def test_coefficientField_transform_altref():
# test coordinates (manually determined).
# original ref image is 2mm isotropic,
# resampled is 1mm. Each tuple contains:
#
# (src, ref2mm, ref1mm)
coords = [((18.414, 26.579, 25.599), (11, 19, 11), (22, 38, 22)),
((14.727, 22.480, 20.340), (8, 17, 8), (16, 34, 16)),
((19.932, 75.616, 27.747), (11, 45, 5), (22, 90, 10))]
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')
src = fslimage.Image(src)
ref2mm = fslimage.Image(ref)
ref1mm = ref2mm.adjust((1, 1, 1))
cfref2mm = fnirt.readFnirt(cf, src, ref2mm)
cfref1mm = fnirt.readFnirt(cf, src, ref1mm)
for srcc, ref2mmc, ref1mmc in coords:
ref2mmc = cfref2mm.transform(ref2mmc, 'voxel', 'voxel')
ref1mmc = cfref1mm.transform(ref1mmc, 'voxel', 'voxel')
assert np.all(np.isclose(ref2mmc, srcc, 1e-4))
assert np.all(np.isclose(ref1mmc, srcc, 1e-4))
def test_readFnirt():
src = op.join(datadir, 'src')
ref = op.join(datadir, 'ref')
coef = op.join(datadir, 'coefficientfield')
disp = op.join(datadir, 'displacementfield')
src = fslimage.Image(src)
ref = fslimage.Image(ref)
coef = fnirt.readFnirt(coef, src, ref)
disp = fnirt.readFnirt(disp, src, ref)
with pytest.raises(ValueError):
fnirt.readFnirt(src, src, ref)
assert isinstance(coef, nonlinear.CoefficientField)
assert isinstance(disp, nonlinear.DeformationField)
assert coef.src.sameSpace(src)
assert coef.ref.sameSpace(ref)
assert disp.src.sameSpace(src)
assert disp.ref.sameSpace(ref)
assert coef.srcSpace == 'fsl'
assert coef.refSpace == 'fsl'
assert disp.srcSpace == 'fsl'
assert disp.refSpace == 'fsl'
def test_coefficientFieldToDeformationField():
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)
rdf = fnirt.readFnirt(df, src, ref)
rdfnp = fnirt.readFnirt(dfnp, src, ref)
adf = nonlinear.convertDeformationType(rdf)
adfnp = nonlinear.convertDeformationType(rdfnp)
rcnv = nonlinear.coefficientFieldToDeformationField(cf)
acnv = nonlinear.coefficientFieldToDeformationField(cf, defType='absolute')
acnvnp = nonlinear.coefficientFieldToDeformationField(cf,
defType='absolute',
premat=False)
rcnvnp = nonlinear.coefficientFieldToDeformationField(cf, premat=False)
tol = dict(atol=1e-5, rtol=1e-5)
assert np.all(np.isclose(rcnv.data, rdf.data, **tol))
assert np.all(np.isclose(acnv.data, adf.data, **tol))
assert np.all(np.isclose(rcnvnp.data, rdfnp.data, **tol))
assert np.all(np.isclose(acnvnp.data, adfnp.data, **tol))
def test_CoefficientField_displacements():
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_no_premat.nii.gz')
src = fslimage.Image(src)
ref = fslimage.Image(ref)
cf = fnirt.readFnirt(cf, src, ref)
df = fnirt.readFnirt(df, src, ref)
ix, iy, iz = ref.shape[:3]
x, y, z = np.meshgrid(np.arange(ix),
np.arange(iy),
np.arange(iz),
indexing='ij')
x = x.flatten()
y = y.flatten()
z = z.flatten()
xyz = np.vstack((x, y, z)).T
disps = cf.displacements(xyz)
disps = disps.reshape(df.shape)
tol = dict(atol=1e-5, rtol=1e-5)
assert np.all(np.isclose(disps, df.data, **tol))
def test_convert_fnirt_coefficient_field():
datadir = op.join(op.dirname(__file__), '..', 'test_transform', 'testdata',
'nonlinear')
srcfile = op.join(datadir, 'src.nii.gz')
reffile = op.join(datadir, 'ref.nii.gz')
cffile = op.join(datadir, 'coefficientfield.nii.gz')
dffile = op.join(datadir, 'displacementfield.nii.gz')
with tempdir.tempdir():
