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]
