diff --git a/tests/test_transform/test_nonlinear.py b/tests/test_transform/test_nonlinear.py
index 9b51c0d4d610860f1e98e179372945443c0c7567..7bc30f8e98faceeaf421b72feab2ad73cc487e47 100644
--- a/tests/test_transform/test_nonlinear.py
+++ b/tests/test_transform/test_nonlinear.py
@@ -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')