# nii -> x5
fsl_convert_x5.main('fnirt -s {} -r {} {} coef.x5'.format(
srcfile, reffile, cffile).split())
# x5 -> nii
fsl_convert_x5.main('fnirt coef.x5 coef.nii.gz'.split())
src = fslimage.Image(srcfile)
ref = fslimage.Image(reffile)
df = fnirt.readFnirt(dffile, src, ref)
dfnii = fnirt.readFnirt('coef.nii.gz', src, ref)
assert dfnii.sameSpace(df)
assert dfnii.src.sameSpace(src)
assert dfnii.ref.sameSpace(ref)
assert dfnii.srcSpace == df.srcSpace
assert dfnii.refSpace == df.refSpace
assert dfnii.deformationType == 'relative'
diff = np.abs(dfnii.data - df.data)
tols = {'rtol': 1e-5, 'atol': 1e-5}
assert np.all(np.isclose(dfnii.data, df.data, **tols))
def test_convert_fnirt_deformation_field():
datadir = op.join(op.dirname(__file__), '..', 'test_transform', 'testdata',
'nonlinear')
srcfile = op.join(datadir, 'src.nii.gz')
reffile = op.join(datadir, 'ref.nii.gz')
dffile = op.join(datadir, 'displacementfield.nii.gz')
with tempdir.tempdir():
# nii -> x5
fsl_convert_x5.main('fnirt -s {} -r {} {} disp.x5'.format(
srcfile, reffile, dffile).split())
# x5 -> nii
fsl_convert_x5.main('fnirt disp.x5 disp.nii.gz'.split())
src = fslimage.Image(srcfile)
ref = fslimage.Image(reffile)
df = fnirt.readFnirt(dffile, src, ref)
dfnii = fnirt.readFnirt('disp.nii.gz', src, ref)
assert dfnii.src.sameSpace(src)
assert dfnii.ref.sameSpace(ref)
assert dfnii.srcSpace == df.srcSpace
assert dfnii.refSpace == df.refSpace
assert dfnii.deformationType == df.deformationType
assert np.all(np.isclose(dfnii.data, df.data))
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_toFnirt():
def check(got, exp):
tol = dict(atol=1e-5, rtol=1e-5)
assert np.all(np.isclose(got.data, exp.data, **tol))
assert got.src.sameSpace(exp.src)
assert got.ref.sameSpace(exp.ref)
assert got.srcSpace == 'fsl'
assert got.refSpace == 'fsl'
basefield, xform = _random_affine_field()
src = basefield.src
ref = basefield.ref
spaces = it.permutations(('voxel', 'fsl', 'world'), 2)
for from_, to in spaces:
field = nonlinear.convertDeformationSpace(basefield, from_, to)
got = fnirt.toFnirt(field)
check(got, basefield)
src = fslimage.Image(op.join(datadir, 'src'))
ref = fslimage.Image(op.join(datadir, 'ref'))
coef = fnirt.readFnirt(op.join(datadir, 'coefficientfield'), src, ref)
got = fnirt.toFnirt(coef)
check(got, coef)
def test_readWriteNonLinearX5():
datadir = op.join(op.dirname(__file__), 'testdata', 'nonlinear')
dffile = op.join(datadir, 'displacementfield.nii.gz')
srcfile = op.join(datadir, 'src.nii.gz')
reffile = op.join(datadir, 'ref.nii.gz')
src = fslimage.Image(srcfile)
ref = fslimage.Image(reffile)
dfield = fnirt.readFnirt(dffile, src, ref)
wdfield = nonlinear.convertDeformationSpace(dfield, 'world', 'world')
with tempdir.tempdir():
# field must be world->world
with pytest.raises(x5.X5Error):
x5.writeNonLinearX5('nonlinear.x5', dfield)
x5.writeNonLinearX5('nonlinear.x5', wdfield)
gotdfield = x5.readNonLinearX5('nonlinear.x5')
assert gotdfield.src.sameSpace(src)
assert gotdfield.ref.sameSpace(ref)
assert gotdfield.srcSpace == wdfield.srcSpace
assert gotdfield.refSpace == wdfield.refSpace
assert gotdfield.deformationType == wdfield.deformationType
assert np.all(np.isclose(gotdfield.data, wdfield.data))
with h5py.File('nonlinear.x5', 'r') as f:
assert f.attrs['Type'] == 'nonlinear'
_check_metadata(f)
