ), - initial_cutoff_value=dict(units='NA', - argstr='-initcutoff %s', ), - minimum_radius_of_curvature=dict(units='mm', - argstr='-curvature %s', + minimum_radius_of_curvature=dict(argstr='-curvature %s', + units='mm', ), - mask_spec=dict(sep=',', + minimum_tract_length=dict(argstr='-minlength %s', units='mm', - position=2, - argstr='-seed %s', ), - out_file=dict(position=-1, + no_mask_interpolation=dict(argstr='-nomaskinterp', + ), + out_file=dict(argstr='%s', genfile=True, - argstr='%s', + position=-1, ), - gradient_encoding_file=dict(position=-2, - mandatory=True, - argstr='-grad %s', + seed_file=dict(argstr='-seed %s', + position=2, ), - include_spec=dict(sep=',', - units='mm', + seed_spec=dict(argstr='-seed %s', position=2, - argstr='-seed %s', + sep=',', + units='mm', + ), + step_size=dict(argstr='-step %s', + units='mm', + ), + stop=dict(argstr='-gzip', ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - mask_file=dict(position=2, - argstr='-exclude %s', + unidirectional=dict(argstr='-unidirectional', ), ) inputs = DiffusionTensorStreamlineTrack.input_spec() @@ -100,6 +101,7 @@ def test_DiffusionTensorStreamlineTrack_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_DiffusionTensorStreamlineTrack_outputs(): output_map = dict(tracked=dict(), ) @@ -108,3 +110,4 @@ def test_DiffusionTensorStreamlineTrack_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/mrtrix/tests/test_auto_Directions2Amplitude.py b/nipype/interfaces/mrtrix/tests/test_auto_Directions2Amplitude.py index b4d4517631..f1c5324fba 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_Directions2Amplitude.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_Directions2Amplitude.py @@ -1,39 +1,40 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.mrtrix.tensors import Directions2Amplitude + def test_Directions2Amplitude_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, - ), - out_file=dict(hash_files=False, - keep_extension=False, - name_source=['in_file'], - name_template='%s_amplitudes.mif', - position=-1, - argstr='%s', + input_map = dict(args=dict(argstr='%s', ), - quiet_display=dict(argstr='-quiet', - ), - args=dict(argstr='%s', - ), - num_peaks=dict(argstr='-num %s', + display_debug=dict(argstr='-debug', ), display_info=dict(argstr='-info', ), - display_debug=dict(argstr='-debug', - ), environ=dict(nohash=True, usedefault=True, ), - in_file=dict(position=-2, + ignore_exception=dict(nohash=True, + usedefault=True, + ), + in_file=dict(argstr='%s', mandatory=True, - argstr='%s', + position=-2, ), - peak_directions=dict(sep=' ', - argstr='-direction %s', + num_peaks=dict(argstr='-num %s', + ), + out_file=dict(argstr='%s', + hash_files=False, + keep_extension=False, + name_source=['in_file'], + name_template='%s_amplitudes.mif', + position=-1, + ), + peak_directions=dict(argstr='-direction %s', + sep=' ', ), peaks_image=dict(argstr='-peaks %s', ), + quiet_display=dict(argstr='-quiet', + ), terminal_output=dict(mandatory=True, nohash=True, ), @@ -43,6 +44,7 @@ def test_Directions2Amplitude_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Directions2Amplitude_outputs(): output_map = dict(out_file=dict(), ) @@ -51,3 +53,4 @@ def test_Directions2Amplitude_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/mrtrix/tests/test_auto_Erode.py b/nipype/interfaces/mrtrix/tests/test_auto_Erode.py index 6b94c346e8..44f9bfdfae 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_Erode.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_Erode.py @@ -1,33 +1,34 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.mrtrix.preprocess import Erode + def test_Erode_inputs(): - input_map = dict(out_filename=dict(position=-1, - genfile=True, - argstr='%s', - ), - ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(args=dict(argstr='%s', ), - dilate=dict(position=1, - argstr='-dilate', + debug=dict(argstr='-debug', + position=1, ), - args=dict(argstr='%s', - ), - quiet=dict(position=1, - argstr='-quiet', - ), - number_of_passes=dict(argstr='-npass %s', + dilate=dict(argstr='-dilate', + position=1, ), environ=dict(nohash=True, usedefault=True, ), - in_file=dict(position=-2, + ignore_exception=dict(nohash=True, + usedefault=True, + ), + in_file=dict(argstr='%s', mandatory=True, - argstr='%s', + position=-2, + ), + number_of_passes=dict(argstr='-npass %s', ), - debug=dict(position=1, - argstr='-debug', + out_filename=dict(argstr='%s', + genfile=True, + position=-1, + ), + quiet=dict(argstr='-quiet', + position=1, ), terminal_output=dict(mandatory=True, nohash=True, @@ -38,6 +39,7 @@ def test_Erode_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Erode_outputs(): output_map = dict(out_file=dict(), ) @@ -46,3 +48,4 @@ def test_Erode_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/mrtrix/tests/test_auto_EstimateResponseForSH.py b/nipype/interfaces/mrtrix/tests/test_auto_EstimateResponseForSH.py index 23a5757eaa..13c1330915 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_EstimateResponseForSH.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_EstimateResponseForSH.py @@ -1,48 +1,50 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.mrtrix.tensors import EstimateResponseForSH + def test_EstimateResponseForSH_inputs(): - input_map = dict(out_filename=dict(position=-1, - genfile=True, - argstr='%s', + input_map = dict(args=dict(argstr='%s', + ), + debug=dict(argstr='-debug', + ), + encoding_file=dict(argstr='-grad %s', + mandatory=True, + position=1, + ), + environ=dict(nohash=True, + usedefault=True, ), ignore_exception=dict(nohash=True, usedefault=True, ), - args=dict(argstr='%s', + in_file=dict(argstr='%s', + mandatory=True, + position=-3, ), - mask_image=dict(position=-2, + mask_image=dict(argstr='%s', mandatory=True, - argstr='%s', + position=-2, ), maximum_harmonic_order=dict(argstr='-lmax %s', ), normalise=dict(argstr='-normalise', ), + out_filename=dict(argstr='%s', + genfile=True, + position=-1, + ), quiet=dict(argstr='-quiet', ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - in_file=dict(position=-3, - mandatory=True, - argstr='%s', - ), - debug=dict(argstr='-debug', - ), - encoding_file=dict(position=1, - mandatory=True, - argstr='-grad %s', - ), ) inputs = EstimateResponseForSH.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_EstimateResponseForSH_outputs(): output_map = dict(response=dict(), ) @@ -51,3 +53,4 @@ def test_EstimateResponseForSH_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/mrtrix/tests/test_auto_FSL2MRTrix.py b/nipype/interfaces/mrtrix/tests/test_auto_FSL2MRTrix.py index bd2860274a..6f8e7f8976 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_FSL2MRTrix.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_FSL2MRTrix.py @@ -1,16 +1,17 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.mrtrix.tensors import FSL2MRTrix + def test_FSL2MRTrix_inputs(): - input_map = dict(invert_y=dict(usedefault=True, + input_map = dict(bval_file=dict(mandatory=True, + ), + bvec_file=dict(mandatory=True, ), invert_x=dict(usedefault=True, ), - invert_z=dict(usedefault=True, + invert_y=dict(usedefault=True, ), - bvec_file=dict(mandatory=True, - ), - bval_file=dict(mandatory=True, + invert_z=dict(usedefault=True, ), out_encoding_file=dict(genfile=True, ), @@ -20,6 +21,7 @@ def test_FSL2MRTrix_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_FSL2MRTrix_outputs(): output_map = dict(encoding_file=dict(), ) @@ -28,3 +30,4 @@ def test_FSL2MRTrix_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/mrtrix/tests/test_auto_FindShPeaks.py b/nipype/interfaces/mrtrix/tests/test_auto_FindShPeaks.py index f0422664ae..cc6784a536 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_FindShPeaks.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_FindShPeaks.py @@ -1,45 +1,46 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.mrtrix.tensors import FindShPeaks + def test_FindShPeaks_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, - ), - display_debug=dict(argstr='-debug', - ), - out_file=dict(hash_files=False, - keep_extension=False, - name_source=['in_file'], - name_template='%s_peak_dirs.mif', - position=-1, - argstr='%s', + input_map = dict(args=dict(argstr='%s', ), - directions_file=dict(position=-2, + directions_file=dict(argstr='%s', mandatory=True, - argstr='%s', - ), - quiet_display=dict(argstr='-quiet', - ), - args=dict(argstr='%s', + position=-2, ), - num_peaks=dict(argstr='-num %s', + display_debug=dict(argstr='-debug', ), display_info=dict(argstr='-info', ), - peak_threshold=dict(argstr='-threshold %s', - ), environ=dict(nohash=True, usedefault=True, ), - in_file=dict(position=-3, + ignore_exception=dict(nohash=True, + usedefault=True, + ), + in_file=dict(argstr='%s', mandatory=True, - argstr='%s', + position=-3, + ), + num_peaks=dict(argstr='-num %s', ), - peak_directions=dict(sep=' ', - argstr='-direction %s', + out_file=dict(argstr='%s', + hash_files=False, + keep_extension=False, + name_source=['in_file'], + name_template='%s_peak_dirs.mif', + position=-1, + ), + peak_directions=dict(argstr='-direction %s', + sep=' ', + ), + peak_threshold=dict(argstr='-threshold %s', ), peaks_image=dict(argstr='-peaks %s', ), + quiet_display=dict(argstr='-quiet', + ), terminal_output=dict(mandatory=True, nohash=True, ), @@ -49,6 +50,7 @@ def test_FindShPeaks_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_FindShPeaks_outputs(): output_map = dict(out_file=dict(), ) @@ -57,3 +59,4 @@ def test_FindShPeaks_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/mrtrix/tests/test_auto_GenerateDirections.py b/nipype/interfaces/mrtrix/tests/test_auto_GenerateDirections.py index 9cc680ef11..5b07ee22bc 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_GenerateDirections.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_GenerateDirections.py @@ -1,33 +1,34 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.mrtrix.tensors import GenerateDirections + def test_GenerateDirections_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, - ), - niter=dict(argstr='-niter %s', + input_map = dict(args=dict(argstr='%s', ), - out_file=dict(hash_files=False, - usedefault=True, - position=-1, - argstr='%s', + display_debug=dict(argstr='-debug', ), - power=dict(argstr='-power %s', + display_info=dict(argstr='-info', ), - quiet_display=dict(argstr='-quiet', + environ=dict(nohash=True, + usedefault=True, ), - args=dict(argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - display_info=dict(argstr='-info', + niter=dict(argstr='-niter %s', ), - display_debug=dict(argstr='-debug', + num_dirs=dict(argstr='%s', + mandatory=True, + position=-2, ), - environ=dict(nohash=True, + out_file=dict(argstr='%s', + hash_files=False, + position=-1, usedefault=True, ), - num_dirs=dict(position=-2, - mandatory=True, - argstr='%s', + power=dict(argstr='-power %s', + ), + quiet_display=dict(argstr='-quiet', ), terminal_output=dict(mandatory=True, nohash=True, @@ -38,6 +39,7 @@ def test_GenerateDirections_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_GenerateDirections_outputs(): output_map = dict(out_file=dict(), ) @@ -46,3 +48,4 @@ def test_GenerateDirections_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/mrtrix/tests/test_auto_GenerateWhiteMatterMask.py b/nipype/interfaces/mrtrix/tests/test_auto_GenerateWhiteMatterMask.py index 700058412c..cd835e1686 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_GenerateWhiteMatterMask.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_GenerateWhiteMatterMask.py @@ -1,42 +1,44 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.mrtrix.preprocess import GenerateWhiteMatterMask + def test_GenerateWhiteMatterMask_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(args=dict(argstr='%s', ), - binary_mask=dict(position=-2, + binary_mask=dict(argstr='%s', mandatory=True, - argstr='%s', + position=-2, + ), + encoding_file=dict(argstr='-grad %s', + mandatory=True, + position=1, + ), + environ=dict(nohash=True, + usedefault=True, ), - args=dict(argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, + ), + in_file=dict(argstr='%s', + mandatory=True, + position=-3, ), noise_level_margin=dict(argstr='-margin %s', ), - out_WMProb_filename=dict(position=-1, + out_WMProb_filename=dict(argstr='%s', genfile=True, - argstr='%s', + position=-1, ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - in_file=dict(position=-3, - mandatory=True, - argstr='%s', - ), - encoding_file=dict(position=1, - mandatory=True, - argstr='-grad %s', - ), ) inputs = GenerateWhiteMatterMask.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_GenerateWhiteMatterMask_outputs(): output_map = dict(WMprobabilitymap=dict(), ) @@ -45,3 +47,4 @@ def test_GenerateWhiteMatterMask_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/mrtrix/tests/test_auto_MRConvert.py b/nipype/interfaces/mrtrix/tests/test_auto_MRConvert.py index 12117bc033..1d5396b989 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_MRConvert.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_MRConvert.py @@ -1,59 +1,60 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.mrtrix.preprocess import MRConvert + def test_MRConvert_inputs(): - input_map = dict(out_filename=dict(position=-1, - genfile=True, - argstr='%s', + input_map = dict(args=dict(argstr='%s', ), - ignore_exception=dict(nohash=True, + environ=dict(nohash=True, usedefault=True, ), - layout=dict(position=2, - argstr='-output %s', - ), extension=dict(position=2, usedefault=True, ), + extract_at_axis=dict(argstr='-coord %s', + position=1, + ), extract_at_coordinate=dict(argstr='%s', - sep=',', position=2, + sep=',', ), - offset_bias=dict(units='mm', - position=3, - argstr='-scale %d', + ignore_exception=dict(nohash=True, + usedefault=True, ), - resample=dict(units='mm', - position=3, - argstr='-scale %d', + in_file=dict(argstr='%s', + mandatory=True, + position=-2, ), - args=dict(argstr='%s', + layout=dict(argstr='-output %s', + position=2, ), - terminal_output=dict(mandatory=True, - nohash=True, + offset_bias=dict(argstr='-scale %d', + position=3, + units='mm', ), - environ=dict(nohash=True, - usedefault=True, + out_filename=dict(argstr='%s', + genfile=True, + position=-1, ), - in_file=dict(position=-2, - mandatory=True, - argstr='%s', + output_datatype=dict(argstr='-output %s', + position=2, + ), + prs=dict(argstr='-prs', + position=3, ), - prs=dict(position=3, - argstr='-prs', + replace_NaN_with_zero=dict(argstr='-zero', + position=3, ), - extract_at_axis=dict(position=1, - argstr='-coord %s', + resample=dict(argstr='-scale %d', + position=3, + units='mm', ), - replace_NaN_with_zero=dict(position=3, - argstr='-zero', + terminal_output=dict(mandatory=True, + nohash=True, ), voxel_dims=dict(argstr='-vox %s', - sep=',', position=3, - ), - output_datatype=dict(position=2, - argstr='-output %s', + sep=',', ), ) inputs = MRConvert.input_spec() @@ -61,6 +62,7 @@ def test_MRConvert_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MRConvert_outputs(): output_map = dict(converted=dict(), ) @@ -69,3 +71,4 @@ def test_MRConvert_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/mrtrix/tests/test_auto_MRMultiply.py b/nipype/interfaces/mrtrix/tests/test_auto_MRMultiply.py index 6aea83edc3..3dbbf1fa3b 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_MRMultiply.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_MRMultiply.py @@ -1,38 +1,40 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.mrtrix.preprocess import MRMultiply + def test_MRMultiply_inputs(): - input_map = dict(out_filename=dict(position=-1, - genfile=True, - argstr='%s', + input_map = dict(args=dict(argstr='%s', ), - ignore_exception=dict(nohash=True, + debug=dict(argstr='-debug', + position=1, + ), + environ=dict(nohash=True, usedefault=True, ), - args=dict(argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, ), in_files=dict(argstr='%s', mandatory=True, position=-2, ), - quiet=dict(position=1, - argstr='-quiet', + out_filename=dict(argstr='%s', + genfile=True, + position=-1, + ), + quiet=dict(argstr='-quiet', + position=1, ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - debug=dict(position=1, - argstr='-debug', - ), ) inputs = MRMultiply.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MRMultiply_outputs(): output_map = dict(out_file=dict(), ) @@ -41,3 +43,4 @@ def test_MRMultiply_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/mrtrix/tests/test_auto_MRTransform.py b/nipype/interfaces/mrtrix/tests/test_auto_MRTransform.py index d66e90d179..859aedb524 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_MRTransform.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_MRTransform.py @@ -1,49 +1,50 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.mrtrix.preprocess import MRTransform + def test_MRTransform_inputs(): - input_map = dict(out_filename=dict(position=-1, - genfile=True, - argstr='%s', - ), - ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(args=dict(argstr='%s', ), - template_image=dict(position=1, - argstr='-template %s', + debug=dict(argstr='-debug', + position=1, ), - invert=dict(position=1, - argstr='-inverse', + environ=dict(nohash=True, + usedefault=True, ), - args=dict(argstr='%s', + flip_x=dict(argstr='-flipx', + position=1, ), - quiet=dict(position=1, - argstr='-quiet', + ignore_exception=dict(nohash=True, + usedefault=True, ), in_files=dict(argstr='%s', mandatory=True, position=-2, ), - debug=dict(position=1, - argstr='-debug', + invert=dict(argstr='-inverse', + position=1, ), - flip_x=dict(position=1, - argstr='-flipx', + out_filename=dict(argstr='%s', + genfile=True, + position=-1, ), - terminal_output=dict(mandatory=True, - nohash=True, + quiet=dict(argstr='-quiet', + position=1, ), - environ=dict(nohash=True, - usedefault=True, + reference_image=dict(argstr='-reference %s', + position=1, ), - reference_image=dict(position=1, - argstr='-reference %s', + replace_transform=dict(argstr='-replace', + position=1, ), - replace_transform=dict(position=1, - argstr='-replace', + template_image=dict(argstr='-template %s', + position=1, ), - transformation_file=dict(position=1, - argstr='-transform %s', + terminal_output=dict(mandatory=True, + nohash=True, + ), + transformation_file=dict(argstr='-transform %s', + position=1, ), ) inputs = MRTransform.input_spec() @@ -51,6 +52,7 @@ def test_MRTransform_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MRTransform_outputs(): output_map = dict(out_file=dict(), ) @@ -59,3 +61,4 @@ def test_MRTransform_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/mrtrix/tests/test_auto_MRTrix2TrackVis.py b/nipype/interfaces/mrtrix/tests/test_auto_MRTrix2TrackVis.py index 26229f5efd..701731fa46 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_MRTrix2TrackVis.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_MRTrix2TrackVis.py @@ -1,21 +1,23 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.mrtrix.convert import MRTrix2TrackVis + def test_MRTrix2TrackVis_inputs(): - input_map = dict(out_filename=dict(genfile=True, - usedefault=True, - ), - image_file=dict(), - registration_image_file=dict(), + input_map = dict(image_file=dict(), in_file=dict(mandatory=True, ), matrix_file=dict(), + out_filename=dict(genfile=True, + usedefault=True, + ), + registration_image_file=dict(), ) inputs = MRTrix2TrackVis.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MRTrix2TrackVis_outputs(): output_map = dict(out_file=dict(), ) @@ -24,3 +26,4 @@ def test_MRTrix2TrackVis_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/mrtrix/tests/test_auto_MRTrixInfo.py b/nipype/interfaces/mrtrix/tests/test_auto_MRTrixInfo.py index 61ceebcb4b..d801f13803 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_MRTrixInfo.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_MRTrixInfo.py @@ -1,21 +1,22 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.mrtrix.preprocess import MRTrixInfo + def test_MRTrixInfo_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, - ), - terminal_output=dict(mandatory=True, - nohash=True, + input_map = dict(args=dict(argstr='%s', ), environ=dict(nohash=True, usedefault=True, ), - in_file=dict(position=-2, + ignore_exception=dict(nohash=True, + usedefault=True, + ), + in_file=dict(argstr='%s', mandatory=True, - argstr='%s', + position=-2, ), - args=dict(argstr='%s', + terminal_output=dict(mandatory=True, + nohash=True, ), ) inputs = MRTrixInfo.input_spec() @@ -23,6 +24,7 @@ def test_MRTrixInfo_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MRTrixInfo_outputs(): output_map = dict() outputs = MRTrixInfo.output_spec() @@ -30,3 +32,4 @@ def test_MRTrixInfo_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/mrtrix/tests/test_auto_MRTrixViewer.py b/nipype/interfaces/mrtrix/tests/test_auto_MRTrixViewer.py index a0d643a449..8dcbf1821f 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_MRTrixViewer.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_MRTrixViewer.py @@ -1,34 +1,36 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.mrtrix.preprocess import MRTrixViewer + def test_MRTrixViewer_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + debug=dict(argstr='-debug', + position=1, + ), + environ=dict(nohash=True, usedefault=True, ), - args=dict(argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, ), in_files=dict(argstr='%s', mandatory=True, position=-2, ), - quiet=dict(position=1, - argstr='-quiet', + quiet=dict(argstr='-quiet', + position=1, ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - debug=dict(position=1, - argstr='-debug', - ), ) inputs = MRTrixViewer.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MRTrixViewer_outputs(): output_map = dict() outputs = MRTrixViewer.output_spec() @@ -36,3 +38,4 @@ def test_MRTrixViewer_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/mrtrix/tests/test_auto_MedianFilter3D.py b/nipype/interfaces/mrtrix/tests/test_auto_MedianFilter3D.py index 51c6b7a3b7..fe5cd18789 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_MedianFilter3D.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_MedianFilter3D.py @@ -1,38 +1,40 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.mrtrix.preprocess import MedianFilter3D + def test_MedianFilter3D_inputs(): - input_map = dict(out_filename=dict(position=-1, - genfile=True, - argstr='%s', + input_map = dict(args=dict(argstr='%s', + ), + debug=dict(argstr='-debug', + position=1, + ), + environ=dict(nohash=True, + usedefault=True, ), ignore_exception=dict(nohash=True, usedefault=True, ), - args=dict(argstr='%s', + in_file=dict(argstr='%s', + mandatory=True, + position=-2, + ), + out_filename=dict(argstr='%s', + genfile=True, + position=-1, ), - quiet=dict(position=1, - argstr='-quiet', + quiet=dict(argstr='-quiet', + position=1, ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - in_file=dict(position=-2, - mandatory=True, - argstr='%s', - ), - debug=dict(position=1, - argstr='-debug', - ), ) inputs = MedianFilter3D.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MedianFilter3D_outputs(): output_map = dict(out_file=dict(), ) @@ -41,3 +43,4 @@ def test_MedianFilter3D_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/mrtrix/tests/test_auto_ProbabilisticSphericallyDeconvolutedStreamlineTrack.py b/nipype/interfaces/mrtrix/tests/test_auto_ProbabilisticSphericallyDeconvolutedStreamlineTrack.py index b0cacf662c..d89946aa4c 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_ProbabilisticSphericallyDeconvolutedStreamlineTrack.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_ProbabilisticSphericallyDeconvolutedStreamlineTrack.py @@ -1,96 +1,97 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.mrtrix.tracking import ProbabilisticSphericallyDeconvolutedStreamlineTrack + def test_ProbabilisticSphericallyDeconvolutedStreamlineTrack_inputs(): - input_map = dict(do_not_precompute=dict(argstr='-noprecomputed', - ), - maximum_number_of_tracks=dict(argstr='-maxnum %d', + input_map = dict(args=dict(argstr='%s', ), - exclude_file=dict(position=2, - argstr='-exclude %s', + cutoff_value=dict(argstr='-cutoff %s', + units='NA', ), - cutoff_value=dict(units='NA', - argstr='-cutoff %s', - ), - seed_file=dict(position=2, - argstr='-seed %s', + desired_number_of_tracks=dict(argstr='-number %d', ), - step_size=dict(units='mm', - argstr='-step %s', + do_not_precompute=dict(argstr='-noprecomputed', ), - in_file=dict(position=-2, - mandatory=True, - argstr='%s', + environ=dict(nohash=True, + usedefault=True, ), - unidirectional=dict(argstr='-unidirectional', + exclude_file=dict(argstr='-exclude %s', + position=2, ), - no_mask_interpolation=dict(argstr='-nomaskinterp', + exclude_spec=dict(argstr='-seed %s', + position=2, + sep=',', + units='mm', ), ignore_exception=dict(nohash=True, usedefault=True, ), - include_file=dict(position=2, - argstr='-include %s', - ), - maximum_tract_length=dict(units='mm', - argstr='-length %s', + in_file=dict(argstr='%s', + mandatory=True, + position=-2, ), - maximum_number_of_trials=dict(argstr='-trials %s', + include_file=dict(argstr='-include %s', + position=2, ), - args=dict(argstr='%s', + include_spec=dict(argstr='-seed %s', + position=2, + sep=',', + units='mm', ), - stop=dict(argstr='-gzip', + initial_cutoff_value=dict(argstr='-initcutoff %s', + units='NA', ), - minimum_tract_length=dict(units='mm', - argstr='-minlength %s', + initial_direction=dict(argstr='-initdirection %s', + units='voxels', ), - inputmodel=dict(position=-3, + inputmodel=dict(argstr='%s', + position=-3, usedefault=True, - argstr='%s', ), - initial_direction=dict(units='voxels', - argstr='-initdirection %s', + mask_file=dict(argstr='-exclude %s', + position=2, ), - exclude_spec=dict(sep=',', - units='mm', + mask_spec=dict(argstr='-seed %s', position=2, - argstr='-seed %s', + sep=',', + units='mm', ), - desired_number_of_tracks=dict(argstr='-number %d', + maximum_number_of_tracks=dict(argstr='-maxnum %d', ), - seed_spec=dict(sep=',', - units='mm', - position=2, - argstr='-seed %s', + maximum_number_of_trials=dict(argstr='-trials %s', ), - initial_cutoff_value=dict(units='NA', - argstr='-initcutoff %s', + maximum_tract_length=dict(argstr='-length %s', + units='mm', ), - minimum_radius_of_curvature=dict(units='mm', - argstr='-curvature %s', + minimum_radius_of_curvature=dict(argstr='-curvature %s', + units='mm', ), - mask_spec=dict(sep=',', + minimum_tract_length=dict(argstr='-minlength %s', units='mm', - position=2, - argstr='-seed %s', ), - out_file=dict(position=-1, + no_mask_interpolation=dict(argstr='-nomaskinterp', + ), + out_file=dict(argstr='%s', genfile=True, - argstr='%s', + position=-1, ), - include_spec=dict(sep=',', - units='mm', + seed_file=dict(argstr='-seed %s', position=2, - argstr='-seed %s', + ), + seed_spec=dict(argstr='-seed %s', + position=2, + sep=',', + units='mm', + ), + step_size=dict(argstr='-step %s', + units='mm', + ), + stop=dict(argstr='-gzip', ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - mask_file=dict(position=2, - argstr='-exclude %s', + unidirectional=dict(argstr='-unidirectional', ), ) inputs = ProbabilisticSphericallyDeconvolutedStreamlineTrack.input_spec() @@ -98,6 +99,7 @@ def test_ProbabilisticSphericallyDeconvolutedStreamlineTrack_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ProbabilisticSphericallyDeconvolutedStreamlineTrack_outputs(): output_map = dict(tracked=dict(), ) @@ -106,3 +108,4 @@ def test_ProbabilisticSphericallyDeconvolutedStreamlineTrack_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/mrtrix/tests/test_auto_SphericallyDeconvolutedStreamlineTrack.py b/nipype/interfaces/mrtrix/tests/test_auto_SphericallyDeconvolutedStreamlineTrack.py index 217574056a..312e51d827 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_SphericallyDeconvolutedStreamlineTrack.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_SphericallyDeconvolutedStreamlineTrack.py @@ -1,101 +1,103 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.mrtrix.tracking import SphericallyDeconvolutedStreamlineTrack + def test_SphericallyDeconvolutedStreamlineTrack_inputs(): - input_map = dict(do_not_precompute=dict(argstr='-noprecomputed', - ), - maximum_number_of_tracks=dict(argstr='-maxnum %d', - ), - exclude_file=dict(position=2, - argstr='-exclude %s', - ), - cutoff_value=dict(units='NA', - argstr='-cutoff %s', + input_map = dict(args=dict(argstr='%s', ), - seed_file=dict(position=2, - argstr='-seed %s', + cutoff_value=dict(argstr='-cutoff %s', + units='NA', ), - step_size=dict(units='mm', - argstr='-step %s', + desired_number_of_tracks=dict(argstr='-number %d', ), - in_file=dict(position=-2, - mandatory=True, - argstr='%s', + do_not_precompute=dict(argstr='-noprecomputed', ), environ=dict(nohash=True, usedefault=True, ), - no_mask_interpolation=dict(argstr='-nomaskinterp', + exclude_file=dict(argstr='-exclude %s', + position=2, + ), + exclude_spec=dict(argstr='-seed %s', + position=2, + sep=',', + units='mm', ), ignore_exception=dict(nohash=True, usedefault=True, ), - include_file=dict(position=2, - argstr='-include %s', + in_file=dict(argstr='%s', + mandatory=True, + position=-2, ), - maximum_tract_length=dict(units='mm', - argstr='-length %s', + include_file=dict(argstr='-include %s', + position=2, ), - args=dict(argstr='%s', + include_spec=dict(argstr='-seed %s', + position=2, + sep=',', + units='mm', ), - stop=dict(argstr='-gzip', + initial_cutoff_value=dict(argstr='-initcutoff %s', + units='NA', ), - minimum_radius_of_curvature=dict(units='mm', - argstr='-curvature %s', + initial_direction=dict(argstr='-initdirection %s', + units='voxels', ), - inputmodel=dict(position=-3, + inputmodel=dict(argstr='%s', + position=-3, usedefault=True, - argstr='%s', ), - initial_direction=dict(units='voxels', - argstr='-initdirection %s', + mask_file=dict(argstr='-exclude %s', + position=2, ), - exclude_spec=dict(sep=',', - units='mm', + mask_spec=dict(argstr='-seed %s', position=2, - argstr='-seed %s', + sep=',', + units='mm', ), - desired_number_of_tracks=dict(argstr='-number %d', + maximum_number_of_tracks=dict(argstr='-maxnum %d', ), - seed_spec=dict(sep=',', + maximum_tract_length=dict(argstr='-length %s', units='mm', - position=2, - argstr='-seed %s', ), - initial_cutoff_value=dict(units='NA', - argstr='-initcutoff %s', - ), - minimum_tract_length=dict(units='mm', - argstr='-minlength %s', + minimum_radius_of_curvature=dict(argstr='-curvature %s', + units='mm', ), - mask_spec=dict(sep=',', + minimum_tract_length=dict(argstr='-minlength %s', units='mm', - position=2, - argstr='-seed %s', ), - out_file=dict(position=-1, + no_mask_interpolation=dict(argstr='-nomaskinterp', + ), + out_file=dict(argstr='%s', genfile=True, - argstr='%s', + position=-1, ), - include_spec=dict(sep=',', - units='mm', + seed_file=dict(argstr='-seed %s', position=2, - argstr='-seed %s', + ), + seed_spec=dict(argstr='-seed %s', + position=2, + sep=',', + units='mm', + ), + step_size=dict(argstr='-step %s', + units='mm', + ), + stop=dict(argstr='-gzip', ), terminal_output=dict(mandatory=True, nohash=True, ), unidirectional=dict(argstr='-unidirectional', ), - mask_file=dict(position=2, - argstr='-exclude %s', - ), ) inputs = SphericallyDeconvolutedStreamlineTrack.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_SphericallyDeconvolutedStreamlineTrack_outputs(): output_map = dict(tracked=dict(), ) @@ -104,3 +106,4 @@ def test_SphericallyDeconvolutedStreamlineTrack_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/mrtrix/tests/test_auto_StreamlineTrack.py b/nipype/interfaces/mrtrix/tests/test_auto_StreamlineTrack.py index bf50902388..47c8b78bc1 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_StreamlineTrack.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_StreamlineTrack.py @@ -1,101 +1,103 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.mrtrix.tracking import StreamlineTrack + def test_StreamlineTrack_inputs(): - input_map = dict(do_not_precompute=dict(argstr='-noprecomputed', - ), - maximum_number_of_tracks=dict(argstr='-maxnum %d', - ), - exclude_file=dict(position=2, - argstr='-exclude %s', - ), - cutoff_value=dict(units='NA', - argstr='-cutoff %s', + input_map = dict(args=dict(argstr='%s', ), - seed_file=dict(position=2, - argstr='-seed %s', + cutoff_value=dict(argstr='-cutoff %s', + units='NA', ), - step_size=dict(units='mm', - argstr='-step %s', + desired_number_of_tracks=dict(argstr='-number %d', ), - in_file=dict(position=-2, - mandatory=True, - argstr='%s', + do_not_precompute=dict(argstr='-noprecomputed', ), environ=dict(nohash=True, usedefault=True, ), - no_mask_interpolation=dict(argstr='-nomaskinterp', + exclude_file=dict(argstr='-exclude %s', + position=2, + ), + exclude_spec=dict(argstr='-seed %s', + position=2, + sep=',', + units='mm', ), ignore_exception=dict(nohash=True, usedefault=True, ), - include_file=dict(position=2, - argstr='-include %s', + in_file=dict(argstr='%s', + mandatory=True, + position=-2, ), - maximum_tract_length=dict(units='mm', - argstr='-length %s', + include_file=dict(argstr='-include %s', + position=2, ), - args=dict(argstr='%s', + include_spec=dict(argstr='-seed %s', + position=2, + sep=',', + units='mm', ), - stop=dict(argstr='-gzip', + initial_cutoff_value=dict(argstr='-initcutoff %s', + units='NA', ), - minimum_radius_of_curvature=dict(units='mm', - argstr='-curvature %s', + initial_direction=dict(argstr='-initdirection %s', + units='voxels', ), - inputmodel=dict(position=-3, + inputmodel=dict(argstr='%s', + position=-3, usedefault=True, - argstr='%s', ), - initial_direction=dict(units='voxels', - argstr='-initdirection %s', + mask_file=dict(argstr='-exclude %s', + position=2, ), - exclude_spec=dict(sep=',', - units='mm', + mask_spec=dict(argstr='-seed %s', position=2, - argstr='-seed %s', + sep=',', + units='mm', ), - desired_number_of_tracks=dict(argstr='-number %d', + maximum_number_of_tracks=dict(argstr='-maxnum %d', ), - seed_spec=dict(sep=',', + maximum_tract_length=dict(argstr='-length %s', units='mm', - position=2, - argstr='-seed %s', ), - initial_cutoff_value=dict(units='NA', - argstr='-initcutoff %s', - ), - minimum_tract_length=dict(units='mm', - argstr='-minlength %s', + minimum_radius_of_curvature=dict(argstr='-curvature %s', + units='mm', ), - mask_spec=dict(sep=',', + minimum_tract_length=dict(argstr='-minlength %s', units='mm', - position=2, - argstr='-seed %s', ), - out_file=dict(position=-1, + no_mask_interpolation=dict(argstr='-nomaskinterp', + ), + out_file=dict(argstr='%s', genfile=True, - argstr='%s', + position=-1, ), - include_spec=dict(sep=',', - units='mm', + seed_file=dict(argstr='-seed %s', position=2, - argstr='-seed %s', + ), + seed_spec=dict(argstr='-seed %s', + position=2, + sep=',', + units='mm', + ), + step_size=dict(argstr='-step %s', + units='mm', + ), + stop=dict(argstr='-gzip', ), terminal_output=dict(mandatory=True, nohash=True, ), unidirectional=dict(argstr='-unidirectional', ), - mask_file=dict(position=2, - argstr='-exclude %s', - ), ) inputs = StreamlineTrack.