diff --git a/tests/test_transform/test_fnirt.py b/tests/test_transform/test_fnirt.py
index 3288972f37b2a1c718f9de973f66d750ae0405cd..eefc68b64e471dc052ff4fb92b637f56a599a8fa 100644
--- a/tests/test_transform/test_fnirt.py
+++ b/tests/test_transform/test_fnirt.py
@@ -39,7 +39,7 @@ def test_readFnirt():
fnirt.readFnirt(src, src, ref)
assert isinstance(coef, nonlinear.CoefficientField)
- assert isinstance(disp, nonlinear.DisplacementField)
+ assert isinstance(disp, nonlinear.DeformationField)
assert coef.src.sameSpace(src)
assert coef.ref.sameSpace(ref)
@@ -68,7 +68,7 @@ def test_toFnirt():
spaces = it.permutations(('voxel', 'fsl', 'world'), 2)
for from_, to in spaces:
- field = nonlinear.convertDisplacementSpace(basefield, from_, to)
+ field = nonlinear.convertDeformationSpace(basefield, from_, to)
got = fnirt.toFnirt(field)
check(got, basefield)
@@ -122,6 +122,6 @@ def test_fromFnirt():
for from_, to in spaces:
cnv = fnirt.fromFnirt(coef, from_, to)
- exp = nonlinear.convertDisplacementSpace(disp, 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))
diff --git a/tests/test_transform/test_nonlinear.py b/tests/test_transform/test_nonlinear.py
index 8b66bdac3fa9bd7782d8c962278108591d8de626..2da07f3868b02578cb20a619f09b499d22ee7ca6 100644
--- a/tests/test_transform/test_nonlinear.py
+++ b/tests/test_transform/test_nonlinear.py
@@ -38,7 +38,7 @@ def _random_field():
np.random.randint(1, 100, 3),
np.random.random(3) * np.pi / 2)
- return nonlinear.DisplacementField(field, src=src, xform=aff)
+ return nonlinear.DeformationField(field, src=src, xform=aff)
def _random_affine_field():
@@ -61,9 +61,9 @@ def _random_affine_field():
field = np.zeros(list(ref.shape[:3]) + [3])
field[:] = (scoords - rcoords).reshape(*it.chain(ref.shape, [3]))
- field = nonlinear.DisplacementField(field, src, ref,
- header=ref.header,
- dispType='relative')
+ field = nonlinear.DeformationField(field, src, ref,
+ header=ref.header,
+ defType='relative')
return field, xform
@@ -78,31 +78,31 @@ def _field_coords(field):
field.getAffine('voxel', 'fsl')).reshape(field.shape)
-def test_detectDisplacementType():
+def test_detectDeformationType():
relfield = _random_field()
coords = _field_coords(relfield)
- absfield = nonlinear.DisplacementField(
+ absfield = nonlinear.DeformationField(
relfield.data + coords,
src=relfield.src,
xform=relfield.voxToWorldMat)
- assert nonlinear.detectDisplacementType(relfield) == 'relative'
- assert nonlinear.detectDisplacementType(absfield) == 'absolute'
+ assert nonlinear.detectDeformationType(relfield) == 'relative'
+ assert nonlinear.detectDeformationType(absfield) == 'absolute'
-def test_convertDisplacementType():
+def test_convertDeformationType():
relfield = _random_field()
coords = _field_coords(relfield)
- absfield = nonlinear.DisplacementField(
+ absfield = nonlinear.DeformationField(
relfield.data + coords,
src=relfield.src,
xform=relfield.voxToWorldMat)
- gotconvrel1 = nonlinear.convertDisplacementType(relfield)
- gotconvabs1 = nonlinear.convertDisplacementType(absfield)
- gotconvrel2 = nonlinear.convertDisplacementType(relfield, 'absolute')
- gotconvabs2 = nonlinear.convertDisplacementType(absfield, 'relative')
+ gotconvrel1 = nonlinear.convertDeformationType(relfield)
+ gotconvabs1 = nonlinear.convertDeformationType(absfield)
+ gotconvrel2 = nonlinear.convertDeformationType(relfield, 'absolute')
+ gotconvabs2 = nonlinear.convertDeformationType(absfield, 'relative')
tol = dict(atol=1e-5, rtol=1e-5)
@@ -112,7 +112,7 @@ def test_convertDisplacementType():
assert np.all(np.isclose(gotconvabs2, relfield.data, **tol))
-def test_convertDisplacementSpace():
