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Commit 7de3cc1e authored by Paul McCarthy's avatar Paul McCarthy :mountain_bicyclist:
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TEST: Test CoefField.transform

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tests/test_transform/test_nonlinear.py
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......@@ -4,10 +4,9 @@ import itertools as it
import os.path as op
import numpy as np
import nibabel as nib
import fsl.data.image as fslimage
import fsl.transform as transform
import fsl.transform.affine as affine
import fsl.transform.nonlinear as nonlinear
import fsl.transform.fnirt as fnirt
......@@ -19,7 +18,7 @@ def _random_image():
vx, vy, vz = np.random.randint(10, 50, 3)
dx, dy, dz = np.random.randint( 1, 10, 3)
data = (np.random.random((vx, vy, vz)) - 0.5) * 10
aff = transform.compose(
aff = affine.compose(
(dx, dy, dz),
np.random.randint(1, 100, 3),
np.random.random(3) * np.pi / 2)
......@@ -34,7 +33,7 @@ def _random_field():
dx, dy, dz = np.random.randint( 1, 10, 3)
field = (np.random.random((vx, vy, vz, 3)) - 0.5) * 10
aff = transform.compose(
aff = affine.compose(
(dx, dy, dz),
np.random.randint(1, 100, 3),
np.random.random(3) * np.pi / 2)
......@@ -47,7 +46,7 @@ def _random_affine_field():
ref = _random_image()
# our test field just encodes an affine
xform = transform.compose(
xform = affine.compose(
np.random.randint(2, 5, 3),
np.random.randint(1, 10, 3),
np.random.random(3))
......@@ -57,8 +56,8 @@ def _random_affine_field():
np.arange(ref.shape[2]), indexing='ij')
rvoxels = np.vstack((rx.flatten(), ry.flatten(), rz.flatten())).T
rcoords = transform.transform(rvoxels, ref.voxToScaledVoxMat)
scoords = transform.transform(rcoords, xform)
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]))
......@@ -74,7 +73,7 @@ def _field_coords(field):
np.arange(vy),
np.arange(vz), indexing='ij')
coords = np.array(coords).transpose((1, 2, 3, 0))
return transform.transform(
return affine.transform(
coords.reshape(-1, 3),
field.getAffine('voxel', 'fsl')).reshape(field.shape)
......@@ -135,15 +134,15 @@ def test_convertDisplacementSpace():
np.random.randint(0, basefield.shape[1], 5),
np.random.randint(0, basefield.shape[2], 5)]
refcoords = np.array(refcoords, dtype=np.int).T
refcoords = transform.transform(refcoords, ref.voxToScaledVoxMat)
refcoords = affine.transform(refcoords, ref.voxToScaledVoxMat)
srccoords = basefield.transform(refcoords)
field = nonlinear.convertDisplacementSpace(basefield, from_, to)
premat = ref.getAffine('fsl', from_)
postmat = src.getAffine('fsl', to)
input = transform.transform(refcoords, premat)
expect = transform.transform(srccoords, postmat)
input = affine.transform(refcoords, premat)
expect = affine.transform(srccoords, postmat)
got = field.transform(input)
enan = np.isnan(expect)
......@@ -163,9 +162,9 @@ def test_DisplacementField_transform():
np.arange(ref.shape[1]),
np.arange(ref.shape[2]), indexing='ij')
rvoxels = np.vstack((rx.flatten(), ry.flatten(), rz.flatten())).T
rcoords = transform.transform(rvoxels, ref.voxToScaledVoxMat)
scoords = transform.transform(rcoords, xform)
svoxels = transform.transform(scoords, src.scaledVoxToVoxMat)
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]))
......@@ -186,9 +185,9 @@ def test_DisplacementField_transform():
# test out of bounds are returned as nan
rvoxels = np.array([[-1, -1, -1],
[ 0, 0, 0]])
rcoords = transform.transform(rvoxels, ref.voxToScaledVoxMat)
scoords = transform.transform(rcoords, xform)
svoxels = transform.transform(scoords, src.scaledVoxToVoxMat)
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, :]))
......@@ -225,6 +224,61 @@ def test_CoefficientField_displacements():
tol = dict(atol=1e-5, rtol=1e-5)
assert np.all(np.isclose(disps, df.data, **tol))
def test_CoefficientField_transform():
nldir = op.join(datadir, 'nonlinear')
src = op.join(nldir, 'src.nii.gz')
ref = op.join(nldir, 'ref.nii.gz')
cf = op.join(nldir, 'coefficientfield.nii.gz')
df = op.join(nldir, 'displacementfield.nii.gz')
dfnp = op.join(nldir, 'displacementfield_no_premat.nii.gz')
src = fslimage.Image(src)
ref = fslimage.Image(ref)
cf = fnirt.readFnirt(cf, src, ref)
df = fnirt.readFnirt(df, src, ref)
dfnp = fnirt.readFnirt(dfnp, src, ref)
spaces = ['fsl', 'voxel', 'world']
spaces = list(it.combinations_with_replacement(spaces, 2))
spaces = spaces + [(r, s) for s, r in spaces]
spaces = list(set(spaces))
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
refcoords = {
'voxel' : rvoxels,
'fsl' : affine.transform(rvoxels, ref.getAffine('voxel', 'fsl')),
'world' : affine.transform(rvoxels, ref.getAffine('voxel', 'world'))
}
srccoords = refcoords['fsl'] + df.data.reshape(-1, 3)
srccoords = {
'voxel' : affine.transform(srccoords, src.getAffine('fsl', 'voxel')),
'fsl' : srccoords,
'world' : affine.transform(srccoords, src.getAffine('fsl', 'world'))
}
srccoordsnp = refcoords['fsl'] + dfnp.data.reshape(-1, 3)
srccoordsnp = {
'voxel' : affine.transform(srccoordsnp, src.getAffine('fsl', 'voxel')),
'fsl' : srccoordsnp,
'world' : affine.transform(srccoordsnp, src.getAffine('fsl', 'world'))
}
tol = dict(atol=1e-5, rtol=1e-5)
for srcspace, refspace in spaces:
got = cf.transform(refcoords[refspace], refspace, srcspace)
gotnp = cf.transform(refcoords[refspace], refspace, srcspace,
premat=False)
assert np.all(np.isclose(got, srccoords[ srcspace], **tol))
assert np.all(np.isclose(gotnp, srccoordsnp[srcspace], **tol))
def test_coefficientFieldToDisplacementField():
nldir = op.join(datadir, 'nonlinear')
......
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