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_StreamlineTrack_outputs(): output_map = dict(tracked=dict(), ) @@ -104,3 +106,4 @@ def test_StreamlineTrack_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/mrtrix/tests/test_auto_Tensor2ApparentDiffusion.py b/nipype/interfaces/mrtrix/tests/test_auto_Tensor2ApparentDiffusion.py index 38d7b065df..6bd4f05a06 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_Tensor2ApparentDiffusion.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_Tensor2ApparentDiffusion.py @@ -1,38 +1,40 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.mrtrix.preprocess import Tensor2ApparentDiffusion + def test_Tensor2ApparentDiffusion_inputs(): - input_map = dict(out_filename=dict(position=-1, - genfile=True, - argstr='%s', + input_map = dict(args=dict(argstr='%s', + ), + debug=dict(argstr='-debug', + position=1, + ), + environ=dict(nohash=True, + usedefault=True, ), ignore_exception=dict(nohash=True, usedefault=True, ), - args=dict(argstr='%s', + in_file=dict(argstr='%s', + mandatory=True, + position=-2, + ), + out_filename=dict(argstr='%s', + genfile=True, + position=-1, ), - quiet=dict(position=1, - argstr='-quiet', + quiet=dict(argstr='-quiet', + position=1, ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - in_file=dict(position=-2, - mandatory=True, - argstr='%s', - ), - debug=dict(position=1, - argstr='-debug', - ), ) inputs = Tensor2ApparentDiffusion.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Tensor2ApparentDiffusion_outputs(): output_map = dict(ADC=dict(), ) @@ -41,3 +43,4 @@ def test_Tensor2ApparentDiffusion_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/mrtrix/tests/test_auto_Tensor2FractionalAnisotropy.py b/nipype/interfaces/mrtrix/tests/test_auto_Tensor2FractionalAnisotropy.py index 7d122737e7..df48a5153c 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_Tensor2FractionalAnisotropy.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_Tensor2FractionalAnisotropy.py @@ -1,38 +1,40 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.mrtrix.preprocess import Tensor2FractionalAnisotropy + def test_Tensor2FractionalAnisotropy_inputs(): - input_map = dict(out_filename=dict(position=-1, - genfile=True, - argstr='%s', + input_map = dict(args=dict(argstr='%s', + ), + debug=dict(argstr='-debug', + position=1, + ), + environ=dict(nohash=True, + usedefault=True, ), ignore_exception=dict(nohash=True, usedefault=True, ), - args=dict(argstr='%s', + in_file=dict(argstr='%s', + mandatory=True, + position=-2, + ), + out_filename=dict(argstr='%s', + genfile=True, + position=-1, ), - quiet=dict(position=1, - argstr='-quiet', + quiet=dict(argstr='-quiet', + position=1, ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - in_file=dict(position=-2, - mandatory=True, - argstr='%s', - ), - debug=dict(position=1, - argstr='-debug', - ), ) inputs = Tensor2FractionalAnisotropy.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Tensor2FractionalAnisotropy_outputs(): output_map = dict(FA=dict(), ) @@ -41,3 +43,4 @@ def test_Tensor2FractionalAnisotropy_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/mrtrix/tests/test_auto_Tensor2Vector.py b/nipype/interfaces/mrtrix/tests/test_auto_Tensor2Vector.py index 1072f31a26..32ea5504e0 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_Tensor2Vector.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_Tensor2Vector.py @@ -1,38 +1,40 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.mrtrix.preprocess import Tensor2Vector + def test_Tensor2Vector_inputs(): - input_map = dict(out_filename=dict(position=-1, - genfile=True, - argstr='%s', + input_map = dict(args=dict(argstr='%s', + ), + debug=dict(argstr='-debug', + position=1, + ), + environ=dict(nohash=True, + usedefault=True, ), ignore_exception=dict(nohash=True, usedefault=True, ), - args=dict(argstr='%s', + in_file=dict(argstr='%s', + mandatory=True, + position=-2, + ), + out_filename=dict(argstr='%s', + genfile=True, + position=-1, ), - quiet=dict(position=1, - argstr='-quiet', + quiet=dict(argstr='-quiet', + position=1, ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - in_file=dict(position=-2, - mandatory=True, - argstr='%s', - ), - debug=dict(position=1, - argstr='-debug', - ), ) inputs = Tensor2Vector.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Tensor2Vector_outputs(): output_map = dict(vector=dict(), ) @@ -41,3 +43,4 @@ def test_Tensor2Vector_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/mrtrix/tests/test_auto_Threshold.py b/nipype/interfaces/mrtrix/tests/test_auto_Threshold.py index 8faf100ba1..d8d028cbf4 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_Threshold.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_Threshold.py @@ -1,48 +1,50 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.mrtrix.preprocess import Threshold + def test_Threshold_inputs(): - input_map = dict(out_filename=dict(position=-1, - genfile=True, - argstr='%s', + input_map = dict(absolute_threshold_value=dict(argstr='-abs %s', + ), + args=dict(argstr='%s', ), - absolute_threshold_value=dict(argstr='-abs %s', + debug=dict(argstr='-debug', + position=1, + ), + environ=dict(nohash=True, + usedefault=True, ), ignore_exception=dict(nohash=True, usedefault=True, ), - invert=dict(position=1, - argstr='-invert', + in_file=dict(argstr='%s', + mandatory=True, + position=-2, ), - args=dict(argstr='%s', + invert=dict(argstr='-invert', + position=1, + ), + out_filename=dict(argstr='%s', + genfile=True, + position=-1, ), percentage_threshold_value=dict(argstr='-percent %s', ), - quiet=dict(position=1, - argstr='-quiet', + quiet=dict(argstr='-quiet', + position=1, + ), + replace_zeros_with_NaN=dict(argstr='-nan', + position=1, ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - in_file=dict(position=-2, - mandatory=True, - argstr='%s', - ), - debug=dict(position=1, - argstr='-debug', - ), - replace_zeros_with_NaN=dict(position=1, - argstr='-nan', - ), ) inputs = Threshold.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Threshold_outputs(): output_map = dict(out_file=dict(), ) @@ -51,3 +53,4 @@ def test_Threshold_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/mrtrix/tests/test_auto_Tracks2Prob.py b/nipype/interfaces/mrtrix/tests/test_auto_Tracks2Prob.py index cb8cdc9c87..eef311d2d3 100644 --- a/nipype/interfaces/mrtrix/tests/test_auto_Tracks2Prob.py +++ b/nipype/interfaces/mrtrix/tests/test_auto_Tracks2Prob.py @@ -1,45 +1,46 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.mrtrix.tracking import Tracks2Prob + def test_Tracks2Prob_inputs(): - input_map = dict(out_filename=dict(position=-1, - genfile=True, - argstr='%s', + input_map = dict(args=dict(argstr='%s', ), - ignore_exception=dict(nohash=True, - usedefault=True, + colour=dict(argstr='-colour', + position=3, ), - template_file=dict(position=1, - argstr='-template %s', + environ=dict(nohash=True, + usedefault=True, ), - resample=dict(units='mm', + fraction=dict(argstr='-fraction', position=3, - argstr='-resample %d', ), - colour=dict(position=3, - argstr='-colour', + ignore_exception=dict(nohash=True, + usedefault=True, ), - args=dict(argstr='%s', + in_file=dict(argstr='%s', + mandatory=True, + position=-2, ), - terminal_output=dict(mandatory=True, - nohash=True, + out_filename=dict(argstr='%s', + genfile=True, + position=-1, ), - environ=dict(nohash=True, - usedefault=True, + output_datatype=dict(argstr='-datatype %s', + position=2, ), - in_file=dict(position=-2, - mandatory=True, - argstr='%s', + resample=dict(argstr='-resample %d', + position=3, + units='mm', ), - fraction=dict(position=3, - argstr='-fraction', + template_file=dict(argstr='-template %s', + position=1, + ), + terminal_output=dict(mandatory=True, + nohash=True, ), voxel_dims=dict(argstr='-vox %s', - sep=',', position=2, - ), - output_datatype=dict(position=2, - argstr='-datatype %s', + sep=',', ), ) inputs = Tracks2Prob.input_spec() @@ -47,6 +48,7 @@ def test_Tracks2Prob_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Tracks2Prob_outputs(): output_map = dict(tract_image=dict(), ) @@ -55,3 +57,4 @@ def test_Tracks2Prob_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/nipy/tests/test_auto_ComputeMask.py b/nipype/interfaces/nipy/tests/test_auto_ComputeMask.py index 8dcff888ae..18b416b991 100644 --- a/nipype/interfaces/nipy/tests/test_auto_ComputeMask.py +++ b/nipype/interfaces/nipy/tests/test_auto_ComputeMask.py @@ -1,13 +1,14 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.nipy.preprocess import ComputeMask + def test_ComputeMask_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(M=dict(), + cc=dict(), + ignore_exception=dict(nohash=True, usedefault=True, ), - cc=dict(), m=dict(), - M=dict(), mean_volume=dict(mandatory=True, ), reference_volume=dict(), @@ -17,6 +18,7 @@ def test_ComputeMask_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ComputeMask_outputs(): output_map = dict(brain_mask=dict(), ) @@ -25,3 +27,4 @@ def test_ComputeMask_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/nipy/tests/test_auto_EstimateContrast.py b/nipype/interfaces/nipy/tests/test_auto_EstimateContrast.py index 76f629411d..c617d192f6 100644 --- a/nipype/interfaces/nipy/tests/test_auto_EstimateContrast.py +++ b/nipype/interfaces/nipy/tests/test_auto_EstimateContrast.py @@ -1,26 +1,27 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.nipy.model import EstimateContrast + def test_EstimateContrast_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(axis=dict(mandatory=True, ), - nvbeta=dict(mandatory=True, + beta=dict(mandatory=True, ), - s2=dict(mandatory=True, + constants=dict(mandatory=True, + ), + contrasts=dict(mandatory=True, ), dof=dict(mandatory=True, ), + ignore_exception=dict(nohash=True, + usedefault=True, + ), mask=dict(), - beta=dict(mandatory=True, + nvbeta=dict(mandatory=True, ), reg_names=dict(mandatory=True, ), - contrasts=dict(mandatory=True, - ), - constants=dict(mandatory=True, - ), - axis=dict(mandatory=True, + s2=dict(mandatory=True, ), ) inputs = EstimateContrast.input_spec() @@ -28,6 +29,7 @@ def test_EstimateContrast_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_EstimateContrast_outputs(): output_map = dict(p_maps=dict(), stat_maps=dict(), @@ -38,3 +40,4 @@ def test_EstimateContrast_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/nipy/tests/test_auto_FitGLM.py b/nipype/interfaces/nipy/tests/test_auto_FitGLM.py index 2f124b80e3..09e70280fe 100644 --- a/nipype/interfaces/nipy/tests/test_auto_FitGLM.py +++ b/nipype/interfaces/nipy/tests/test_auto_FitGLM.py @@ -1,28 +1,29 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.nipy.model import FitGLM + def test_FitGLM_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, - ), - session_info=dict(mandatory=True, + input_map = dict(TR=dict(mandatory=True, ), drift_model=dict(usedefault=True, ), - normalize_design_matrix=dict(usedefault=True, + hrf_model=dict(usedefault=True, ), - TR=dict(mandatory=True, + ignore_exception=dict(nohash=True, + usedefault=True, ), mask=dict(), - save_residuals=dict(usedefault=True, + method=dict(usedefault=True, ), - plot_design_matrix=dict(usedefault=True, + model=dict(usedefault=True, ), - hrf_model=dict(usedefault=True, + normalize_design_matrix=dict(usedefault=True, ), - model=dict(usedefault=True, + plot_design_matrix=dict(usedefault=True, ), - method=dict(usedefault=True, + save_residuals=dict(usedefault=True, + ), + session_info=dict(mandatory=True, ), ) inputs = FitGLM.input_spec() @@ -30,19 +31,21 @@ def test_FitGLM_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_FitGLM_outputs(): output_map = dict(a=dict(), - nvbeta=dict(), - s2=dict(), - dof=dict(), + axis=dict(), beta=dict(), - residuals=dict(), - reg_names=dict(), constants=dict(), - axis=dict(), + dof=dict(), + nvbeta=dict(), + reg_names=dict(), + residuals=dict(), + s2=dict(), ) outputs = FitGLM.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/nipy/tests/test_auto_FmriRealign4d.py b/nipype/interfaces/nipy/tests/test_auto_FmriRealign4d.py index 2cd655ee1e..c3b3ccb4c8 100644 --- a/nipype/interfaces/nipy/tests/test_auto_FmriRealign4d.py +++ b/nipype/interfaces/nipy/tests/test_auto_FmriRealign4d.py @@ -1,27 +1,28 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.nipy.preprocess import FmriRealign4d + def test_FmriRealign4d_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(between_loops=dict(usedefault=True, + ), + ignore_exception=dict(nohash=True, usedefault=True, ), - time_interp=dict(requires=['slice_order'], + in_file=dict(mandatory=True, ), - tr_slices=dict(requires=['time_interp'], + loops=dict(usedefault=True, ), - tr=dict(mandatory=True, + slice_order=dict(requires=['time_interp'], ), speedup=dict(usedefault=True, ), - between_loops=dict(usedefault=True, - ), start=dict(usedefault=True, ), - in_file=dict(mandatory=True, + time_interp=dict(requires=['slice_order'], ), - slice_order=dict(requires=['time_interp'], + tr=dict(mandatory=True, ), - loops=dict(usedefault=True, + tr_slices=dict(requires=['time_interp'], ), ) inputs = FmriRealign4d.input_spec() @@ -29,6 +30,7 @@ def test_FmriRealign4d_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_FmriRealign4d_outputs(): output_map = dict(out_file=dict(), par_file=dict(), @@ -38,3 +40,4 @@ def test_FmriRealign4d_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/nipy/tests/test_auto_Similarity.py b/nipype/interfaces/nipy/tests/test_auto_Similarity.py index 1e78ef36e8..548fe5f117 100644 --- a/nipype/interfaces/nipy/tests/test_auto_Similarity.py +++ b/nipype/interfaces/nipy/tests/test_auto_Similarity.py @@ -1,14 +1,15 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.nipy.utils import Similarity + def test_Similarity_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, ), - metric=dict(usedefault=True, - ), mask1=dict(), mask2=dict(), + metric=dict(usedefault=True, + ), volume1=dict(mandatory=True, ), volume2=dict(mandatory=True, @@ -19,6 +20,7 @@ def test_Similarity_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Similarity_outputs(): output_map = dict(similarity=dict(), ) @@ -27,3 +29,4 @@ def test_Similarity_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/nipy/tests/test_auto_SpaceTimeRealigner.py b/nipype/interfaces/nipy/tests/test_auto_SpaceTimeRealigner.py index c647489205..3786e760b0 100644 --- a/nipype/interfaces/nipy/tests/test_auto_SpaceTimeRealigner.py +++ b/nipype/interfaces/nipy/tests/test_auto_SpaceTimeRealigner.py @@ -1,24 +1,26 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.nipy.preprocess import SpaceTimeRealigner + def test_SpaceTimeRealigner_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, ), - slice_info=dict(requires=['slice_times'], - ), - tr=dict(requires=['slice_times'], - ), in_file=dict(mandatory=True, min_ver='0.4.0.dev', ), + slice_info=dict(requires=['slice_times'], + ), slice_times=dict(), + tr=dict(requires=['slice_times'], + ), ) inputs = SpaceTimeRealigner.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_SpaceTimeRealigner_outputs(): output_map = dict(out_file=dict(), par_file=dict(), @@ -28,3 +30,4 @@ def test_SpaceTimeRealigner_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/nipy/tests/test_auto_Trim.py b/nipype/interfaces/nipy/tests/test_auto_Trim.py index f9cc85ae45..0b9b3f881f 100644 --- a/nipype/interfaces/nipy/tests/test_auto_Trim.py +++ b/nipype/interfaces/nipy/tests/test_auto_Trim.py @@ -1,17 +1,18 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.nipy.preprocess import Trim + def test_Trim_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, - ), - out_file=dict(), - begin_index=dict(usedefault=True, + input_map = dict(begin_index=dict(usedefault=True, ), end_index=dict(usedefault=True, ), + ignore_exception=dict(nohash=True, + usedefault=True, + ), in_file=dict(mandatory=True, ), + out_file=dict(), suffix=dict(usedefault=True, ), ) @@ -20,6 +21,7 @@ def test_Trim_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Trim_outputs(): output_map = dict(out_file=dict(), ) @@ -28,3 +30,4 @@ def test_Trim_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/nitime/tests/test_auto_CoherenceAnalyzer.py b/nipype/interfaces/nitime/tests/test_auto_CoherenceAnalyzer.py index 8a37b1e91c..0c0f134af3 100644 --- a/nipype/interfaces/nitime/tests/test_auto_CoherenceAnalyzer.py +++ b/nipype/interfaces/nitime/tests/test_auto_CoherenceAnalyzer.py @@ -1,40 +1,43 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.nitime.analysis import CoherenceAnalyzer + def test_CoherenceAnalyzer_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(NFFT=dict(usedefault=True, ), TR=dict(), - in_TS=dict(), - n_overlap=dict(usedefault=True, - ), figure_type=dict(usedefault=True, ), - output_figure_file=dict(), - in_file=dict(requires=('TR',), + frequency_range=dict(usedefault=True, ), - NFFT=dict(usedefault=True, + ignore_exception=dict(nohash=True, + usedefault=True, ), - frequency_range=dict(usedefault=True, + in_TS=dict(), + in_file=dict(requires=('TR',), + ), + n_overlap=dict(usedefault=True, ), output_csv_file=dict(), + output_figure_file=dict(), ) inputs = CoherenceAnalyzer.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_CoherenceAnalyzer_outputs(): - output_map = dict(coherence_fig=dict(), - timedelay_fig=dict(), - timedelay_array=dict(), + output_map = dict(coherence_array=dict(), coherence_csv=dict(), + coherence_fig=dict(), + timedelay_array=dict(), timedelay_csv=dict(), - coherence_array=dict(), + timedelay_fig=dict(), ) outputs = CoherenceAnalyzer.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIexport.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIexport.py index 8513f972b3..e28d8f6faa 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIexport.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIexport.py @@ -1,31 +1,33 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.slicer.diffusion.diffusion import DTIexport + def test_DTIexport_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + environ=dict(nohash=True, usedefault=True, ), - outputFile=dict(position=-1, - hash_files=False, - argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - inputTensor=dict(position=-2, - argstr='%s', + inputTensor=dict(argstr='%s', + position=-2, ), - args=dict(argstr='%s', + outputFile=dict(argstr='%s', + hash_files=False, + position=-1, ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), ) inputs = DTIexport.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_DTIexport_outputs(): output_map = dict(outputFile=dict(position=-1, ), @@ -35,3 +37,4 @@ def test_DTIexport_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIimport.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIimport.py index ba6e8a43a6..1d6e88d70b 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIimport.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DTIimport.py @@ -1,26 +1,27 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.slicer.diffusion.diffusion import DTIimport + def test_DTIimport_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + environ=dict(nohash=True, usedefault=True, ), - testingmode=dict(argstr='--testingmode ', + ignore_exception=dict(nohash=True, + usedefault=True, + ), + inputFile=dict(argstr='%s', + position=-2, ), - args=dict(argstr='%s', + outputTensor=dict(argstr='%s', + hash_files=False, + position=-1, ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - outputTensor=dict(position=-1, - hash_files=False, - argstr='%s', - ), - inputFile=dict(position=-2, - argstr='%s', + testingmode=dict(argstr='--testingmode ', ), ) inputs = DTIimport.input_spec() @@ -28,6 +29,7 @@ def test_DTIimport_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_DTIimport_outputs(): output_map = dict(outputTensor=dict(position=-1, ), @@ -37,3 +39,4 @@ def test_DTIimport_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIJointRicianLMMSEFilter.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIJointRicianLMMSEFilter.py index a0f0b6423b..6561309c01 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIJointRicianLMMSEFilter.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIJointRicianLMMSEFilter.py @@ -1,18 +1,27 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.slicer.diffusion.diffusion import DWIJointRicianLMMSEFilter + def test_DWIJointRicianLMMSEFilter_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + compressOutput=dict(argstr='--compressOutput ', + ), + environ=dict(nohash=True, usedefault=True, ), - outputVolume=dict(position=-1, - hash_files=False, - argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - args=dict(argstr='%s', + inputVolume=dict(argstr='%s', + position=-2, ), ng=dict(argstr='--ng %d', ), + outputVolume=dict(argstr='%s', + hash_files=False, + position=-1, + ), re=dict(argstr='--re %s', sep=',', ), @@ -22,20 +31,13 @@ def test_DWIJointRicianLMMSEFilter_inputs(): terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - compressOutput=dict(argstr='--compressOutput ', - ), - inputVolume=dict(position=-2, - argstr='%s', - ), ) inputs = DWIJointRicianLMMSEFilter.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_DWIJointRicianLMMSEFilter_outputs(): output_map = dict(outputVolume=dict(position=-1, ), @@ -45,3 +47,4 @@ def test_DWIJointRicianLMMSEFilter_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIRicianLMMSEFilter.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIRicianLMMSEFilter.py index 2a7dbc3da5..34c252b340 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIRicianLMMSEFilter.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIRicianLMMSEFilter.py @@ -1,27 +1,36 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.slicer.diffusion.diffusion import DWIRicianLMMSEFilter + def test_DWIRicianLMMSEFilter_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + compressOutput=dict(argstr='--compressOutput ', + ), + environ=dict(nohash=True, usedefault=True, ), - outputVolume=dict(position=-1, - hash_files=False, - argstr='%s', + hrf=dict(argstr='--hrf %f', ), - minnstd=dict(argstr='--minnstd %d', + ignore_exception=dict(nohash=True, + usedefault=True, + ), + inputVolume=dict(argstr='%s', + position=-2, + ), + iter=dict(argstr='--iter %d', ), maxnstd=dict(argstr='--maxnstd %d', ), - mnvf=dict(argstr='--mnvf %d', + minnstd=dict(argstr='--minnstd %d', ), mnve=dict(argstr='--mnve %d', ), - args=dict(argstr='%s', - ), - iter=dict(argstr='--iter %d', + mnvf=dict(argstr='--mnvf %d', ), - uav=dict(argstr='--uav ', + outputVolume=dict(argstr='%s', + hash_files=False, + position=-1, ), re=dict(argstr='--re %s', sep=',', @@ -32,15 +41,7 @@ def test_DWIRicianLMMSEFilter_inputs(): terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - compressOutput=dict(argstr='--compressOutput ', - ), - inputVolume=dict(position=-2, - argstr='%s', - ), - hrf=dict(argstr='--hrf %f', + uav=dict(argstr='--uav ', ), ) inputs = DWIRicianLMMSEFilter.input_spec() @@ -48,6 +49,7 @@ def test_DWIRicianLMMSEFilter_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_DWIRicianLMMSEFilter_outputs(): output_map = dict(outputVolume=dict(position=-1, ), @@ -57,3 +59,4 @@ def test_DWIRicianLMMSEFilter_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIToDTIEstimation.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIToDTIEstimation.py index a191037f98..529fce2d1f 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIToDTIEstimation.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DWIToDTIEstimation.py @@ -1,45 +1,47 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.slicer.diffusion.diffusion import DWIToDTIEstimation + def test_DWIToDTIEstimation_inputs(): - input_map = dict(outputBaseline=dict(position=-1, - hash_files=False, - argstr='%s', + input_map = dict(args=dict(argstr='%s', + ), + enumeration=dict(argstr='--enumeration %s', + ), + environ=dict(nohash=True, + usedefault=True, ), ignore_exception=dict(nohash=True, usedefault=True, ), - args=dict(argstr='%s', + inputVolume=dict(argstr='%s', + position=-3, ), mask=dict(argstr='--mask %s', ), - enumeration=dict(argstr='--enumeration %s', - ), - terminal_output=dict(mandatory=True, - nohash=True, - ), - environ=dict(nohash=True, - usedefault=True, - ), - outputTensor=dict(position=-2, + outputBaseline=dict(argstr='%s', hash_files=False, - argstr='%s', + position=-1, ), - inputVolume=dict(position=-3, - argstr='%s', + outputTensor=dict(argstr='%s', + hash_files=False, + position=-2, ), shiftNeg=dict(argstr='--shiftNeg ', ), + terminal_output=dict(mandatory=True, + nohash=True, + ), ) inputs = DWIToDTIEstimation.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_DWIToDTIEstimation_outputs(): - output_map = dict(outputTensor=dict(position=-2, + output_map = dict(outputBaseline=dict(position=-1, ), - outputBaseline=dict(position=-1, + outputTensor=dict(position=-2, ), ) outputs = DWIToDTIEstimation.output_spec() @@ -47,3 +49,4 @@ def test_DWIToDTIEstimation_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionTensorScalarMeasurements.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionTensorScalarMeasurements.py index fa55dd01dd..12efd49ea0 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionTensorScalarMeasurements.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionTensorScalarMeasurements.py @@ -1,33 +1,35 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.slicer.diffusion.diffusion import DiffusionTensorScalarMeasurements + def test_DiffusionTensorScalarMeasurements_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + enumeration=dict(argstr='--enumeration %s', + ), + environ=dict(nohash=True, usedefault=True, ), - outputScalar=dict(position=-1, - hash_files=False, - argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - args=dict(argstr='%s', + inputVolume=dict(argstr='%s', + position=-3, ), - enumeration=dict(argstr='--enumeration %s', + outputScalar=dict(argstr='%s', + hash_files=False, + position=-1, ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - inputVolume=dict(position=-3, - argstr='%s', - ), ) inputs = DiffusionTensorScalarMeasurements.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_DiffusionTensorScalarMeasurements_outputs(): output_map = dict(outputScalar=dict(position=-1, ), @@ -37,3 +39,4 @@ def test_DiffusionTensorScalarMeasurements_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionWeightedVolumeMasking.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionWeightedVolumeMasking.py index 48b00dd62c..a1abb60b86 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionWeightedVolumeMasking.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_DiffusionWeightedVolumeMasking.py @@ -1,32 +1,33 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.slicer.diffusion.diffusion import DiffusionWeightedVolumeMasking + def test_DiffusionWeightedVolumeMasking_inputs(): - input_map = dict(outputBaseline=dict(position=-2, - hash_files=False, - argstr='%s', - ), - thresholdMask=dict(position=-1, - hash_files=False, - argstr='%s', + input_map = dict(args=dict(argstr='%s', ), - args=dict(argstr='%s', + environ=dict(nohash=True, + usedefault=True, ), ignore_exception=dict(nohash=True, usedefault=True, ), - removeislands=dict(argstr='--removeislands ', + inputVolume=dict(argstr='%s', + position=-4, ), otsuomegathreshold=dict(argstr='--otsuomegathreshold %f', ), + outputBaseline=dict(argstr='%s', + hash_files=False, + position=-2, + ), + removeislands=dict(argstr='--removeislands ', + ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - inputVolume=dict(position=-4, - argstr='%s', + thresholdMask=dict(argstr='%s', + hash_files=False, + position=-1, ), ) inputs = DiffusionWeightedVolumeMasking.input_spec() @@ -34,6 +35,7 @@ def test_DiffusionWeightedVolumeMasking_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_DiffusionWeightedVolumeMasking_outputs(): output_map = dict(outputBaseline=dict(position=-2, ), @@ -45,3 +47,4 @@ def test_DiffusionWeightedVolumeMasking_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_ResampleDTIVolume.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_ResampleDTIVolume.py index 6de8786150..c2d236277f 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_ResampleDTIVolume.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_ResampleDTIVolume.py @@ -1,76 +1,77 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.slicer.diffusion.diffusion import ResampleDTIVolume + def test_ResampleDTIVolume_inputs(): - input_map = dict(origin=dict(argstr='--origin %s', + input_map = dict(Inverse_ITK_Transformation=dict(argstr='--Inverse_ITK_Transformation ', ), - correction=dict(argstr='--correction %s', + Reference=dict(argstr='--Reference %s', ), - defField=dict(argstr='--defField %s', + args=dict(argstr='%s', ), - window_function=dict(argstr='--window_function %s', + centered_transform=dict(argstr='--centered_transform ', ), - image_center=dict(argstr='--image_center %s', + correction=dict(argstr='--correction %s', ), - transform_tensor_method=dict(argstr='--transform_tensor_method %s', + defField=dict(argstr='--defField %s', ), - size=dict(argstr='--size %s', - sep=',', + default_pixel_value=dict(argstr='--default_pixel_value %f', ), - spline_order=dict(argstr='--spline_order %d', + direction_matrix=dict(argstr='--direction_matrix %s', + sep=',', ), - transform=dict(argstr='--transform %s', + environ=dict(nohash=True, + usedefault=True, ), - centered_transform=dict(argstr='--centered_transform ', + hfieldtype=dict(argstr='--hfieldtype %s', ), - transform_order=dict(argstr='--transform_order %s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - Inverse_ITK_Transformation=dict(argstr='--Inverse_ITK_Transformation ', + image_center=dict(argstr='--image_center %s', ), - direction_matrix=dict(argstr='--direction_matrix %s', - sep=',', + inputVolume=dict(argstr='%s', + position=-2, ), interpolation=dict(argstr='--interpolation %s', ), - ignore_exception=dict(nohash=True, - usedefault=True, + notbulk=dict(argstr='--notbulk ', ), - outputVolume=dict(position=-1, + number_of_thread=dict(argstr='--number_of_thread %d', + ), + origin=dict(argstr='--origin %s', + ), + outputVolume=dict(argstr='%s', hash_files=False, - argstr='%s', + position=-1, ), - number_of_thread=dict(argstr='--number_of_thread %d', + rotation_point=dict(argstr='--rotation_point %s', ), - args=dict(argstr='%s', + size=dict(argstr='--size %s', + sep=',', + ), + spaceChange=dict(argstr='--spaceChange ', ), spacing=dict(argstr='--spacing %s', sep=',', ), - hfieldtype=dict(argstr='--hfieldtype %s', - ), - rotation_point=dict(argstr='--rotation_point %s', + spline_order=dict(argstr='--spline_order %d', ), terminal_output=dict(mandatory=True, nohash=True, ), - notbulk=dict(argstr='--notbulk ', - ), - default_pixel_value=dict(argstr='--default_pixel_value %f', + transform=dict(argstr='--transform %s', ), transform_matrix=dict(argstr='--transform_matrix %s', sep=',', ), - Reference=dict(argstr='--Reference %s', - ), - transformationFile=dict(argstr='--transformationFile %s', + transform_order=dict(argstr='--transform_order %s', ), - environ=dict(nohash=True, - usedefault=True, + transform_tensor_method=dict(argstr='--transform_tensor_method %s', ), - inputVolume=dict(position=-2, - argstr='%s', + transformationFile=dict(argstr='--transformationFile %s', ), - spaceChange=dict(argstr='--spaceChange ', + window_function=dict(argstr='--window_function %s', ), ) inputs = ResampleDTIVolume.input_spec() @@ -78,6 +79,7 @@ def test_ResampleDTIVolume_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ResampleDTIVolume_outputs(): output_map = dict(outputVolume=dict(position=-1, ), @@ -87,3 +89,4 @@ def test_ResampleDTIVolume_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/slicer/diffusion/tests/test_auto_TractographyLabelMapSeeding.py b/nipype/interfaces/slicer/diffusion/tests/test_auto_TractographyLabelMapSeeding.py index 474f05c0f2..baa593b212 100644 --- a/nipype/interfaces/slicer/diffusion/tests/test_auto_TractographyLabelMapSeeding.py +++ b/nipype/interfaces/slicer/diffusion/tests/test_auto_TractographyLabelMapSeeding.py @@ -1,55 +1,56 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.slicer.diffusion.diffusion import TractographyLabelMapSeeding + def test_TractographyLabelMapSeeding_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, - ), - minimumlength=dict(argstr='--minimumlength %f', - ), - inputroi=dict(argstr='--inputroi %s', + input_map = dict(InputVolume=dict(argstr='%s', + position=-2, ), - stoppingcurvature=dict(argstr='--stoppingcurvature %f', - ), - integrationsteplength=dict(argstr='--integrationsteplength %f', + OutputFibers=dict(argstr='%s', + hash_files=False, + position=-1, ), args=dict(argstr='%s', ), - stoppingmode=dict(argstr='--stoppingmode %s', + clthreshold=dict(argstr='--clthreshold %f', ), - useindexspace=dict(argstr='--useindexspace ', + environ=dict(nohash=True, + usedefault=True, ), - outputdirectory=dict(hash_files=False, - argstr='--outputdirectory %s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - seedspacing=dict(argstr='--seedspacing %f', + inputroi=dict(argstr='--inputroi %s', + ), + integrationsteplength=dict(argstr='--integrationsteplength %f', ), label=dict(argstr='--label %d', ), - randomgrid=dict(argstr='--randomgrid ', + maximumlength=dict(argstr='--maximumlength %f', ), - environ=dict(nohash=True, - usedefault=True, + minimumlength=dict(argstr='--minimumlength %f', ), - clthreshold=dict(argstr='--clthreshold %f', + name=dict(argstr='--name %s', ), - stoppingvalue=dict(argstr='--stoppingvalue %f', + outputdirectory=dict(argstr='--outputdirectory %s', + hash_files=False, ), - InputVolume=dict(position=-2, - argstr='%s', + randomgrid=dict(argstr='--randomgrid ', ), - writetofile=dict(argstr='--writetofile ', + seedspacing=dict(argstr='--seedspacing %f', ), - maximumlength=dict(argstr='--maximumlength %f', + stoppingcurvature=dict(argstr='--stoppingcurvature %f', ), - OutputFibers=dict(position=-1, - hash_files=False, - argstr='%s', + stoppingmode=dict(argstr='--stoppingmode %s', + ), + stoppingvalue=dict(argstr='--stoppingvalue %f', ), terminal_output=dict(mandatory=True, nohash=True, ), - name=dict(argstr='--name %s', + useindexspace=dict(argstr='--useindexspace ', + ), + writetofile=dict(argstr='--writetofile ', ), ) inputs = TractographyLabelMapSeeding.input_spec() @@ -57,6 +58,7 @@ def test_TractographyLabelMapSeeding_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_TractographyLabelMapSeeding_outputs(): output_map = dict(OutputFibers=dict(position=-1, ), @@ -67,3 +69,4 @@ def test_TractographyLabelMapSeeding_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_AddScalarVolumes.py b/nipype/interfaces/slicer/filtering/tests/test_auto_AddScalarVolumes.py index b6ebbe30b5..bc50b4e7f9 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_AddScalarVolumes.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_AddScalarVolumes.py @@ -1,36 +1,38 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.slicer.filtering.arithmetic import AddScalarVolumes + def test_AddScalarVolumes_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + environ=dict(nohash=True, usedefault=True, ), - outputVolume=dict(position=-1, - hash_files=False, - argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, + ), + inputVolume1=dict(argstr='%s', + position=-3, ), - args=dict(argstr='%s', + inputVolume2=dict(argstr='%s', + position=-2, ), - inputVolume2=dict(position=-2, - argstr='%s', + order=dict(argstr='--order %s', ), - inputVolume1=dict(position=-3, - argstr='%s', + outputVolume=dict(argstr='%s', + hash_files=False, + position=-1, ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - order=dict(argstr='--order %s', - ), ) inputs = AddScalarVolumes.