def test_JointFusion_radius():
at = JointFusion()
set_radius = lambda attr,x,y,z: setattr(at.inputs, attr, [x, y, z])
for attr in ['patch_radius', 'search_radius']:
for x in range(5):
set_radius(attr, x, x + 1, x**x)
yield assert_equal, at._format_arg(attr, None, getattr(at.inputs, attr))[4:], '{0}x{1}x{2}'.format(x, x + 1, x**x)
def test_JointFusion_radius():
at = JointFusion()
set_radius = lambda attr,x,y,z: setattr(at.inputs, attr, [x, y, z])
for attr in ['patch_radius', 'search_radius']:
for x in range(5):
set_radius(attr, x, x + 1, x**x)
yield assert_equal, at._format_arg(attr, None, getattr(at.inputs, attr))[4:], '{0}x{1}x{2}'.format(x, x + 1, x**x)
def test_JointFusion_cmd():
at = JointFusion()
at.inputs.dimension = 3
at.inputs.modalities = 1
at.inputs.method = 'Joint[0.1,2]'
at.inputs.output_label_image = 'fusion_labelimage_output.nii'
warped_intensity_images = [example_data('im1.nii'),
example_data('im2.nii')]
at.inputs.warped_intensity_images = warped_intensity_images
segmentation_images = [example_data('segmentation0.nii.gz'),
example_data('segmentation1.nii.gz')]
at.inputs.warped_label_images = segmentation_images
T1_image = example_data('T1.nii')
at.inputs.target_image = T1_image
at.inputs.patch_radius = [3, 2, 1]
at.inputs.search_radius = [1, 2, 3]
expected_command = ('jointfusion 3 1 -m Joint[0.1,2] -rp 3x2x1 -rs 1x2x3'
' -tg %s -g %s -g %s -l %s -l %s'
' fusion_labelimage_output.nii') % (T1_image,
warped_intensity_images[0],
warped_intensity_images[1],
segmentation_images[0],
segmentation_images[1])
assert at.cmdline == expected_command
# setting intensity or labels with unequal lengths raises error
with pytest.raises(AssertionError):
at._format_arg('warped_intensity_images', InputMultiPath, warped_intensity_images + [example_data('im3.nii')])
def test_JointFusion_cmd():
at = JointFusion()
at.inputs.dimension = 3
at.inputs.modalities = 1
at.inputs.method = 'Joint[0.1,2]'
at.inputs.output_label_image = 'fusion_labelimage_output.nii'
warped_intensity_images = [
example_data('im1.nii'),
example_data('im2.nii')
]
at.inputs.warped_intensity_images = warped_intensity_images
segmentation_images = [
example_data('segmentation0.nii.gz'),
example_data('segmentation1.nii.gz')
]
at.inputs.warped_label_images = segmentation_images
T1_image = example_data('T1.nii')
at.inputs.target_image = T1_image
at.inputs.patch_radius = [3, 2, 1]
at.inputs.search_radius = [1, 2, 3]
expected_command = ('jointfusion 3 1 -m Joint[0.1,2] -rp 3x2x1 -rs 1x2x3'
' -tg %s -g %s -g %s -l %s -l %s'
' fusion_labelimage_output.nii') % (
T1_image, warped_intensity_images[0],
warped_intensity_images[1], segmentation_images[0],
segmentation_images[1])
assert at.cmdline == expected_command
# setting intensity or labels with unequal lengths raises error
with pytest.raises(AssertionError):
at._format_arg('warped_intensity_images', InputMultiPath,
warped_intensity_images + [example_data('im3.nii')])
def test_JointFusion_cmd():
at = JointFusion()
at.inputs.dimension = 3
at.inputs.modalities = 1
at.inputs.method = 'Joint[0.1,2]'
at.inputs.output_label_image = 'fusion_labelimage_output.nii'
at.inputs.warped_intensity_images = ['im1.nii', 'im2.nii']
at.inputs.warped_label_images = [
'segmentation0.nii.gz', 'segmentation1.nii.gz'
]
at.inputs.target_image = 'T1.nii'