_check_deformation(f['/Transform'], wdfield)
_check_space(f['/A'], ref)
_check_space(f['/B'], src)
def test_fromFnirt():
basefield, basexform = _random_affine_field()
src = basefield.src
ref = basefield.ref
spaces = list(it.permutations(('voxel', 'fsl', 'world'), 2))
for from_, to in spaces:
got = fnirt.fromFnirt(basefield, from_, to)
assert got.srcSpace == to
assert got.refSpace == from_
coords = [
np.random.randint(0, basefield.shape[0], 5),
np.random.randint(0, basefield.shape[1], 5),
np.random.randint(0, basefield.shape[2], 5)
]
coords = np.array(coords).T
coords = affine.transform(coords, ref.getAffine('voxel', from_))
aff = affine.concat(src.getAffine('fsl', to), basexform,
ref.getAffine(from_, 'fsl'))
got = got.transform(coords)
exp = affine.transform(coords, aff)
enan = np.isnan(exp)
gnan = np.isnan(got)
assert np.all(np.isclose(enan, gnan))
assert np.all(np.isclose(exp[~enan], got[~gnan]))
# Converting from a FNIRT coefficient field
src = fslimage.Image(op.join(datadir, 'src'))
ref = fslimage.Image(op.join(datadir, 'ref'))
coef = fnirt.readFnirt(op.join(datadir, 'coefficientfield'), src, ref)
disp = fnirt.readFnirt(op.join(datadir, 'displacementfield'), src, ref)
for from_, to in spaces:
cnv = fnirt.fromFnirt(coef, from_, to)
exp = nonlinear.convertDeformationSpace(disp, from_, to)
tol = dict(atol=1e-5, rtol=1e-5)
assert np.all(np.isclose(cnv.data, exp.data, **tol))
def get_for_row(self, afq_object, row):
nearest_warp, nearest_space = self.fnames[row['ses']][row['subject']]
our_templ = afq_object.reg_template_img
subj = Image(row['dwi_file'])
their_templ = Image(nearest_space)
warp = readFnirt(nearest_warp, their_templ, subj)
return ConformedFnirtMapping(warp, our_templ.affine)
def fnirtToX5(args):
"""Convert a non-linear FNIRT transformation into an X5 transformation
file.
"""
src = args.source
ref = args.reference
field = fnirt.readFnirt(args.input, src=src, ref=ref)
field = fnirt.fromFnirt(field, 'world', 'world')
x5.writeNonLinearX5(args.output, field)
def get_for_subses(self, subses_dict, reg_template, reg_subject):
nearest_warp, nearest_space = self.fnames[subses_dict['ses']][
subses_dict['subject']]
our_templ = reg_template
subj = Image(subses_dict['dwi_file'])
their_templ = Image(nearest_space)
warp = readFnirt(nearest_warp, their_templ, subj)
return ConformedFnirtMapping(warp, our_templ.affine)
def test_readFnirt_defType_intent():
src = op.join(datadir, 'src.nii.gz')
ref = op.join(datadir, 'ref.nii.gz')
coef = op.join(datadir, 'coefficientfield.nii.gz')
disp = op.join(datadir, 'displacementfield.nii.gz')
src = fslimage.Image(src)
ref = fslimage.Image(ref)
field = fnirt.readFnirt(disp, src, ref, defType='absolute')
assert field.deformationType == 'absolute'
field = fnirt.readFnirt(disp, src, ref, defType='relative')
assert field.deformationType == 'relative'
img = nib.load(coef)
img.header['intent_code'] = 0
with tempdir.tempdir():
img.to_filename('field.nii.gz')
with pytest.raises(ValueError):
fnirt.readFnirt('field', src, ref)
field = fnirt.readFnirt('field',
src,
ref,
intent=constants.FSL_CUBIC_SPLINE_COEFFICIENTS)
assert isinstance(field, nonlinear.CoefficientField)
field = fnirt.readFnirt('field',
src,
ref,
intent=constants.FSL_FNIRT_DISPLACEMENT_FIELD)
assert isinstance(field, nonlinear.DeformationField)