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_AddScalarVolumes_outputs(): output_map = dict(outputVolume=dict(position=-1, ), @@ -40,3 +42,4 @@ def test_AddScalarVolumes_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_CastScalarVolume.py b/nipype/interfaces/slicer/filtering/tests/test_auto_CastScalarVolume.py index 477e10d2c8..24dc9b8a57 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_CastScalarVolume.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_CastScalarVolume.py @@ -1,24 +1,25 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.slicer.filtering.arithmetic import CastScalarVolume + def test_CastScalarVolume_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(InputVolume=dict(argstr='%s', + position=-2, ), - OutputVolume=dict(position=-1, + OutputVolume=dict(argstr='%s', hash_files=False, - argstr='%s', + position=-1, ), args=dict(argstr='%s', ), - terminal_output=dict(mandatory=True, - nohash=True, - ), environ=dict(nohash=True, usedefault=True, ), - InputVolume=dict(position=-2, - argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, + ), + terminal_output=dict(mandatory=True, + nohash=True, ), type=dict(argstr='--type %s', ), @@ -28,6 +29,7 @@ def test_CastScalarVolume_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_CastScalarVolume_outputs(): output_map = dict(OutputVolume=dict(position=-1, ), @@ -37,3 +39,4 @@ def test_CastScalarVolume_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_CheckerBoardFilter.py b/nipype/interfaces/slicer/filtering/tests/test_auto_CheckerBoardFilter.py index 1c9270c1bd..e2a0a8092f 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_CheckerBoardFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_CheckerBoardFilter.py @@ -1,37 +1,39 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.slicer.filtering.checkerboardfilter import CheckerBoardFilter + def test_CheckerBoardFilter_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + checkerPattern=dict(argstr='--checkerPattern %s', + sep=',', + ), + environ=dict(nohash=True, usedefault=True, ), - outputVolume=dict(position=-1, - hash_files=False, - argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - args=dict(argstr='%s', + inputVolume1=dict(argstr='%s', + position=-3, ), - inputVolume2=dict(position=-2, - argstr='%s', + inputVolume2=dict(argstr='%s', + position=-2, ), - inputVolume1=dict(position=-3, - argstr='%s', + outputVolume=dict(argstr='%s', + hash_files=False, + position=-1, ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - checkerPattern=dict(argstr='--checkerPattern %s', - sep=',', - ), ) inputs = CheckerBoardFilter.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_CheckerBoardFilter_outputs(): output_map = dict(outputVolume=dict(position=-1, ), @@ -41,3 +43,4 @@ def test_CheckerBoardFilter_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_CurvatureAnisotropicDiffusion.py b/nipype/interfaces/slicer/filtering/tests/test_auto_CurvatureAnisotropicDiffusion.py index a6b0b9a4a3..b84fe48fdd 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_CurvatureAnisotropicDiffusion.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_CurvatureAnisotropicDiffusion.py @@ -1,30 +1,31 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.slicer.filtering.denoising import CurvatureAnisotropicDiffusion + def test_CurvatureAnisotropicDiffusion_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + conductance=dict(argstr='--conductance %f', + ), + environ=dict(nohash=True, usedefault=True, ), - outputVolume=dict(position=-1, - hash_files=False, - argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - timeStep=dict(argstr='--timeStep %f', + inputVolume=dict(argstr='%s', + position=-2, ), - args=dict(argstr='%s', + iterations=dict(argstr='--iterations %d', ), - conductance=dict(argstr='--conductance %f', + outputVolume=dict(argstr='%s', + hash_files=False, + position=-1, ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - iterations=dict(argstr='--iterations %d', - ), - inputVolume=dict(position=-2, - argstr='%s', + timeStep=dict(argstr='--timeStep %f', ), ) inputs = CurvatureAnisotropicDiffusion.input_spec() @@ -32,6 +33,7 @@ def test_CurvatureAnisotropicDiffusion_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_CurvatureAnisotropicDiffusion_outputs(): output_map = dict(outputVolume=dict(position=-1, ), @@ -41,3 +43,4 @@ def test_CurvatureAnisotropicDiffusion_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_ExtractSkeleton.py b/nipype/interfaces/slicer/filtering/tests/test_auto_ExtractSkeleton.py index ab37b2466b..02d8c1cd4e 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_ExtractSkeleton.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_ExtractSkeleton.py @@ -1,31 +1,32 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.slicer.filtering.extractskeleton import ExtractSkeleton + def test_ExtractSkeleton_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(InputImageFileName=dict(argstr='%s', + position=-2, ), - OutputImageFileName=dict(position=-1, + OutputImageFileName=dict(argstr='%s', hash_files=False, - argstr='%s', + position=-1, ), args=dict(argstr='%s', ), - numPoints=dict(argstr='--numPoints %d', + dontPrune=dict(argstr='--dontPrune ', ), - InputImageFileName=dict(position=-2, - argstr='%s', + environ=dict(nohash=True, + usedefault=True, + ), + ignore_exception=dict(nohash=True, + usedefault=True, + ), + numPoints=dict(argstr='--numPoints %d', ), pointsFile=dict(argstr='--pointsFile %s', ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - dontPrune=dict(argstr='--dontPrune ', - ), type=dict(argstr='--type %s', ), ) @@ -34,6 +35,7 @@ def test_ExtractSkeleton_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ExtractSkeleton_outputs(): output_map = dict(OutputImageFileName=dict(position=-1, ), @@ -43,3 +45,4 @@ def test_ExtractSkeleton_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_GaussianBlurImageFilter.py b/nipype/interfaces/slicer/filtering/tests/test_auto_GaussianBlurImageFilter.py index 86563fa3d2..f43d973517 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_GaussianBlurImageFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_GaussianBlurImageFilter.py @@ -1,33 +1,35 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.slicer.filtering.denoising import GaussianBlurImageFilter + def test_GaussianBlurImageFilter_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + environ=dict(nohash=True, + usedefault=True, + ), + ignore_exception=dict(nohash=True, usedefault=True, ), - outputVolume=dict(position=-1, + inputVolume=dict(argstr='%s', + position=-2, + ), + outputVolume=dict(argstr='%s', hash_files=False, - argstr='%s', + position=-1, ), - args=dict(argstr='%s', + sigma=dict(argstr='--sigma %f', ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - inputVolume=dict(position=-2, - argstr='%s', - ), - sigma=dict(argstr='--sigma %f', - ), ) inputs = GaussianBlurImageFilter.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_GaussianBlurImageFilter_outputs(): output_map = dict(outputVolume=dict(position=-1, ), @@ -37,3 +39,4 @@ def test_GaussianBlurImageFilter_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_GradientAnisotropicDiffusion.py b/nipype/interfaces/slicer/filtering/tests/test_auto_GradientAnisotropicDiffusion.py index eabbd74003..692a379097 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_GradientAnisotropicDiffusion.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_GradientAnisotropicDiffusion.py @@ -1,30 +1,31 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.slicer.filtering.denoising import GradientAnisotropicDiffusion + def test_GradientAnisotropicDiffusion_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + conductance=dict(argstr='--conductance %f', + ), + environ=dict(nohash=True, usedefault=True, ), - outputVolume=dict(position=-1, - hash_files=False, - argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - timeStep=dict(argstr='--timeStep %f', + inputVolume=dict(argstr='%s', + position=-2, ), - args=dict(argstr='%s', + iterations=dict(argstr='--iterations %d', ), - conductance=dict(argstr='--conductance %f', + outputVolume=dict(argstr='%s', + hash_files=False, + position=-1, ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - iterations=dict(argstr='--iterations %d', - ), - inputVolume=dict(position=-2, - argstr='%s', + timeStep=dict(argstr='--timeStep %f', ), ) inputs = GradientAnisotropicDiffusion.input_spec() @@ -32,6 +33,7 @@ def test_GradientAnisotropicDiffusion_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_GradientAnisotropicDiffusion_outputs(): output_map = dict(outputVolume=dict(position=-1, ), @@ -41,3 +43,4 @@ def test_GradientAnisotropicDiffusion_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleFillHoleImageFilter.py b/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleFillHoleImageFilter.py index a5b1b70267..9188142311 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleFillHoleImageFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleFillHoleImageFilter.py @@ -1,31 +1,33 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.slicer.filtering.morphology import GrayscaleFillHoleImageFilter + def test_GrayscaleFillHoleImageFilter_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + environ=dict(nohash=True, usedefault=True, ), - outputVolume=dict(position=-1, - hash_files=False, - argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, + ), + inputVolume=dict(argstr='%s', + position=-2, ), - args=dict(argstr='%s', + outputVolume=dict(argstr='%s', + hash_files=False, + position=-1, ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - inputVolume=dict(position=-2, - argstr='%s', - ), ) inputs = GrayscaleFillHoleImageFilter.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_GrayscaleFillHoleImageFilter_outputs(): output_map = dict(outputVolume=dict(position=-1, ), @@ -35,3 +37,4 @@ def test_GrayscaleFillHoleImageFilter_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleGrindPeakImageFilter.py b/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleGrindPeakImageFilter.py index e6ec3c9676..4a087d3730 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleGrindPeakImageFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_GrayscaleGrindPeakImageFilter.py @@ -1,31 +1,33 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.slicer.filtering.morphology import GrayscaleGrindPeakImageFilter + def test_GrayscaleGrindPeakImageFilter_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + environ=dict(nohash=True, usedefault=True, ), - outputVolume=dict(position=-1, - hash_files=False, - argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, + ), + inputVolume=dict(argstr='%s', + position=-2, ), - args=dict(argstr='%s', + outputVolume=dict(argstr='%s', + hash_files=False, + position=-1, ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - inputVolume=dict(position=-2, - argstr='%s', - ), ) inputs = GrayscaleGrindPeakImageFilter.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_GrayscaleGrindPeakImageFilter_outputs(): output_map = dict(outputVolume=dict(position=-1, ), @@ -35,3 +37,4 @@ def test_GrayscaleGrindPeakImageFilter_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_HistogramMatching.py b/nipype/interfaces/slicer/filtering/tests/test_auto_HistogramMatching.py index acc1a811d8..e96aa78ddb 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_HistogramMatching.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_HistogramMatching.py @@ -1,40 +1,42 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.slicer.filtering.histogrammatching import HistogramMatching + def test_HistogramMatching_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + environ=dict(nohash=True, usedefault=True, ), - outputVolume=dict(position=-1, - hash_files=False, - argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, + ), + inputVolume=dict(argstr='%s', + position=-3, ), numberOfHistogramLevels=dict(argstr='--numberOfHistogramLevels %d', ), - args=dict(argstr='%s', + numberOfMatchPoints=dict(argstr='--numberOfMatchPoints %d', + ), + outputVolume=dict(argstr='%s', + hash_files=False, + position=-1, ), - referenceVolume=dict(position=-2, - argstr='%s', + referenceVolume=dict(argstr='%s', + position=-2, ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - inputVolume=dict(position=-3, - argstr='%s', - ), threshold=dict(argstr='--threshold ', ), - numberOfMatchPoints=dict(argstr='--numberOfMatchPoints %d', - ), ) inputs = HistogramMatching.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_HistogramMatching_outputs(): output_map = dict(outputVolume=dict(position=-1, ), @@ -44,3 +46,4 @@ def test_HistogramMatching_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_ImageLabelCombine.py b/nipype/interfaces/slicer/filtering/tests/test_auto_ImageLabelCombine.py index 127a738120..5a74ba8953 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_ImageLabelCombine.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_ImageLabelCombine.py @@ -1,29 +1,30 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.slicer.filtering.imagelabelcombine import ImageLabelCombine + def test_ImageLabelCombine_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(InputLabelMap_A=dict(argstr='%s', + position=-3, ), - OutputLabelMap=dict(position=-1, + InputLabelMap_B=dict(argstr='%s', + position=-2, + ), + OutputLabelMap=dict(argstr='%s', hash_files=False, - argstr='%s', + position=-1, ), args=dict(argstr='%s', ), - terminal_output=dict(mandatory=True, - nohash=True, - ), environ=dict(nohash=True, usedefault=True, ), - InputLabelMap_A=dict(position=-3, - argstr='%s', + first_overwrites=dict(argstr='--first_overwrites ', ), - InputLabelMap_B=dict(position=-2, - argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - first_overwrites=dict(argstr='--first_overwrites ', + terminal_output=dict(mandatory=True, + nohash=True, ), ) inputs = ImageLabelCombine.input_spec() @@ -31,6 +32,7 @@ def test_ImageLabelCombine_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ImageLabelCombine_outputs(): output_map = dict(OutputLabelMap=dict(position=-1, ), @@ -40,3 +42,4 @@ def test_ImageLabelCombine_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_MaskScalarVolume.py b/nipype/interfaces/slicer/filtering/tests/test_auto_MaskScalarVolume.py index cdefff3c25..64c63c8c45 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_MaskScalarVolume.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_MaskScalarVolume.py @@ -1,38 +1,40 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.slicer.filtering.arithmetic import MaskScalarVolume + def test_MaskScalarVolume_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(InputVolume=dict(argstr='%s', + position=-3, ), - OutputVolume=dict(position=-1, - hash_files=False, - argstr='%s', + MaskVolume=dict(argstr='%s', + position=-2, ), - MaskVolume=dict(position=-2, - argstr='%s', + OutputVolume=dict(argstr='%s', + hash_files=False, + position=-1, ), args=dict(argstr='%s', ), - label=dict(argstr='--label %d', - ), - terminal_output=dict(mandatory=True, - nohash=True, - ), environ=dict(nohash=True, usedefault=True, ), - InputVolume=dict(position=-3, - argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, + ), + label=dict(argstr='--label %d', ), replace=dict(argstr='--replace %d', ), + terminal_output=dict(mandatory=True, + nohash=True, + ), ) inputs = MaskScalarVolume.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MaskScalarVolume_outputs(): output_map = dict(OutputVolume=dict(position=-1, ), @@ -42,3 +44,4 @@ def test_MaskScalarVolume_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_MedianImageFilter.py b/nipype/interfaces/slicer/filtering/tests/test_auto_MedianImageFilter.py index e11cc3b7e6..d796bc9de2 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_MedianImageFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_MedianImageFilter.py @@ -1,34 +1,36 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.slicer.filtering.denoising import MedianImageFilter + def test_MedianImageFilter_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + environ=dict(nohash=True, usedefault=True, ), - outputVolume=dict(position=-1, - hash_files=False, - argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, + ), + inputVolume=dict(argstr='%s', + position=-2, ), neighborhood=dict(argstr='--neighborhood %s', sep=',', ), - args=dict(argstr='%s', + outputVolume=dict(argstr='%s', + hash_files=False, + position=-1, ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - inputVolume=dict(position=-2, - argstr='%s', - ), ) inputs = MedianImageFilter.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MedianImageFilter_outputs(): output_map = dict(outputVolume=dict(position=-1, ), @@ -38,3 +40,4 @@ def test_MedianImageFilter_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_MultiplyScalarVolumes.py b/nipype/interfaces/slicer/filtering/tests/test_auto_MultiplyScalarVolumes.py index 4b0ac29c0f..58a5014daf 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_MultiplyScalarVolumes.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_MultiplyScalarVolumes.py @@ -1,36 +1,38 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.slicer.filtering.arithmetic import MultiplyScalarVolumes + def test_MultiplyScalarVolumes_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + environ=dict(nohash=True, usedefault=True, ), - outputVolume=dict(position=-1, - hash_files=False, - argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, + ), + inputVolume1=dict(argstr='%s', + position=-3, ), - args=dict(argstr='%s', + inputVolume2=dict(argstr='%s', + position=-2, ), - inputVolume2=dict(position=-2, - argstr='%s', + order=dict(argstr='--order %s', ), - inputVolume1=dict(position=-3, - argstr='%s', + outputVolume=dict(argstr='%s', + hash_files=False, + position=-1, ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - order=dict(argstr='--order %s', - ), ) inputs = MultiplyScalarVolumes.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MultiplyScalarVolumes_outputs(): output_map = dict(outputVolume=dict(position=-1, ), @@ -40,3 +42,4 @@ def test_MultiplyScalarVolumes_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_N4ITKBiasFieldCorrection.py b/nipype/interfaces/slicer/filtering/tests/test_auto_N4ITKBiasFieldCorrection.py index 3bdf30e148..ad4684946a 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_N4ITKBiasFieldCorrection.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_N4ITKBiasFieldCorrection.py @@ -1,46 +1,47 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.slicer.filtering.n4itkbiasfieldcorrection import N4ITKBiasFieldCorrection + def test_N4ITKBiasFieldCorrection_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(args=dict(argstr='%s', ), - meshresolution=dict(argstr='--meshresolution %s', - sep=',', + bsplineorder=dict(argstr='--bsplineorder %d', ), - weightimage=dict(argstr='--weightimage %s', + convergencethreshold=dict(argstr='--convergencethreshold %f', + ), + environ=dict(nohash=True, + usedefault=True, ), histogramsharpening=dict(argstr='--histogramsharpening %s', sep=',', ), - args=dict(argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, + ), + inputimage=dict(argstr='--inputimage %s', + ), + iterations=dict(argstr='--iterations %s', + sep=',', ), maskimage=dict(argstr='--maskimage %s', ), - outputbiasfield=dict(hash_files=False, - argstr='--outputbiasfield %s', + meshresolution=dict(argstr='--meshresolution %s', + sep=',', ), - convergencethreshold=dict(argstr='--convergencethreshold %f', + outputbiasfield=dict(argstr='--outputbiasfield %s', + hash_files=False, ), - inputimage=dict(argstr='--inputimage %s', + outputimage=dict(argstr='--outputimage %s', + hash_files=False, ), shrinkfactor=dict(argstr='--shrinkfactor %d', ), + splinedistance=dict(argstr='--splinedistance %f', + ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - iterations=dict(argstr='--iterations %s', - sep=',', - ), - bsplineorder=dict(argstr='--bsplineorder %d', - ), - splinedistance=dict(argstr='--splinedistance %f', - ), - outputimage=dict(hash_files=False, - argstr='--outputimage %s', + weightimage=dict(argstr='--weightimage %s', ), ) inputs = N4ITKBiasFieldCorrection.input_spec() @@ -48,12 +49,14 @@ def test_N4ITKBiasFieldCorrection_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_N4ITKBiasFieldCorrection_outputs(): - output_map = dict(outputimage=dict(), - outputbiasfield=dict(), + output_map = dict(outputbiasfield=dict(), + outputimage=dict(), ) outputs = N4ITKBiasFieldCorrection.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_ResampleScalarVectorDWIVolume.py b/nipype/interfaces/slicer/filtering/tests/test_auto_ResampleScalarVectorDWIVolume.py index 3b75a21ea2..061262ae83 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_ResampleScalarVectorDWIVolume.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_ResampleScalarVectorDWIVolume.py @@ -1,72 +1,73 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.slicer.filtering.resamplescalarvectordwivolume import ResampleScalarVectorDWIVolume + def test_ResampleScalarVectorDWIVolume_inputs(): - input_map = dict(origin=dict(argstr='--origin %s', - ), - defField=dict(argstr='--defField %s', - ), - window_function=dict(argstr='--window_function %s', - ), - image_center=dict(argstr='--image_center %s', + input_map = dict(Inverse_ITK_Transformation=dict(argstr='--Inverse_ITK_Transformation ', ), - size=dict(argstr='--size %s', - sep=',', - ), - spline_order=dict(argstr='--spline_order %d', + Reference=dict(argstr='--Reference %s', ), - transform=dict(argstr='--transform %s', + args=dict(argstr='%s', ), centered_transform=dict(argstr='--centered_transform ', ), - transform_order=dict(argstr='--transform_order %s', + defField=dict(argstr='--defField %s', ), - Inverse_ITK_Transformation=dict(argstr='--Inverse_ITK_Transformation ', + default_pixel_value=dict(argstr='--default_pixel_value %f', ), direction_matrix=dict(argstr='--direction_matrix %s', sep=',', ), - interpolation=dict(argstr='--interpolation %s', + environ=dict(nohash=True, + usedefault=True, + ), + hfieldtype=dict(argstr='--hfieldtype %s', ), ignore_exception=dict(nohash=True, usedefault=True, ), - outputVolume=dict(position=-1, - hash_files=False, - argstr='%s', + image_center=dict(argstr='--image_center %s', + ), + inputVolume=dict(argstr='%s', + position=-2, + ), + interpolation=dict(argstr='--interpolation %s', + ), + notbulk=dict(argstr='--notbulk ', ), number_of_thread=dict(argstr='--number_of_thread %d', ), - args=dict(argstr='%s', + origin=dict(argstr='--origin %s', ), - spacing=dict(argstr='--spacing %s', + outputVolume=dict(argstr='%s', + hash_files=False, + position=-1, + ), + rotation_point=dict(argstr='--rotation_point %s', + ), + size=dict(argstr='--size %s', sep=',', ), - hfieldtype=dict(argstr='--hfieldtype %s', + spaceChange=dict(argstr='--spaceChange ', ), - rotation_point=dict(argstr='--rotation_point %s', + spacing=dict(argstr='--spacing %s', + sep=',', + ), + spline_order=dict(argstr='--spline_order %d', ), terminal_output=dict(mandatory=True, nohash=True, ), - notbulk=dict(argstr='--notbulk ', - ), - default_pixel_value=dict(argstr='--default_pixel_value %f', + transform=dict(argstr='--transform %s', ), transform_matrix=dict(argstr='--transform_matrix %s', sep=',', ), - Reference=dict(argstr='--Reference %s', + transform_order=dict(argstr='--transform_order %s', ), transformationFile=dict(argstr='--transformationFile %s', ), - environ=dict(nohash=True, - usedefault=True, - ), - inputVolume=dict(position=-2, - argstr='%s', - ), - spaceChange=dict(argstr='--spaceChange ', + window_function=dict(argstr='--window_function %s', ), ) inputs = ResampleScalarVectorDWIVolume.input_spec() @@ -74,6 +75,7 @@ def test_ResampleScalarVectorDWIVolume_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ResampleScalarVectorDWIVolume_outputs(): output_map = dict(outputVolume=dict(position=-1, ), @@ -83,3 +85,4 @@ def test_ResampleScalarVectorDWIVolume_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_SubtractScalarVolumes.py b/nipype/interfaces/slicer/filtering/tests/test_auto_SubtractScalarVolumes.py index a21ca2face..49ad811395 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_SubtractScalarVolumes.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_SubtractScalarVolumes.py @@ -1,36 +1,38 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.slicer.filtering.arithmetic import SubtractScalarVolumes + def test_SubtractScalarVolumes_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + environ=dict(nohash=True, usedefault=True, ), - outputVolume=dict(position=-1, - hash_files=False, - argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, + ), + inputVolume1=dict(argstr='%s', + position=-3, ), - args=dict(argstr='%s', + inputVolume2=dict(argstr='%s', + position=-2, ), - inputVolume2=dict(position=-2, - argstr='%s', + order=dict(argstr='--order %s', ), - inputVolume1=dict(position=-3, - argstr='%s', + outputVolume=dict(argstr='%s', + hash_files=False, + position=-1, ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - order=dict(argstr='--order %s', - ), ) inputs = SubtractScalarVolumes.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_SubtractScalarVolumes_outputs(): output_map = dict(outputVolume=dict(position=-1, ), @@ -40,3 +42,4 @@ def test_SubtractScalarVolumes_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_ThresholdScalarVolume.py b/nipype/interfaces/slicer/filtering/tests/test_auto_ThresholdScalarVolume.py index 8a7b9330df..9a57b52f74 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_ThresholdScalarVolume.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_ThresholdScalarVolume.py @@ -1,34 +1,35 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.slicer.filtering.thresholdscalarvolume import ThresholdScalarVolume + def test_ThresholdScalarVolume_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, - ), - upper=dict(argstr='--upper %d', - ), - lower=dict(argstr='--lower %d', + input_map = dict(InputVolume=dict(argstr='%s', + position=-2, ), - OutputVolume=dict(position=-1, + OutputVolume=dict(argstr='%s', hash_files=False, - argstr='%s', + position=-1, ), args=dict(argstr='%s', ), - thresholdtype=dict(argstr='--thresholdtype %s', + environ=dict(nohash=True, + usedefault=True, + ), + ignore_exception=dict(nohash=True, + usedefault=True, + ), + lower=dict(argstr='--lower %d', ), outsidevalue=dict(argstr='--outsidevalue %d', ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), threshold=dict(argstr='--threshold %d', ), - InputVolume=dict(position=-2, - argstr='%s', + thresholdtype=dict(argstr='--thresholdtype %s', + ), + upper=dict(argstr='--upper %d', ), ) inputs = ThresholdScalarVolume.input_spec() @@ -36,6 +37,7 @@ def test_ThresholdScalarVolume_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ThresholdScalarVolume_outputs(): output_map = dict(OutputVolume=dict(position=-1, ), @@ -45,3 +47,4 @@ def test_ThresholdScalarVolume_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/slicer/filtering/tests/test_auto_VotingBinaryHoleFillingImageFilter.py b/nipype/interfaces/slicer/filtering/tests/test_auto_VotingBinaryHoleFillingImageFilter.py index ce7113f4ac..ea471f5252 100644 --- a/nipype/interfaces/slicer/filtering/tests/test_auto_VotingBinaryHoleFillingImageFilter.py +++ b/nipype/interfaces/slicer/filtering/tests/test_auto_VotingBinaryHoleFillingImageFilter.py @@ -1,40 +1,42 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.slicer.filtering.votingbinaryholefillingimagefilter import VotingBinaryHoleFillingImageFilter + def test_VotingBinaryHoleFillingImageFilter_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + background=dict(argstr='--background %d', + ), + environ=dict(nohash=True, usedefault=True, ), foreground=dict(argstr='--foreground %d', ), - radius=dict(argstr='--radius %s', - sep=',', + ignore_exception=dict(nohash=True, + usedefault=True, + ), + inputVolume=dict(argstr='%s', + position=-2, ), majorityThreshold=dict(argstr='--majorityThreshold %d', ), - outputVolume=dict(position=-1, + outputVolume=dict(argstr='%s', hash_files=False, - argstr='%s', + position=-1, ), - args=dict(argstr='%s', + radius=dict(argstr='--radius %s', + sep=',', ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - background=dict(argstr='--background %d', - ), - inputVolume=dict(position=-2, - argstr='%s', - ), ) inputs = VotingBinaryHoleFillingImageFilter.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_VotingBinaryHoleFillingImageFilter_outputs(): output_map = dict(outputVolume=dict(position=-1, ), @@ -44,3 +46,4 @@ def test_VotingBinaryHoleFillingImageFilter_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/slicer/legacy/diffusion/tests/test_auto_DWIUnbiasedNonLocalMeansFilter.py b/nipype/interfaces/slicer/legacy/diffusion/tests/test_auto_DWIUnbiasedNonLocalMeansFilter.py index 79b03ff78c..e5f07c3c8b 100644 --- a/nipype/interfaces/slicer/legacy/diffusion/tests/test_auto_DWIUnbiasedNonLocalMeansFilter.py +++ b/nipype/interfaces/slicer/legacy/diffusion/tests/test_auto_DWIUnbiasedNonLocalMeansFilter.py @@ -1,37 +1,38 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.slicer.legacy.diffusion.denoising import DWIUnbiasedNonLocalMeansFilter + def test_DWIUnbiasedNonLocalMeansFilter_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, - ), - outputVolume=dict(position=-1, - hash_files=False, - argstr='%s', + input_map = dict(args=dict(argstr='%s', ), - rs=dict(argstr='--rs %s', - sep=',', + environ=dict(nohash=True, + usedefault=True, ), hp=dict(argstr='--hp %f', ), - args=dict(argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, + ), + inputVolume=dict(argstr='%s', + position=-2, ), ng=dict(argstr='--ng %d', ), - re=dict(argstr='--re %s', - sep=',', + outputVolume=dict(argstr='%s', + hash_files=False, + position=-1, ), - terminal_output=dict(mandatory=True, - nohash=True, + rc=dict(argstr='--rc %s', + sep=',', ), - environ=dict(nohash=True, - usedefault=True, + re=dict(argstr='--re %s', + sep=',', ), - rc=dict(argstr='--rc %s', + rs=dict(argstr='--rs %s', sep=',', ), - inputVolume=dict(position=-2, - argstr='%s', + terminal_output=dict(mandatory=True, + nohash=True, ), ) inputs = DWIUnbiasedNonLocalMeansFilter.input_spec() @@ -39,6 +40,7 @@ def test_DWIUnbiasedNonLocalMeansFilter_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_DWIUnbiasedNonLocalMeansFilter_outputs(): output_map = dict(outputVolume=dict(position=-1, ), @@ -48,3 +50,4 @@ def test_DWIUnbiasedNonLocalMeansFilter_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_AffineRegistration.py b/nipype/interfaces/slicer/legacy/tests/test_auto_AffineRegistration.py index ef32233bf0..29e15b59ea 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_AffineRegistration.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_AffineRegistration.py @@ -1,43 +1,44 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.slicer.legacy.registration import AffineRegistration + def test_AffineRegistration_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(FixedImageFileName=dict(argstr='%s', + position=-2, + ), + MovingImageFileName=dict(argstr='%s', + position=-1, + ), + args=dict(argstr='%s', + ), + environ=dict(nohash=True, usedefault=True, ), - initialtransform=dict(argstr='--initialtransform %s', + fixedsmoothingfactor=dict(argstr='--fixedsmoothingfactor %d', ), histogrambins=dict(argstr='--histogrambins %d', ), - translationscale=dict(argstr='--translationscale %f', + ignore_exception=dict(nohash=True, + usedefault=True, ), - movingsmoothingfactor=dict(argstr='--movingsmoothingfactor %d', + initialtransform=dict(argstr='--initialtransform %s', ), - args=dict(argstr='%s', + iterations=dict(argstr='--iterations %d', ), - outputtransform=dict(hash_files=False, - argstr='--outputtransform %s', + movingsmoothingfactor=dict(argstr='--movingsmoothingfactor %d', ), - spatialsamples=dict(argstr='--spatialsamples %d', + outputtransform=dict(argstr='--outputtransform %s', + hash_files=False, ), - resampledmovingfilename=dict(hash_files=False, - argstr='--resampledmovingfilename %s', + resampledmovingfilename=dict(argstr='--resampledmovingfilename %s', + hash_files=False, ), - MovingImageFileName=dict(position=-1, - argstr='%s', + spatialsamples=dict(argstr='--spatialsamples %d', ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - iterations=dict(argstr='--iterations %d', - ), - FixedImageFileName=dict(position=-2, - argstr='%s', - ), - fixedsmoothingfactor=dict(argstr='--fixedsmoothingfactor %d', + translationscale=dict(argstr='--translationscale %f', ), ) inputs = AffineRegistration.input_spec() @@ -45,12 +46,14 @@ def test_AffineRegistration_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_AffineRegistration_outputs(): - output_map = dict(resampledmovingfilename=dict(), - outputtransform=dict(), + output_map = dict(outputtransform=dict(), + resampledmovingfilename=dict(), ) outputs = AffineRegistration.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineDeformableRegistration.py b/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineDeformableRegistration.py index 60fcf371e6..00738fb176 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineDeformableRegistration.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineDeformableRegistration.py @@ -1,48 +1,49 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.slicer.legacy.registration import BSplineDeformableRegistration + def test_BSplineDeformableRegistration_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, - ), - initialtransform=dict(argstr='--initialtransform %s', + input_map = dict(FixedImageFileName=dict(argstr='%s', + position=-2, ), - maximumDeformation=dict(argstr='--maximumDeformation %f', + MovingImageFileName=dict(argstr='%s', + position=-1, ), - gridSize=dict(argstr='--gridSize %d', + args=dict(argstr='%s', ), - MovingImageFileName=dict(position=-1, - argstr='%s', + constrain=dict(argstr='--constrain ', ), default=dict(argstr='--default %d', ), - histogrambins=dict(argstr='--histogrambins %d', + environ=dict(nohash=True, + usedefault=True, ), - args=dict(argstr='%s', + gridSize=dict(argstr='--gridSize %d', ), - outputtransform=dict(hash_files=False, - argstr='--outputtransform %s', + histogrambins=dict(argstr='--histogrambins %d', ), - spatialsamples=dict(argstr='--spatialsamples %d', + ignore_exception=dict(nohash=True, + usedefault=True, ), - resampledmovingfilename=dict(hash_files=False, - argstr='--resampledmovingfilename %s', + initialtransform=dict(argstr='--initialtransform %s', ), - terminal_output=dict(mandatory=True, - nohash=True, + iterations=dict(argstr='--iterations %d', ), - environ=dict(nohash=True, - usedefault=True, + maximumDeformation=dict(argstr='--maximumDeformation %f', ), - iterations=dict(argstr='--iterations %d', + outputtransform=dict(argstr='--outputtransform %s', + hash_files=False, ), - outputwarp=dict(hash_files=False, - argstr='--outputwarp %s', + outputwarp=dict(argstr='--outputwarp %s', + hash_files=False, ), - constrain=dict(argstr='--constrain ', + resampledmovingfilename=dict(argstr='--resampledmovingfilename %s', + hash_files=False, ), - FixedImageFileName=dict(position=-2, - argstr='%s', + spatialsamples=dict(argstr='--spatialsamples %d', + ), + terminal_output=dict(mandatory=True, + nohash=True, ), ) inputs = BSplineDeformableRegistration.input_spec() @@ -50,13 +51,15 @@ def test_BSplineDeformableRegistration_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_BSplineDeformableRegistration_outputs(): - output_map = dict(resampledmovingfilename=dict(), - outputtransform=dict(), + output_map = dict(outputtransform=dict(), outputwarp=dict(), + resampledmovingfilename=dict(), ) outputs = BSplineDeformableRegistration.