Ejemplo n.º 1
0
def test_SUSAN_outputs():
    output_map = dict(smoothed_file=dict(), )
    outputs = SUSAN.output_spec()

    for key, metadata in output_map.items():
        for metakey, value in metadata.items():
            yield assert_equal, getattr(outputs.traits()[key], metakey), value
Ejemplo n.º 2
0
def test_SUSAN_outputs():
    output_map = dict(smoothed_file=dict(),
    )
    outputs = SUSAN.output_spec()

    for key, metadata in output_map.items():
        for metakey, value in metadata.items():
            yield assert_equal, getattr(outputs.traits()[key], metakey), value
Ejemplo n.º 3
0
def test_SUSAN_inputs():
    input_map = dict(
        args=dict(argstr='%s', ),
        brightness_threshold=dict(
            argstr='%.10f',
            mandatory=True,
            position=2,
        ),
        dimension=dict(
            argstr='%d',
            position=4,
            usedefault=True,
        ),
        environ=dict(
            nohash=True,
            usedefault=True,
        ),
        fwhm=dict(
            argstr='%.10f',
            mandatory=True,
            position=3,
        ),
        ignore_exception=dict(
            nohash=True,
            usedefault=True,
        ),
        in_file=dict(
            argstr='%s',
            mandatory=True,
            position=1,
        ),
        out_file=dict(
            argstr='%s',
            genfile=True,
            hash_files=False,
            position=-1,
        ),
        output_type=dict(),
        terminal_output=dict(
            mandatory=True,
            nohash=True,
        ),
        usans=dict(
            argstr='',
            position=6,
            usedefault=True,
        ),
        use_median=dict(
            argstr='%d',
            position=5,
            usedefault=True,
        ),
    )
    inputs = SUSAN.input_spec()

    for key, metadata in input_map.items():
        for metakey, value in metadata.items():
            yield assert_equal, getattr(inputs.traits()[key], metakey), value
Ejemplo n.º 4
0
def test_SUSAN_inputs():
    input_map = dict(args=dict(argstr='%s',
    ),
    brightness_threshold=dict(argstr='%.10f',
    mandatory=True,
    position=2,
    ),
    dimension=dict(argstr='%d',
    position=4,
    usedefault=True,
    ),
    environ=dict(nohash=True,
    usedefault=True,
    ),
    fwhm=dict(argstr='%.10f',
    mandatory=True,
    position=3,
    ),
    ignore_exception=dict(nohash=True,
    usedefault=True,
    ),
    in_file=dict(argstr='%s',
    mandatory=True,
    position=1,
    ),
    out_file=dict(argstr='%s',
    genfile=True,
    hash_files=False,
    position=-1,
    ),
    output_type=dict(),
    terminal_output=dict(mandatory=True,
    nohash=True,
    ),
    usans=dict(argstr='',
    position=6,
    usedefault=True,
    ),
    use_median=dict(argstr='%d',
    position=5,
    usedefault=True,
    ),
    )
    inputs = SUSAN.input_spec()

    for key, metadata in input_map.items():
        for metakey, value in metadata.items():
            yield assert_equal, getattr(inputs.traits()[key], metakey), value
Ejemplo n.º 5
0
    func_data = func_nifti1.get_data()
    func_data = func_data.astype(float)

    brain_values = where(func_data > 0)
    median_thresh = median(brain_values)
    bright_thresh = 0.75 * median_thresh

    return (bright_thresh)


brightthresh_filt = Node(name='brightthresh_filt',
                         interface=Function(input_names=['func'],
                                            output_names=['bright_thresh'],
                                            function=brightthresh))

smooth_filt = Node(SUSAN(fwhm=fwhm), name='smooth_filt')

brightthresh_orig = Node(name='brightthresh_orig',
                         interface=Function(input_names=['func'],
                                            output_names=['bright_thresh'],
                                            function=brightthresh))

smooth_orig = Node(SUSAN(fwhm=fwhm), name='smooth_orig')

# In[8]:

## Preprocessing Workflow

# workflowname.connect([(node1,node2,[('node1output','node2input')]),
#                    (node2,node3,[('node2output','node3input')])
#                    ])