def test_applyDeformation_premat():
src2ref = affine.compose(
np.random.randint(2, 5, 3),
np.random.randint(1, 10, 3),
[0, 0, 0])
ref2src = affine.invert(src2ref)
srcdata = np.random.randint(1, 65536, (10, 10, 10))
refdata = np.random.randint(1, 65536, (10, 10, 10))
src = fslimage.Image(srcdata)
ref = fslimage.Image(refdata, xform=src2ref)
field = _affine_field(src, ref, ref2src, 'world', 'world')
# First try a down-sampled version
# of the original source image
altsrc, xf = resample.resample(src, (5, 5, 5), origin='corner')
altsrc = fslimage.Image(altsrc, xform=xf, header=src.header)
expect, xf = resample.resampleToReference(
altsrc, ref, matrix=src2ref, order=1, mode='nearest')
premat = affine.concat(src .getAffine('world', 'voxel'),
altsrc.getAffine('voxel', 'world'))
result = nonlinear.applyDeformation(
altsrc, field, order=1, mode='nearest', premat=premat)
assert np.all(np.isclose(expect, result))
# Now try a down-sampled ROI
# of the original source image
altsrc = roi.roi(src, [(2, 9), (2, 9), (2, 9)])
altsrc, xf = resample.resample(altsrc, (4, 4, 4))
altsrc = fslimage.Image(altsrc, xform=xf, header=src.header)
expect, xf = resample.resampleToReference(
altsrc, ref, matrix=src2ref, order=1, mode='nearest')
premat = affine.concat(src .getAffine('world', 'voxel'),
altsrc.getAffine('voxel', 'world'))
result = nonlinear.applyDeformation(
altsrc, field, order=1, mode='nearest', premat=premat)
assert np.all(np.isclose(expect, result))
# down-sampled and offset ROI
# of the original source image
altsrc = roi.roi(src, [(-5, 8), (-5, 8), (-5, 8)])
altsrc, xf = resample.resample(altsrc, (6, 6, 6))
altsrc = fslimage.Image(altsrc, xform=xf, header=src.header)
expect, xf = resample.resampleToReference(
altsrc, ref, matrix=src2ref, order=1, mode='nearest')
premat = affine.concat(src .getAffine('world', 'voxel'),
altsrc.getAffine('voxel', 'world'))
result = nonlinear.applyDeformation(
altsrc, field, order=1, mode='nearest', premat=premat)
assert np.all(np.isclose(expect, result))
def test_applyDeformation_worldAligned():
refv2w = affine.scaleOffsetXform([1, 1, 1], [10, 10, 10])
fieldv2w = affine.scaleOffsetXform([2, 2, 2], [10.5, 10.5, 10.5])
src2ref = refv2w
ref2src = affine.invert(src2ref)
srcdata = np.random.randint(1, 65536, (10, 10, 10))
src = fslimage.Image(srcdata)
ref = fslimage.Image(srcdata, xform=src2ref)
field = _affine_field(src, ref, ref2src, 'world', 'world',
shape=(5, 5, 5), fv2w=fieldv2w)
field = nonlinear.DeformationField(
nonlinear.convertDeformationType(field, 'absolute'),
header=field.header,
src=src,
ref=ref,
srcSpace='world',
refSpace='world',
defType='absolute')
expect, xf = resample.resampleToReference(
src, ref, matrix=src2ref, order=1, mode='constant', cval=0)
result = nonlinear.applyDeformation(
src, field, order=1, mode='constant', cval=0)
expect = expect[1:-1, 1:-1, 1:-1]
result = result[1:-1, 1:-1, 1:-1]
assert np.all(np.isclose(expect, result))
def test_applyDeformation_altref():
src2ref = affine.compose(
np.random.randint(2, 5, 3),
np.random.randint(1, 10, 3),
np.random.random(3))
ref2src = affine.invert(src2ref)
srcdata = np.random.randint(1, 65536, (10, 10, 10))
refdata = np.random.randint(1, 65536, (10, 10, 10))
src = fslimage.Image(srcdata)
ref = fslimage.Image(refdata, xform=src2ref)
field = _affine_field(src, ref, ref2src, 'world', 'world')
altrefxform = affine.concat(
src2ref,
affine.scaleOffsetXform([1, 1, 1], [5, 0, 0]))
altref = fslimage.Image(refdata, xform=altrefxform)
expect, xf = resample.resampleToReference(
src, altref, matrix=src2ref, order=1, mode='constant', cval=0)
result = nonlinear.applyDeformation(
src, field, ref=altref, order=1, mode='constant', cval=0)
# boundary voxels can get truncated
# (4 is the altref-ref overlap boundary)
expect[4, :, :] = 0
result[4, :, :] = 0
expect = expect[1:-1, 1:-1, 1:-1]
result = result[1:-1, 1:-1, 1:-1]
assert np.all(np.isclose(expect, result))
def applyNonlinear(args):
"""Applies a non-linear X5 transformation file to the input.
:arg args: ``argparse.Namespace`` object
:returns: The transformed input as an :class:`.Image` object
"""
field = x5.readNonLinearX5(args.xform)
if args.ref is None: ref = field.ref
else: ref = args.ref
result = nonlinear.applyDeformation(args.input,
field,
ref=ref,
order=args.interp,
mode='constant')
return fslimage.Image(result, header=ref.header)
def test_applyDeformation():
src2ref = affine.compose(np.random.randint(2, 5, 3),
np.random.randint(1, 10, 3), np.random.random(3))
ref2src = affine.invert(src2ref)
srcdata = np.random.randint(1, 65536, (10, 10, 10))
refdata = np.random.randint(1, 65536, (10, 10, 10))
src = fslimage.Image(srcdata)
ref = fslimage.Image(refdata, xform=src2ref)
field = _affine_field(src, ref, ref2src, 'world', 'world')
expect, xf = resample.resampleToReference(src,
ref,
matrix=src2ref,
order=1,
mode='nearest')
result = nonlinear.applyDeformation(src, field, order=1, mode='nearest')
assert np.all(np.isclose(expect, result))
def transform_inverse(self, data, **kwargs):
data_img = Image(
nib.Nifti1Image(data.astype(np.float32), self.ref_affine))
xform_data = np.asarray(applyDeformation(data_img, self.warp).data)
return xform_data