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineToDeformationField.py b/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineToDeformationField.py index 6592190d2a..185ec5cc97 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineToDeformationField.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_BSplineToDeformationField.py @@ -1,24 +1,25 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.slicer.legacy.converters import BSplineToDeformationField + def test_BSplineToDeformationField_inputs(): - input_map = dict(tfm=dict(argstr='--tfm %s', + input_map = dict(args=dict(argstr='%s', ), - ignore_exception=dict(nohash=True, + defImage=dict(argstr='--defImage %s', + hash_files=False, + ), + environ=dict(nohash=True, usedefault=True, ), - args=dict(argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - defImage=dict(hash_files=False, - argstr='--defImage %s', + refImage=dict(argstr='--refImage %s', ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - refImage=dict(argstr='--refImage %s', + tfm=dict(argstr='--tfm %s', ), ) inputs = BSplineToDeformationField.input_spec() @@ -26,6 +27,7 @@ def test_BSplineToDeformationField_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_BSplineToDeformationField_outputs(): output_map = dict(defImage=dict(), ) @@ -34,3 +36,4 @@ def test_BSplineToDeformationField_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_ExpertAutomatedRegistration.py b/nipype/interfaces/slicer/legacy/tests/test_auto_ExpertAutomatedRegistration.py index 5bd0ceae52..ec4b9dca36 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_ExpertAutomatedRegistration.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_ExpertAutomatedRegistration.py @@ -1,84 +1,86 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.slicer.legacy.registration import ExpertAutomatedRegistration + def test_ExpertAutomatedRegistration_inputs(): - input_map = dict(metric=dict(argstr='--metric %s', - ), - bsplineSamplingRatio=dict(argstr='--bsplineSamplingRatio %f', - ), - movingLandmarks=dict(argstr='--movingLandmarks %s...', + input_map = dict(affineMaxIterations=dict(argstr='--affineMaxIterations %d', ), - expectedRotation=dict(argstr='--expectedRotation %f', + affineSamplingRatio=dict(argstr='--affineSamplingRatio %f', ), - registration=dict(argstr='--registration %s', + args=dict(argstr='%s', ), - fixedLandmarks=dict(argstr='--fixedLandmarks %s...', + bsplineMaxIterations=dict(argstr='--bsplineMaxIterations %d', ), - affineMaxIterations=dict(argstr='--affineMaxIterations %d', + bsplineSamplingRatio=dict(argstr='--bsplineSamplingRatio %f', ), - fixedImage=dict(position=-2, - argstr='%s', + controlPointSpacing=dict(argstr='--controlPointSpacing %d', ), - rigidMaxIterations=dict(argstr='--rigidMaxIterations %d', + environ=dict(nohash=True, + usedefault=True, ), expectedOffset=dict(argstr='--expectedOffset %f', ), - affineSamplingRatio=dict(argstr='--affineSamplingRatio %f', + expectedRotation=dict(argstr='--expectedRotation %f', ), expectedScale=dict(argstr='--expectedScale %f', ), - interpolation=dict(argstr='--interpolation %s', + expectedSkew=dict(argstr='--expectedSkew %f', + ), + fixedImage=dict(argstr='%s', + position=-2, + ), + fixedImageMask=dict(argstr='--fixedImageMask %s', + ), + fixedLandmarks=dict(argstr='--fixedLandmarks %s...', ), ignore_exception=dict(nohash=True, usedefault=True, ), - sampleFromOverlap=dict(argstr='--sampleFromOverlap ', + initialization=dict(argstr='--initialization %s', ), - controlPointSpacing=dict(argstr='--controlPointSpacing %d', + interpolation=dict(argstr='--interpolation %s', ), - initialization=dict(argstr='--initialization %s', + loadTransform=dict(argstr='--loadTransform %s', ), - args=dict(argstr='%s', + metric=dict(argstr='--metric %s', ), - numberOfThreads=dict(argstr='--numberOfThreads %d', + minimizeMemory=dict(argstr='--minimizeMemory ', ), - rigidSamplingRatio=dict(argstr='--rigidSamplingRatio %f', + movingImage=dict(argstr='%s', + position=-1, ), - terminal_output=dict(mandatory=True, - nohash=True, + movingLandmarks=dict(argstr='--movingLandmarks %s...', ), - randomNumberSeed=dict(argstr='--randomNumberSeed %d', + numberOfThreads=dict(argstr='--numberOfThreads %d', ), - resampledImage=dict(hash_files=False, - argstr='--resampledImage %s', + randomNumberSeed=dict(argstr='--randomNumberSeed %d', ), - loadTransform=dict(argstr='--loadTransform %s', + registration=dict(argstr='--registration %s', ), - fixedImageMask=dict(argstr='--fixedImageMask %s', + resampledImage=dict(argstr='--resampledImage %s', + hash_files=False, ), - saveTransform=dict(hash_files=False, - argstr='--saveTransform %s', + rigidMaxIterations=dict(argstr='--rigidMaxIterations %d', ), - movingImage=dict(position=-1, - argstr='%s', + rigidSamplingRatio=dict(argstr='--rigidSamplingRatio %f', ), - bsplineMaxIterations=dict(argstr='--bsplineMaxIterations %d', + sampleFromOverlap=dict(argstr='--sampleFromOverlap ', ), - expectedSkew=dict(argstr='--expectedSkew %f', + saveTransform=dict(argstr='--saveTransform %s', + hash_files=False, ), - environ=dict(nohash=True, - usedefault=True, + terminal_output=dict(mandatory=True, + nohash=True, ), verbosityLevel=dict(argstr='--verbosityLevel %s', ), - minimizeMemory=dict(argstr='--minimizeMemory ', - ), ) inputs = ExpertAutomatedRegistration.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ExpertAutomatedRegistration_outputs(): output_map = dict(resampledImage=dict(), saveTransform=dict(), @@ -88,3 +90,4 @@ def test_ExpertAutomatedRegistration_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_LinearRegistration.py b/nipype/interfaces/slicer/legacy/tests/test_auto_LinearRegistration.py index c83938a3f1..908bff95d2 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_LinearRegistration.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_LinearRegistration.py @@ -1,47 +1,48 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.slicer.legacy.registration import LinearRegistration + def test_LinearRegistration_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(FixedImageFileName=dict(argstr='%s', + position=-2, ), - initialtransform=dict(argstr='--initialtransform %s', - ), - histogrambins=dict(argstr='--histogrambins %d', - ), - translationscale=dict(argstr='--translationscale %f', - ), - movingsmoothingfactor=dict(argstr='--movingsmoothingfactor %d', + MovingImageFileName=dict(argstr='%s', + position=-1, ), args=dict(argstr='%s', ), - outputtransform=dict(hash_files=False, - argstr='--outputtransform %s', + environ=dict(nohash=True, + usedefault=True, ), - spatialsamples=dict(argstr='--spatialsamples %d', + fixedsmoothingfactor=dict(argstr='--fixedsmoothingfactor %d', ), - resampledmovingfilename=dict(hash_files=False, - argstr='--resampledmovingfilename %s', + histogrambins=dict(argstr='--histogrambins %d', ), - MovingImageFileName=dict(position=-1, - argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - terminal_output=dict(mandatory=True, - nohash=True, + initialtransform=dict(argstr='--initialtransform %s', ), - learningrate=dict(argstr='--learningrate %s', + iterations=dict(argstr='--iterations %s', sep=',', ), - iterations=dict(argstr='--iterations %s', + learningrate=dict(argstr='--learningrate %s', sep=',', ), - environ=dict(nohash=True, - usedefault=True, + movingsmoothingfactor=dict(argstr='--movingsmoothingfactor %d', ), - FixedImageFileName=dict(position=-2, - argstr='%s', + outputtransform=dict(argstr='--outputtransform %s', + hash_files=False, ), - fixedsmoothingfactor=dict(argstr='--fixedsmoothingfactor %d', + resampledmovingfilename=dict(argstr='--resampledmovingfilename %s', + hash_files=False, + ), + spatialsamples=dict(argstr='--spatialsamples %d', + ), + terminal_output=dict(mandatory=True, + nohash=True, + ), + translationscale=dict(argstr='--translationscale %f', ), ) inputs = LinearRegistration.input_spec() @@ -49,12 +50,14 @@ def test_LinearRegistration_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_LinearRegistration_outputs(): - output_map = dict(resampledmovingfilename=dict(), - outputtransform=dict(), + output_map = dict(outputtransform=dict(), + resampledmovingfilename=dict(), ) outputs = LinearRegistration.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_MultiResolutionAffineRegistration.py b/nipype/interfaces/slicer/legacy/tests/test_auto_MultiResolutionAffineRegistration.py index 4903e603eb..7456e7fc70 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_MultiResolutionAffineRegistration.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_MultiResolutionAffineRegistration.py @@ -1,43 +1,44 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.slicer.legacy.registration import MultiResolutionAffineRegistration + def test_MultiResolutionAffineRegistration_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + environ=dict(nohash=True, usedefault=True, ), - numIterations=dict(argstr='--numIterations %d', + fixedImage=dict(argstr='%s', + position=-2, ), fixedImageMask=dict(argstr='--fixedImageMask %s', ), - args=dict(argstr='%s', + fixedImageROI=dict(argstr='--fixedImageROI %s', ), - saveTransform=dict(hash_files=False, - argstr='--saveTransform %s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - stepTolerance=dict(argstr='--stepTolerance %f', + metricTolerance=dict(argstr='--metricTolerance %f', ), - resampledImage=dict(hash_files=False, - argstr='--resampledImage %s', + movingImage=dict(argstr='%s', + position=-1, ), - movingImage=dict(position=-1, - argstr='%s', + numIterations=dict(argstr='--numIterations %d', ), - terminal_output=dict(mandatory=True, - nohash=True, + numLineIterations=dict(argstr='--numLineIterations %d', ), - environ=dict(nohash=True, - usedefault=True, + resampledImage=dict(argstr='--resampledImage %s', + hash_files=False, ), - metricTolerance=dict(argstr='--metricTolerance %f', + saveTransform=dict(argstr='--saveTransform %s', + hash_files=False, ), stepSize=dict(argstr='--stepSize %f', ), - numLineIterations=dict(argstr='--numLineIterations %d', - ), - fixedImageROI=dict(argstr='--fixedImageROI %s', + stepTolerance=dict(argstr='--stepTolerance %f', ), - fixedImage=dict(position=-2, - argstr='%s', + terminal_output=dict(mandatory=True, + nohash=True, ), ) inputs = MultiResolutionAffineRegistration.input_spec() @@ -45,6 +46,7 @@ def test_MultiResolutionAffineRegistration_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MultiResolutionAffineRegistration_outputs(): output_map = dict(resampledImage=dict(), saveTransform=dict(), @@ -54,3 +56,4 @@ def test_MultiResolutionAffineRegistration_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdImageFilter.py b/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdImageFilter.py index 01f239e607..99cfcaaedd 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdImageFilter.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdImageFilter.py @@ -1,37 +1,39 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.slicer.legacy.filtering import OtsuThresholdImageFilter + def test_OtsuThresholdImageFilter_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + environ=dict(nohash=True, usedefault=True, ), - outputVolume=dict(position=-1, - hash_files=False, - argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - numberOfBins=dict(argstr='--numberOfBins %d', + inputVolume=dict(argstr='%s', + position=-2, ), insideValue=dict(argstr='--insideValue %d', ), - args=dict(argstr='%s', + numberOfBins=dict(argstr='--numberOfBins %d', + ), + outputVolume=dict(argstr='%s', + hash_files=False, + position=-1, ), outsideValue=dict(argstr='--outsideValue %d', ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - inputVolume=dict(position=-2, - argstr='%s', - ), ) inputs = OtsuThresholdImageFilter.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_OtsuThresholdImageFilter_outputs(): output_map = dict(outputVolume=dict(position=-1, ), @@ -41,3 +43,4 @@ def test_OtsuThresholdImageFilter_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdSegmentation.py b/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdSegmentation.py index e6fde407c7..bc4cb8406f 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdSegmentation.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_OtsuThresholdSegmentation.py @@ -1,32 +1,33 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.slicer.legacy.segmentation import OtsuThresholdSegmentation + def test_OtsuThresholdSegmentation_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, - ), - outputVolume=dict(position=-1, - hash_files=False, - argstr='%s', - ), - numberOfBins=dict(argstr='--numberOfBins %d', + input_map = dict(args=dict(argstr='%s', ), brightObjects=dict(argstr='--brightObjects ', ), + environ=dict(nohash=True, + usedefault=True, + ), faceConnected=dict(argstr='--faceConnected ', ), - args=dict(argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, + ), + inputVolume=dict(argstr='%s', + position=-2, ), minimumObjectSize=dict(argstr='--minimumObjectSize %d', ), - terminal_output=dict(mandatory=True, - nohash=True, + numberOfBins=dict(argstr='--numberOfBins %d', ), - environ=dict(nohash=True, - usedefault=True, + outputVolume=dict(argstr='%s', + hash_files=False, + position=-1, ), - inputVolume=dict(position=-2, - argstr='%s', + terminal_output=dict(mandatory=True, + nohash=True, ), ) inputs = OtsuThresholdSegmentation.input_spec() @@ -34,6 +35,7 @@ def test_OtsuThresholdSegmentation_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_OtsuThresholdSegmentation_outputs(): output_map = dict(outputVolume=dict(position=-1, ), @@ -43,3 +45,4 @@ def test_OtsuThresholdSegmentation_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_ResampleScalarVolume.py b/nipype/interfaces/slicer/legacy/tests/test_auto_ResampleScalarVolume.py index 884b3eb9d9..3b54ce3bc0 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_ResampleScalarVolume.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_ResampleScalarVolume.py @@ -1,36 +1,38 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.slicer.legacy.filtering import ResampleScalarVolume + def test_ResampleScalarVolume_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(InputVolume=dict(argstr='%s', + position=-2, ), - OutputVolume=dict(position=-1, + OutputVolume=dict(argstr='%s', hash_files=False, - argstr='%s', + position=-1, ), args=dict(argstr='%s', ), - spacing=dict(argstr='--spacing %s', - sep=',', - ), - terminal_output=dict(mandatory=True, - nohash=True, - ), environ=dict(nohash=True, usedefault=True, ), - InputVolume=dict(position=-2, - argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, ), interpolation=dict(argstr='--interpolation %s', ), + spacing=dict(argstr='--spacing %s', + sep=',', + ), + terminal_output=dict(mandatory=True, + nohash=True, + ), ) inputs = ResampleScalarVolume.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ResampleScalarVolume_outputs(): output_map = dict(OutputVolume=dict(position=-1, ), @@ -40,3 +42,4 @@ def test_ResampleScalarVolume_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/slicer/legacy/tests/test_auto_RigidRegistration.py b/nipype/interfaces/slicer/legacy/tests/test_auto_RigidRegistration.py index 039bcf6be4..115aab9921 100644 --- a/nipype/interfaces/slicer/legacy/tests/test_auto_RigidRegistration.py +++ b/nipype/interfaces/slicer/legacy/tests/test_auto_RigidRegistration.py @@ -1,49 +1,50 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.slicer.legacy.registration import RigidRegistration + def test_RigidRegistration_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(FixedImageFileName=dict(argstr='%s', + position=-2, ), - initialtransform=dict(argstr='--initialtransform %s', + MovingImageFileName=dict(argstr='%s', + position=-1, ), - testingmode=dict(argstr='--testingmode ', + args=dict(argstr='%s', ), - histogrambins=dict(argstr='--histogrambins %d', + environ=dict(nohash=True, + usedefault=True, ), - translationscale=dict(argstr='--translationscale %f', + fixedsmoothingfactor=dict(argstr='--fixedsmoothingfactor %d', ), - movingsmoothingfactor=dict(argstr='--movingsmoothingfactor %d', + histogrambins=dict(argstr='--histogrambins %d', ), - args=dict(argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - outputtransform=dict(hash_files=False, - argstr='--outputtransform %s', + initialtransform=dict(argstr='--initialtransform %s', ), - spatialsamples=dict(argstr='--spatialsamples %d', + iterations=dict(argstr='--iterations %s', + sep=',', ), - resampledmovingfilename=dict(hash_files=False, - argstr='--resampledmovingfilename %s', + learningrate=dict(argstr='--learningrate %s', + sep=',', ), - MovingImageFileName=dict(position=-1, - argstr='%s', + movingsmoothingfactor=dict(argstr='--movingsmoothingfactor %d', ), - terminal_output=dict(mandatory=True, - nohash=True, + outputtransform=dict(argstr='--outputtransform %s', + hash_files=False, ), - learningrate=dict(argstr='--learningrate %s', - sep=',', + resampledmovingfilename=dict(argstr='--resampledmovingfilename %s', + hash_files=False, ), - iterations=dict(argstr='--iterations %s', - sep=',', + spatialsamples=dict(argstr='--spatialsamples %d', ), - environ=dict(nohash=True, - usedefault=True, + terminal_output=dict(mandatory=True, + nohash=True, ), - FixedImageFileName=dict(position=-2, - argstr='%s', + testingmode=dict(argstr='--testingmode ', ), - fixedsmoothingfactor=dict(argstr='--fixedsmoothingfactor %d', + translationscale=dict(argstr='--translationscale %f', ), ) inputs = RigidRegistration.input_spec() @@ -51,12 +52,14 @@ def test_RigidRegistration_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_RigidRegistration_outputs(): - output_map = dict(resampledmovingfilename=dict(), - outputtransform=dict(), + output_map = dict(outputtransform=dict(), + resampledmovingfilename=dict(), ) outputs = RigidRegistration.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/slicer/quantification/tests/test_auto_IntensityDifferenceMetric.py b/nipype/interfaces/slicer/quantification/tests/test_auto_IntensityDifferenceMetric.py index 197efdc536..e100678469 100644 --- a/nipype/interfaces/slicer/quantification/tests/test_auto_IntensityDifferenceMetric.py +++ b/nipype/interfaces/slicer/quantification/tests/test_auto_IntensityDifferenceMetric.py @@ -1,44 +1,46 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.slicer.quantification.changequantification import IntensityDifferenceMetric + def test_IntensityDifferenceMetric_inputs(): - input_map = dict(followupVolume=dict(position=-2, - argstr='%s', - ), - outputVolume=dict(position=-1, - hash_files=False, - argstr='%s', - ), - ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(args=dict(argstr='%s', ), - baselineVolume=dict(position=-4, - argstr='%s', + baselineSegmentationVolume=dict(argstr='%s', + position=-3, ), - args=dict(argstr='%s', + baselineVolume=dict(argstr='%s', + position=-4, ), changingBandSize=dict(argstr='--changingBandSize %d', ), - terminal_output=dict(mandatory=True, - nohash=True, - ), environ=dict(nohash=True, usedefault=True, ), - reportFileName=dict(hash_files=False, - argstr='--reportFileName %s', + followupVolume=dict(argstr='%s', + position=-2, + ), + ignore_exception=dict(nohash=True, + usedefault=True, + ), + outputVolume=dict(argstr='%s', + hash_files=False, + position=-1, ), - baselineSegmentationVolume=dict(position=-3, - argstr='%s', + reportFileName=dict(argstr='--reportFileName %s', + hash_files=False, ), sensitivityThreshold=dict(argstr='--sensitivityThreshold %f', ), + terminal_output=dict(mandatory=True, + nohash=True, + ), ) inputs = IntensityDifferenceMetric.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_IntensityDifferenceMetric_outputs(): output_map = dict(outputVolume=dict(position=-1, ), @@ -49,3 +51,4 @@ def test_IntensityDifferenceMetric_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/slicer/quantification/tests/test_auto_PETStandardUptakeValueComputation.py b/nipype/interfaces/slicer/quantification/tests/test_auto_PETStandardUptakeValueComputation.py index 34d2b0912e..018d8dad74 100644 --- a/nipype/interfaces/slicer/quantification/tests/test_auto_PETStandardUptakeValueComputation.py +++ b/nipype/interfaces/slicer/quantification/tests/test_auto_PETStandardUptakeValueComputation.py @@ -1,45 +1,47 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.slicer.quantification.petstandarduptakevaluecomputation import PETStandardUptakeValueComputation + def test_PETStandardUptakeValueComputation_inputs(): - input_map = dict(petVolume=dict(argstr='--petVolume %s', + input_map = dict(OutputLabel=dict(argstr='--OutputLabel %s', ), - ignore_exception=dict(nohash=True, - usedefault=True, + OutputLabelValue=dict(argstr='--OutputLabelValue %s', ), - color=dict(argstr='--color %s', + SUVMax=dict(argstr='--SUVMax %s', + ), + SUVMean=dict(argstr='--SUVMean %s', + ), + SUVMin=dict(argstr='--SUVMin %s', ), args=dict(argstr='%s', ), - OutputLabel=dict(argstr='--OutputLabel %s', + color=dict(argstr='--color %s', ), - csvFile=dict(hash_files=False, - argstr='--csvFile %s', + csvFile=dict(argstr='--csvFile %s', + hash_files=False, ), - OutputLabelValue=dict(argstr='--OutputLabelValue %s', + environ=dict(nohash=True, + usedefault=True, + ), + ignore_exception=dict(nohash=True, + usedefault=True, ), labelMap=dict(argstr='--labelMap %s', ), petDICOMPath=dict(argstr='--petDICOMPath %s', ), + petVolume=dict(argstr='--petVolume %s', + ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - SUVMax=dict(argstr='--SUVMax %s', - ), - SUVMin=dict(argstr='--SUVMin %s', - ), - SUVMean=dict(argstr='--SUVMean %s', - ), ) inputs = PETStandardUptakeValueComputation.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_PETStandardUptakeValueComputation_outputs(): output_map = dict(csvFile=dict(), ) @@ -48,3 +50,4 @@ def test_PETStandardUptakeValueComputation_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/slicer/registration/tests/test_auto_ACPCTransform.py b/nipype/interfaces/slicer/registration/tests/test_auto_ACPCTransform.py index da6e388286..eaf05fe165 100644 --- a/nipype/interfaces/slicer/registration/tests/test_auto_ACPCTransform.py +++ b/nipype/interfaces/slicer/registration/tests/test_auto_ACPCTransform.py @@ -1,33 +1,35 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.slicer.registration.specialized import ACPCTransform + def test_ACPCTransform_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, - ), - debugSwitch=dict(argstr='--debugSwitch ', + input_map = dict(acpc=dict(argstr='--acpc %s...', ), args=dict(argstr='%s', ), - outputTransform=dict(hash_files=False, - argstr='--outputTransform %s', - ), - terminal_output=dict(mandatory=True, - nohash=True, + debugSwitch=dict(argstr='--debugSwitch ', ), environ=dict(nohash=True, usedefault=True, ), - acpc=dict(argstr='--acpc %s...', + ignore_exception=dict(nohash=True, + usedefault=True, ), midline=dict(argstr='--midline %s...', ), + outputTransform=dict(argstr='--outputTransform %s', + hash_files=False, + ), + terminal_output=dict(mandatory=True, + nohash=True, + ), ) inputs = ACPCTransform.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ACPCTransform_outputs(): output_map = dict(outputTransform=dict(), ) @@ -36,3 +38,4 @@ def test_ACPCTransform_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSDemonWarp.py b/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSDemonWarp.py index db4fec63e4..929e69985c 100644 --- a/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSDemonWarp.py +++ b/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSDemonWarp.py @@ -1,107 +1,108 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.slicer.registration.specialized import BRAINSDemonWarp + def test_BRAINSDemonWarp_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, - ), - outputPixelType=dict(argstr='--outputPixelType %s', + input_map = dict(args=dict(argstr='%s', ), - medianFilterSize=dict(argstr='--medianFilterSize %s', + arrayOfPyramidLevelIterations=dict(argstr='--arrayOfPyramidLevelIterations %s', sep=',', ), backgroundFillValue=dict(argstr='--backgroundFillValue %d', ), - upperThresholdForBOBF=dict(argstr='--upperThresholdForBOBF %d', + checkerboardPatternSubdivisions=dict(argstr='--checkerboardPatternSubdivisions %s', + sep=',', ), - promptUser=dict(argstr='--promptUser ', + environ=dict(nohash=True, + usedefault=True, ), - smoothDisplacementFieldSigma=dict(argstr='--smoothDisplacementFieldSigma %f', + fixedBinaryVolume=dict(argstr='--fixedBinaryVolume %s', ), - histogramMatch=dict(argstr='--histogramMatch ', + fixedVolume=dict(argstr='--fixedVolume %s', ), - interpolationMode=dict(argstr='--interpolationMode %s', + gradient_type=dict(argstr='--gradient_type %s', ), - fixedVolume=dict(argstr='--fixedVolume %s', + gui=dict(argstr='--gui ', + ), + histogramMatch=dict(argstr='--histogramMatch ', + ), + ignore_exception=dict(nohash=True, + usedefault=True, ), initializeWithDisplacementField=dict(argstr='--initializeWithDisplacementField %s', ), - numberOfBCHApproximationTerms=dict(argstr='--numberOfBCHApproximationTerms %d', + initializeWithTransform=dict(argstr='--initializeWithTransform %s', ), inputPixelType=dict(argstr='--inputPixelType %s', ), - minimumMovingPyramid=dict(argstr='--minimumMovingPyramid %s', - sep=',', + interpolationMode=dict(argstr='--interpolationMode %s', ), - registrationFilterType=dict(argstr='--registrationFilterType %s', + lowerThresholdForBOBF=dict(argstr='--lowerThresholdForBOBF %d', ), - upFieldSmoothing=dict(argstr='--upFieldSmoothing %f', + maskProcessingMode=dict(argstr='--maskProcessingMode %s', ), - initializeWithTransform=dict(argstr='--initializeWithTransform %s', + max_step_length=dict(argstr='--max_step_length %f', ), - numberOfHistogramBins=dict(argstr='--numberOfHistogramBins %d', + medianFilterSize=dict(argstr='--medianFilterSize %s', + sep=',', ), minimumFixedPyramid=dict(argstr='--minimumFixedPyramid %s', sep=',', ), - outputNormalized=dict(argstr='--outputNormalized ', - ), - outputVolume=dict(hash_files=False, - argstr='--outputVolume %s', + minimumMovingPyramid=dict(argstr='--minimumMovingPyramid %s', + sep=',', ), - outputCheckerboardVolume=dict(hash_files=False, - argstr='--outputCheckerboardVolume %s', + movingBinaryVolume=dict(argstr='--movingBinaryVolume %s', ), movingVolume=dict(argstr='--movingVolume %s', ), - max_step_length=dict(argstr='--max_step_length %f', + neighborhoodForBOBF=dict(argstr='--neighborhoodForBOBF %s', + sep=',', ), - fixedBinaryVolume=dict(argstr='--fixedBinaryVolume %s', + numberOfBCHApproximationTerms=dict(argstr='--numberOfBCHApproximationTerms %d', ), - args=dict(argstr='%s', + numberOfHistogramBins=dict(argstr='--numberOfHistogramBins %d', ), - arrayOfPyramidLevelIterations=dict(argstr='--arrayOfPyramidLevelIterations %s', - sep=',', + numberOfMatchPoints=dict(argstr='--numberOfMatchPoints %d', + ), + numberOfPyramidLevels=dict(argstr='--numberOfPyramidLevels %d', ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), - movingBinaryVolume=dict(argstr='--movingBinaryVolume %s', + outputCheckerboardVolume=dict(argstr='--outputCheckerboardVolume %s', + hash_files=False, ), - neighborhoodForBOBF=dict(argstr='--neighborhoodForBOBF %s', - sep=',', + outputDebug=dict(argstr='--outputDebug ', ), - outputDisplacementFieldVolume=dict(hash_files=False, - argstr='--outputDisplacementFieldVolume %s', + outputDisplacementFieldPrefix=dict(argstr='--outputDisplacementFieldPrefix %s', ), - checkerboardPatternSubdivisions=dict(argstr='--checkerboardPatternSubdivisions %s', - sep=',', + outputDisplacementFieldVolume=dict(argstr='--outputDisplacementFieldVolume %s', + hash_files=False, ), - seedForBOBF=dict(argstr='--seedForBOBF %s', - sep=',', + outputNormalized=dict(argstr='--outputNormalized ', ), - outputDisplacementFieldPrefix=dict(argstr='--outputDisplacementFieldPrefix %s', + outputPixelType=dict(argstr='--outputPixelType %s', ), - numberOfPyramidLevels=dict(argstr='--numberOfPyramidLevels %d', + outputVolume=dict(argstr='--outputVolume %s', + hash_files=False, ), - gui=dict(argstr='--gui ', + promptUser=dict(argstr='--promptUser ', ), - outputDebug=dict(argstr='--outputDebug ', + registrationFilterType=dict(argstr='--registrationFilterType %s', ), - maskProcessingMode=dict(argstr='--maskProcessingMode %s', + seedForBOBF=dict(argstr='--seedForBOBF %s', + sep=',', ), - use_vanilla_dem=dict(argstr='--use_vanilla_dem ', + smoothDisplacementFieldSigma=dict(argstr='--smoothDisplacementFieldSigma %f', ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - lowerThresholdForBOBF=dict(argstr='--lowerThresholdForBOBF %d', + upFieldSmoothing=dict(argstr='--upFieldSmoothing %f', ), - numberOfMatchPoints=dict(argstr='--numberOfMatchPoints %d', + upperThresholdForBOBF=dict(argstr='--upperThresholdForBOBF %d', ), - gradient_type=dict(argstr='--gradient_type %s', + use_vanilla_dem=dict(argstr='--use_vanilla_dem ', ), ) inputs = BRAINSDemonWarp.input_spec() @@ -109,13 +110,15 @@ def test_BRAINSDemonWarp_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_BRAINSDemonWarp_outputs(): - output_map = dict(outputVolume=dict(), - outputCheckerboardVolume=dict(), + output_map = dict(outputCheckerboardVolume=dict(), outputDisplacementFieldVolume=dict(), + outputVolume=dict(), ) outputs = BRAINSDemonWarp.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSFit.py b/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSFit.py index 04a66d8d4d..fd1dc98d68 100644 --- a/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSFit.py +++ b/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSFit.py @@ -1,150 +1,151 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.slicer.registration.brainsfit import BRAINSFit + def test_BRAINSFit_inputs(): - input_map = dict(initialTransform=dict(argstr='--initialTransform %s', + input_map = dict(NEVER_USE_THIS_FLAG_IT_IS_OUTDATED_00=dict(argstr='--NEVER_USE_THIS_FLAG_IT_IS_OUTDATED_00 ', ), - permitParameterVariation=dict(argstr='--permitParameterVariation %s', - sep=',', + NEVER_USE_THIS_FLAG_IT_IS_OUTDATED_01=dict(argstr='--NEVER_USE_THIS_FLAG_IT_IS_OUTDATED_01 ', ), - costFunctionConvergenceFactor=dict(argstr='--costFunctionConvergenceFactor %f', + NEVER_USE_THIS_FLAG_IT_IS_OUTDATED_02=dict(argstr='--NEVER_USE_THIS_FLAG_IT_IS_OUTDATED_02 ', ), - medianFilterSize=dict(argstr='--medianFilterSize %s', - sep=',', + ROIAutoClosingSize=dict(argstr='--ROIAutoClosingSize %f', ), - backgroundFillValue=dict(argstr='--backgroundFillValue %f', + ROIAutoDilateSize=dict(argstr='--ROIAutoDilateSize %f', ), - relaxationFactor=dict(argstr='--relaxationFactor %f', + args=dict(argstr='%s', ), - translationScale=dict(argstr='--translationScale %f', + backgroundFillValue=dict(argstr='--backgroundFillValue %f', ), - bsplineTransform=dict(hash_files=False, - argstr='--bsplineTransform %s', + bsplineTransform=dict(argstr='--bsplineTransform %s', + hash_files=False, ), - numberOfMatchPoints=dict(argstr='--numberOfMatchPoints %d', + costFunctionConvergenceFactor=dict(argstr='--costFunctionConvergenceFactor %f', ), - numberOfIterations=dict(argstr='--numberOfIterations %s', - sep=',', + costMetric=dict(argstr='--costMetric %s', ), - histogramMatch=dict(argstr='--histogramMatch ', + debugLevel=dict(argstr='--debugLevel %d', ), - failureExitCode=dict(argstr='--failureExitCode %d', + environ=dict(nohash=True, + usedefault=True, ), - NEVER_USE_THIS_FLAG_IT_IS_OUTDATED_02=dict(argstr='--NEVER_USE_THIS_FLAG_IT_IS_OUTDATED_02 ', + failureExitCode=dict(argstr='--failureExitCode %d', ), - maskProcessingMode=dict(argstr='--maskProcessingMode %s', + fixedBinaryVolume=dict(argstr='--fixedBinaryVolume %s', ), - maskInferiorCutOffFromCenter=dict(argstr='--maskInferiorCutOffFromCenter %f', + fixedVolume=dict(argstr='--fixedVolume %s', ), - NEVER_USE_THIS_FLAG_IT_IS_OUTDATED_01=dict(argstr='--NEVER_USE_THIS_FLAG_IT_IS_OUTDATED_01 ', + fixedVolumeTimeIndex=dict(argstr='--fixedVolumeTimeIndex %d', ), - reproportionScale=dict(argstr='--reproportionScale %f', + forceMINumberOfThreads=dict(argstr='--forceMINumberOfThreads %d', ), - skewScale=dict(argstr='--skewScale %f', + gui=dict(argstr='--gui ', ), - NEVER_USE_THIS_FLAG_IT_IS_OUTDATED_00=dict(argstr='--NEVER_USE_THIS_FLAG_IT_IS_OUTDATED_00 ', + histogramMatch=dict(argstr='--histogramMatch ', ), - fixedVolume=dict(argstr='--fixedVolume %s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - costMetric=dict(argstr='--costMetric %s', + initialTransform=dict(argstr='--initialTransform %s', ), - useCachingOfBSplineWeightsMode=dict(argstr='--useCachingOfBSplineWeightsMode %s', + initializeTransformMode=dict(argstr='--initializeTransformMode %s', ), - useScaleSkewVersor3D=dict(argstr='--useScaleSkewVersor3D ', + interpolationMode=dict(argstr='--interpolationMode %s', ), - useExplicitPDFDerivativesMode=dict(argstr='--useExplicitPDFDerivativesMode %s', + linearTransform=dict(argstr='--linearTransform %s', + hash_files=False, ), - outputTransform=dict(hash_files=False, - argstr='--outputTransform %s', + maskInferiorCutOffFromCenter=dict(argstr='--maskInferiorCutOffFromCenter %f', ), - useBSpline=dict(argstr='--useBSpline ', + maskProcessingMode=dict(argstr='--maskProcessingMode %s', ), - fixedVolumeTimeIndex=dict(argstr='--fixedVolumeTimeIndex %d', + maxBSplineDisplacement=dict(argstr='--maxBSplineDisplacement %f', ), - promptUser=dict(argstr='--promptUser ', + maximumStepLength=dict(argstr='--maximumStepLength %f', ), - environ=dict(nohash=True, - usedefault=True, + medianFilterSize=dict(argstr='--medianFilterSize %s', + sep=',', ), - linearTransform=dict(hash_files=False, - argstr='--linearTransform %s', + minimumStepLength=dict(argstr='--minimumStepLength %s', + sep=',', ), - maxBSplineDisplacement=dict(argstr='--maxBSplineDisplacement %f', + movingBinaryVolume=dict(argstr='--movingBinaryVolume %s', ), - numberOfHistogramBins=dict(argstr='--numberOfHistogramBins %d', + movingVolume=dict(argstr='--movingVolume %s', ), - outputMovingVolumeROI=dict(hash_files=False, - argstr='--outputMovingVolumeROI %s', + movingVolumeTimeIndex=dict(argstr='--movingVolumeTimeIndex %d', ), - ignore_exception=dict(nohash=True, - usedefault=True, + numberOfHistogramBins=dict(argstr='--numberOfHistogramBins %d', ), - outputVolume=dict(hash_files=False, - argstr='--outputVolume %s', + numberOfIterations=dict(argstr='--numberOfIterations %s', + sep=',', ), - projectedGradientTolerance=dict(argstr='--projectedGradientTolerance %f', + numberOfMatchPoints=dict(argstr='--numberOfMatchPoints %d', ), - movingVolume=dict(argstr='--movingVolume %s', + numberOfSamples=dict(argstr='--numberOfSamples %d', ), - fixedBinaryVolume=dict(argstr='--fixedBinaryVolume %s', + numberOfThreads=dict(argstr='--numberOfThreads %d', ), - args=dict(argstr='%s', + outputFixedVolumeROI=dict(argstr='--outputFixedVolumeROI %s', + hash_files=False, ), - splineGridSize=dict(argstr='--splineGridSize %s', - sep=',', + outputMovingVolumeROI=dict(argstr='--outputMovingVolumeROI %s', + hash_files=False, ), - initializeTransformMode=dict(argstr='--initializeTransformMode %s', + outputTransform=dict(argstr='--outputTransform %s', + hash_files=False, ), - movingBinaryVolume=dict(argstr='--movingBinaryVolume %s', + outputVolume=dict(argstr='--outputVolume %s', + hash_files=False, ), outputVolumePixelType=dict(argstr='--outputVolumePixelType %s', ), - terminal_output=dict(mandatory=True, - nohash=True, - ), - numberOfThreads=dict(argstr='--numberOfThreads %d', + permitParameterVariation=dict(argstr='--permitParameterVariation %s', + sep=',', ), - writeTransformOnFailure=dict(argstr='--writeTransformOnFailure ', + projectedGradientTolerance=dict(argstr='--projectedGradientTolerance %f', ), - debugLevel=dict(argstr='--debugLevel %d', + promptUser=dict(argstr='--promptUser ', ), - useScaleVersor3D=dict(argstr='--useScaleVersor3D ', + relaxationFactor=dict(argstr='--relaxationFactor %f', ), - minimumStepLength=dict(argstr='--minimumStepLength %s', - sep=',', + removeIntensityOutliers=dict(argstr='--removeIntensityOutliers %f', ), - transformType=dict(argstr='--transformType %s', - sep=',', + reproportionScale=dict(argstr='--reproportionScale %f', ), scaleOutputValues=dict(argstr='--scaleOutputValues ', ), - useAffine=dict(argstr='--useAffine ', + skewScale=dict(argstr='--skewScale %f', ), - gui=dict(argstr='--gui ', + splineGridSize=dict(argstr='--splineGridSize %s', + sep=',', ), - ROIAutoDilateSize=dict(argstr='--ROIAutoDilateSize %f', + strippedOutputTransform=dict(argstr='--strippedOutputTransform %s', + hash_files=False, ), - numberOfSamples=dict(argstr='--numberOfSamples %d', + terminal_output=dict(mandatory=True, + nohash=True, ), - interpolationMode=dict(argstr='--interpolationMode %s', + transformType=dict(argstr='--transformType %s', + sep=',', ), - maximumStepLength=dict(argstr='--maximumStepLength %f', + translationScale=dict(argstr='--translationScale %f', ), - forceMINumberOfThreads=dict(argstr='--forceMINumberOfThreads %d', + useAffine=dict(argstr='--useAffine ', ), - strippedOutputTransform=dict(hash_files=False, - argstr='--strippedOutputTransform %s', + useBSpline=dict(argstr='--useBSpline ', ), - movingVolumeTimeIndex=dict(argstr='--movingVolumeTimeIndex %d', + useCachingOfBSplineWeightsMode=dict(argstr='--useCachingOfBSplineWeightsMode %s', ), - ROIAutoClosingSize=dict(argstr='--ROIAutoClosingSize %f', + useExplicitPDFDerivativesMode=dict(argstr='--useExplicitPDFDerivativesMode %s', ), useRigid=dict(argstr='--useRigid ', ), - outputFixedVolumeROI=dict(hash_files=False, - argstr='--outputFixedVolumeROI %s', + useScaleSkewVersor3D=dict(argstr='--useScaleSkewVersor3D ', + ), + useScaleVersor3D=dict(argstr='--useScaleVersor3D ', ), - removeIntensityOutliers=dict(argstr='--removeIntensityOutliers %f', + writeTransformOnFailure=dict(argstr='--writeTransformOnFailure ', ), ) inputs = BRAINSFit.input_spec() @@ -152,17 +153,19 @@ def test_BRAINSFit_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_BRAINSFit_outputs(): - output_map = dict(outputVolume=dict(), - bsplineTransform=dict(), - outputTransform=dict(), + output_map = dict(bsplineTransform=dict(), + linearTransform=dict(), outputFixedVolumeROI=dict(), - strippedOutputTransform=dict(), outputMovingVolumeROI=dict(), - linearTransform=dict(), + outputTransform=dict(), + outputVolume=dict(), + strippedOutputTransform=dict(), ) outputs = BRAINSFit.