def test_BuildConnectome_outputs():
output_map = dict(out_file=dict(), )
outputs = BuildConnectome.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_BuildConnectome_outputs():
output_map = dict(out_file=dict(),
)
outputs = BuildConnectome.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_BuildConnectome_inputs():
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=-3,
),
in_parc=dict(argstr='%s',
position=-2,
),
in_scalar=dict(argstr='-image %s',
),
in_weights=dict(argstr='-tck_weights_in %s',
),
keep_unassigned=dict(argstr='-keep_unassigned',
),
metric=dict(argstr='-metric %s',
),
nthreads=dict(argstr='-nthreads %d',
nohash=True,
),
out_file=dict(argstr='%s',
mandatory=True,
position=-1,
usedefault=True,
),
search_forward=dict(argstr='-assignment_forward_search %f',
),
search_radius=dict(argstr='-assignment_radial_search %f',
),
search_reverse=dict(argstr='-assignment_reverse_search %f',
),
terminal_output=dict(nohash=True,
),
vox_lookup=dict(argstr='-assignment_voxel_lookup',
),
zero_diagonal=dict(argstr='-zero_diagonal',
),
)
inputs = BuildConnectome.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_BuildConnectome_inputs():
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=-3,
),
in_parc=dict(
argstr='%s',
position=-2,
),
in_scalar=dict(argstr='-image %s', ),
in_weights=dict(argstr='-tck_weights_in %s', ),
keep_unassigned=dict(argstr='-keep_unassigned', ),
metric=dict(argstr='-metric %s', ),
nthreads=dict(
argstr='-nthreads %d',
nohash=True,
),
out_file=dict(
argstr='%s',
mandatory=True,
position=-1,
usedefault=True,
),
search_forward=dict(argstr='-assignment_forward_search %f', ),
search_radius=dict(argstr='-assignment_radial_search %f', ),
search_reverse=dict(argstr='-assignment_reverse_search %f', ),
terminal_output=dict(nohash=True, ),
vox_lookup=dict(argstr='-assignment_voxel_lookup', ),
zero_diagonal=dict(argstr='-zero_diagonal', ),
)
inputs = BuildConnectome.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 create_workflow(self, flow, inputnode, outputnode):
#conflow = pe.Workflow(name='MRTRix_connectome_pipeline')
#connectome_inputnode = pe.Node(interface=util.IdentityInterface(fields=['intck','fod_file','roi_volumes']),name='inputnode')
#connectome_outputnode = pe.Node(interface=util.IdentityInterface(fields=['connectome']),name='outputnode')
def get_first(output):
return output[0]
# Additional maps
map_merge = pe.Node(interface=util.Merge(4),
name="merge_additional_maps")
flow.connect([
(inputnode, map_merge, [('gFA', 'in1'), ('skewness', 'in2'),
('kurtosis', 'in3'), ('P0', 'in4')])
#(map_merge,cmtk_mrtrixcmat, [('out','additional_maps')]),
])
#print "INTCK : ",intck
if self.config.fiber_filter:
fibers_filter = pe.Node(
interface=FilterTractogram(out_file='streamlines_weights.txt'),
name='fibers_filter')
flow.connect([(inputnode, fibers_filter, [('track_file',
'in_tracks')])])
# if inputnode.inputs.diffusion_model == 'Deterministic':
# flow.connect([
# (inputnode,fibers_filter,[('track_file','in_tracks')])
# ])
# else:
# flow.connect([
# (inputnode,fibers_filter,[(('track_file',get_first),'in_tracks')]),
# ])
flow.connect([(inputnode, fibers_filter, [('fod_file', 'in_fod')])
])
connectome_builder = pe.Node(interface=BuildConnectome(),
name='connectome_builder')
#connectome_builder.inputs.zero_diagonal = True
#Test if trackfile is a list of tracks filename (Probabilistic tracking) or only a filename (Deterministic tracking)
flow.connect([(inputnode, connectome_builder, [('track_file',
'in_file')])])
# if inputnode.inputs.diffusion_model == 'Deterministic':
# print "Deterministic"
# flow.connect([
# (inputnode,connectome_builder,[('track_file','in_file')])
# ])
# else:
# print "Probabilistic"
# flow.connect([
# (inputnode,connectome_builder,[(('track_file',get_first),'in_file')])
# ])
flow.connect([
(inputnode, connectome_builder, [(('roi_volumes_registered',
get_first), 'in_parc')]),
])
if self.config.fiber_filter:
flow.connect([(fibers_filter, connectome_builder,
[('out_weights', 'in_weights')])])
flow.connect([(inputnode, outputnode, [('track_file',
'streamline_final_file')]),
(connectome_builder, outputnode,
[('out_file', 'connectivity_matrices')])])
