def _affine_field(src, ref, xform, srcSpace, refSpace, shape=None, fv2w=None):
if shape is None: shape = ref.shape[:3]
if fv2w is None: fv2w = ref.getAffine('voxel', 'world')
rx, ry, rz = np.meshgrid(np.arange(shape[0]),
np.arange(shape[1]),
np.arange(shape[2]),
indexing='ij')
rvoxels = np.vstack((rx.flatten(), ry.flatten(), rz.flatten())).T
f2r = affine.concat(ref.getAffine('world', refSpace), fv2w)
rcoords = affine.transform(rvoxels, f2r)
scoords = affine.transform(rcoords, xform)
field = np.zeros(list(shape[:3]) + [3])
field[:] = (scoords - rcoords).reshape(*it.chain(shape, [3]))
field = nonlinear.DeformationField(field,
src,
ref,
srcSpace=srcSpace,
refSpace=refSpace,
xform=fv2w,
header=ref.header,
defType='relative')
return field
def _random_affine_field():
src = _random_image()
ref = _random_image()
# our test field just encodes an affine
xform = affine.compose(np.random.randint(2, 5, 3),
np.random.randint(1, 10, 3), np.random.random(3))
rx, ry, rz = np.meshgrid(np.arange(ref.shape[0]),
np.arange(ref.shape[1]),
np.arange(ref.shape[2]),
indexing='ij')
rvoxels = np.vstack((rx.flatten(), ry.flatten(), rz.flatten())).T
rcoords = affine.transform(rvoxels, ref.voxToScaledVoxMat)
scoords = affine.transform(rcoords, xform)
field = np.zeros(list(ref.shape[:3]) + [3])
field[:] = (scoords - rcoords).reshape(*it.chain(ref.shape, [3]))
field = nonlinear.DeformationField(field,
src,
ref,
header=ref.header,
defType='relative')
return field, xform
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_detectDeformationType():
relfield = _random_field()
coords = _field_coords(relfield)
absfield = nonlinear.DeformationField(relfield.data + coords,
src=relfield.src,
xform=relfield.voxToWorldMat)
assert nonlinear.detectDeformationType(relfield) == 'relative'
assert nonlinear.detectDeformationType(absfield) == 'absolute'
def _random_field():
src = _random_image()
vx, vy, vz = np.random.randint(10, 50, 3)
dx, dy, dz = np.random.randint(1, 10, 3)
field = (np.random.random((vx, vy, vz, 3)) - 0.5) * 10
aff = affine.compose((dx, dy, dz), np.random.randint(1, 100, 3),
np.random.random(3) * np.pi / 2)
return nonlinear.DeformationField(field, src=src, xform=aff)
def test_DeformationField_transform():
relfield, xform = _random_affine_field()
src = relfield.src
ref = relfield.ref
rx, ry, rz = np.meshgrid(np.arange(ref.shape[0]),
np.arange(ref.shape[1]),
np.arange(ref.shape[2]),
indexing='ij')
rvoxels = np.vstack((rx.flatten(), ry.flatten(), rz.flatten())).T
rcoords = affine.transform(rvoxels, ref.voxToScaledVoxMat)
scoords = affine.transform(rcoords, xform)
svoxels = affine.transform(scoords, src.scaledVoxToVoxMat)
absfield = np.zeros(list(ref.shape[:3]) + [3])
absfield[:] = scoords.reshape(*it.chain(ref.shape, [3]))
absfield = nonlinear.DeformationField(absfield,
src,
ref,
header=ref.header,
defType='absolute')
got = relfield.transform(rcoords)
assert np.all(np.isclose(got, scoords))
got = absfield.transform(rcoords)
assert np.all(np.isclose(got, scoords))
# test single set of coords
got = absfield.transform(rcoords[0])
assert np.all(np.isclose(got, scoords[0]))
got = relfield.transform(rvoxels, from_='voxel', to='voxel')
assert np.all(np.isclose(got, svoxels))
got = absfield.transform(rvoxels, from_='voxel', to='voxel')
assert np.all(np.isclose(got, svoxels))
# test out of bounds are returned as nan
rvoxels = np.array([[-1, -1, -1], [0, 0, 0]])
rcoords = affine.transform(rvoxels, ref.voxToScaledVoxMat)
scoords = affine.transform(rcoords, xform)
svoxels = affine.transform(scoords, src.scaledVoxToVoxMat)
got = relfield.transform(rcoords)
assert np.all(np.isnan(got[0, :]))
assert np.all(np.isclose(got[1, :], scoords[1, :]))
got = absfield.transform(rcoords)
assert np.all(np.isnan(got[0, :]))
assert np.all(np.isclose(got[1, :], scoords[1, :]))
def test_convertDeformationType():
relfield = _random_field()
coords = _field_coords(relfield)
absfield = nonlinear.DeformationField(relfield.data + coords,
src=relfield.src,
xform=relfield.voxToWorldMat)
gotconvrel1 = nonlinear.convertDeformationType(relfield)
gotconvabs1 = nonlinear.convertDeformationType(absfield)
gotconvrel2 = nonlinear.convertDeformationType(relfield, 'absolute')
gotconvabs2 = nonlinear.convertDeformationType(absfield, 'relative')
tol = dict(atol=1e-3, rtol=1e-3)
assert np.all(np.isclose(gotconvrel1, absfield.data, **tol))
assert np.all(np.isclose(gotconvabs1, relfield.data, **tol))
assert np.all(np.isclose(gotconvrel2, absfield.data, **tol))
assert np.all(np.isclose(gotconvabs2, relfield.data, **tol))