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSResample.py b/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSResample.py index 8048ad36b4..48620e85d3 100644 --- a/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSResample.py +++ b/nipype/interfaces/slicer/registration/tests/test_auto_BRAINSResample.py @@ -1,39 +1,40 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.slicer.registration.brainsresample import BRAINSResample + def test_BRAINSResample_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, - ), - outputVolume=dict(hash_files=False, - argstr='--outputVolume %s', - ), - pixelType=dict(argstr='--pixelType %s', + input_map = dict(args=dict(argstr='%s', ), defaultValue=dict(argstr='--defaultValue %f', ), - args=dict(argstr='%s', - ), deformationVolume=dict(argstr='--deformationVolume %s', ), - interpolationMode=dict(argstr='--interpolationMode %s', + environ=dict(nohash=True, + usedefault=True, ), gridSpacing=dict(argstr='--gridSpacing %s', sep=',', ), - referenceVolume=dict(argstr='--referenceVolume %s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - terminal_output=dict(mandatory=True, - nohash=True, + inputVolume=dict(argstr='--inputVolume %s', + ), + interpolationMode=dict(argstr='--interpolationMode %s', + ), + inverseTransform=dict(argstr='--inverseTransform ', ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), - inputVolume=dict(argstr='--inputVolume %s', + outputVolume=dict(argstr='--outputVolume %s', + hash_files=False, ), - inverseTransform=dict(argstr='--inverseTransform ', + pixelType=dict(argstr='--pixelType %s', ), - environ=dict(nohash=True, - usedefault=True, + referenceVolume=dict(argstr='--referenceVolume %s', + ), + terminal_output=dict(mandatory=True, + nohash=True, ), warpTransform=dict(argstr='--warpTransform %s', ), @@ -43,6 +44,7 @@ def test_BRAINSResample_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_BRAINSResample_outputs(): output_map = dict(outputVolume=dict(), ) @@ -51,3 +53,4 @@ def test_BRAINSResample_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/slicer/registration/tests/test_auto_FiducialRegistration.py b/nipype/interfaces/slicer/registration/tests/test_auto_FiducialRegistration.py index 228f7c058a..88a80028b9 100644 --- a/nipype/interfaces/slicer/registration/tests/test_auto_FiducialRegistration.py +++ b/nipype/interfaces/slicer/registration/tests/test_auto_FiducialRegistration.py @@ -1,30 +1,31 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.slicer.registration.specialized import FiducialRegistration + def test_FiducialRegistration_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + environ=dict(nohash=True, usedefault=True, ), - transformType=dict(argstr='--transformType %s', + fixedLandmarks=dict(argstr='--fixedLandmarks %s...', ), - rms=dict(argstr='--rms %f', + ignore_exception=dict(nohash=True, + usedefault=True, ), - outputMessage=dict(argstr='--outputMessage %s', + movingLandmarks=dict(argstr='--movingLandmarks %s...', ), - args=dict(argstr='%s', + outputMessage=dict(argstr='--outputMessage %s', ), - saveTransform=dict(hash_files=False, - argstr='--saveTransform %s', + rms=dict(argstr='--rms %f', ), - movingLandmarks=dict(argstr='--movingLandmarks %s...', + saveTransform=dict(argstr='--saveTransform %s', + hash_files=False, ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - fixedLandmarks=dict(argstr='--fixedLandmarks %s...', + transformType=dict(argstr='--transformType %s', ), ) inputs = FiducialRegistration.input_spec() @@ -32,6 +33,7 @@ def test_FiducialRegistration_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_FiducialRegistration_outputs(): output_map = dict(saveTransform=dict(), ) @@ -40,3 +42,4 @@ def test_FiducialRegistration_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/slicer/registration/tests/test_auto_VBRAINSDemonWarp.py b/nipype/interfaces/slicer/registration/tests/test_auto_VBRAINSDemonWarp.py index 98c6ac1992..1656cb76a0 100644 --- a/nipype/interfaces/slicer/registration/tests/test_auto_VBRAINSDemonWarp.py +++ b/nipype/interfaces/slicer/registration/tests/test_auto_VBRAINSDemonWarp.py @@ -1,109 +1,110 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.slicer.registration.specialized import VBRAINSDemonWarp + def test_VBRAINSDemonWarp_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, - ), - outputPixelType=dict(argstr='--outputPixelType %s', + input_map = dict(args=dict(argstr='%s', ), - medianFilterSize=dict(argstr='--medianFilterSize %s', + arrayOfPyramidLevelIterations=dict(argstr='--arrayOfPyramidLevelIterations %s', sep=',', ), backgroundFillValue=dict(argstr='--backgroundFillValue %d', ), - upperThresholdForBOBF=dict(argstr='--upperThresholdForBOBF %d', + checkerboardPatternSubdivisions=dict(argstr='--checkerboardPatternSubdivisions %s', + sep=',', ), - promptUser=dict(argstr='--promptUser ', + environ=dict(nohash=True, + usedefault=True, ), - smoothDisplacementFieldSigma=dict(argstr='--smoothDisplacementFieldSigma %f', + fixedBinaryVolume=dict(argstr='--fixedBinaryVolume %s', + ), + fixedVolume=dict(argstr='--fixedVolume %s...', + ), + gradient_type=dict(argstr='--gradient_type %s', + ), + gui=dict(argstr='--gui ', ), histogramMatch=dict(argstr='--histogramMatch ', ), - fixedVolume=dict(argstr='--fixedVolume %s...', + ignore_exception=dict(nohash=True, + usedefault=True, ), initializeWithDisplacementField=dict(argstr='--initializeWithDisplacementField %s', ), - numberOfBCHApproximationTerms=dict(argstr='--numberOfBCHApproximationTerms %d', + initializeWithTransform=dict(argstr='--initializeWithTransform %s', ), inputPixelType=dict(argstr='--inputPixelType %s', ), - minimumMovingPyramid=dict(argstr='--minimumMovingPyramid %s', - sep=',', + interpolationMode=dict(argstr='--interpolationMode %s', ), - registrationFilterType=dict(argstr='--registrationFilterType %s', + lowerThresholdForBOBF=dict(argstr='--lowerThresholdForBOBF %d', ), - upFieldSmoothing=dict(argstr='--upFieldSmoothing %f', + makeBOBF=dict(argstr='--makeBOBF ', ), - initializeWithTransform=dict(argstr='--initializeWithTransform %s', + max_step_length=dict(argstr='--max_step_length %f', ), - numberOfHistogramBins=dict(argstr='--numberOfHistogramBins %d', + medianFilterSize=dict(argstr='--medianFilterSize %s', + sep=',', ), minimumFixedPyramid=dict(argstr='--minimumFixedPyramid %s', sep=',', ), - outputNormalized=dict(argstr='--outputNormalized ', - ), - outputVolume=dict(hash_files=False, - argstr='--outputVolume %s', + minimumMovingPyramid=dict(argstr='--minimumMovingPyramid %s', + sep=',', ), - outputCheckerboardVolume=dict(hash_files=False, - argstr='--outputCheckerboardVolume %s', + movingBinaryVolume=dict(argstr='--movingBinaryVolume %s', ), movingVolume=dict(argstr='--movingVolume %s...', ), - max_step_length=dict(argstr='--max_step_length %f', + neighborhoodForBOBF=dict(argstr='--neighborhoodForBOBF %s', + sep=',', ), - fixedBinaryVolume=dict(argstr='--fixedBinaryVolume %s', + numberOfBCHApproximationTerms=dict(argstr='--numberOfBCHApproximationTerms %d', ), - args=dict(argstr='%s', + numberOfHistogramBins=dict(argstr='--numberOfHistogramBins %d', ), - weightFactors=dict(argstr='--weightFactors %s', - sep=',', + numberOfMatchPoints=dict(argstr='--numberOfMatchPoints %d', ), - numberOfThreads=dict(argstr='--numberOfThreads %d', + numberOfPyramidLevels=dict(argstr='--numberOfPyramidLevels %d', ), - movingBinaryVolume=dict(argstr='--movingBinaryVolume %s', + numberOfThreads=dict(argstr='--numberOfThreads %d', ), - neighborhoodForBOBF=dict(argstr='--neighborhoodForBOBF %s', - sep=',', + outputCheckerboardVolume=dict(argstr='--outputCheckerboardVolume %s', + hash_files=False, ), - outputDisplacementFieldVolume=dict(hash_files=False, - argstr='--outputDisplacementFieldVolume %s', + outputDebug=dict(argstr='--outputDebug ', ), - makeBOBF=dict(argstr='--makeBOBF ', + outputDisplacementFieldPrefix=dict(argstr='--outputDisplacementFieldPrefix %s', ), - checkerboardPatternSubdivisions=dict(argstr='--checkerboardPatternSubdivisions %s', - sep=',', + outputDisplacementFieldVolume=dict(argstr='--outputDisplacementFieldVolume %s', + hash_files=False, ), - seedForBOBF=dict(argstr='--seedForBOBF %s', - sep=',', + outputNormalized=dict(argstr='--outputNormalized ', ), - outputDisplacementFieldPrefix=dict(argstr='--outputDisplacementFieldPrefix %s', + outputPixelType=dict(argstr='--outputPixelType %s', ), - numberOfPyramidLevels=dict(argstr='--numberOfPyramidLevels %d', + outputVolume=dict(argstr='--outputVolume %s', + hash_files=False, ), - gui=dict(argstr='--gui ', + promptUser=dict(argstr='--promptUser ', ), - outputDebug=dict(argstr='--outputDebug ', + registrationFilterType=dict(argstr='--registrationFilterType %s', ), - interpolationMode=dict(argstr='--interpolationMode %s', + seedForBOBF=dict(argstr='--seedForBOBF %s', + sep=',', ), - use_vanilla_dem=dict(argstr='--use_vanilla_dem ', + smoothDisplacementFieldSigma=dict(argstr='--smoothDisplacementFieldSigma %f', ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - lowerThresholdForBOBF=dict(argstr='--lowerThresholdForBOBF %d', + upFieldSmoothing=dict(argstr='--upFieldSmoothing %f', ), - numberOfMatchPoints=dict(argstr='--numberOfMatchPoints %d', + upperThresholdForBOBF=dict(argstr='--upperThresholdForBOBF %d', ), - gradient_type=dict(argstr='--gradient_type %s', + use_vanilla_dem=dict(argstr='--use_vanilla_dem ', ), - arrayOfPyramidLevelIterations=dict(argstr='--arrayOfPyramidLevelIterations %s', + weightFactors=dict(argstr='--weightFactors %s', sep=',', ), ) @@ -112,13 +113,15 @@ def test_VBRAINSDemonWarp_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_VBRAINSDemonWarp_outputs(): - output_map = dict(outputVolume=dict(), - outputCheckerboardVolume=dict(), + output_map = dict(outputCheckerboardVolume=dict(), outputDisplacementFieldVolume=dict(), + outputVolume=dict(), ) outputs = VBRAINSDemonWarp.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/slicer/segmentation/tests/test_auto_BRAINSROIAuto.py b/nipype/interfaces/slicer/segmentation/tests/test_auto_BRAINSROIAuto.py index 4837e6c86e..ed4c7dc815 100644 --- a/nipype/interfaces/slicer/segmentation/tests/test_auto_BRAINSROIAuto.py +++ b/nipype/interfaces/slicer/segmentation/tests/test_auto_BRAINSROIAuto.py @@ -1,44 +1,46 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.slicer.segmentation.specialized import BRAINSROIAuto + def test_BRAINSROIAuto_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(ROIAutoDilateSize=dict(argstr='--ROIAutoDilateSize %f', ), - outputClippedVolumeROI=dict(hash_files=False, - argstr='--outputClippedVolumeROI %s', + args=dict(argstr='%s', ), - otsuPercentileThreshold=dict(argstr='--otsuPercentileThreshold %f', + closingSize=dict(argstr='--closingSize %f', ), - args=dict(argstr='%s', + environ=dict(nohash=True, + usedefault=True, + ), + ignore_exception=dict(nohash=True, + usedefault=True, ), - ROIAutoDilateSize=dict(argstr='--ROIAutoDilateSize %f', + inputVolume=dict(argstr='--inputVolume %s', ), numberOfThreads=dict(argstr='--numberOfThreads %d', ), - closingSize=dict(argstr='--closingSize %f', + otsuPercentileThreshold=dict(argstr='--otsuPercentileThreshold %f', + ), + outputClippedVolumeROI=dict(argstr='--outputClippedVolumeROI %s', + hash_files=False, + ), + outputROIMaskVolume=dict(argstr='--outputROIMaskVolume %s', + hash_files=False, ), outputVolumePixelType=dict(argstr='--outputVolumePixelType %s', ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), thresholdCorrectionFactor=dict(argstr='--thresholdCorrectionFactor %f', ), - inputVolume=dict(argstr='--inputVolume %s', - ), - outputROIMaskVolume=dict(hash_files=False, - argstr='--outputROIMaskVolume %s', - ), ) inputs = BRAINSROIAuto.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_BRAINSROIAuto_outputs(): output_map = dict(outputClippedVolumeROI=dict(), outputROIMaskVolume=dict(), @@ -48,3 +50,4 @@ def test_BRAINSROIAuto_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/slicer/segmentation/tests/test_auto_EMSegmentCommandLine.py b/nipype/interfaces/slicer/segmentation/tests/test_auto_EMSegmentCommandLine.py index 9e6b407433..03052c4345 100644 --- a/nipype/interfaces/slicer/segmentation/tests/test_auto_EMSegmentCommandLine.py +++ b/nipype/interfaces/slicer/segmentation/tests/test_auto_EMSegmentCommandLine.py @@ -1,62 +1,63 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.slicer.segmentation.specialized import EMSegmentCommandLine + def test_EMSegmentCommandLine_inputs(): - input_map = dict(verbose=dict(argstr='--verbose ', - ), - resultMRMLSceneFileName=dict(hash_files=False, - argstr='--resultMRMLSceneFileName %s', + input_map = dict(args=dict(argstr='%s', ), - resultVolumeFileName=dict(hash_files=False, - argstr='--resultVolumeFileName %s', + atlasVolumeFileNames=dict(argstr='--atlasVolumeFileNames %s...', ), disableCompression=dict(argstr='--disableCompression ', ), - targetVolumeFileNames=dict(argstr='--targetVolumeFileNames %s...', + disableMultithreading=dict(argstr='--disableMultithreading %d', ), - atlasVolumeFileNames=dict(argstr='--atlasVolumeFileNames %s...', + dontUpdateIntermediateData=dict(argstr='--dontUpdateIntermediateData %d', ), - registrationPackage=dict(argstr='--registrationPackage %s', + dontWriteResults=dict(argstr='--dontWriteResults ', ), - taskPreProcessingSetting=dict(argstr='--taskPreProcessingSetting %s', + environ=dict(nohash=True, + usedefault=True, + ), + generateEmptyMRMLSceneAndQuit=dict(argstr='--generateEmptyMRMLSceneAndQuit %s', + hash_files=False, ), ignore_exception=dict(nohash=True, usedefault=True, ), - parametersMRMLNodeName=dict(argstr='--parametersMRMLNodeName %s', + intermediateResultsDirectory=dict(argstr='--intermediateResultsDirectory %s', ), - registrationDeformableType=dict(argstr='--registrationDeformableType %d', + keepTempFiles=dict(argstr='--keepTempFiles ', ), - args=dict(argstr='%s', + loadAtlasNonCentered=dict(argstr='--loadAtlasNonCentered ', ), - terminal_output=dict(mandatory=True, - nohash=True, + loadTargetCentered=dict(argstr='--loadTargetCentered ', ), - disableMultithreading=dict(argstr='--disableMultithreading %d', + mrmlSceneFileName=dict(argstr='--mrmlSceneFileName %s', ), - loadTargetCentered=dict(argstr='--loadTargetCentered ', + parametersMRMLNodeName=dict(argstr='--parametersMRMLNodeName %s', ), - generateEmptyMRMLSceneAndQuit=dict(hash_files=False, - argstr='--generateEmptyMRMLSceneAndQuit %s', + registrationAffineType=dict(argstr='--registrationAffineType %d', ), - keepTempFiles=dict(argstr='--keepTempFiles ', + registrationDeformableType=dict(argstr='--registrationDeformableType %d', ), - dontWriteResults=dict(argstr='--dontWriteResults ', + registrationPackage=dict(argstr='--registrationPackage %s', ), - registrationAffineType=dict(argstr='--registrationAffineType %d', + resultMRMLSceneFileName=dict(argstr='--resultMRMLSceneFileName %s', + hash_files=False, ), resultStandardVolumeFileName=dict(argstr='--resultStandardVolumeFileName %s', ), - dontUpdateIntermediateData=dict(argstr='--dontUpdateIntermediateData %d', + resultVolumeFileName=dict(argstr='--resultVolumeFileName %s', + hash_files=False, ), - environ=dict(nohash=True, - usedefault=True, + targetVolumeFileNames=dict(argstr='--targetVolumeFileNames %s...', ), - mrmlSceneFileName=dict(argstr='--mrmlSceneFileName %s', + taskPreProcessingSetting=dict(argstr='--taskPreProcessingSetting %s', ), - intermediateResultsDirectory=dict(argstr='--intermediateResultsDirectory %s', + terminal_output=dict(mandatory=True, + nohash=True, ), - loadAtlasNonCentered=dict(argstr='--loadAtlasNonCentered ', + verbose=dict(argstr='--verbose ', ), ) inputs = EMSegmentCommandLine.input_spec() @@ -64,6 +65,7 @@ def test_EMSegmentCommandLine_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_EMSegmentCommandLine_outputs(): output_map = dict(generateEmptyMRMLSceneAndQuit=dict(), resultMRMLSceneFileName=dict(), @@ -74,3 +76,4 @@ def test_EMSegmentCommandLine_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/slicer/segmentation/tests/test_auto_RobustStatisticsSegmenter.py b/nipype/interfaces/slicer/segmentation/tests/test_auto_RobustStatisticsSegmenter.py index de6d6ddd0e..a0d972de99 100644 --- a/nipype/interfaces/slicer/segmentation/tests/test_auto_RobustStatisticsSegmenter.py +++ b/nipype/interfaces/slicer/segmentation/tests/test_auto_RobustStatisticsSegmenter.py @@ -1,37 +1,38 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.slicer.segmentation.specialized import RobustStatisticsSegmenter + def test_RobustStatisticsSegmenter_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(args=dict(argstr='%s', + ), + curvatureWeight=dict(argstr='--curvatureWeight %f', ), - originalImageFileName=dict(position=-3, - argstr='%s', + environ=dict(nohash=True, + usedefault=True, ), expectedVolume=dict(argstr='--expectedVolume %f', ), - args=dict(argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - curvatureWeight=dict(argstr='--curvatureWeight %f', + intensityHomogeneity=dict(argstr='--intensityHomogeneity %f', ), - segmentedImageFileName=dict(position=-1, - hash_files=False, - argstr='%s', + labelImageFileName=dict(argstr='%s', + position=-2, ), labelValue=dict(argstr='--labelValue %d', ), - terminal_output=dict(mandatory=True, - nohash=True, - ), - environ=dict(nohash=True, - usedefault=True, + maxRunningTime=dict(argstr='--maxRunningTime %f', ), - labelImageFileName=dict(position=-2, - argstr='%s', + originalImageFileName=dict(argstr='%s', + position=-3, ), - intensityHomogeneity=dict(argstr='--intensityHomogeneity %f', + segmentedImageFileName=dict(argstr='%s', + hash_files=False, + position=-1, ), - maxRunningTime=dict(argstr='--maxRunningTime %f', + terminal_output=dict(mandatory=True, + nohash=True, ), ) inputs = RobustStatisticsSegmenter.input_spec() @@ -39,6 +40,7 @@ def test_RobustStatisticsSegmenter_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_RobustStatisticsSegmenter_outputs(): output_map = dict(segmentedImageFileName=dict(position=-1, ), @@ -48,3 +50,4 @@ def test_RobustStatisticsSegmenter_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/slicer/segmentation/tests/test_auto_SimpleRegionGrowingSegmentation.py b/nipype/interfaces/slicer/segmentation/tests/test_auto_SimpleRegionGrowingSegmentation.py index 87bc935d50..e0361ebb5d 100644 --- a/nipype/interfaces/slicer/segmentation/tests/test_auto_SimpleRegionGrowingSegmentation.py +++ b/nipype/interfaces/slicer/segmentation/tests/test_auto_SimpleRegionGrowingSegmentation.py @@ -1,45 +1,47 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.slicer.segmentation.simpleregiongrowingsegmentation import SimpleRegionGrowingSegmentation + def test_SimpleRegionGrowingSegmentation_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + environ=dict(nohash=True, usedefault=True, ), - outputVolume=dict(position=-1, - hash_files=False, - argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - neighborhood=dict(argstr='--neighborhood %d', + inputVolume=dict(argstr='%s', + position=-2, ), - timestep=dict(argstr='--timestep %f', - ), - args=dict(argstr='%s', + iterations=dict(argstr='--iterations %d', ), labelvalue=dict(argstr='--labelvalue %d', ), - smoothingIterations=dict(argstr='--smoothingIterations %d', - ), - seed=dict(argstr='--seed %s...', + multiplier=dict(argstr='--multiplier %f', ), - environ=dict(nohash=True, - usedefault=True, + neighborhood=dict(argstr='--neighborhood %d', ), - iterations=dict(argstr='--iterations %d', + outputVolume=dict(argstr='%s', + hash_files=False, + position=-1, ), - multiplier=dict(argstr='--multiplier %f', + seed=dict(argstr='--seed %s...', ), - inputVolume=dict(position=-2, - argstr='%s', + smoothingIterations=dict(argstr='--smoothingIterations %d', ), terminal_output=dict(mandatory=True, nohash=True, ), + timestep=dict(argstr='--timestep %f', + ), ) inputs = SimpleRegionGrowingSegmentation.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_SimpleRegionGrowingSegmentation_outputs(): output_map = dict(outputVolume=dict(position=-1, ), @@ -49,3 +51,4 @@ def test_SimpleRegionGrowingSegmentation_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/slicer/tests/test_auto_DicomToNrrdConverter.py b/nipype/interfaces/slicer/tests/test_auto_DicomToNrrdConverter.py index 6dda6e5c12..e83381b6a1 100644 --- a/nipype/interfaces/slicer/tests/test_auto_DicomToNrrdConverter.py +++ b/nipype/interfaces/slicer/tests/test_auto_DicomToNrrdConverter.py @@ -1,39 +1,41 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.slicer.converters import DicomToNrrdConverter + def test_DicomToNrrdConverter_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(args=dict(argstr='%s', ), - outputVolume=dict(argstr='--outputVolume %s', + environ=dict(nohash=True, + usedefault=True, ), - smallGradientThreshold=dict(argstr='--smallGradientThreshold %f', + ignore_exception=dict(nohash=True, + usedefault=True, ), inputDicomDirectory=dict(argstr='--inputDicomDirectory %s', ), - args=dict(argstr='%s', + outputDirectory=dict(argstr='--outputDirectory %s', + hash_files=False, ), - outputDirectory=dict(hash_files=False, - argstr='--outputDirectory %s', + outputVolume=dict(argstr='--outputVolume %s', + ), + smallGradientThreshold=dict(argstr='--smallGradientThreshold %f', ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), useBMatrixGradientDirections=dict(argstr='--useBMatrixGradientDirections ', ), - writeProtocolGradientsFile=dict(argstr='--writeProtocolGradientsFile ', - ), useIdentityMeaseurementFrame=dict(argstr='--useIdentityMeaseurementFrame ', ), + writeProtocolGradientsFile=dict(argstr='--writeProtocolGradientsFile ', + ), ) inputs = DicomToNrrdConverter.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_DicomToNrrdConverter_outputs(): output_map = dict(outputDirectory=dict(), ) @@ -42,3 +44,4 @@ def test_DicomToNrrdConverter_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/slicer/tests/test_auto_EMSegmentTransformToNewFormat.py b/nipype/interfaces/slicer/tests/test_auto_EMSegmentTransformToNewFormat.py index ad18cbf917..43e4f8e24c 100644 --- a/nipype/interfaces/slicer/tests/test_auto_EMSegmentTransformToNewFormat.py +++ b/nipype/interfaces/slicer/tests/test_auto_EMSegmentTransformToNewFormat.py @@ -1,31 +1,33 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.slicer.utilities import EMSegmentTransformToNewFormat + def test_EMSegmentTransformToNewFormat_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + environ=dict(nohash=True, usedefault=True, ), - args=dict(argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, ), inputMRMLFileName=dict(argstr='--inputMRMLFileName %s', ), + outputMRMLFileName=dict(argstr='--outputMRMLFileName %s', + hash_files=False, + ), templateFlag=dict(argstr='--templateFlag ', ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), - outputMRMLFileName=dict(hash_files=False, - argstr='--outputMRMLFileName %s', - ), ) inputs = EMSegmentTransformToNewFormat.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_EMSegmentTransformToNewFormat_outputs(): output_map = dict(outputMRMLFileName=dict(), ) @@ -34,3 +36,4 @@ def test_EMSegmentTransformToNewFormat_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/slicer/tests/test_auto_GrayscaleModelMaker.py b/nipype/interfaces/slicer/tests/test_auto_GrayscaleModelMaker.py index f426cf5948..f86ac81c8b 100644 --- a/nipype/interfaces/slicer/tests/test_auto_GrayscaleModelMaker.py +++ b/nipype/interfaces/slicer/tests/test_auto_GrayscaleModelMaker.py @@ -1,43 +1,45 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.slicer.surface import GrayscaleModelMaker + def test_GrayscaleModelMaker_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(InputVolume=dict(argstr='%s', + position=-2, + ), + OutputGeometry=dict(argstr='%s', + hash_files=False, + position=-1, + ), + args=dict(argstr='%s', + ), + decimate=dict(argstr='--decimate %f', + ), + environ=dict(nohash=True, usedefault=True, ), - name=dict(argstr='--name %s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - smooth=dict(argstr='--smooth %d', + name=dict(argstr='--name %s', ), pointnormals=dict(argstr='--pointnormals ', ), - args=dict(argstr='%s', + smooth=dict(argstr='--smooth %d', ), splitnormals=dict(argstr='--splitnormals ', ), - OutputGeometry=dict(position=-1, - hash_files=False, - argstr='%s', - ), - decimate=dict(argstr='--decimate %f', - ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), threshold=dict(argstr='--threshold %f', ), - InputVolume=dict(position=-2, - argstr='%s', - ), ) inputs = GrayscaleModelMaker.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_GrayscaleModelMaker_outputs(): output_map = dict(OutputGeometry=dict(position=-1, ), @@ -47,3 +49,4 @@ def test_GrayscaleModelMaker_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/slicer/tests/test_auto_LabelMapSmoothing.py b/nipype/interfaces/slicer/tests/test_auto_LabelMapSmoothing.py index 6f319e26af..e2d6c4b9fd 100644 --- a/nipype/interfaces/slicer/tests/test_auto_LabelMapSmoothing.py +++ b/nipype/interfaces/slicer/tests/test_auto_LabelMapSmoothing.py @@ -1,32 +1,33 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.slicer.surface import LabelMapSmoothing + def test_LabelMapSmoothing_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(args=dict(argstr='%s', ), - outputVolume=dict(position=-1, - hash_files=False, - argstr='%s', + environ=dict(nohash=True, + usedefault=True, ), - numberOfIterations=dict(argstr='--numberOfIterations %d', + gaussianSigma=dict(argstr='--gaussianSigma %f', ), - args=dict(argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - maxRMSError=dict(argstr='--maxRMSError %f', + inputVolume=dict(argstr='%s', + position=-2, ), - terminal_output=dict(mandatory=True, - nohash=True, + labelToSmooth=dict(argstr='--labelToSmooth %d', ), - environ=dict(nohash=True, - usedefault=True, + maxRMSError=dict(argstr='--maxRMSError %f', ), - labelToSmooth=dict(argstr='--labelToSmooth %d', + numberOfIterations=dict(argstr='--numberOfIterations %d', ), - inputVolume=dict(position=-2, - argstr='%s', + outputVolume=dict(argstr='%s', + hash_files=False, + position=-1, ), - gaussianSigma=dict(argstr='--gaussianSigma %f', + terminal_output=dict(mandatory=True, + nohash=True, ), ) inputs = LabelMapSmoothing.input_spec() @@ -34,6 +35,7 @@ def test_LabelMapSmoothing_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_LabelMapSmoothing_outputs(): output_map = dict(outputVolume=dict(position=-1, ), @@ -43,3 +45,4 @@ def test_LabelMapSmoothing_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/slicer/tests/test_auto_MergeModels.py b/nipype/interfaces/slicer/tests/test_auto_MergeModels.py index 3d84f09d3b..fd30b629a4 100644 --- a/nipype/interfaces/slicer/tests/test_auto_MergeModels.py +++ b/nipype/interfaces/slicer/tests/test_auto_MergeModels.py @@ -1,27 +1,28 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.slicer.surface import MergeModels + def test_MergeModels_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(Model1=dict(argstr='%s', + position=-3, ), - Model2=dict(position=-2, - argstr='%s', + Model2=dict(argstr='%s', + position=-2, ), - Model1=dict(position=-3, - argstr='%s', + ModelOutput=dict(argstr='%s', + hash_files=False, + position=-1, ), args=dict(argstr='%s', ), - terminal_output=dict(mandatory=True, - nohash=True, - ), environ=dict(nohash=True, usedefault=True, ), - ModelOutput=dict(position=-1, - hash_files=False, - argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, + ), + terminal_output=dict(mandatory=True, + nohash=True, ), ) inputs = MergeModels.input_spec() @@ -29,6 +30,7 @@ def test_MergeModels_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MergeModels_outputs(): output_map = dict(ModelOutput=dict(position=-1, ), @@ -38,3 +40,4 @@ def test_MergeModels_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/slicer/tests/test_auto_ModelMaker.py b/nipype/interfaces/slicer/tests/test_auto_ModelMaker.py index 78621e2717..38821dccd3 100644 --- a/nipype/interfaces/slicer/tests/test_auto_ModelMaker.py +++ b/nipype/interfaces/slicer/tests/test_auto_ModelMaker.py @@ -1,56 +1,57 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.slicer.surface import ModelMaker + def test_ModelMaker_inputs(): - input_map = dict(color=dict(argstr='--color %s', - ), - labels=dict(argstr='--labels %s', - sep=',', + input_map = dict(InputVolume=dict(argstr='%s', + position=-1, ), - jointsmooth=dict(argstr='--jointsmooth ', + args=dict(argstr='%s', ), - modelSceneFile=dict(hash_files=False, - argstr='--modelSceneFile %s...', + color=dict(argstr='--color %s', ), - InputVolume=dict(position=-1, - argstr='%s', + debug=dict(argstr='--debug ', ), - saveIntermediateModels=dict(argstr='--saveIntermediateModels ', + decimate=dict(argstr='--decimate %f', ), - skipUnNamed=dict(argstr='--skipUnNamed ', + end=dict(argstr='--end %d', ), - generateAll=dict(argstr='--generateAll ', + environ=dict(nohash=True, + usedefault=True, ), filtertype=dict(argstr='--filtertype %s', ), - start=dict(argstr='--start %d', - ), - pad=dict(argstr='--pad ', + generateAll=dict(argstr='--generateAll ', ), ignore_exception=dict(nohash=True, usedefault=True, ), - args=dict(argstr='%s', - ), - splitnormals=dict(argstr='--splitnormals ', + jointsmooth=dict(argstr='--jointsmooth ', ), - terminal_output=dict(mandatory=True, - nohash=True, + labels=dict(argstr='--labels %s', + sep=',', ), - end=dict(argstr='--end %d', + modelSceneFile=dict(argstr='--modelSceneFile %s...', + hash_files=False, ), name=dict(argstr='--name %s', ), + pad=dict(argstr='--pad ', + ), pointnormals=dict(argstr='--pointnormals ', ), + saveIntermediateModels=dict(argstr='--saveIntermediateModels ', + ), + skipUnNamed=dict(argstr='--skipUnNamed ', + ), smooth=dict(argstr='--smooth %d', ), - decimate=dict(argstr='--decimate %f', + splitnormals=dict(argstr='--splitnormals ', ), - environ=dict(nohash=True, - usedefault=True, + start=dict(argstr='--start %d', ), - debug=dict(argstr='--debug ', + terminal_output=dict(mandatory=True, + nohash=True, ), ) inputs = ModelMaker.input_spec() @@ -58,6 +59,7 @@ def test_ModelMaker_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ModelMaker_outputs(): output_map = dict(modelSceneFile=dict(exists=True, ), @@ -67,3 +69,4 @@ def test_ModelMaker_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/slicer/tests/test_auto_ModelToLabelMap.py b/nipype/interfaces/slicer/tests/test_auto_ModelToLabelMap.py index 344f28d4a6..4ed262e1ad 100644 --- a/nipype/interfaces/slicer/tests/test_auto_ModelToLabelMap.py +++ b/nipype/interfaces/slicer/tests/test_auto_ModelToLabelMap.py @@ -1,29 +1,30 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.slicer.surface import ModelToLabelMap + def test_ModelToLabelMap_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(InputVolume=dict(argstr='%s', + position=-3, ), - OutputVolume=dict(position=-1, + OutputVolume=dict(argstr='%s', hash_files=False, - argstr='%s', - ), - distance=dict(argstr='--distance %f', + position=-1, ), args=dict(argstr='%s', ), - surface=dict(position=-2, - argstr='%s', - ), - terminal_output=dict(mandatory=True, - nohash=True, + distance=dict(argstr='--distance %f', ), environ=dict(nohash=True, usedefault=True, ), - InputVolume=dict(position=-3, - argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, + ), + surface=dict(argstr='%s', + position=-2, + ), + terminal_output=dict(mandatory=True, + nohash=True, ), ) inputs = ModelToLabelMap.input_spec() @@ -31,6 +32,7 @@ def test_ModelToLabelMap_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ModelToLabelMap_outputs(): output_map = dict(OutputVolume=dict(position=-1, ), @@ -40,3 +42,4 @@ def test_ModelToLabelMap_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/slicer/tests/test_auto_OrientScalarVolume.py b/nipype/interfaces/slicer/tests/test_auto_OrientScalarVolume.py index 4e45902940..d2512a64e9 100644 --- a/nipype/interfaces/slicer/tests/test_auto_OrientScalarVolume.py +++ b/nipype/interfaces/slicer/tests/test_auto_OrientScalarVolume.py @@ -1,33 +1,35 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.slicer.converters import OrientScalarVolume + def test_OrientScalarVolume_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + environ=dict(nohash=True, usedefault=True, ), - outputVolume=dict(position=-1, - hash_files=False, - argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - args=dict(argstr='%s', + inputVolume1=dict(argstr='%s', + position=-2, ), orientation=dict(argstr='--orientation %s', ), - inputVolume1=dict(position=-2, - argstr='%s', + outputVolume=dict(argstr='%s', + hash_files=False, + position=-1, ), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), ) inputs = OrientScalarVolume.