Пример #1
0
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 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
Пример #4
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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()
Пример #5
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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
Пример #6
0
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