def test_ApplyTransform_outputs(): output_map = dict(out_file=dict()) outputs = ApplyTransform.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value
def test_ApplyTransform_outputs(): output_map = dict(out_file=dict(), ) outputs = ApplyTransform.output_spec() for key, metadata in output_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(outputs.traits()[key], metakey), value
def test_ApplyTransform_inputs(): input_map = dict( ignore_exception=dict( nohash=True, usedefault=True, ), in_file=dict( copyfile=True, mandatory=True, ), mat=dict(mandatory=True, ), matlab_cmd=dict(), mfile=dict(usedefault=True, ), out_file=dict(genfile=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_inputs(): input_map = dict( ignore_exception=dict(nohash=True, usedefault=True), in_file=dict(copyfile=True, mandatory=True), mat=dict(mandatory=True), matlab_cmd=dict(), mfile=dict(usedefault=True), out_file=dict(genfile=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
spm.SPMCommand.set_mlab_paths(matlab_cmd=matlab_cmd, use_mcr=True) # Test whether spm version is printed to the screen spm.SPMCommand().version # Setting the parameters from collected arguments transf_mat_path = '/data/mat_file/transform.mat' tpm_path = '/data/tpm_file/TPM.nii' #Create vbm_spm12 dir if not os.path.exists(vbm_out + "/vbm_spm12"): os.makedirs(vbm_out + "/vbm_spm12") # Reorientation node and settings reorient = pe.Node(interface=ApplyTransform(), name='reorient') reorient.inputs.mat = transf_mat_path reorient.inputs.in_file = nifti_file reorient.inputs.out_file = vbm_out + "/vbm_spm12/Re.nii" # Segementation Node and settings segmentation = pe.Node(interface=NewSegment(), name='segmentation') segmentation.inputs.channel_info = (0.0001, 60, (False, False)) Tis1 = ((tpm_path, 1), 1, (True, False), (True, True)) Tis2 = ((tpm_path, 2), 1, (True, False), (True, True)) Tis3 = ((tpm_path, 3), 2, (True, False), (True, True)) Tis4 = ((tpm_path, 4), 3, (True, False), (True, True)) Tis5 = ((tpm_path, 5), 4, (True, False), (True, True)) Tis6 = ((tpm_path, 6), 2, (True, False), (True, True)) segmentation.inputs.tissues = [Tis1, Tis2, Tis3, Tis4, Tis5, Tis6]