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_OrientScalarVolume_outputs(): output_map = dict(outputVolume=dict(position=-1, ), @@ -37,3 +39,4 @@ def test_OrientScalarVolume_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/slicer/tests/test_auto_ProbeVolumeWithModel.py b/nipype/interfaces/slicer/tests/test_auto_ProbeVolumeWithModel.py index 3aa0e57483..d3a20a40fc 100644 --- a/nipype/interfaces/slicer/tests/test_auto_ProbeVolumeWithModel.py +++ b/nipype/interfaces/slicer/tests/test_auto_ProbeVolumeWithModel.py @@ -1,27 +1,28 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.slicer.surface import ProbeVolumeWithModel + def test_ProbeVolumeWithModel_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(InputModel=dict(argstr='%s', + position=-2, ), - args=dict(argstr='%s', + InputVolume=dict(argstr='%s', + position=-3, ), - OutputModel=dict(position=-1, + OutputModel=dict(argstr='%s', hash_files=False, - argstr='%s', - ), - InputModel=dict(position=-2, - argstr='%s', + position=-1, ), - terminal_output=dict(mandatory=True, - nohash=True, + args=dict(argstr='%s', ), environ=dict(nohash=True, usedefault=True, ), - InputVolume=dict(position=-3, - argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, + ), + terminal_output=dict(mandatory=True, + nohash=True, ), ) inputs = ProbeVolumeWithModel.input_spec() @@ -29,6 +30,7 @@ def test_ProbeVolumeWithModel_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ProbeVolumeWithModel_outputs(): output_map = dict(OutputModel=dict(position=-1, ), @@ -38,3 +40,4 @@ def test_ProbeVolumeWithModel_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/slicer/tests/test_auto_SlicerCommandLine.py b/nipype/interfaces/slicer/tests/test_auto_SlicerCommandLine.py index b7f25b6393..3225ac99e5 100644 --- a/nipype/interfaces/slicer/tests/test_auto_SlicerCommandLine.py +++ b/nipype/interfaces/slicer/tests/test_auto_SlicerCommandLine.py @@ -1,17 +1,18 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.slicer.base import SlicerCommandLine + def test_SlicerCommandLine_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, - ), - terminal_output=dict(mandatory=True, - nohash=True, + input_map = dict(args=dict(argstr='%s', ), environ=dict(nohash=True, usedefault=True, ), - args=dict(argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, + ), + terminal_output=dict(mandatory=True, + nohash=True, ), ) inputs = SlicerCommandLine.input_spec() @@ -19,3 +20,4 @@ def test_SlicerCommandLine_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/spm/tests/test_auto_Analyze2nii.py b/nipype/interfaces/spm/tests/test_auto_Analyze2nii.py index d081957618..808a8ad374 100644 --- a/nipype/interfaces/spm/tests/test_auto_Analyze2nii.py +++ b/nipype/interfaces/spm/tests/test_auto_Analyze2nii.py @@ -1,42 +1,45 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.spm.utils import Analyze2nii + def test_Analyze2nii_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(analyze_file=dict(mandatory=True, + ), + ignore_exception=dict(nohash=True, usedefault=True, ), - analyze_file=dict(mandatory=True, + matlab_cmd=dict(), + mfile=dict(usedefault=True, ), paths=dict(), + use_mcr=dict(), use_v8struct=dict(min_ver='8', usedefault=True, ), - use_mcr=dict(), - matlab_cmd=dict(), - mfile=dict(usedefault=True, - ), ) inputs = Analyze2nii.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Analyze2nii_outputs(): output_map = dict(ignore_exception=dict(nohash=True, usedefault=True, ), - paths=dict(), - use_v8struct=dict(min_ver='8', - usedefault=True, - ), - use_mcr=dict(), matlab_cmd=dict(), mfile=dict(usedefault=True, ), nifti_file=dict(), + paths=dict(), + use_mcr=dict(), + use_v8struct=dict(min_ver='8', + usedefault=True, + ), ) outputs = Analyze2nii.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/spm/tests/test_auto_ApplyDeformations.py b/nipype/interfaces/spm/tests/test_auto_ApplyDeformations.py index 8233d78e75..caeeb179b8 100644 --- a/nipype/interfaces/spm/tests/test_auto_ApplyDeformations.py +++ b/nipype/interfaces/spm/tests/test_auto_ApplyDeformations.py @@ -1,35 +1,37 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.spm.preprocess import ApplyDeformations + def test_ApplyDeformations_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(deformation_field=dict(field='comp{1}.def', + mandatory=True, ), - paths=dict(), - use_v8struct=dict(min_ver='8', + ignore_exception=dict(nohash=True, usedefault=True, ), - interp=dict(field='interp', - ), in_files=dict(field='fnames', mandatory=True, ), - use_mcr=dict(), - deformation_field=dict(field='comp{1}.def', - mandatory=True, + interp=dict(field='interp', ), matlab_cmd=dict(), mfile=dict(usedefault=True, ), + paths=dict(), reference_volume=dict(field='comp{2}.id.space', mandatory=True, ), + use_mcr=dict(), + use_v8struct=dict(min_ver='8', + usedefault=True, + ), ) inputs = ApplyDeformations.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ApplyDeformations_outputs(): output_map = dict(out_files=dict(), ) @@ -38,3 +40,4 @@ def test_ApplyDeformations_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/spm/tests/test_auto_ApplyInverseDeformation.py b/nipype/interfaces/spm/tests/test_auto_ApplyInverseDeformation.py index b7bba72dd9..c7fe241ce8 100644 --- a/nipype/interfaces/spm/tests/test_auto_ApplyInverseDeformation.py +++ b/nipype/interfaces/spm/tests/test_auto_ApplyInverseDeformation.py @@ -1,34 +1,35 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.spm.utils import ApplyInverseDeformation + def test_ApplyInverseDeformation_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(bounding_box=dict(field='comp{1}.inv.comp{1}.sn2def.bb', ), - paths=dict(), - target=dict(field='comp{1}.inv.space', + deformation=dict(field='comp{1}.inv.comp{1}.sn2def.matname', + xor=['deformation_field'], ), - use_v8struct=dict(min_ver='8', + deformation_field=dict(field='comp{1}.inv.comp{1}.def', + xor=['deformation'], + ), + ignore_exception=dict(nohash=True, usedefault=True, ), - use_mcr=dict(), in_files=dict(field='fnames', mandatory=True, ), - voxel_sizes=dict(field='comp{1}.inv.comp{1}.sn2def.vox', - ), - bounding_box=dict(field='comp{1}.inv.comp{1}.sn2def.bb', + interpolation=dict(field='interp', ), matlab_cmd=dict(), mfile=dict(usedefault=True, ), - deformation_field=dict(field='comp{1}.inv.comp{1}.def', - xor=['deformation'], + paths=dict(), + target=dict(field='comp{1}.inv.space', ), - deformation=dict(field='comp{1}.inv.comp{1}.sn2def.matname', - xor=['deformation_field'], + use_mcr=dict(), + use_v8struct=dict(min_ver='8', + usedefault=True, ), - interpolation=dict(field='interp', + voxel_sizes=dict(field='comp{1}.inv.comp{1}.sn2def.vox', ), ) inputs = ApplyInverseDeformation.input_spec() @@ -36,6 +37,7 @@ def test_ApplyInverseDeformation_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ApplyInverseDeformation_outputs(): output_map = dict(out_files=dict(), ) @@ -44,3 +46,4 @@ def test_ApplyInverseDeformation_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/spm/tests/test_auto_ApplyTransform.py b/nipype/interfaces/spm/tests/test_auto_ApplyTransform.py index d5fc08e3da..c908dadd88 100644 --- a/nipype/interfaces/spm/tests/test_auto_ApplyTransform.py +++ b/nipype/interfaces/spm/tests/test_auto_ApplyTransform.py @@ -1,29 +1,31 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.spm.utils import ApplyTransform + def test_ApplyTransform_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, ), - paths=dict(), - mat=dict(mandatory=True, - ), - use_v8struct=dict(min_ver='8', - usedefault=True, - ), - use_mcr=dict(), - matlab_cmd=dict(), in_file=dict(copyfile=True, mandatory=True, ), + mat=dict(mandatory=True, + ), + matlab_cmd=dict(), mfile=dict(usedefault=True, ), + paths=dict(), + use_mcr=dict(), + use_v8struct=dict(min_ver='8', + usedefault=True, + ), ) inputs = ApplyTransform.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ApplyTransform_outputs(): output_map = dict(out_file=dict(), ) @@ -32,3 +34,4 @@ def test_ApplyTransform_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/spm/tests/test_auto_CalcCoregAffine.py b/nipype/interfaces/spm/tests/test_auto_CalcCoregAffine.py index 27e8a42141..325838471a 100644 --- a/nipype/interfaces/spm/tests/test_auto_CalcCoregAffine.py +++ b/nipype/interfaces/spm/tests/test_auto_CalcCoregAffine.py @@ -1,31 +1,33 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.spm.utils import CalcCoregAffine + def test_CalcCoregAffine_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, ), + invmat=dict(), + mat=dict(), + matlab_cmd=dict(), + mfile=dict(usedefault=True, + ), + moving=dict(copyfile=False, + mandatory=True, + ), paths=dict(), target=dict(mandatory=True, ), + use_mcr=dict(), use_v8struct=dict(min_ver='8', usedefault=True, ), - use_mcr=dict(), - moving=dict(copyfile=False, - mandatory=True, - ), - mfile=dict(usedefault=True, - ), - matlab_cmd=dict(), - invmat=dict(), - mat=dict(), ) inputs = CalcCoregAffine.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_CalcCoregAffine_outputs(): output_map = dict(invmat=dict(), mat=dict(), @@ -35,3 +37,4 @@ def test_CalcCoregAffine_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/spm/tests/test_auto_Coregister.py b/nipype/interfaces/spm/tests/test_auto_Coregister.py index ad96f63bbe..1e64bba9cc 100644 --- a/nipype/interfaces/spm/tests/test_auto_Coregister.py +++ b/nipype/interfaces/spm/tests/test_auto_Coregister.py @@ -1,47 +1,48 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.spm.preprocess import Coregister + def test_Coregister_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, - ), - paths=dict(), - write_mask=dict(field='roptions.mask', + input_map = dict(apply_to_files=dict(copyfile=True, + field='other', ), - write_wrap=dict(field='roptions.wrap', + cost_function=dict(field='eoptions.cost_fun', ), - write_interp=dict(field='roptions.interp', + fwhm=dict(field='eoptions.fwhm', ), - use_v8struct=dict(min_ver='8', + ignore_exception=dict(nohash=True, usedefault=True, ), - cost_function=dict(field='eoptions.cost_fun', + jobtype=dict(usedefault=True, + ), + matlab_cmd=dict(), + mfile=dict(usedefault=True, ), - use_mcr=dict(), out_prefix=dict(field='roptions.prefix', usedefault=True, ), + paths=dict(), + separation=dict(field='eoptions.sep', + ), source=dict(copyfile=True, - mandatory=True, field='source', + mandatory=True, ), - mfile=dict(usedefault=True, + target=dict(copyfile=False, + field='ref', + mandatory=True, ), - matlab_cmd=dict(), tolerance=dict(field='eoptions.tol', ), - separation=dict(field='eoptions.sep', - ), - apply_to_files=dict(copyfile=True, - field='other', + use_mcr=dict(), + use_v8struct=dict(min_ver='8', + usedefault=True, ), - fwhm=dict(field='eoptions.fwhm', + write_interp=dict(field='roptions.interp', ), - jobtype=dict(usedefault=True, + write_mask=dict(field='roptions.mask', ), - target=dict(copyfile=False, - mandatory=True, - field='ref', + write_wrap=dict(field='roptions.wrap', ), ) inputs = Coregister.input_spec() @@ -49,6 +50,7 @@ def test_Coregister_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Coregister_outputs(): output_map = dict(coregistered_files=dict(), coregistered_source=dict(), @@ -58,3 +60,4 @@ def test_Coregister_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/spm/tests/test_auto_CreateWarped.py b/nipype/interfaces/spm/tests/test_auto_CreateWarped.py index b6ff847e3a..c00bbc3bdc 100644 --- a/nipype/interfaces/spm/tests/test_auto_CreateWarped.py +++ b/nipype/interfaces/spm/tests/test_auto_CreateWarped.py @@ -1,36 +1,38 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.spm.preprocess import CreateWarped + def test_CreateWarped_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, - ), - paths=dict(), - mfile=dict(usedefault=True, - ), - image_files=dict(copyfile=False, + input_map = dict(flowfield_files=dict(copyfile=False, + field='crt_warped.flowfields', mandatory=True, - field='crt_warped.images', ), - use_v8struct=dict(min_ver='8', + ignore_exception=dict(nohash=True, usedefault=True, ), - flowfield_files=dict(copyfile=False, + image_files=dict(copyfile=False, + field='crt_warped.images', mandatory=True, - field='crt_warped.flowfields', ), interp=dict(field='crt_warped.interp', ), - use_mcr=dict(), - matlab_cmd=dict(), iterations=dict(field='crt_warped.K', ), + matlab_cmd=dict(), + mfile=dict(usedefault=True, + ), + paths=dict(), + use_mcr=dict(), + use_v8struct=dict(min_ver='8', + usedefault=True, + ), ) inputs = CreateWarped.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_CreateWarped_outputs(): output_map = dict(warped_files=dict(), ) @@ -39,3 +41,4 @@ def test_CreateWarped_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/spm/tests/test_auto_DARTEL.py b/nipype/interfaces/spm/tests/test_auto_DARTEL.py index c1d38205b4..4637f65556 100644 --- a/nipype/interfaces/spm/tests/test_auto_DARTEL.py +++ b/nipype/interfaces/spm/tests/test_auto_DARTEL.py @@ -1,44 +1,47 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.spm.preprocess import DARTEL + def test_DARTEL_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, ), - paths=dict(), - iteration_parameters=dict(field='warp.settings.param', - ), - use_v8struct=dict(min_ver='8', - usedefault=True, - ), - use_mcr=dict(), - template_prefix=dict(field='warp.settings.template', - usedefault=True, - ), image_files=dict(copyfile=False, - mandatory=True, field='warp.images', + mandatory=True, ), - matlab_cmd=dict(), - optimization_parameters=dict(field='warp.settings.optim', + iteration_parameters=dict(field='warp.settings.param', ), + matlab_cmd=dict(), mfile=dict(usedefault=True, ), + optimization_parameters=dict(field='warp.settings.optim', + ), + paths=dict(), regularization_form=dict(field='warp.settings.rform', ), + template_prefix=dict(field='warp.settings.template', + usedefault=True, + ), + use_mcr=dict(), + use_v8struct=dict(min_ver='8', + usedefault=True, + ), ) inputs = DARTEL.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_DARTEL_outputs(): output_map = dict(dartel_flow_fields=dict(), - template_files=dict(), final_template_file=dict(), + template_files=dict(), ) outputs = DARTEL.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/spm/tests/test_auto_DARTELNorm2MNI.py b/nipype/interfaces/spm/tests/test_auto_DARTELNorm2MNI.py index 9aa3f62713..80cce2b51f 100644 --- a/nipype/interfaces/spm/tests/test_auto_DARTELNorm2MNI.py +++ b/nipype/interfaces/spm/tests/test_auto_DARTELNorm2MNI.py @@ -1,36 +1,37 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.spm.preprocess import DARTELNorm2MNI + def test_DARTELNorm2MNI_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, - ), - paths=dict(), - voxel_size=dict(field='mni_norm.vox', - ), - template_file=dict(copyfile=False, + input_map = dict(apply_to_files=dict(copyfile=False, + field='mni_norm.data.subjs.images', mandatory=True, - field='mni_norm.template', ), - use_v8struct=dict(min_ver='8', - usedefault=True, + bounding_box=dict(field='mni_norm.bb', ), flowfield_files=dict(field='mni_norm.data.subjs.flowfields', mandatory=True, ), - use_mcr=dict(), - bounding_box=dict(field='mni_norm.bb', + fwhm=dict(field='mni_norm.fwhm', ), - mfile=dict(usedefault=True, + ignore_exception=dict(nohash=True, + usedefault=True, ), matlab_cmd=dict(), - apply_to_files=dict(copyfile=False, + mfile=dict(usedefault=True, + ), + modulate=dict(field='mni_norm.preserve', + ), + paths=dict(), + template_file=dict(copyfile=False, + field='mni_norm.template', mandatory=True, - field='mni_norm.data.subjs.images', ), - fwhm=dict(field='mni_norm.fwhm', + use_mcr=dict(), + use_v8struct=dict(min_ver='8', + usedefault=True, ), - modulate=dict(field='mni_norm.preserve', + voxel_size=dict(field='mni_norm.vox', ), ) inputs = DARTELNorm2MNI.input_spec() @@ -38,12 +39,14 @@ def test_DARTELNorm2MNI_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_DARTELNorm2MNI_outputs(): - output_map = dict(normalized_files=dict(), - normalization_parameter_file=dict(), + output_map = dict(normalization_parameter_file=dict(), + normalized_files=dict(), ) outputs = DARTELNorm2MNI.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/spm/tests/test_auto_DicomImport.py b/nipype/interfaces/spm/tests/test_auto_DicomImport.py index d86d9af485..6fe2bbc65a 100644 --- a/nipype/interfaces/spm/tests/test_auto_DicomImport.py +++ b/nipype/interfaces/spm/tests/test_auto_DicomImport.py @@ -1,32 +1,33 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.spm.utils import DicomImport + def test_DicomImport_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(format=dict(field='convopts.format', usedefault=True, ), - paths=dict(), - format=dict(field='convopts.format', + icedims=dict(field='convopts.icedims', usedefault=True, ), - use_v8struct=dict(min_ver='8', + ignore_exception=dict(nohash=True, usedefault=True, ), - use_mcr=dict(), in_files=dict(field='data', mandatory=True, ), - output_dir_struct=dict(field='root', - usedefault=True, + matlab_cmd=dict(), + mfile=dict(usedefault=True, ), - icedims=dict(field='convopts.icedims', + output_dir=dict(field='outdir', usedefault=True, ), - matlab_cmd=dict(), - output_dir=dict(field='outdir', + output_dir_struct=dict(field='root', usedefault=True, ), - mfile=dict(usedefault=True, + paths=dict(), + use_mcr=dict(), + use_v8struct=dict(min_ver='8', + usedefault=True, ), ) inputs = DicomImport.input_spec() @@ -34,6 +35,7 @@ def test_DicomImport_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_DicomImport_outputs(): output_map = dict(out_files=dict(), ) @@ -42,3 +44,4 @@ def test_DicomImport_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/spm/tests/test_auto_EstimateContrast.py b/nipype/interfaces/spm/tests/test_auto_EstimateContrast.py index fb15c55e22..e8eda5c50a 100644 --- a/nipype/interfaces/spm/tests/test_auto_EstimateContrast.py +++ b/nipype/interfaces/spm/tests/test_auto_EstimateContrast.py @@ -1,33 +1,34 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.spm.model import EstimateContrast + def test_EstimateContrast_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, - ), - paths=dict(), - spm_mat_file=dict(copyfile=True, + input_map = dict(beta_images=dict(copyfile=False, mandatory=True, - field='spmmat', ), - use_v8struct=dict(min_ver='8', + contrasts=dict(mandatory=True, + ), + group_contrast=dict(xor=['use_derivs'], + ), + ignore_exception=dict(nohash=True, usedefault=True, ), - use_derivs=dict(xor=['group_contrast'], + matlab_cmd=dict(), + mfile=dict(usedefault=True, ), - use_mcr=dict(), + paths=dict(), residual_image=dict(copyfile=False, mandatory=True, ), - beta_images=dict(copyfile=False, + spm_mat_file=dict(copyfile=True, + field='spmmat', mandatory=True, ), - mfile=dict(usedefault=True, - ), - contrasts=dict(mandatory=True, + use_derivs=dict(xor=['group_contrast'], ), - matlab_cmd=dict(), - group_contrast=dict(xor=['use_derivs'], + use_mcr=dict(), + use_v8struct=dict(min_ver='8', + usedefault=True, ), ) inputs = EstimateContrast.input_spec() @@ -35,15 +36,17 @@ def test_EstimateContrast_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_EstimateContrast_outputs(): - output_map = dict(spm_mat_file=dict(), - spmT_images=dict(), + output_map = dict(con_images=dict(), ess_images=dict(), spmF_images=dict(), - con_images=dict(), + spmT_images=dict(), + spm_mat_file=dict(), ) outputs = EstimateContrast.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/spm/tests/test_auto_EstimateModel.py b/nipype/interfaces/spm/tests/test_auto_EstimateModel.py index d561966925..bb4af3a99e 100644 --- a/nipype/interfaces/spm/tests/test_auto_EstimateModel.py +++ b/nipype/interfaces/spm/tests/test_auto_EstimateModel.py @@ -1,41 +1,44 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.spm.model import EstimateModel + def test_EstimateModel_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(estimation_method=dict(field='method', + mandatory=True, + ), + flags=dict(), + ignore_exception=dict(nohash=True, usedefault=True, ), + matlab_cmd=dict(), + mfile=dict(usedefault=True, + ), paths=dict(), spm_mat_file=dict(copyfile=True, - mandatory=True, field='spmmat', + mandatory=True, ), + use_mcr=dict(), use_v8struct=dict(min_ver='8', usedefault=True, ), - use_mcr=dict(), - estimation_method=dict(field='method', - mandatory=True, - ), - flags=dict(), - mfile=dict(usedefault=True, - ), - matlab_cmd=dict(), ) inputs = EstimateModel.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_EstimateModel_outputs(): - output_map = dict(residual_image=dict(), - spm_mat_file=dict(), - RPVimage=dict(), - mask_image=dict(), + output_map = dict(RPVimage=dict(), beta_images=dict(), + mask_image=dict(), + residual_image=dict(), + spm_mat_file=dict(), ) outputs = EstimateModel.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/spm/tests/test_auto_FactorialDesign.py b/nipype/interfaces/spm/tests/test_auto_FactorialDesign.py index 84e75dee06..9dd4b77790 100644 --- a/nipype/interfaces/spm/tests/test_auto_FactorialDesign.py +++ b/nipype/interfaces/spm/tests/test_auto_FactorialDesign.py @@ -1,47 +1,48 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.spm.model import FactorialDesign + def test_FactorialDesign_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(covariates=dict(field='cov', ), - paths=dict(), - use_implicit_threshold=dict(field='masking.im', + explicit_mask_file=dict(field='masking.em', ), global_calc_mean=dict(field='globalc.g_mean', xor=['global_calc_omit', 'global_calc_values'], ), - use_v8struct=dict(min_ver='8', - usedefault=True, - ), - threshold_mask_absolute=dict(field='masking.tm.tma.athresh', - xor=['threshold_mask_none', 'threshold_mask_relative'], - ), - use_mcr=dict(), - threshold_mask_none=dict(field='masking.tm.tm_none', - xor=['threshold_mask_absolute', 'threshold_mask_relative'], - ), - covariates=dict(field='cov', - ), global_calc_omit=dict(field='globalc.g_omit', xor=['global_calc_mean', 'global_calc_values'], ), - matlab_cmd=dict(), global_calc_values=dict(field='globalc.g_user.global_uval', xor=['global_calc_mean', 'global_calc_omit'], ), + global_normalization=dict(field='globalm.glonorm', + ), + ignore_exception=dict(nohash=True, + usedefault=True, + ), + matlab_cmd=dict(), mfile=dict(usedefault=True, ), no_grand_mean_scaling=dict(field='globalm.gmsca.gmsca_no', ), - explicit_mask_file=dict(field='masking.em', + paths=dict(), + spm_mat_dir=dict(field='dir', + ), + threshold_mask_absolute=dict(field='masking.tm.tma.athresh', + xor=['threshold_mask_none', 'threshold_mask_relative'], + ), + threshold_mask_none=dict(field='masking.tm.tm_none', + xor=['threshold_mask_absolute', 'threshold_mask_relative'], ), threshold_mask_relative=dict(field='masking.tm.tmr.rthresh', xor=['threshold_mask_absolute', 'threshold_mask_none'], ), - spm_mat_dir=dict(field='dir', + use_implicit_threshold=dict(field='masking.im', ), - global_normalization=dict(field='globalm.glonorm', + use_mcr=dict(), + use_v8struct=dict(min_ver='8', + usedefault=True, ), ) inputs = FactorialDesign.input_spec() @@ -49,6 +50,7 @@ def test_FactorialDesign_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_FactorialDesign_outputs(): output_map = dict(spm_mat_file=dict(), ) @@ -57,3 +59,4 @@ def test_FactorialDesign_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/spm/tests/test_auto_Level1Design.py b/nipype/interfaces/spm/tests/test_auto_Level1Design.py index 724bb1eca0..d5086b728c 100644 --- a/nipype/interfaces/spm/tests/test_auto_Level1Design.py +++ b/nipype/interfaces/spm/tests/test_auto_Level1Design.py @@ -1,54 +1,56 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.spm.model import Level1Design + def test_Level1Design_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(bases=dict(field='bases', + mandatory=True, + ), + factor_info=dict(field='fact', ), - paths=dict(), global_intensity_normalization=dict(field='global', ), + ignore_exception=dict(nohash=True, + usedefault=True, + ), + interscan_interval=dict(field='timing.RT', + mandatory=True, + ), mask_image=dict(field='mask', ), mask_threshold=dict(usedefault=True, ), - session_info=dict(field='sess', - mandatory=True, + matlab_cmd=dict(), + mfile=dict(usedefault=True, + ), + microtime_onset=dict(field='timing.fmri_t0', ), microtime_resolution=dict(field='timing.fmri_t', ), - use_v8struct=dict(min_ver='8', - usedefault=True, + model_serial_correlations=dict(field='cvi', ), - use_mcr=dict(), - interscan_interval=dict(field='timing.RT', + paths=dict(), + session_info=dict(field='sess', mandatory=True, ), + spm_mat_dir=dict(field='dir', + ), timing_units=dict(field='timing.units', mandatory=True, ), - factor_info=dict(field='fact', + use_mcr=dict(), + use_v8struct=dict(min_ver='8', + usedefault=True, ), volterra_expansion_order=dict(field='volt', ), - bases=dict(field='bases', - mandatory=True, - ), - mfile=dict(usedefault=True, - ), - model_serial_correlations=dict(field='cvi', - ), - microtime_onset=dict(field='timing.fmri_t0', - ), - matlab_cmd=dict(), - spm_mat_dir=dict(field='dir', - ), ) inputs = Level1Design.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Level1Design_outputs(): output_map = dict(spm_mat_file=dict(), ) @@ -57,3 +59,4 @@ def test_Level1Design_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/spm/tests/test_auto_MultipleRegressionDesign.py b/nipype/interfaces/spm/tests/test_auto_MultipleRegressionDesign.py index 3141af0491..b200958cdd 100644 --- a/nipype/interfaces/spm/tests/test_auto_MultipleRegressionDesign.py +++ b/nipype/interfaces/spm/tests/test_auto_MultipleRegressionDesign.py @@ -1,55 +1,56 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.spm.model import MultipleRegressionDesign + def test_MultipleRegressionDesign_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(covariates=dict(field='cov', ), - paths=dict(), - use_implicit_threshold=dict(field='masking.im', + explicit_mask_file=dict(field='masking.em', ), global_calc_mean=dict(field='globalc.g_mean', xor=['global_calc_omit', 'global_calc_values'], ), - use_v8struct=dict(min_ver='8', - usedefault=True, + global_calc_omit=dict(field='globalc.g_omit', + xor=['global_calc_mean', 'global_calc_values'], ), - include_intercept=dict(field='des.mreg.incint', - usedefault=True, + global_calc_values=dict(field='globalc.g_user.global_uval', + xor=['global_calc_mean', 'global_calc_omit'], ), - threshold_mask_absolute=dict(field='masking.tm.tma.athresh', - xor=['threshold_mask_none', 'threshold_mask_relative'], + global_normalization=dict(field='globalm.glonorm', ), - use_mcr=dict(), - threshold_mask_none=dict(field='masking.tm.tm_none', - xor=['threshold_mask_absolute', 'threshold_mask_relative'], + ignore_exception=dict(nohash=True, + usedefault=True, ), in_files=dict(field='des.mreg.scans', mandatory=True, ), - global_calc_omit=dict(field='globalc.g_omit', - xor=['global_calc_mean', 'global_calc_values'], + include_intercept=dict(field='des.mreg.incint', + usedefault=True, ), matlab_cmd=dict(), - global_calc_values=dict(field='globalc.g_user.global_uval', - xor=['global_calc_mean', 'global_calc_omit'], - ), mfile=dict(usedefault=True, ), no_grand_mean_scaling=dict(field='globalm.gmsca.gmsca_no', ), + paths=dict(), spm_mat_dir=dict(field='dir', ), - covariates=dict(field='cov', + threshold_mask_absolute=dict(field='masking.tm.tma.athresh', + xor=['threshold_mask_none', 'threshold_mask_relative'], + ), + threshold_mask_none=dict(field='masking.tm.tm_none', + xor=['threshold_mask_absolute', 'threshold_mask_relative'], ), threshold_mask_relative=dict(field='masking.tm.tmr.rthresh', xor=['threshold_mask_absolute', 'threshold_mask_none'], ), - explicit_mask_file=dict(field='masking.em', + use_implicit_threshold=dict(field='masking.im', ), - user_covariates=dict(field='des.mreg.mcov', + use_mcr=dict(), + use_v8struct=dict(min_ver='8', + usedefault=True, ), - global_normalization=dict(field='globalm.glonorm', + user_covariates=dict(field='des.mreg.mcov', ), ) inputs = MultipleRegressionDesign.input_spec() @@ -57,6 +58,7 @@ def test_MultipleRegressionDesign_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MultipleRegressionDesign_outputs(): output_map = dict(spm_mat_file=dict(), ) @@ -65,3 +67,4 @@ def test_MultipleRegressionDesign_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/spm/tests/test_auto_NewSegment.py b/nipype/interfaces/spm/tests/test_auto_NewSegment.py index 3753aa2e82..051b92695f 100644 --- a/nipype/interfaces/spm/tests/test_auto_NewSegment.py +++ b/nipype/interfaces/spm/tests/test_auto_NewSegment.py @@ -1,33 +1,34 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.spm.preprocess import NewSegment + def test_NewSegment_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(affine_regularization=dict(field='warp.affreg', + ), + channel_files=dict(copyfile=False, + field='channel', + mandatory=True, + ), + channel_info=dict(field='channel', + ), + ignore_exception=dict(nohash=True, usedefault=True, ), + matlab_cmd=dict(), + mfile=dict(usedefault=True, + ), paths=dict(), - write_deformation_fields=dict(field='warp.write', + sampling_distance=dict(field='warp.samp', ), tissues=dict(field='tissue', ), - sampling_distance=dict(field='warp.samp', - ), + use_mcr=dict(), use_v8struct=dict(min_ver='8', usedefault=True, ), warping_regularization=dict(field='warp.reg', ), - use_mcr=dict(), - affine_regularization=dict(field='warp.affreg', - ), - channel_files=dict(copyfile=False, - mandatory=True, - field='channel', - ), - mfile=dict(usedefault=True, - ), - matlab_cmd=dict(), - channel_info=dict(field='channel', + write_deformation_fields=dict(field='warp.write', ), ) inputs = NewSegment.input_spec() @@ -35,19 +36,21 @@ def test_NewSegment_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_NewSegment_outputs(): - output_map = dict(modulated_class_images=dict(), - normalized_class_images=dict(), + output_map = dict(bias_corrected_images=dict(), bias_field_images=dict(), - bias_corrected_images=dict(), - inverse_deformation_field=dict(), dartel_input_images=dict(), - transformation_mat=dict(), - native_class_images=dict(), forward_deformation_field=dict(), + inverse_deformation_field=dict(), + modulated_class_images=dict(), + native_class_images=dict(), + normalized_class_images=dict(), + transformation_mat=dict(), ) outputs = NewSegment.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/spm/tests/test_auto_Normalize.py b/nipype/interfaces/spm/tests/test_auto_Normalize.py index c8cc4913be..5eda31f292 100644 --- a/nipype/interfaces/spm/tests/test_auto_Normalize.py +++ b/nipype/interfaces/spm/tests/test_auto_Normalize.py @@ -1,68 +1,69 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.spm.preprocess import Normalize + def test_Normalize_inputs(): - input_map = dict(write_interp=dict(field='roptions.interp', + input_map = dict(DCT_period_cutoff=dict(field='eoptions.cutoff', ), - use_v8struct=dict(min_ver='8', - usedefault=True, + affine_regularization_type=dict(field='eoptions.regype', ), - write_voxel_sizes=dict(field='roptions.vox', + apply_to_files=dict(copyfile=True, + field='subj.resample', ), - write_bounding_box=dict(field='roptions.bb', + ignore_exception=dict(nohash=True, + usedefault=True, + ), + jobtype=dict(usedefault=True, ), matlab_cmd=dict(), - write_wrap=dict(field='roptions.wrap', + mfile=dict(usedefault=True, + ), + nonlinear_iterations=dict(field='eoptions.nits', + ), + nonlinear_regularization=dict(field='eoptions.reg', + ), + out_prefix=dict(field='roptions.prefix', + usedefault=True, ), parameter_file=dict(copyfile=False, - xor=['source', 'template'], field='subj.matname', mandatory=True, + xor=['source', 'template'], ), paths=dict(), - nonlinear_iterations=dict(field='eoptions.nits', - ), source=dict(copyfile=True, - xor=['parameter_file'], field='subj.source', mandatory=True, - ), - template=dict(copyfile=False, xor=['parameter_file'], - field='eoptions.template', - mandatory=True, ), source_image_smoothing=dict(field='eoptions.smosrc', ), source_weight=dict(copyfile=False, field='subj.wtsrc', ), - ignore_exception=dict(nohash=True, - usedefault=True, - ), - mfile=dict(usedefault=True, - ), - write_preserve=dict(field='roptions.preserve', + template=dict(copyfile=False, + field='eoptions.template', + mandatory=True, + xor=['parameter_file'], ), - affine_regularization_type=dict(field='eoptions.regype', + template_image_smoothing=dict(field='eoptions.smoref', ), - out_prefix=dict(field='roptions.prefix', - usedefault=True, + template_weight=dict(copyfile=False, + field='eoptions.weight', ), use_mcr=dict(), - DCT_period_cutoff=dict(field='eoptions.cutoff', + use_v8struct=dict(min_ver='8', + usedefault=True, ), - nonlinear_regularization=dict(field='eoptions.reg', + write_bounding_box=dict(field='roptions.bb', ), - apply_to_files=dict(copyfile=True, - field='subj.resample', + write_interp=dict(field='roptions.interp', ), - template_weight=dict(copyfile=False, - field='eoptions.weight', + write_preserve=dict(field='roptions.preserve', ), - template_image_smoothing=dict(field='eoptions.smoref', + write_voxel_sizes=dict(field='roptions.vox', ), - jobtype=dict(usedefault=True, + write_wrap=dict(field='roptions.wrap', ), ) inputs = Normalize.input_spec() @@ -70,13 +71,15 @@ def test_Normalize_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Normalize_outputs(): - output_map = dict(normalized_source=dict(), + output_map = dict(normalization_parameters=dict(), normalized_files=dict(), - normalization_parameters=dict(), + normalized_source=dict(), ) outputs = Normalize.