def test_ApplyTransformsToPoints_outputs(): output_map = dict(output_file=dict(), ) outputs = ApplyTransformsToPoints.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_ApplyTransformsToPoints_inputs(): input_map = dict(args=dict(argstr='%s', ), dimension=dict(argstr='--dimensionality %d', ), environ=dict(nohash=True, usedefault=True, ), ignore_exception=dict(nohash=True, usedefault=True, ), input_file=dict(argstr='--input %s', mandatory=True, ), invert_transform_flags=dict(), num_threads=dict(nohash=True, usedefault=True, ), output_file=dict(argstr='--output %s', hash_files=False, name_source=['input_file'], name_template='%s_transformed.csv', ), terminal_output=dict(mandatory=True, nohash=True, ), transforms=dict(argstr='%s', mandatory=True, ), ) inputs = ApplyTransformsToPoints.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 apply_transform_2_points(input_csv, transforms, output_csv): at = ApplyTransformsToPoints() at.inputs.dimension = 2 at.inputs.input_file = input_csv at.inputs.transforms = transforms at.inputs.invert_transform_flags = [False, False] at.inputs.output_file = output_csv args = shlex.split(at.cmdline) p = subprocess.Popen(args) p.wait()
def _tr_points_wf(): wf = pe.Workflow('trpointswf') inputspec = pe.Node(IdentityInterface(['T1', 'model', 'points']), 'inputspec') reg = pe.Node(ants_registration_affine_node(write_composite_transform=False), name='register') convertpoints = pe.Node(ConvertPoints(in_format='tsv', out_format='ants'), 'convert_points') trpoints = pe.Node(ApplyTransformsToPoints(dimension=3), name='transform_points') convertpoints2 = pe.Node(ConvertPoints(in_format='ants', out_format='tsv'), 'convert_points2') outputspec = pe.Node(IdentityInterface(['out_points']), 'outputspec') wf.connect([(inputspec, reg, [('T1', 'moving_image'), ('model', 'fixed_image')]), (inputspec, convertpoints, [('points', 'in_file')]), (reg, trpoints, [('forward_transforms', 'transforms')]), (convertpoints, trpoints, [('out_file', 'input_file')]), (trpoints, convertpoints2, [('output_file', 'in_file')]), (convertpoints2, outputspec, [('out_file', 'out_points')])]) return wf
def test_ApplyTransformsToPoints_inputs(): input_map = dict( args=dict(argstr='%s', ), dimension=dict(argstr='--dimensionality %d', ), environ=dict( nohash=True, usedefault=True, ), ignore_exception=dict( nohash=True, usedefault=True, ), input_file=dict( argstr='--input %s', mandatory=True, ), invert_transform_flags=dict(), num_threads=dict( nohash=True, usedefault=True, ), output_file=dict( argstr='--output %s', hash_files=False, name_source=['input_file'], name_template='%s_transformed.csv', ), terminal_output=dict( mandatory=True, nohash=True, ), transforms=dict( argstr='%s', mandatory=True, ), ) inputs = ApplyTransformsToPoints.input_spec() for key, metadata in input_map.items(): for metakey, value in metadata.items(): yield assert_equal, getattr(inputs.traits()[key], metakey), value