+def test_convertDeformationSpace():
basefield, xform = _random_affine_field()
src = basefield.src
@@ -137,7 +137,7 @@ def test_convertDisplacementSpace():
refcoords = affine.transform(refcoords, ref.voxToScaledVoxMat)
srccoords = basefield.transform(refcoords)
- field = nonlinear.convertDisplacementSpace(basefield, from_, to)
+ field = nonlinear.convertDeformationSpace(basefield, from_, to)
premat = ref.getAffine('fsl', from_)
postmat = src.getAffine('fsl', to)
@@ -152,7 +152,7 @@ def test_convertDisplacementSpace():
assert np.all(np.isclose(expect[~enan], got[~gnan]))
-def test_DisplacementField_transform():
+def test_DeformationField_transform():
relfield, xform = _random_affine_field()
src = relfield.src
@@ -168,9 +168,9 @@ def test_DisplacementField_transform():
absfield = np.zeros(list(ref.shape[:3]) + [3])
absfield[:] = scoords.reshape(*it.chain(ref.shape, [3]))
- absfield = nonlinear.DisplacementField(absfield, src, ref,
- header=ref.header,
- dispType='absolute')
+ absfield = nonlinear.DeformationField(absfield, src, ref,
+ header=ref.header,
+ defType='absolute')
got = relfield.transform(rcoords)
assert np.all(np.isclose(got, scoords))
@@ -279,7 +279,7 @@ def test_CoefficientField_transform():
assert np.all(np.isclose(gotnp, srccoordsnp[srcspace], **tol))
-def test_coefficientFieldToDisplacementField():
+def test_coefficientFieldToDeformationField():
nldir = op.join(datadir, 'nonlinear')
src = op.join(nldir, 'src.nii.gz')
@@ -293,50 +293,20 @@ def test_coefficientFieldToDisplacementField():
cf = fnirt.readFnirt(cf, src, ref)
rdf = fnirt.readFnirt(df, src, ref)
rdfnp = fnirt.readFnirt(dfnp, src, ref)
- adf = nonlinear.convertDisplacementType(rdf)
- adfnp = nonlinear.convertDisplacementType(rdfnp)
-
- rcnv = nonlinear.coefficientFieldToDisplacementField(cf)
- acnv = nonlinear.coefficientFieldToDisplacementField(cf,
- dispType='absolute')
- acnvnp = nonlinear.coefficientFieldToDisplacementField(cf,
- dispType='absolute',
- premat=False)
- rcnvnp = nonlinear.coefficientFieldToDisplacementField(cf,
- premat=False)
+ 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_DisplacementFIeld_srcToRefMat():
-
- field1 = _random_field()
- xform = affine.compose(
- np.random.randint( 1, 10, 3),
- np.random.randint(1, 100, 3),
- np.random.random(3) * np.pi / 2)
-
- field2 = nonlinear.DisplacementField(
- field1.data,
- xform=field1.voxToWorldMat,
- src=field1.src,
- ref=field1.ref,
- srcToRefMat=xform)
-
- x = np.random.randint(0, field1.shape[0], 100)
- y = np.random.randint(0, field1.shape[1], 100)
- z = np.random.randint(0, field1.shape[2], 100)
-
- coords = np.array([x, y, z]).T
- coords = affine.transform(
- coords, field1.ref.getAffine('voxel', 'fsl'))
-
- coordsf1 = field1.transform(coords)
- coordsf2 = field2.transform(coords)
- coordsf1 = affine.transform(coordsf1, affine.invert(xform))
-
- assert np.all(np.isclose(coordsf1, coordsf2))
diff --git a/tests/test_transform/test_x5.py b/tests/test_transform/test_x5.py
index ec96672039626fc7d36e0468128ca0966a84578a..3a92ece655197f3fa77051c858b9fcd03bc7bb57 100644
--- a/tests/test_transform/test_x5.py
+++ b/tests/test_transform/test_x5.py
@@ -9,6 +9,8 @@
import os.path as op
import numpy as np
+import pytest
+
import h5py
import fsl.data.image as fslimage
@@ -27,8 +29,8 @@ def _check_metadata(group):
def _check_affine(group, xform):
- assert group.attrs['Type'] == 'linear'
- gotxform = np.array(group['Transform'])
+ assert group.attrs['Type'] == 'affine'
+ gotxform = np.array(group['Matrix'])
assert np.all(np.isclose(gotxform, xform))
@@ -39,28 +41,12 @@ def _check_space(group, img):