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/spm/tests/test_auto_OneSampleTTestDesign.py b/nipype/interfaces/spm/tests/test_auto_OneSampleTTestDesign.py index 9532355ff7..6ff8bdc031 100644 --- a/nipype/interfaces/spm/tests/test_auto_OneSampleTTestDesign.py +++ b/nipype/interfaces/spm/tests/test_auto_OneSampleTTestDesign.py @@ -1,50 +1,51 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.spm.model import OneSampleTTestDesign + def test_OneSampleTTestDesign_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(covariates=dict(field='cov', ), - paths=dict(), - use_implicit_threshold=dict(field='masking.im', + explicit_mask_file=dict(field='masking.em', ), global_calc_mean=dict(field='globalc.g_mean', xor=['global_calc_omit', 'global_calc_values'], ), - use_v8struct=dict(min_ver='8', - usedefault=True, + global_calc_omit=dict(field='globalc.g_omit', + xor=['global_calc_mean', 'global_calc_values'], ), - threshold_mask_absolute=dict(field='masking.tm.tma.athresh', - xor=['threshold_mask_none', 'threshold_mask_relative'], + global_calc_values=dict(field='globalc.g_user.global_uval', + xor=['global_calc_mean', 'global_calc_omit'], ), - use_mcr=dict(), - threshold_mask_none=dict(field='masking.tm.tm_none', - xor=['threshold_mask_absolute', 'threshold_mask_relative'], + global_normalization=dict(field='globalm.glonorm', + ), + ignore_exception=dict(nohash=True, + usedefault=True, ), in_files=dict(field='des.t1.scans', mandatory=True, ), - global_calc_omit=dict(field='globalc.g_omit', - xor=['global_calc_mean', 'global_calc_values'], - ), matlab_cmd=dict(), - global_calc_values=dict(field='globalc.g_user.global_uval', - xor=['global_calc_mean', 'global_calc_omit'], - ), mfile=dict(usedefault=True, ), no_grand_mean_scaling=dict(field='globalm.gmsca.gmsca_no', ), - explicit_mask_file=dict(field='masking.em', + paths=dict(), + spm_mat_dir=dict(field='dir', + ), + threshold_mask_absolute=dict(field='masking.tm.tma.athresh', + xor=['threshold_mask_none', 'threshold_mask_relative'], ), - covariates=dict(field='cov', + threshold_mask_none=dict(field='masking.tm.tm_none', + xor=['threshold_mask_absolute', 'threshold_mask_relative'], ), threshold_mask_relative=dict(field='masking.tm.tmr.rthresh', xor=['threshold_mask_absolute', 'threshold_mask_none'], ), - spm_mat_dir=dict(field='dir', + use_implicit_threshold=dict(field='masking.im', ), - global_normalization=dict(field='globalm.glonorm', + use_mcr=dict(), + use_v8struct=dict(min_ver='8', + usedefault=True, ), ) inputs = OneSampleTTestDesign.input_spec() @@ -52,6 +53,7 @@ def test_OneSampleTTestDesign_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_OneSampleTTestDesign_outputs(): output_map = dict(spm_mat_file=dict(), ) @@ -60,3 +62,4 @@ def test_OneSampleTTestDesign_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/spm/tests/test_auto_PairedTTestDesign.py b/nipype/interfaces/spm/tests/test_auto_PairedTTestDesign.py index cf77fdf0d9..71045cccdf 100644 --- a/nipype/interfaces/spm/tests/test_auto_PairedTTestDesign.py +++ b/nipype/interfaces/spm/tests/test_auto_PairedTTestDesign.py @@ -1,54 +1,55 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.spm.model import PairedTTestDesign + def test_PairedTTestDesign_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(ancova=dict(field='des.pt.ancova', ), - paths=dict(), - use_implicit_threshold=dict(field='masking.im', + covariates=dict(field='cov', ), - no_grand_mean_scaling=dict(field='globalm.gmsca.gmsca_no', + explicit_mask_file=dict(field='masking.em', ), global_calc_mean=dict(field='globalc.g_mean', xor=['global_calc_omit', 'global_calc_values'], ), - use_v8struct=dict(min_ver='8', - usedefault=True, - ), - ancova=dict(field='des.pt.ancova', - ), - threshold_mask_absolute=dict(field='masking.tm.tma.athresh', - xor=['threshold_mask_none', 'threshold_mask_relative'], - ), - use_mcr=dict(), - threshold_mask_none=dict(field='masking.tm.tm_none', - xor=['threshold_mask_absolute', 'threshold_mask_relative'], - ), - covariates=dict(field='cov', - ), global_calc_omit=dict(field='globalc.g_omit', xor=['global_calc_mean', 'global_calc_values'], ), - matlab_cmd=dict(), global_calc_values=dict(field='globalc.g_user.global_uval', xor=['global_calc_mean', 'global_calc_omit'], ), + global_normalization=dict(field='globalm.glonorm', + ), + grand_mean_scaling=dict(field='des.pt.gmsca', + ), + ignore_exception=dict(nohash=True, + usedefault=True, + ), + matlab_cmd=dict(), mfile=dict(usedefault=True, ), + no_grand_mean_scaling=dict(field='globalm.gmsca.gmsca_no', + ), paired_files=dict(field='des.pt.pair', mandatory=True, ), - explicit_mask_file=dict(field='masking.em', + paths=dict(), + spm_mat_dir=dict(field='dir', + ), + threshold_mask_absolute=dict(field='masking.tm.tma.athresh', + xor=['threshold_mask_none', 'threshold_mask_relative'], + ), + threshold_mask_none=dict(field='masking.tm.tm_none', + xor=['threshold_mask_absolute', 'threshold_mask_relative'], ), threshold_mask_relative=dict(field='masking.tm.tmr.rthresh', xor=['threshold_mask_absolute', 'threshold_mask_none'], ), - spm_mat_dir=dict(field='dir', - ), - grand_mean_scaling=dict(field='des.pt.gmsca', + use_implicit_threshold=dict(field='masking.im', ), - global_normalization=dict(field='globalm.glonorm', + use_mcr=dict(), + use_v8struct=dict(min_ver='8', + usedefault=True, ), ) inputs = PairedTTestDesign.input_spec() @@ -56,6 +57,7 @@ def test_PairedTTestDesign_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_PairedTTestDesign_outputs(): output_map = dict(spm_mat_file=dict(), ) @@ -64,3 +66,4 @@ def test_PairedTTestDesign_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/spm/tests/test_auto_Realign.py b/nipype/interfaces/spm/tests/test_auto_Realign.py index 4b90565ff9..9fdf39973d 100644 --- a/nipype/interfaces/spm/tests/test_auto_Realign.py +++ b/nipype/interfaces/spm/tests/test_auto_Realign.py @@ -1,53 +1,54 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.spm.preprocess import Realign + def test_Realign_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(fwhm=dict(field='eoptions.fwhm', ), - paths=dict(), - write_mask=dict(field='roptions.mask', + ignore_exception=dict(nohash=True, + usedefault=True, ), - register_to_mean=dict(field='eoptions.rtm', + in_files=dict(copyfile=True, + field='data', mandatory=True, - usedefault=True, ), - weight_img=dict(field='eoptions.weight', + interp=dict(field='eoptions.interp', ), - write_wrap=dict(field='roptions.wrap', + jobtype=dict(usedefault=True, ), - write_interp=dict(field='roptions.interp', + matlab_cmd=dict(), + mfile=dict(usedefault=True, ), - use_v8struct=dict(min_ver='8', + out_prefix=dict(field='roptions.prefix', usedefault=True, ), - interp=dict(field='eoptions.interp', + paths=dict(), + quality=dict(field='eoptions.quality', ), - out_prefix=dict(field='roptions.prefix', + register_to_mean=dict(field='eoptions.rtm', + mandatory=True, usedefault=True, ), + separation=dict(field='eoptions.sep', + ), use_mcr=dict(), - write_which=dict(minlen=2, - maxlen=2, - field='roptions.which', + use_v8struct=dict(min_ver='8', usedefault=True, ), - mfile=dict(usedefault=True, - ), - matlab_cmd=dict(), - jobtype=dict(usedefault=True, - ), - separation=dict(field='eoptions.sep', + weight_img=dict(field='eoptions.weight', ), wrap=dict(field='eoptions.wrap', ), - quality=dict(field='eoptions.quality', + write_interp=dict(field='roptions.interp', ), - fwhm=dict(field='eoptions.fwhm', + write_mask=dict(field='roptions.mask', ), - in_files=dict(copyfile=True, - mandatory=True, - field='data', + write_which=dict(field='roptions.which', + maxlen=2, + minlen=2, + usedefault=True, + ), + write_wrap=dict(field='roptions.wrap', ), ) inputs = Realign.input_spec() @@ -55,14 +56,16 @@ def test_Realign_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Realign_outputs(): - output_map = dict(realignment_parameters=dict(), + output_map = dict(mean_image=dict(), modified_in_files=dict(), realigned_files=dict(), - mean_image=dict(), + realignment_parameters=dict(), ) outputs = Realign.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/spm/tests/test_auto_Reslice.py b/nipype/interfaces/spm/tests/test_auto_Reslice.py index 70903441f4..79dbd7a095 100644 --- a/nipype/interfaces/spm/tests/test_auto_Reslice.py +++ b/nipype/interfaces/spm/tests/test_auto_Reslice.py @@ -1,31 +1,33 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.spm.utils import Reslice + def test_Reslice_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, ), - paths=dict(), - out_file=dict(), - use_v8struct=dict(min_ver='8', - usedefault=True, + in_file=dict(mandatory=True, ), interp=dict(usedefault=True, ), - use_mcr=dict(), matlab_cmd=dict(), - in_file=dict(mandatory=True, - ), mfile=dict(usedefault=True, ), + out_file=dict(), + paths=dict(), space_defining=dict(mandatory=True, ), + use_mcr=dict(), + use_v8struct=dict(min_ver='8', + usedefault=True, + ), ) inputs = Reslice.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Reslice_outputs(): output_map = dict(out_file=dict(), ) @@ -34,3 +36,4 @@ def test_Reslice_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/spm/tests/test_auto_ResliceToReference.py b/nipype/interfaces/spm/tests/test_auto_ResliceToReference.py index 9a94e069fc..a79e81bd71 100644 --- a/nipype/interfaces/spm/tests/test_auto_ResliceToReference.py +++ b/nipype/interfaces/spm/tests/test_auto_ResliceToReference.py @@ -1,28 +1,29 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.spm.utils import ResliceToReference + def test_ResliceToReference_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, - ), - paths=dict(), - target=dict(field='comp{1}.id.space', + input_map = dict(bounding_box=dict(field='comp{2}.idbbvox.bb', ), - use_v8struct=dict(min_ver='8', + ignore_exception=dict(nohash=True, usedefault=True, ), - use_mcr=dict(), in_files=dict(field='fnames', mandatory=True, ), - voxel_sizes=dict(field='comp{2}.idbbvox.vox', - ), - bounding_box=dict(field='comp{2}.idbbvox.bb', + interpolation=dict(field='interp', ), matlab_cmd=dict(), mfile=dict(usedefault=True, ), - interpolation=dict(field='interp', + paths=dict(), + target=dict(field='comp{1}.id.space', + ), + use_mcr=dict(), + use_v8struct=dict(min_ver='8', + usedefault=True, + ), + voxel_sizes=dict(field='comp{2}.idbbvox.vox', ), ) inputs = ResliceToReference.input_spec() @@ -30,6 +31,7 @@ def test_ResliceToReference_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ResliceToReference_outputs(): output_map = dict(out_files=dict(), ) @@ -38,3 +40,4 @@ def test_ResliceToReference_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/spm/tests/test_auto_SPMCommand.py b/nipype/interfaces/spm/tests/test_auto_SPMCommand.py index 9bfe27d5fc..105fe06fec 100644 --- a/nipype/interfaces/spm/tests/test_auto_SPMCommand.py +++ b/nipype/interfaces/spm/tests/test_auto_SPMCommand.py @@ -1,21 +1,23 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.spm.base import SPMCommand + def test_SPMCommand_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, ), + matlab_cmd=dict(), + mfile=dict(usedefault=True, + ), paths=dict(), + use_mcr=dict(), use_v8struct=dict(min_ver='8', usedefault=True, ), - use_mcr=dict(), - matlab_cmd=dict(), - mfile=dict(usedefault=True, - ), ) inputs = SPMCommand.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/spm/tests/test_auto_Segment.py b/nipype/interfaces/spm/tests/test_auto_Segment.py index b3b0744702..022fa279c1 100644 --- a/nipype/interfaces/spm/tests/test_auto_Segment.py +++ b/nipype/interfaces/spm/tests/test_auto_Segment.py @@ -1,49 +1,50 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.spm.preprocess import Segment + def test_Segment_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, - ), - paths=dict(), - clean_masks=dict(field='output.cleanup', + input_map = dict(affine_regularization=dict(field='opts.regtype', ), bias_fwhm=dict(field='opts.biasfwhm', ), - mask_image=dict(field='opts.msk', - ), bias_regularization=dict(field='opts.biasreg', ), - warp_frequency_cutoff=dict(field='opts.warpco', + clean_masks=dict(field='output.cleanup', ), - affine_regularization=dict(field='opts.regtype', + csf_output_type=dict(field='output.CSF', ), - use_v8struct=dict(min_ver='8', - usedefault=True, + data=dict(copyfile=False, + field='data', + mandatory=True, ), - warping_regularization=dict(field='opts.warpreg', + gaussians_per_class=dict(field='opts.ngaus', ), - use_mcr=dict(), gm_output_type=dict(field='output.GM', ), - tissue_prob_maps=dict(field='opts.tpm', + ignore_exception=dict(nohash=True, + usedefault=True, ), - sampling_distance=dict(field='opts.samp', + mask_image=dict(field='opts.msk', ), matlab_cmd=dict(), - gaussians_per_class=dict(field='opts.ngaus', - ), mfile=dict(usedefault=True, ), + paths=dict(), + sampling_distance=dict(field='opts.samp', + ), save_bias_corrected=dict(field='output.biascor', ), - data=dict(copyfile=False, - mandatory=True, - field='data', + tissue_prob_maps=dict(field='opts.tpm', ), - wm_output_type=dict(field='output.WM', + use_mcr=dict(), + use_v8struct=dict(min_ver='8', + usedefault=True, ), - csf_output_type=dict(field='output.CSF', + warp_frequency_cutoff=dict(field='opts.warpco', + ), + warping_regularization=dict(field='opts.warpreg', + ), + wm_output_type=dict(field='output.WM', ), ) inputs = Segment.input_spec() @@ -51,25 +52,27 @@ def test_Segment_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Segment_outputs(): output_map = dict(bias_corrected_image=dict(), - native_csf_image=dict(), - normalized_wm_image=dict(), - modulated_wm_image=dict(), - modulated_input_image=dict(new_name='bias_corrected_image', - deprecated='0.10', - ), - native_wm_image=dict(), inverse_transformation_mat=dict(), - transformation_mat=dict(), - normalized_csf_image=dict(), - modulated_gm_image=dict(), modulated_csf_image=dict(), + modulated_gm_image=dict(), + modulated_input_image=dict(deprecated='0.10', + new_name='bias_corrected_image', + ), + modulated_wm_image=dict(), + native_csf_image=dict(), native_gm_image=dict(), + native_wm_image=dict(), + normalized_csf_image=dict(), normalized_gm_image=dict(), + normalized_wm_image=dict(), + transformation_mat=dict(), ) outputs = Segment.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/spm/tests/test_auto_SliceTiming.py b/nipype/interfaces/spm/tests/test_auto_SliceTiming.py index f7a8c40c9a..4a1812759e 100644 --- a/nipype/interfaces/spm/tests/test_auto_SliceTiming.py +++ b/nipype/interfaces/spm/tests/test_auto_SliceTiming.py @@ -1,46 +1,48 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.spm.preprocess import SliceTiming + def test_SliceTiming_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, ), - paths=dict(), - mfile=dict(usedefault=True, + in_files=dict(copyfile=False, + field='scans', + mandatory=True, ), - use_v8struct=dict(min_ver='8', - usedefault=True, + matlab_cmd=dict(), + mfile=dict(usedefault=True, ), - time_repetition=dict(field='tr', + num_slices=dict(field='nslices', mandatory=True, ), out_prefix=dict(field='prefix', usedefault=True, ), - in_files=dict(copyfile=False, - mandatory=True, - field='scans', - ), - num_slices=dict(field='nslices', + paths=dict(), + ref_slice=dict(field='refslice', mandatory=True, ), - matlab_cmd=dict(), - ref_slice=dict(field='refslice', + slice_order=dict(field='so', mandatory=True, ), - use_mcr=dict(), time_acquisition=dict(field='ta', mandatory=True, ), - slice_order=dict(field='so', + time_repetition=dict(field='tr', mandatory=True, ), + use_mcr=dict(), + use_v8struct=dict(min_ver='8', + usedefault=True, + ), ) inputs = SliceTiming.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_SliceTiming_outputs(): output_map = dict(timecorrected_files=dict(), ) @@ -49,3 +51,4 @@ def test_SliceTiming_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/spm/tests/test_auto_Smooth.py b/nipype/interfaces/spm/tests/test_auto_Smooth.py index 10c3c0b26f..e0d54046c1 100644 --- a/nipype/interfaces/spm/tests/test_auto_Smooth.py +++ b/nipype/interfaces/spm/tests/test_auto_Smooth.py @@ -1,30 +1,31 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.spm.preprocess import Smooth + def test_Smooth_inputs(): - input_map = dict(implicit_masking=dict(field='im', + input_map = dict(data_type=dict(field='dtype', + ), + fwhm=dict(field='fwhm', ), ignore_exception=dict(nohash=True, usedefault=True, ), - mfile=dict(usedefault=True, - ), - data_type=dict(field='dtype', - ), - paths=dict(), - use_v8struct=dict(min_ver='8', - usedefault=True, + implicit_masking=dict(field='im', ), in_files=dict(copyfile=False, - mandatory=True, field='data', + mandatory=True, + ), + matlab_cmd=dict(), + mfile=dict(usedefault=True, ), out_prefix=dict(field='prefix', usedefault=True, ), - matlab_cmd=dict(), + paths=dict(), use_mcr=dict(), - fwhm=dict(field='fwhm', + use_v8struct=dict(min_ver='8', + usedefault=True, ), ) inputs = Smooth.input_spec() @@ -32,6 +33,7 @@ def test_Smooth_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Smooth_outputs(): output_map = dict(smoothed_files=dict(), ) @@ -40,3 +42,4 @@ def test_Smooth_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/spm/tests/test_auto_Threshold.py b/nipype/interfaces/spm/tests/test_auto_Threshold.py index 42a50afc8a..8d2aecb6b8 100644 --- a/nipype/interfaces/spm/tests/test_auto_Threshold.py +++ b/nipype/interfaces/spm/tests/test_auto_Threshold.py @@ -1,39 +1,40 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.spm.model import Threshold + def test_Threshold_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(contrast_index=dict(mandatory=True, ), - paths=dict(), - spm_mat_file=dict(copyfile=True, - mandatory=True, + extent_fdr_p_threshold=dict(usedefault=True, ), - force_activation=dict(usedefault=True, + extent_threshold=dict(usedefault=True, ), - use_v8struct=dict(min_ver='8', - usedefault=True, + force_activation=dict(usedefault=True, ), - use_mcr=dict(), - use_fwe_correction=dict(usedefault=True, + height_threshold=dict(usedefault=True, ), - extent_threshold=dict(usedefault=True, + height_threshold_type=dict(usedefault=True, ), - contrast_index=dict(mandatory=True, + ignore_exception=dict(nohash=True, + usedefault=True, ), matlab_cmd=dict(), - extent_fdr_p_threshold=dict(usedefault=True, - ), mfile=dict(usedefault=True, ), - use_topo_fdr=dict(usedefault=True, - ), - height_threshold_type=dict(usedefault=True, + paths=dict(), + spm_mat_file=dict(copyfile=True, + mandatory=True, ), stat_image=dict(copyfile=False, mandatory=True, ), - height_threshold=dict(usedefault=True, + use_fwe_correction=dict(usedefault=True, + ), + use_mcr=dict(), + use_topo_fdr=dict(usedefault=True, + ), + use_v8struct=dict(min_ver='8', + usedefault=True, ), ) inputs = Threshold.input_spec() @@ -41,16 +42,18 @@ def test_Threshold_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Threshold_outputs(): - output_map = dict(thresholded_map=dict(), + output_map = dict(activation_forced=dict(), + cluster_forming_thr=dict(), n_clusters=dict(), - activation_forced=dict(), - pre_topo_n_clusters=dict(), pre_topo_fdr_map=dict(), - cluster_forming_thr=dict(), + pre_topo_n_clusters=dict(), + thresholded_map=dict(), ) outputs = Threshold.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/spm/tests/test_auto_ThresholdStatistics.py b/nipype/interfaces/spm/tests/test_auto_ThresholdStatistics.py index 81f16c86a2..42837d595a 100644 --- a/nipype/interfaces/spm/tests/test_auto_ThresholdStatistics.py +++ b/nipype/interfaces/spm/tests/test_auto_ThresholdStatistics.py @@ -1,42 +1,44 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.spm.model import ThresholdStatistics + def test_ThresholdStatistics_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, - ), - paths=dict(), - spm_mat_file=dict(copyfile=True, - mandatory=True, + input_map = dict(contrast_index=dict(mandatory=True, ), - use_v8struct=dict(min_ver='8', - usedefault=True, - ), - use_mcr=dict(), extent_threshold=dict(usedefault=True, ), - contrast_index=dict(mandatory=True, - ), - matlab_cmd=dict(), height_threshold=dict(mandatory=True, ), + ignore_exception=dict(nohash=True, + usedefault=True, + ), + matlab_cmd=dict(), mfile=dict(usedefault=True, ), + paths=dict(), + spm_mat_file=dict(copyfile=True, + mandatory=True, + ), stat_image=dict(copyfile=False, mandatory=True, ), + use_mcr=dict(), + use_v8struct=dict(min_ver='8', + usedefault=True, + ), ) inputs = ThresholdStatistics.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_ThresholdStatistics_outputs(): - output_map = dict(voxelwise_P_RF=dict(), - voxelwise_P_FDR=dict(), - voxelwise_P_Bonf=dict(), - clusterwise_P_FDR=dict(), + output_map = dict(clusterwise_P_FDR=dict(), clusterwise_P_RF=dict(), + voxelwise_P_Bonf=dict(), + voxelwise_P_FDR=dict(), + voxelwise_P_RF=dict(), voxelwise_P_uncor=dict(), ) outputs = ThresholdStatistics.output_spec() @@ -44,3 +46,4 @@ def test_ThresholdStatistics_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/spm/tests/test_auto_TwoSampleTTestDesign.py b/nipype/interfaces/spm/tests/test_auto_TwoSampleTTestDesign.py index bf8c0aaa03..ff21621c32 100644 --- a/nipype/interfaces/spm/tests/test_auto_TwoSampleTTestDesign.py +++ b/nipype/interfaces/spm/tests/test_auto_TwoSampleTTestDesign.py @@ -1,35 +1,24 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.spm.model import TwoSampleTTestDesign + def test_TwoSampleTTestDesign_inputs(): - input_map = dict(use_v8struct=dict(min_ver='8', - usedefault=True, - ), - matlab_cmd=dict(), - explicit_mask_file=dict(field='masking.em', - ), - paths=dict(), - unequal_variance=dict(field='des.t2.variance', + input_map = dict(covariates=dict(field='cov', ), - covariates=dict(field='cov', + dependent=dict(field='des.t2.dept', ), - mfile=dict(usedefault=True, + explicit_mask_file=dict(field='masking.em', ), - threshold_mask_absolute=dict(field='masking.tm.tma.athresh', - xor=['threshold_mask_none', 'threshold_mask_relative'], + global_calc_mean=dict(field='globalc.g_mean', + xor=['global_calc_omit', 'global_calc_values'], ), global_calc_omit=dict(field='globalc.g_omit', xor=['global_calc_mean', 'global_calc_values'], ), - ignore_exception=dict(nohash=True, - usedefault=True, - ), - use_implicit_threshold=dict(field='masking.im', - ), - global_calc_mean=dict(field='globalc.g_mean', - xor=['global_calc_omit', 'global_calc_values'], + global_calc_values=dict(field='globalc.g_user.global_uval', + xor=['global_calc_mean', 'global_calc_omit'], ), - dependent=dict(field='des.t2.dept', + global_normalization=dict(field='globalm.glonorm', ), group1_files=dict(field='des.t2.scans1', mandatory=True, @@ -37,28 +26,41 @@ def test_TwoSampleTTestDesign_inputs(): group2_files=dict(field='des.t2.scans2', mandatory=True, ), - threshold_mask_none=dict(field='masking.tm.tm_none', - xor=['threshold_mask_absolute', 'threshold_mask_relative'], - ), - use_mcr=dict(), - spm_mat_dir=dict(field='dir', + ignore_exception=dict(nohash=True, + usedefault=True, ), - global_normalization=dict(field='globalm.glonorm', + matlab_cmd=dict(), + mfile=dict(usedefault=True, ), no_grand_mean_scaling=dict(field='globalm.gmsca.gmsca_no', ), - global_calc_values=dict(field='globalc.g_user.global_uval', - xor=['global_calc_mean', 'global_calc_omit'], + paths=dict(), + spm_mat_dir=dict(field='dir', + ), + threshold_mask_absolute=dict(field='masking.tm.tma.athresh', + xor=['threshold_mask_none', 'threshold_mask_relative'], + ), + threshold_mask_none=dict(field='masking.tm.tm_none', + xor=['threshold_mask_absolute', 'threshold_mask_relative'], ), threshold_mask_relative=dict(field='masking.tm.tmr.rthresh', xor=['threshold_mask_absolute', 'threshold_mask_none'], ), + unequal_variance=dict(field='des.t2.variance', + ), + use_implicit_threshold=dict(field='masking.im', + ), + use_mcr=dict(), + use_v8struct=dict(min_ver='8', + usedefault=True, + ), ) inputs = TwoSampleTTestDesign.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_TwoSampleTTestDesign_outputs(): output_map = dict(spm_mat_file=dict(), ) @@ -67,3 +69,4 @@ def test_TwoSampleTTestDesign_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/spm/tests/test_auto_VBMSegment.py b/nipype/interfaces/spm/tests/test_auto_VBMSegment.py index b19532c848..1e9f0d58b6 100644 --- a/nipype/interfaces/spm/tests/test_auto_VBMSegment.py +++ b/nipype/interfaces/spm/tests/test_auto_VBMSegment.py @@ -1,137 +1,140 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.spm.preprocess import VBMSegment + def test_VBMSegment_inputs(): - input_map = dict(csf_dartel=dict(field='estwrite.output.CSF.dartel', + input_map = dict(bias_corrected_affine=dict(field='estwrite.output.bias.affine', usedefault=True, ), - csf_modulated_normalized=dict(field='estwrite.output.CSF.modulated', + bias_corrected_native=dict(field='estwrite.output.bias.native', usedefault=True, ), - cleanup_partitions=dict(field='estwrite.extopts.cleanup', + bias_corrected_normalized=dict(field='estwrite.output.bias.warped', usedefault=True, ), - gm_dartel=dict(field='estwrite.output.GM.dartel', + bias_fwhm=dict(field='estwrite.opts.biasfwhm', usedefault=True, ), - use_v8struct=dict(min_ver='8', + bias_regularization=dict(field='estwrite.opts.biasreg', usedefault=True, ), - dartel_template=dict(field='estwrite.extopts.dartelwarp.normhigh.darteltpm', - ), - warping_regularization=dict(field='estwrite.opts.warpreg', + cleanup_partitions=dict(field='estwrite.extopts.cleanup', usedefault=True, ), - use_sanlm_denoising_filter=dict(field='estwrite.extopts.sanlm', + csf_dartel=dict(field='estwrite.output.CSF.dartel', usedefault=True, ), - matlab_cmd=dict(), - csf_normalized=dict(field='estwrite.output.CSF.warped', + csf_modulated_normalized=dict(field='estwrite.output.CSF.modulated', usedefault=True, ), - pve_label_dartel=dict(field='estwrite.output.label.dartel', + csf_native=dict(field='estwrite.output.CSF.native', usedefault=True, ), - bias_corrected_normalized=dict(field='estwrite.output.bias.warped', + csf_normalized=dict(field='estwrite.output.CSF.warped', usedefault=True, ), - paths=dict(), - sampling_distance=dict(field='estwrite.opts.samp', - usedefault=True, + dartel_template=dict(field='estwrite.extopts.dartelwarp.normhigh.darteltpm', ), - wm_native=dict(field='estwrite.output.WM.native', + deformation_field=dict(field='estwrite.output.warps', usedefault=True, ), - wm_modulated_normalized=dict(field='estwrite.output.WM.modulated', + display_results=dict(field='estwrite.extopts.print', usedefault=True, ), - pve_label_native=dict(field='estwrite.output.label.native', + gaussians_per_class=dict(usedefault=True, + ), + gm_dartel=dict(field='estwrite.output.GM.dartel', usedefault=True, ), - bias_corrected_affine=dict(field='estwrite.output.bias.affine', + gm_modulated_normalized=dict(field='estwrite.output.GM.modulated', usedefault=True, ), gm_native=dict(field='estwrite.output.GM.native', usedefault=True, ), - gm_modulated_normalized=dict(field='estwrite.output.GM.modulated', + gm_normalized=dict(field='estwrite.output.GM.warped', usedefault=True, ), - bias_corrected_native=dict(field='estwrite.output.bias.native', + ignore_exception=dict(nohash=True, usedefault=True, ), - ignore_exception=dict(nohash=True, + in_files=dict(copyfile=False, + field='estwrite.data', + mandatory=True, + ), + jacobian_determinant=dict(field='estwrite.jacobian.warped', usedefault=True, ), - spatial_normalization=dict(usedefault=True, + matlab_cmd=dict(), + mfile=dict(usedefault=True, ), - csf_native=dict(field='estwrite.output.CSF.native', + mrf_weighting=dict(field='estwrite.extopts.mrf', usedefault=True, ), - gm_normalized=dict(field='estwrite.output.GM.warped', + paths=dict(), + pve_label_dartel=dict(field='estwrite.output.label.dartel', usedefault=True, ), - display_results=dict(field='estwrite.extopts.print', + pve_label_native=dict(field='estwrite.output.label.native', usedefault=True, ), - jacobian_determinant=dict(field='estwrite.jacobian.warped', + pve_label_normalized=dict(field='estwrite.output.label.warped', usedefault=True, ), + sampling_distance=dict(field='estwrite.opts.samp', + usedefault=True, + ), + spatial_normalization=dict(usedefault=True, + ), tissues=dict(field='estwrite.tpm', ), use_mcr=dict(), - wm_dartel=dict(field='estwrite.output.WM.dartel', + use_sanlm_denoising_filter=dict(field='estwrite.extopts.sanlm', usedefault=True, ), - bias_regularization=dict(field='estwrite.opts.biasreg', + use_v8struct=dict(min_ver='8', usedefault=True, ), - mrf_weighting=dict(field='estwrite.extopts.mrf', + warping_regularization=dict(field='estwrite.opts.warpreg', usedefault=True, ), - bias_fwhm=dict(field='estwrite.opts.biasfwhm', + wm_dartel=dict(field='estwrite.output.WM.dartel', usedefault=True, ), - in_files=dict(copyfile=False, - mandatory=True, - field='estwrite.data', - ), - deformation_field=dict(field='estwrite.output.warps', + wm_modulated_normalized=dict(field='estwrite.output.WM.modulated', usedefault=True, ), - mfile=dict(usedefault=True, - ), - wm_normalized=dict(field='estwrite.output.WM.warped', + wm_native=dict(field='estwrite.output.WM.native', usedefault=True, ), - pve_label_normalized=dict(field='estwrite.output.label.warped', + wm_normalized=dict(field='estwrite.output.WM.warped', usedefault=True, ), - gaussians_per_class=dict(usedefault=True, - ), ) inputs = VBMSegment.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_VBMSegment_outputs(): - output_map = dict(modulated_class_images=dict(), - pve_label_registered_images=dict(), - normalized_class_images=dict(), - normalized_bias_corrected_images=dict(), - bias_corrected_images=dict(), - pve_label_normalized_images=dict(), - inverse_deformation_field=dict(), + output_map = dict(bias_corrected_images=dict(), dartel_input_images=dict(), - transformation_mat=dict(), - pve_label_native_images=dict(), - native_class_images=dict(), forward_deformation_field=dict(), + inverse_deformation_field=dict(), jacobian_determinant_images=dict(), + modulated_class_images=dict(), + native_class_images=dict(), + normalized_bias_corrected_images=dict(), + normalized_class_images=dict(), + pve_label_native_images=dict(), + pve_label_normalized_images=dict(), + pve_label_registered_images=dict(), + transformation_mat=dict(), ) outputs = VBMSegment.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/tests/test_auto_AssertEqual.py b/nipype/interfaces/tests/test_auto_AssertEqual.py index 60cf50abb7..c0dd821b0c 100644 --- a/nipype/interfaces/tests/test_auto_AssertEqual.py +++ b/nipype/interfaces/tests/test_auto_AssertEqual.py @@ -1,6 +1,7 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.utility import AssertEqual + def test_AssertEqual_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, @@ -15,3 +16,4 @@ def test_AssertEqual_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/tests/test_auto_BaseInterface.py b/nipype/interfaces/tests/test_auto_BaseInterface.py index 0ec8e55c9b..de4c191e36 100644 --- a/nipype/interfaces/tests/test_auto_BaseInterface.py +++ b/nipype/interfaces/tests/test_auto_BaseInterface.py @@ -1,6 +1,7 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.base import BaseInterface + def test_BaseInterface_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, @@ -11,3 +12,4 @@ def test_BaseInterface_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/tests/test_auto_C3dAffineTool.py b/nipype/interfaces/tests/test_auto_C3dAffineTool.py index 848efd4644..dcaaebf533 100644 --- a/nipype/interfaces/tests/test_auto_C3dAffineTool.py +++ b/nipype/interfaces/tests/test_auto_C3dAffineTool.py @@ -1,33 +1,34 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.c3 import C3dAffineTool + def test_C3dAffineTool_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + environ=dict(nohash=True, usedefault=True, ), - terminal_output=dict(mandatory=True, - nohash=True, + fsl2ras=dict(argstr='-fsl2ras', + position=4, ), - args=dict(argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, ), - fsl2ras=dict(position=4, - argstr='-fsl2ras', + itk_transform=dict(argstr='-oitk %s', + hash_files=False, + position=5, ), - source_file=dict(position=2, - argstr='-src %s', + reference_file=dict(argstr='-ref %s', + position=1, ), - environ=dict(nohash=True, - usedefault=True, + source_file=dict(argstr='-src %s', + position=2, ), - reference_file=dict(position=1, - argstr='-ref %s', + terminal_output=dict(mandatory=True, + nohash=True, ), - transform_file=dict(position=3, - argstr='%s', - ), - itk_transform=dict(position=5, - hash_files=False, - argstr='-oitk %s', + transform_file=dict(argstr='%s', + position=3, ), ) inputs = C3dAffineTool.input_spec() @@ -35,6 +36,7 @@ def test_C3dAffineTool_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_C3dAffineTool_outputs(): output_map = dict(itk_transform=dict(), ) @@ -43,3 +45,4 @@ def test_C3dAffineTool_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/tests/test_auto_CommandLine.py b/nipype/interfaces/tests/test_auto_CommandLine.py index caa4772767..4114623254 100644 --- a/nipype/interfaces/tests/test_auto_CommandLine.py +++ b/nipype/interfaces/tests/test_auto_CommandLine.py @@ -1,17 +1,18 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.base import CommandLine + def test_CommandLine_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, - ), - terminal_output=dict(mandatory=True, - nohash=True, + input_map = dict(args=dict(argstr='%s', ), environ=dict(nohash=True, usedefault=True, ), - args=dict(argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, + ), + terminal_output=dict(mandatory=True, + nohash=True, ), ) inputs = CommandLine.input_spec() @@ -19,3 +20,4 @@ def test_CommandLine_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/tests/test_auto_CopyMeta.py b/nipype/interfaces/tests/test_auto_CopyMeta.py index 56da32aa06..8bfff5fb85 100644 --- a/nipype/interfaces/tests/test_auto_CopyMeta.py +++ b/nipype/interfaces/tests/test_auto_CopyMeta.py @@ -1,10 +1,11 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.dcmstack import CopyMeta + def test_CopyMeta_inputs(): - input_map = dict(exclude_classes=dict(), - dest_file=dict(mandatory=True, + input_map = dict(dest_file=dict(mandatory=True, ), + exclude_classes=dict(), include_classes=dict(), src_file=dict(mandatory=True, ), @@ -14,6 +15,7 @@ def test_CopyMeta_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_CopyMeta_outputs(): output_map = dict(dest_file=dict(), ) @@ -22,3 +24,4 @@ def test_CopyMeta_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/tests/test_auto_DataFinder.py b/nipype/interfaces/tests/test_auto_DataFinder.py index 3c7178f962..039b41ba94 100644 --- a/nipype/interfaces/tests/test_auto_DataFinder.py +++ b/nipype/interfaces/tests/test_auto_DataFinder.py @@ -1,25 +1,27 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.io import DataFinder + def test_DataFinder_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, ), ignore_regexes=dict(), - min_depth=dict(), - unpack_single=dict(usedefault=True, - ), match_regex=dict(usedefault=True, ), max_depth=dict(), + min_depth=dict(), root_paths=dict(mandatory=True, ), + unpack_single=dict(usedefault=True, + ), ) inputs = DataFinder.