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
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
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
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
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')])
# ])