_check_affine(group['Mapping'], img.voxToWorldMat)
-def _check_nonlinear_common(group, field):
- assert group.attrs['Type'] == 'nonlinear'
-
- if isinstance(field, nonlinear.DisplacementField):
- assert group.attrs['SubType'] == 'displacement'
- assert group.attrs['Representation'] == field.displacementType
-
- elif isinstance(field, nonlinear.CoefficientField):
- assert group.attrs['SubType'] == 'coefficient'
- if field.fieldType == 'cubic':
- assert group.attrs['Representation'] == 'cubic bspline'
- elif field.fieldType == 'quadratic':
- assert group.attrs['Representation'] == 'quadratic bspline'
-
- _check_space(group['From'], field.src)
- _check_space(group['To'], field.ref)
-
- pre = field.ref.getAffine('world', 'fsl')
- post = field.src.getAffine('fsl', 'world')
-
- _check_affine(group['Pre'], pre)
- _check_affine(group['Post'], post)
+def _check_deformation(group, field):
+ assert group.attrs['Type'] == 'deformation'
+ assert group.attrs['SubType'] == field.deformationType
+ xform = np.array(group['Matrix'])
+ assert np.all(np.isclose(xform, field.data))
+ _check_affine(group['Mapping'], field.voxToWorldMat)
def test_readWriteLinearX5():
@@ -84,73 +70,43 @@ def test_readWriteLinearX5():
with h5py.File('linear.x5', 'r') as f:
_check_metadata(f)
- _check_affine(f['/'], xform)
- _check_space( f['/From'], src)
- _check_space( f['/To'], ref)
+ assert f.attrs['Type'] == 'linear'
+ _check_affine(f['/Transform'], xform)
+ _check_space( f['/A'], src)
+ _check_space( f['/B'], ref)
-def test_readWriteNonLinearX5_DisplacementField():
+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)
+ src = fslimage.Image(srcfile)
+ ref = fslimage.Image(reffile)
+ dfield = fnirt.readFnirt(dffile, src, ref)
+ wdfield = nonlinear.convertDeformationSpace(dfield, 'world', 'world')
with tempdir.tempdir():
- x5.writeNonLinearX5('nonlinear.x5', dfield)
+
+ # 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 == dfield.srcSpace
- assert gotdfield.refSpace == dfield.refSpace
- assert gotdfield.displacementType == dfield.displacementType
- assert np.all(np.isclose(gotdfield.data, dfield.data))
+ 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_nonlinear_common(f['/'], dfield)
-
- xform = np.array(f['/Transform'])
- assert np.all(np.isclose(xform, dfield.data))
-
-
-
-def test_readWriteNonLinearX5_CoefficientField():
- datadir = op.join(op.dirname(__file__), 'testdata', 'nonlinear')
- cffile = op.join(datadir, 'coefficientfield.nii.gz')
- srcfile = op.join(datadir, 'src.nii.gz')
- reffile = op.join(datadir, 'ref.nii.gz')
-
- src = fslimage.Image(srcfile)
- ref = fslimage.Image(reffile)
-
- cfield = fnirt.readFnirt(cffile, src, ref)
-
- with tempdir.tempdir():
- x5.writeNonLinearX5('nonlinear.x5', cfield)
-
- gotcfield = x5.readNonLinearX5('nonlinear.x5')
-
- assert gotcfield.src.sameSpace(src)
- assert gotcfield.ref.sameSpace(ref)
- assert gotcfield.srcSpace == cfield.srcSpace
- assert gotcfield.refSpace == cfield.refSpace
- assert gotcfield.knotSpacing == cfield.knotSpacing
-
- assert np.all(np.isclose(gotcfield.fieldToRefMat, cfield.fieldToRefMat))
- assert np.all(np.isclose(gotcfield.srcToRefMat, cfield.srcToRefMat))
- assert np.all(np.isclose(gotcfield.data, cfield.data))
-
- with h5py.File('nonlinear.x5', 'r') as f:
- _check_metadata(f)
- _check_nonlinear_common(f['/'], cfield)
-
- _check_affine(f['/InitialAlignment'], cfield.srcToRefMat)
- _check_affine(f['/Parameters/ReferenceToField'], cfield.refToFieldMat)
- assert np.all(np.isclose(f['/Parameters'].attrs['Spacing'], cfield.knotSpacing))
+ _check_deformation(f['/Transform'], wdfield)
+ _check_space( f['/A'], ref)
+ _check_space( f['/B'], src)