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_DataFinder_outputs(): output_map = dict() outputs = DataFinder.output_spec() @@ -27,3 +29,4 @@ def test_DataFinder_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/tests/test_auto_DataGrabber.py b/nipype/interfaces/tests/test_auto_DataGrabber.py index 16f96d07c1..1d630a8941 100644 --- a/nipype/interfaces/tests/test_auto_DataGrabber.py +++ b/nipype/interfaces/tests/test_auto_DataGrabber.py @@ -1,24 +1,26 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.io import DataGrabber + def test_DataGrabber_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(base_directory=dict(), + ignore_exception=dict(nohash=True, usedefault=True, ), raise_on_empty=dict(usedefault=True, ), sort_filelist=dict(mandatory=True, ), - template_args=dict(), template=dict(mandatory=True, ), - base_directory=dict(), + template_args=dict(), ) inputs = DataGrabber.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_DataGrabber_outputs(): output_map = dict() outputs = DataGrabber.output_spec() @@ -26,3 +28,4 @@ def test_DataGrabber_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/tests/test_auto_DataSink.py b/nipype/interfaces/tests/test_auto_DataSink.py index 175198ec47..15305f3694 100644 --- a/nipype/interfaces/tests/test_auto_DataSink.py +++ b/nipype/interfaces/tests/test_auto_DataSink.py @@ -1,27 +1,29 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.io import DataSink + def test_DataSink_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(_outputs=dict(usedefault=True, ), + base_directory=dict(), container=dict(), - strip_dir=dict(), - remove_dest_dir=dict(usedefault=True, - ), - _outputs=dict(usedefault=True, + ignore_exception=dict(nohash=True, + usedefault=True, ), - substitutions=dict(), parameterization=dict(usedefault=True, ), - base_directory=dict(), regexp_substitutions=dict(), + remove_dest_dir=dict(usedefault=True, + ), + strip_dir=dict(), + substitutions=dict(), ) inputs = DataSink.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_DataSink_outputs(): output_map = dict(out_file=dict(), ) @@ -30,3 +32,4 @@ def test_DataSink_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/tests/test_auto_Dcm2nii.py b/nipype/interfaces/tests/test_auto_Dcm2nii.py index 69cab3445d..086a340864 100644 --- a/nipype/interfaces/tests/test_auto_Dcm2nii.py +++ b/nipype/interfaces/tests/test_auto_Dcm2nii.py @@ -1,54 +1,55 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.dcm2nii import Dcm2nii + def test_Dcm2nii_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(anonymize=dict(argstr='-a', + position=2, ), - gzip_output=dict(position=0, - usedefault=True, - argstr='-g', + args=dict(argstr='%s', + position=9, ), - config_file=dict(position=7, + config_file=dict(argstr='-b %s', genfile=True, - argstr='-b %s', + position=7, ), - args=dict(position=9, - argstr='%s', + convert_all_pars=dict(argstr='-v', + position=8, ), - convert_all_pars=dict(position=8, - argstr='-v', - ), - reorient_and_crop=dict(position=5, - argstr='-x', + environ=dict(nohash=True, + usedefault=True, ), - reorient=dict(position=4, - argstr='-r', + gzip_output=dict(argstr='-g', + position=0, + usedefault=True, ), - source_names=dict(position=10, - mandatory=True, - argstr='%s', + id_in_filename=dict(argstr='-i', + position=3, + usedefault=True, ), - terminal_output=dict(mandatory=True, - nohash=True, + ignore_exception=dict(nohash=True, + usedefault=True, ), - environ=dict(nohash=True, + nii_output=dict(argstr='-n', + position=1, usedefault=True, ), - output_dir=dict(position=6, + output_dir=dict(argstr='-o %s', genfile=True, - argstr='-o %s', + position=6, ), - anonymize=dict(position=2, - argstr='-a', + reorient=dict(argstr='-r', + position=4, ), - id_in_filename=dict(position=3, - usedefault=True, - argstr='-i', + reorient_and_crop=dict(argstr='-x', + position=5, ), - nii_output=dict(position=1, - usedefault=True, - argstr='-n', + source_names=dict(argstr='%s', + mandatory=True, + position=10, + ), + terminal_output=dict(mandatory=True, + nohash=True, ), ) inputs = Dcm2nii.input_spec() @@ -56,11 +57,12 @@ def test_Dcm2nii_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Dcm2nii_outputs(): - output_map = dict(reoriented_and_cropped_files=dict(), - converted_files=dict(), + output_map = dict(bvals=dict(), bvecs=dict(), - bvals=dict(), + converted_files=dict(), + reoriented_and_cropped_files=dict(), reoriented_files=dict(), ) outputs = Dcm2nii.output_spec() @@ -68,3 +70,4 @@ def test_Dcm2nii_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/tests/test_auto_DcmStack.py b/nipype/interfaces/tests/test_auto_DcmStack.py index 005d078a47..a001bc17a6 100644 --- a/nipype/interfaces/tests/test_auto_DcmStack.py +++ b/nipype/interfaces/tests/test_auto_DcmStack.py @@ -1,21 +1,23 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.dcmstack import DcmStack + def test_DcmStack_inputs(): - input_map = dict(out_format=dict(), - embed_meta=dict(), - out_ext=dict(usedefault=True, - ), - dicom_files=dict(mandatory=True, + input_map = dict(dicom_files=dict(mandatory=True, ), + embed_meta=dict(), exclude_regexes=dict(), include_regexes=dict(), + out_ext=dict(usedefault=True, + ), + out_format=dict(), ) inputs = DcmStack.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_DcmStack_outputs(): output_map = dict(out_file=dict(), ) @@ -24,3 +26,4 @@ def test_DcmStack_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/tests/test_auto_FreeSurferSource.py b/nipype/interfaces/tests/test_auto_FreeSurferSource.py index 1075bf18b9..e447e354da 100644 --- a/nipype/interfaces/tests/test_auto_FreeSurferSource.py +++ b/nipype/interfaces/tests/test_auto_FreeSurferSource.py @@ -1,14 +1,15 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.io import FreeSurferSource + def test_FreeSurferSource_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(hemi=dict(usedefault=True, + ), + ignore_exception=dict(nohash=True, usedefault=True, ), subject_id=dict(mandatory=True, ), - hemi=dict(usedefault=True, - ), subjects_dir=dict(mandatory=True, ), ) @@ -17,82 +18,83 @@ def test_FreeSurferSource_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_FreeSurferSource_outputs(): - output_map = dict(curv=dict(loc='surf', - ), - curv_stats=dict(altkey='curv', + output_map = dict(BA_stats=dict(altkey='BA', loc='stats', ), + T1=dict(loc='mri', + ), annot=dict(altkey='*annot', loc='label', ), - sphere=dict(loc='surf', - ), - inflated=dict(loc='surf', - ), - BA_stats=dict(altkey='BA', + aparc_a2009s_stats=dict(altkey='aparc.a2009s', loc='stats', ), - ribbon=dict(altkey='*ribbon', + aparc_aseg=dict(altkey='aparc*aseg', loc='mri', ), - sulc=dict(loc='surf', + aparc_stats=dict(altkey='aparc', + loc='stats', ), - entorhinal_exvivo_stats=dict(altkey='entorhinal_exvivo', + aseg=dict(loc='mri', + ), + aseg_stats=dict(altkey='aseg', loc='stats', ), + brain=dict(loc='mri', + ), brainmask=dict(loc='mri', ), - thickness=dict(loc='surf', + curv=dict(loc='surf', ), - sphere_reg=dict(altkey='sphere.reg', - loc='surf', + curv_stats=dict(altkey='curv', + loc='stats', ), - rawavg=dict(loc='mri', + entorhinal_exvivo_stats=dict(altkey='entorhinal_exvivo', + loc='stats', ), - white=dict(loc='surf', + filled=dict(loc='mri', ), - orig=dict(loc='mri', + inflated=dict(loc='surf', ), - nu=dict(loc='mri', + label=dict(altkey='*label', + loc='label', ), norm=dict(loc='mri', ), - wm=dict(loc='mri', + nu=dict(loc='mri', ), - wmparc=dict(loc='mri', + orig=dict(loc='mri', ), - T1=dict(loc='mri', + pial=dict(loc='surf', ), - volume=dict(loc='surf', + rawavg=dict(loc='mri', ), - aseg=dict(loc='mri', + ribbon=dict(altkey='*ribbon', + loc='mri', ), - aparc_stats=dict(altkey='aparc', - loc='stats', + smoothwm=dict(loc='surf', ), - brain=dict(loc='mri', + sphere=dict(loc='surf', ), - aparc_a2009s_stats=dict(altkey='aparc.a2009s', - loc='stats', + sphere_reg=dict(altkey='sphere.reg', + loc='surf', ), - label=dict(altkey='*label', - loc='label', + sulc=dict(loc='surf', ), - aseg_stats=dict(altkey='aseg', - loc='stats', + thickness=dict(loc='surf', ), - filled=dict(loc='mri', + volume=dict(loc='surf', ), - pial=dict(loc='surf', + white=dict(loc='surf', ), - wmparc_stats=dict(altkey='wmparc', - loc='stats', + wm=dict(loc='mri', ), - aparc_aseg=dict(altkey='aparc*aseg', - loc='mri', + wmparc=dict(loc='mri', ), - smoothwm=dict(loc='surf', + wmparc_stats=dict(altkey='wmparc', + loc='stats', ), ) outputs = FreeSurferSource.output_spec() @@ -100,3 +102,4 @@ def test_FreeSurferSource_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/tests/test_auto_Function.py b/nipype/interfaces/tests/test_auto_Function.py index d3d541fc0c..e627635a7f 100644 --- a/nipype/interfaces/tests/test_auto_Function.py +++ b/nipype/interfaces/tests/test_auto_Function.py @@ -1,11 +1,12 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.utility import Function + def test_Function_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(function_str=dict(mandatory=True, ), - function_str=dict(mandatory=True, + ignore_exception=dict(nohash=True, + usedefault=True, ), ) inputs = Function.input_spec() @@ -13,6 +14,7 @@ def test_Function_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Function_outputs(): output_map = dict() outputs = Function.output_spec() @@ -20,3 +22,4 @@ def test_Function_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/tests/test_auto_GroupAndStack.py b/nipype/interfaces/tests/test_auto_GroupAndStack.py index cfeebf074b..3f290762ed 100644 --- a/nipype/interfaces/tests/test_auto_GroupAndStack.py +++ b/nipype/interfaces/tests/test_auto_GroupAndStack.py @@ -1,21 +1,23 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.dcmstack import GroupAndStack + def test_GroupAndStack_inputs(): - input_map = dict(out_format=dict(), - embed_meta=dict(), - out_ext=dict(usedefault=True, - ), - dicom_files=dict(mandatory=True, + input_map = dict(dicom_files=dict(mandatory=True, ), + embed_meta=dict(), exclude_regexes=dict(), include_regexes=dict(), + out_ext=dict(usedefault=True, + ), + out_format=dict(), ) inputs = GroupAndStack.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_GroupAndStack_outputs(): output_map = dict(out_list=dict(), ) @@ -24,3 +26,4 @@ def test_GroupAndStack_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/tests/test_auto_IOBase.py b/nipype/interfaces/tests/test_auto_IOBase.py index e1d42957cd..e2f9541d95 100644 --- a/nipype/interfaces/tests/test_auto_IOBase.py +++ b/nipype/interfaces/tests/test_auto_IOBase.py @@ -1,6 +1,7 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.io import IOBase + def test_IOBase_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, @@ -11,3 +12,4 @@ def test_IOBase_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/tests/test_auto_IdentityInterface.py b/nipype/interfaces/tests/test_auto_IdentityInterface.py index 7d5b3c343f..9821b3bcf1 100644 --- a/nipype/interfaces/tests/test_auto_IdentityInterface.py +++ b/nipype/interfaces/tests/test_auto_IdentityInterface.py @@ -1,6 +1,7 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.utility import IdentityInterface + def test_IdentityInterface_inputs(): input_map = dict() inputs = IdentityInterface.input_spec() @@ -8,6 +9,7 @@ def test_IdentityInterface_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_IdentityInterface_outputs(): output_map = dict() outputs = IdentityInterface.output_spec() @@ -15,3 +17,4 @@ def test_IdentityInterface_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/tests/test_auto_LookupMeta.py b/nipype/interfaces/tests/test_auto_LookupMeta.py index 73525cbcf7..7ae4c19491 100644 --- a/nipype/interfaces/tests/test_auto_LookupMeta.py +++ b/nipype/interfaces/tests/test_auto_LookupMeta.py @@ -1,6 +1,7 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.dcmstack import LookupMeta + def test_LookupMeta_inputs(): input_map = dict(in_file=dict(mandatory=True, ), @@ -12,6 +13,7 @@ def test_LookupMeta_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_LookupMeta_outputs(): output_map = dict() outputs = LookupMeta.output_spec() @@ -19,3 +21,4 @@ def test_LookupMeta_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/tests/test_auto_MatlabCommand.py b/nipype/interfaces/tests/test_auto_MatlabCommand.py index 7ef38a2710..26fc235dd7 100644 --- a/nipype/interfaces/tests/test_auto_MatlabCommand.py +++ b/nipype/interfaces/tests/test_auto_MatlabCommand.py @@ -1,46 +1,47 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.matlab import MatlabCommand + def test_MatlabCommand_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + environ=dict(nohash=True, usedefault=True, ), - paths=dict(), - prescript=dict(usedefault=True, + ignore_exception=dict(nohash=True, + usedefault=True, ), - script=dict(position=-1, - mandatory=True, - argstr='-r "%s;exit"', + logfile=dict(argstr='-logfile %s', ), - args=dict(argstr='%s', + mfile=dict(usedefault=True, ), - single_comp_thread=dict(argstr='-singleCompThread', + nodesktop=dict(argstr='-nodesktop', nohash=True, - ), - script_file=dict(usedefault=True, + usedefault=True, ), nosplash=dict(argstr='-nosplash', nohash=True, usedefault=True, ), + paths=dict(), postscript=dict(usedefault=True, ), - terminal_output=dict(mandatory=True, - nohash=True, - ), - environ=dict(nohash=True, - usedefault=True, + prescript=dict(usedefault=True, ), - mfile=dict(usedefault=True, + script=dict(argstr='-r "%s;exit"', + mandatory=True, + position=-1, ), - logfile=dict(argstr='-logfile %s', + script_file=dict(usedefault=True, ), - uses_mcr=dict(xor=['nodesktop', 'nosplash', 'single_comp_thread'], + single_comp_thread=dict(argstr='-singleCompThread', nohash=True, ), - nodesktop=dict(argstr='-nodesktop', + terminal_output=dict(mandatory=True, nohash=True, - usedefault=True, + ), + uses_mcr=dict(nohash=True, + xor=['nodesktop', 'nosplash', 'single_comp_thread'], ), ) inputs = MatlabCommand.input_spec() @@ -48,3 +49,4 @@ def test_MatlabCommand_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/tests/test_auto_Merge.py b/nipype/interfaces/tests/test_auto_Merge.py index 333eb5b084..161fe247f6 100644 --- a/nipype/interfaces/tests/test_auto_Merge.py +++ b/nipype/interfaces/tests/test_auto_Merge.py @@ -1,13 +1,14 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.utility import Merge + def test_Merge_inputs(): - input_map = dict(no_flatten=dict(usedefault=True, + input_map = dict(axis=dict(usedefault=True, ), ignore_exception=dict(nohash=True, usedefault=True, ), - axis=dict(usedefault=True, + no_flatten=dict(usedefault=True, ), ) inputs = Merge.input_spec() @@ -15,6 +16,7 @@ def test_Merge_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Merge_outputs(): output_map = dict(out=dict(), ) @@ -23,3 +25,4 @@ def test_Merge_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/tests/test_auto_MergeNifti.py b/nipype/interfaces/tests/test_auto_MergeNifti.py index cf504f0a79..b0a99aee5a 100644 --- a/nipype/interfaces/tests/test_auto_MergeNifti.py +++ b/nipype/interfaces/tests/test_auto_MergeNifti.py @@ -1,20 +1,22 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.dcmstack import MergeNifti + def test_MergeNifti_inputs(): - input_map = dict(out_format=dict(), - sort_order=dict(), - in_files=dict(mandatory=True, + input_map = dict(in_files=dict(mandatory=True, ), merge_dim=dict(), out_ext=dict(usedefault=True, ), + out_format=dict(), + sort_order=dict(), ) inputs = MergeNifti.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MergeNifti_outputs(): output_map = dict(out_file=dict(), ) @@ -23,3 +25,4 @@ def test_MergeNifti_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/tests/test_auto_MeshFix.py b/nipype/interfaces/tests/test_auto_MeshFix.py index 7c6e17ed50..48c6ad33b5 100644 --- a/nipype/interfaces/tests/test_auto_MeshFix.py +++ b/nipype/interfaces/tests/test_auto_MeshFix.py @@ -1,98 +1,100 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.meshfix import MeshFix + def test_MeshFix_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(args=dict(argstr='%s', + ), + cut_inner=dict(argstr='--cut-inner %d', ), cut_outer=dict(argstr='--cut-outer %d', ), - x_shift=dict(argstr='--smooth %d', + decouple_inin=dict(argstr='--decouple-inin %d', ), - remove_handles=dict(argstr='--remove-handles', + decouple_outin=dict(argstr='--decouple-outin %d', ), - join_closest_components=dict(xor=['join_closest_components'], - argstr='-jc', + decouple_outout=dict(argstr='--decouple-outout %d', ), dilation=dict(argstr='--dilate %d', ), - in_file2=dict(position=2, - argstr='%s', + dont_clean=dict(argstr='--no-clean', ), - in_file1=dict(position=1, - mandatory=True, - argstr='%s', + environ=dict(nohash=True, + usedefault=True, + ), + epsilon_angle=dict(argstr='-a %f', + ), + finetuning_distance=dict(argstr='%f', + requires=['finetuning_substeps'], + ), + finetuning_inwards=dict(argstr='--fineTuneIn ', + requires=['finetuning_distance', 'finetuning_substeps'], ), finetuning_outwards=dict(argstr='--fineTuneIn ', - xor=['finetuning_inwards'], requires=['finetuning_distance', 'finetuning_substeps'], + xor=['finetuning_inwards'], ), - decouple_outin=dict(argstr='--decouple-outin %d', + finetuning_substeps=dict(argstr='%d', + requires=['finetuning_distance'], ), - dont_clean=dict(argstr='--no-clean', + ignore_exception=dict(nohash=True, + usedefault=True, ), - number_of_biggest_shells=dict(argstr='--shells %d', + in_file1=dict(argstr='%s', + mandatory=True, + position=1, ), - finetuning_distance=dict(requires=['finetuning_substeps'], - argstr='%f', + in_file2=dict(argstr='%s', + position=2, ), - save_as_freesurfer_mesh=dict(xor=['save_as_vrml', 'save_as_stl'], - argstr='--fsmesh', + join_closest_components=dict(argstr='-jc', + xor=['join_closest_components'], ), - uniform_remeshing_steps=dict(requires=['uniform_remeshing_vertices'], - argstr='-u %d', + join_overlapping_largest_components=dict(argstr='-j', + xor=['join_closest_components'], ), - save_as_stl=dict(xor=['save_as_vmrl', 'save_as_freesurfer_mesh'], - argstr='--stl', + laplacian_smoothing_steps=dict(argstr='--smooth %d', ), - cut_inner=dict(argstr='--cut-inner %d', + number_of_biggest_shells=dict(argstr='--shells %d', ), out_filename=dict(argstr='-o %s', genfile=True, ), - finetuning_inwards=dict(requires=['finetuning_distance', 'finetuning_substeps'], - argstr='--fineTuneIn ', - ), - decouple_outout=dict(argstr='--decouple-outout %d', - ), - args=dict(argstr='%s', - ), - set_intersections_to_one=dict(argstr='--intersect', - ), - save_as_vmrl=dict(xor=['save_as_stl', 'save_as_freesurfer_mesh'], - argstr='--wrl', - ), - uniform_remeshing_vertices=dict(requires=['uniform_remeshing_steps'], - argstr='--vertices %d', - ), - finetuning_substeps=dict(requires=['finetuning_distance'], - argstr='%d', + output_type=dict(usedefault=True, ), quiet_mode=dict(argstr='-q', ), - laplacian_smoothing_steps=dict(argstr='--smooth %d', - ), - epsilon_angle=dict(argstr='-a %f', + remove_handles=dict(argstr='--remove-handles', ), - join_overlapping_largest_components=dict(xor=['join_closest_components'], - argstr='-j', + save_as_freesurfer_mesh=dict(argstr='--fsmesh', + xor=['save_as_vrml', 'save_as_stl'], ), - environ=dict(nohash=True, - usedefault=True, + save_as_stl=dict(argstr='--stl', + xor=['save_as_vmrl', 'save_as_freesurfer_mesh'], ), - decouple_inin=dict(argstr='--decouple-inin %d', + save_as_vmrl=dict(argstr='--wrl', + xor=['save_as_stl', 'save_as_freesurfer_mesh'], ), - output_type=dict(usedefault=True, + set_intersections_to_one=dict(argstr='--intersect', ), terminal_output=dict(mandatory=True, nohash=True, ), + uniform_remeshing_steps=dict(argstr='-u %d', + requires=['uniform_remeshing_vertices'], + ), + uniform_remeshing_vertices=dict(argstr='--vertices %d', + requires=['uniform_remeshing_steps'], + ), + x_shift=dict(argstr='--smooth %d', + ), ) inputs = MeshFix.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_MeshFix_outputs(): output_map = dict(mesh_file=dict(), ) @@ -101,3 +103,4 @@ def test_MeshFix_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/tests/test_auto_MpiCommandLine.py b/nipype/interfaces/tests/test_auto_MpiCommandLine.py index 1c2f180e71..5435bf2c28 100644 --- a/nipype/interfaces/tests/test_auto_MpiCommandLine.py +++ b/nipype/interfaces/tests/test_auto_MpiCommandLine.py @@ -1,19 +1,20 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.base import MpiCommandLine + def test_MpiCommandLine_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(args=dict(argstr='%s', + ), + environ=dict(nohash=True, usedefault=True, ), - args=dict(argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, ), n_procs=dict(), terminal_output=dict(mandatory=True, nohash=True, ), - environ=dict(nohash=True, - usedefault=True, - ), use_mpi=dict(usedefault=True, ), ) @@ -22,3 +23,4 @@ def test_MpiCommandLine_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/tests/test_auto_MySQLSink.py b/nipype/interfaces/tests/test_auto_MySQLSink.py index 6785e16856..58869d63b8 100644 --- a/nipype/interfaces/tests/test_auto_MySQLSink.py +++ b/nipype/interfaces/tests/test_auto_MySQLSink.py @@ -1,27 +1,29 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.io import MySQLSink + def test_MySQLSink_inputs(): - input_map = dict(username=dict(), - ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(config=dict(mandatory=True, + xor=['host'], ), database_name=dict(mandatory=True, ), - host=dict(xor=['config'], - mandatory=True, + host=dict(mandatory=True, requires=['username', 'password'], usedefault=True, + xor=['config'], ), - table_name=dict(mandatory=True, + ignore_exception=dict(nohash=True, + usedefault=True, ), password=dict(), - config=dict(mandatory=True, - xor=['host'], + table_name=dict(mandatory=True, ), + username=dict(), ) inputs = MySQLSink.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/tests/test_auto_NiftiGeneratorBase.py b/nipype/interfaces/tests/test_auto_NiftiGeneratorBase.py index 8afd3cb878..848f94990c 100644 --- a/nipype/interfaces/tests/test_auto_NiftiGeneratorBase.py +++ b/nipype/interfaces/tests/test_auto_NiftiGeneratorBase.py @@ -1,6 +1,7 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.dcmstack import NiftiGeneratorBase + def test_NiftiGeneratorBase_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, @@ -11,3 +12,4 @@ def test_NiftiGeneratorBase_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/tests/test_auto_Rename.py b/nipype/interfaces/tests/test_auto_Rename.py index f36c9e137d..758191e890 100644 --- a/nipype/interfaces/tests/test_auto_Rename.py +++ b/nipype/interfaces/tests/test_auto_Rename.py @@ -1,21 +1,23 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.utility import Rename + def test_Rename_inputs(): - input_map = dict(use_fullpath=dict(usedefault=True, - ), - format_string=dict(mandatory=True, + input_map = dict(format_string=dict(mandatory=True, ), - keep_ext=dict(), in_file=dict(mandatory=True, ), + keep_ext=dict(), parse_string=dict(), + use_fullpath=dict(usedefault=True, + ), ) inputs = Rename.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Rename_outputs(): output_map = dict(out_file=dict(), ) @@ -24,3 +26,4 @@ def test_Rename_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/tests/test_auto_SEMLikeCommandLine.py b/nipype/interfaces/tests/test_auto_SEMLikeCommandLine.py index c364cb836b..e1f96e87ff 100644 --- a/nipype/interfaces/tests/test_auto_SEMLikeCommandLine.py +++ b/nipype/interfaces/tests/test_auto_SEMLikeCommandLine.py @@ -1,17 +1,18 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.base import SEMLikeCommandLine + def test_SEMLikeCommandLine_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, - ), - terminal_output=dict(mandatory=True, - nohash=True, + input_map = dict(args=dict(argstr='%s', ), environ=dict(nohash=True, usedefault=True, ), - args=dict(argstr='%s', + ignore_exception=dict(nohash=True, + usedefault=True, + ), + terminal_output=dict(mandatory=True, + nohash=True, ), ) inputs = SEMLikeCommandLine.input_spec() @@ -19,3 +20,4 @@ def test_SEMLikeCommandLine_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/tests/test_auto_SQLiteSink.py b/nipype/interfaces/tests/test_auto_SQLiteSink.py index 27ae726b80..6a7a064291 100644 --- a/nipype/interfaces/tests/test_auto_SQLiteSink.py +++ b/nipype/interfaces/tests/test_auto_SQLiteSink.py @@ -1,17 +1,19 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.io import SQLiteSink + def test_SQLiteSink_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(database_file=dict(mandatory=True, + ), + ignore_exception=dict(nohash=True, usedefault=True, ), table_name=dict(mandatory=True, ), - database_file=dict(mandatory=True, - ), ) inputs = SQLiteSink.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/tests/test_auto_Select.py b/nipype/interfaces/tests/test_auto_Select.py index d98f2c0979..85649f42e6 100644 --- a/nipype/interfaces/tests/test_auto_Select.py +++ b/nipype/interfaces/tests/test_auto_Select.py @@ -1,6 +1,7 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.utility import Select + def test_Select_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, @@ -15,6 +16,7 @@ def test_Select_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Select_outputs(): output_map = dict(out=dict(), ) @@ -23,3 +25,4 @@ def test_Select_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/tests/test_auto_SelectFiles.py b/nipype/interfaces/tests/test_auto_SelectFiles.py index c75ec00cd0..edec59dbe5 100644 --- a/nipype/interfaces/tests/test_auto_SelectFiles.py +++ b/nipype/interfaces/tests/test_auto_SelectFiles.py @@ -1,23 +1,25 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.io import SelectFiles + def test_SelectFiles_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(base_directory=dict(), + force_lists=dict(usedefault=True, ), - sort_filelist=dict(usedefault=True, + ignore_exception=dict(nohash=True, + usedefault=True, ), raise_on_empty=dict(usedefault=True, ), - force_lists=dict(usedefault=True, + sort_filelist=dict(usedefault=True, ), - base_directory=dict(), ) inputs = SelectFiles.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_SelectFiles_outputs(): output_map = dict() outputs = SelectFiles.output_spec() @@ -25,3 +27,4 @@ def test_SelectFiles_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/tests/test_auto_SlicerCommandLine.py b/nipype/interfaces/tests/test_auto_SlicerCommandLine.py index 9106d38656..ef9fd18e82 100644 --- a/nipype/interfaces/tests/test_auto_SlicerCommandLine.py +++ b/nipype/interfaces/tests/test_auto_SlicerCommandLine.py @@ -1,18 +1,19 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.dynamic_slicer import SlicerCommandLine + def test_SlicerCommandLine_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, - ), - terminal_output=dict(mandatory=True, - nohash=True, + input_map = dict(args=dict(argstr='%s', ), environ=dict(nohash=True, usedefault=True, ), + ignore_exception=dict(nohash=True, + usedefault=True, + ), module=dict(), - args=dict(argstr='%s', + terminal_output=dict(mandatory=True, + nohash=True, ), ) inputs = SlicerCommandLine.input_spec() @@ -20,6 +21,7 @@ def test_SlicerCommandLine_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_SlicerCommandLine_outputs(): output_map = dict() outputs = SlicerCommandLine.output_spec() @@ -27,3 +29,4 @@ def test_SlicerCommandLine_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/tests/test_auto_Split.py b/nipype/interfaces/tests/test_auto_Split.py index 5d4f97d89a..9c7fbf27c3 100644 --- a/nipype/interfaces/tests/test_auto_Split.py +++ b/nipype/interfaces/tests/test_auto_Split.py @@ -1,6 +1,7 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.utility import Split + def test_Split_inputs(): input_map = dict(ignore_exception=dict(nohash=True, usedefault=True, @@ -15,6 +16,7 @@ def test_Split_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_Split_outputs(): output_map = dict() outputs = Split.output_spec() @@ -22,3 +24,4 @@ def test_Split_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/tests/test_auto_SplitNifti.py b/nipype/interfaces/tests/test_auto_SplitNifti.py index 901443f7f8..a38efc2679 100644 --- a/nipype/interfaces/tests/test_auto_SplitNifti.py +++ b/nipype/interfaces/tests/test_auto_SplitNifti.py @@ -1,19 +1,21 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.dcmstack import SplitNifti + def test_SplitNifti_inputs(): - input_map = dict(out_format=dict(), - split_dim=dict(), - in_file=dict(mandatory=True, + input_map = dict(in_file=dict(mandatory=True, ), out_ext=dict(usedefault=True, ), + out_format=dict(), + split_dim=dict(), ) inputs = SplitNifti.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_SplitNifti_outputs(): output_map = dict(out_list=dict(), ) @@ -22,3 +24,4 @@ def test_SplitNifti_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/tests/test_auto_StdOutCommandLine.py b/nipype/interfaces/tests/test_auto_StdOutCommandLine.py index 9cd8f0a4e2..ee64d2f0e1 100644 --- a/nipype/interfaces/tests/test_auto_StdOutCommandLine.py +++ b/nipype/interfaces/tests/test_auto_StdOutCommandLine.py @@ -1,21 +1,22 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.base import StdOutCommandLine + def test_StdOutCommandLine_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, - ), - terminal_output=dict(mandatory=True, - nohash=True, + input_map = dict(args=dict(argstr='%s', ), environ=dict(nohash=True, usedefault=True, ), - out_file=dict(position=-1, + ignore_exception=dict(nohash=True, + usedefault=True, + ), + out_file=dict(argstr='> %s', genfile=True, - argstr='> %s', + position=-1, ), - args=dict(argstr='%s', + terminal_output=dict(mandatory=True, + nohash=True, ), ) inputs = StdOutCommandLine.input_spec() @@ -23,3 +24,4 @@ def test_StdOutCommandLine_inputs(): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/tests/test_auto_XNATSink.py b/nipype/interfaces/tests/test_auto_XNATSink.py index 666b1da5d0..5fd01e583d 100644 --- a/nipype/interfaces/tests/test_auto_XNATSink.py +++ b/nipype/interfaces/tests/test_auto_XNATSink.py @@ -1,37 +1,39 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.io import XNATSink + def test_XNATSink_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, - usedefault=True, + input_map = dict(_outputs=dict(usedefault=True, ), - _outputs=dict(usedefault=True, + assessor_id=dict(xor=['reconstruction_id'], ), - subject_id=dict(mandatory=True, + cache_dir=dict(), + config=dict(mandatory=True, + xor=['server'], ), - share=dict(usedefault=True, + experiment_id=dict(mandatory=True, ), - server=dict(xor=['config'], - mandatory=True, - requires=['user', 'pwd'], + ignore_exception=dict(nohash=True, + usedefault=True, ), - reconstruction_id=dict(xor=['assessor_id'], + project_id=dict(mandatory=True, ), pwd=dict(), - cache_dir=dict(), - assessor_id=dict(xor=['reconstruction_id'], + reconstruction_id=dict(xor=['assessor_id'], ), - user=dict(), - experiment_id=dict(mandatory=True, + server=dict(mandatory=True, + requires=['user', 'pwd'], + xor=['config'], ), - project_id=dict(mandatory=True, + share=dict(usedefault=True, ), - config=dict(mandatory=True, - xor=['server'], + subject_id=dict(mandatory=True, ), + user=dict(), ) inputs = XNATSink.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + diff --git a/nipype/interfaces/tests/test_auto_XNATSource.py b/nipype/interfaces/tests/test_auto_XNATSource.py index 20b53fe04e..ab86a880f4 100644 --- a/nipype/interfaces/tests/test_auto_XNATSource.py +++ b/nipype/interfaces/tests/test_auto_XNATSource.py @@ -1,30 +1,32 @@ # AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT from nipype.testing import assert_equal from nipype.interfaces.io import XNATSource + def test_XNATSource_inputs(): - input_map = dict(ignore_exception=dict(nohash=True, + input_map = dict(cache_dir=dict(), + config=dict(mandatory=True, + xor=['server'], + ), + ignore_exception=dict(nohash=True, usedefault=True, ), + pwd=dict(), + query_template=dict(mandatory=True, + ), query_template_args=dict(usedefault=True, ), - server=dict(xor=['config'], - mandatory=True, + server=dict(mandatory=True, requires=['user', 'pwd'], + xor=['config'], ), - pwd=dict(), - cache_dir=dict(), user=dict(), - config=dict(mandatory=True, - xor=['server'], - ), - query_template=dict(mandatory=True, - ), ) inputs = XNATSource.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value + def test_XNATSource_outputs(): output_map = dict() outputs = XNATSource.output_spec() @@ -32,3 +34,4 @@ def test_XNATSource_outputs(): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value + diff --git a/tools/checkspecs.py b/tools/checkspecs.py index 2b5afbc8f1..ec70f01a9e 100644 --- a/tools/checkspecs.py +++ b/tools/checkspecs.py @@ -207,11 +207,12 @@ def test_specs(self, uri): cmd = ['# AUTO-GENERATED by tools/checkspecs.py - DO NOT EDIT', 'from nipype.testing import assert_equal', 'from %s import %s' % (uri, c), + '', 'def test_%s_inputs():' % c] input_fields = '' - for traitname, trait in classinst.input_spec().traits(transient=None).items(): + for traitname, trait in sorted(classinst.input_spec().traits(transient=None).items()): input_fields += '%s=dict(' % traitname - for key, value in trait.__dict__.items(): + for key, value in sorted(trait.__dict__.items()): if key in in_built or key == 'desc': continue if isinstance(value, basestring): @@ -229,10 +230,10 @@ def test_specs(self, uri): for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value"""] - fp.writelines('\n'.join(cmd) + '\n') + fp.writelines('\n'.join(cmd) + '\n\n') - for traitname, trait in classinst.input_spec().traits(transient=None).items(): - for key in trait.__dict__: + for traitname, trait in sorted(classinst.input_spec().traits(transient=None).items()): + for key in sorted(trait.__dict__): if key in in_built: continue parent_metadata = [] @@ -251,9 +252,9 @@ def test_specs(self, uri): with open(testfile, 'at') as fp: cmd = ['def test_%s_outputs():' % c] input_fields = '' - for traitname, trait in classinst.output_spec().traits(transient=None).items(): + for traitname, trait in sorted(classinst.output_spec().traits(transient=None).items()): input_fields += '%s=dict(' % traitname - for key, value in trait.__dict__.items(): + for key, value in sorted(trait.__dict__.items()): if key in in_built or key == 'desc': continue if isinstance(value, basestring): @@ -271,10 +272,10 @@ def test_specs(self, uri): for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value"""] - fp.writelines('\n'.join(cmd) + '\n') + fp.writelines('\n'.join(cmd) + '\n\n') - for traitname, trait in classinst.output_spec().traits(transient=None).items(): - for key in trait.__dict__: + for traitname, trait in sorted(classinst.output_spec().traits(transient=None).items()): + for key in sorted(trait.__dict__): if key in in_built: continue parent_metadata = []