at.inputs.patch_radius = [3, 2, 1]
at.inputs.search_radius = [1, 2, 3]
yield assert_equal, at.cmdline, 'jointfusion 3 1' + \
' -m Joint[0.1,2]' + \
' -rp 3x2x1' + \
' -rs 1x2x3' + \
' -tg T1.nii' + \
' -g im1.nii' + \
' -g im2.nii' + \
' -l segmentation0.nii.gz' + \
' -l segmentation1.nii.gz' + \
' fusion_labelimage_output.nii',
"Command line generation failure", True
# setting intensity or labels with unequal lengths raises error
yield assert_raises, AssertionError, at._format_arg, 'warped_intensity_images', InputMultiPath, [
'im1.nii', 'im2.nii', 'im3.nii'
]
def test_JointFusion_dimension():
at = JointFusion()
set_dimension = lambda d: setattr(at.inputs, 'dimension', int(d))
for d in range(2, 5):
set_dimension(d)
yield assert_equal, at.inputs.dimension, int(d)
for d in [0, 1, 6, 7]:
yield assert_raises, TraitError, set_dimension, d
def __init__(self,
atlas_segmentation_image=['path', 'path'],
atlas_image=[['path']],
target_image=['path'],
**options):
from nipype.interfaces.ants import JointFusion
at = JointFusion()
at.inputs.warped_label_images = warped_label_images
at.inputs.warped_intensity_images = warped_intensity_images
at.inputs.output_label_image = output_label_image
at.inputs.target_image = target_image
at.inputs.modalities = modalities
at.inputs.dimension = dimension
for ef in options:
setattr(at.inputs, ef, options[ef])
self.res = at.run()
def test_JointFusion_dimension():
at = JointFusion()
set_dimension = lambda d: setattr(at.inputs, "dimension", int(d))
for d in range(2, 5):
set_dimension(d)
assert at.inputs.dimension == int(d)
for d in [0, 1, 6, 7]:
with pytest.raises(TraitError):
set_dimension(d)
def test_JointFusion_method(a, b):
at = JointFusion()
set_method = lambda a, b: setattr(at.inputs, 'method', 'Joint[%.1f,%d]'.format(a, b))
_a = a / 10.0
set_method(_a, b)
# set directly
assert at.inputs.method == 'Joint[%.1f,%d]'.format(_a, b)
aprime = _a + 0.1
bprime = b + 1
at.inputs.alpha = aprime
at.inputs.beta = bprime
# set with alpha/beta
assert at.inputs.method == 'Joint[%.1f,%d]'.format(aprime, bprime)
def test_JointFusion_method():
at = JointFusion()
set_method = lambda a, b: setattr(at.inputs, 'method', 'Joint[%.1f,%d]'.format(a, b))
for a in range(10):
_a = a / 10.0
for b in range(10):
set_method(_a, b)
# set directly
yield assert_equal, at.inputs.method, 'Joint[%.1f,%d]'.format(_a, b)
aprime = _a + 0.1
bprime = b + 1
at.inputs.alpha = aprime
at.inputs.beta = bprime
# set with alpha/beta
yield assert_equal, at.inputs.method, 'Joint[%.1f,%d]'.format(aprime, bprime)
def test_JointFusion_modalities():
at = JointFusion()
set_modalities = lambda m: setattr(at.inputs, 'modalities', int(m))
for m in range(1, 5):
set_modalities(m)
yield assert_equal, at.inputs.modalities, int(m)
def test_JointFusion_radius(attr, x):
at = JointFusion()
setattr(at.inputs, attr, [x, x + 1, x**x])
assert at._format_arg(attr, None, getattr(
at.inputs, attr))[4:] == "{0}x{1}x{2}".format(x, x + 1, x**x)
def test_JointFusion_modalities(m):
at = JointFusion()
setattr(at.inputs, "modalities", int(m))
assert at.inputs.modalities == int(m)
def test_JointFusion_radius(attr, x):
at = JointFusion()
setattr(at.inputs, attr, [x, x+1, x**x])
assert at._format_arg(attr, None, getattr(at.inputs, attr))[4:] == '{0}x{1}x{2}'.format(x, x + 1, x**x)