diff --git a/tests/test_scripts/test_fsl_apply_x5.py b/tests/test_scripts/test_fsl_apply_x5.py
index 57a56959f929d1117e118a7b0440404428a934eb..96c2740b1ca537ed96b5e22b786e226a5f47a2b0 100644
--- a/tests/test_scripts/test_fsl_apply_x5.py
+++ b/tests/test_scripts/test_fsl_apply_x5.py
@@ -6,6 +6,7 @@ import numpy as np
import fsl.scripts.fsl_apply_x5 as fsl_apply_x5
import fsl.data.image as fslimage
import fsl.utils.image.resample as resample
+import fsl.utils.image.roi as roi
import fsl.transform.x5 as x5
import fsl.transform.affine as affine
import fsl.utils.tempdir as tempdir
@@ -20,9 +21,13 @@ def _random_affine():
np.random.random(3))
-def _random_image(aff):
- vx, vy, vz = np.random.randint(10, 50, 3)
- data = (np.random.random((vx, vy, vz)) - 0.5) * 10
+def _random_image(aff, shape=None):
+
+ if shape is None:
+ shape = np.random.randint(10, 50, 3)
+
+ data = (np.random.random(shape) - 0.5) * 10
+
return fslimage.Image(data, xform=aff)
@@ -129,3 +134,118 @@ def test_nonlinear_altref():
assert result.sameSpace(altref)
assert np.all(result.data == expect)
+
+
+def test_linear_altsrc():
+ with tempdir.tempdir():
+
+ src2ref = _random_affine()
+ src = _random_image(np.eye(4), (20, 20, 20))
+ ref = _random_image(src2ref)
+
+ x5.writeLinearX5('xform.x5', src2ref, src, ref)
+
+ src.save('src')
+ ref.save('ref')
+
+ srclo, xf = resample.resample(src, (10, 10, 10))
+ srclo = fslimage.Image(srclo, xform=xf)
+ srchi, xf = resample.resample(src, (40, 40, 40))
+ srchi = fslimage.Image(srchi, xform=xf)
+
+ srcoff = roi.roi(src, [(-10, 10), (-10, 10), (-10, 10)])
+
+ srclo .save('srclo')
+ srchi .save('srchi')
+ srcoff.save('srcoff')
+
+ fsl_apply_x5.main('src xform.x5 out' .split())
+ fsl_apply_x5.main('srclo xform.x5 outlo' .split())
+ fsl_apply_x5.main('srchi xform.x5 outhi' .split())
+ fsl_apply_x5.main('srcoff xform.x5 outoff'.split())
+
+ out = fslimage.Image('out')
+ outlo = fslimage.Image('outlo')
+ outhi = fslimage.Image('outhi')
+ outoff = fslimage.Image('outoff')
+
+ exp = resample.resampleToReference(src, ref, matrix=src2ref)[0]
+ explo = resample.resampleToReference(srclo, ref, matrix=src2ref)[0]
+ exphi = resample.resampleToReference(srchi, ref, matrix=src2ref)[0]
+ expoff = resample.resampleToReference(srcoff, ref, matrix=src2ref)[0]
+
+ assert out .sameSpace(ref)
+ assert outlo .sameSpace(ref)
+ assert outhi .sameSpace(ref)
+ assert outoff.sameSpace(ref)
+
+ assert np.all(np.isclose(out .data, exp))
+ assert np.all(np.isclose(outlo .data, explo))
+ assert np.all(np.isclose(outhi .data, exphi))
+ assert np.all(np.isclose(outoff.data, expoff))
+
+
+def test_nonlinear_altsrc():
+ with tempdir.tempdir():
+
+ src2ref = _random_affine()
+ ref2src = affine.invert(src2ref)
+ src = _random_image(np.eye(4), (20, 20, 20))
+ ref = _random_image(src2ref, (20, 20, 20))
+
+ field = _affine_field(src, ref, ref2src, 'world', 'world')
+
+ x5.writeNonLinearX5('xform.x5', field)
+
+ src.save('src')
+ ref.save('ref')
+
+ srclo, xf = resample.resample(src, (10, 10, 10), origin='corner')
+ srclo = fslimage.Image(srclo, xform=xf)
+ srchi, xf = resample.resample(src, (40, 40, 40), origin='corner')
+ srchi = fslimage.Image(srchi, xform=xf)
+
+ srcoff = roi.roi(src, [(-10, 10), (-10, 10), (-10, 10)])
+
+ srclo .save('srclo')
+ srchi .save('srchi')
+ srcoff.save('srcoff')
+
+ # The up-sampled source image is subject to
+ # an unavoidable interpolation, as the
+ # deformation field coordinates are affine-
+ # transformed to the space of the alternate
+ # source image. So in this test case we use
+ # nearest-neighbour interp, so that we can
+ # get the same output as a standard linear
+ # resample
+ fsl_apply_x5.main('src xform.x5 out' .split())
+ fsl_apply_x5.main('srclo xform.x5 outlo' .split())
+ fsl_apply_x5.main('srchi xform.x5 outhi -i nearest'.split())
+ fsl_apply_x5.main('srcoff xform.x5 outoff' .split())
+
+ out = fslimage.Image('out')
+ outlo = fslimage.Image('outlo')
+ outhi = fslimage.Image('outhi')
+ outoff = fslimage.Image('outoff')
+
+ exp, x1 = resample.resampleToReference(src, ref, matrix=src2ref, mode='constant')
+ explo, x2 = resample.resampleToReference(srclo, ref, matrix=src2ref, mode='constant')
+ exphi, x3 = resample.resampleToReference(srchi, ref, matrix=src2ref, mode='constant', order=0)
+ expoff, x4 = resample.resampleToReference(srcoff, ref, matrix=src2ref, mode='constant')
+
+ assert out .sameSpace(ref)
+ assert outlo .sameSpace(ref)
+ assert outhi .sameSpace(ref)
+ assert outoff.sameSpace(ref)
+
+ # We get boundary issues just at the first
+ # voxel, so I'm masking that voxel out
+ for img in (out, outlo, outhi, outoff,
+ exp, explo, exphi, expoff):
+ img[0, 0, 0] = 0
+
+ assert np.all(np.isclose(out .data, exp))
+ assert np.all(np.isclose(outlo .data, explo))
+ assert np.all(np.isclose(outhi .data, exphi))
+ assert np.all(np.isclose(outoff.data, expoff))
diff --git a/tests/test_transform/test_nonlinear.py b/tests/test_transform/test_nonlinear.py
index 27f79d7de7e37245010954438b2a79432571e512..694162c3b3496cec470c68d57eb3142506e25cf0 100644
--- a/tests/test_transform/test_nonlinear.py
+++ b/tests/test_transform/test_nonlinear.py
@@ -7,6 +7,7 @@ import numpy as np
import fsl.data.image as fslimage
import fsl.utils.image.resample as resample
+import fsl.utils.image.roi as roi
import fsl.transform.affine as affine
import fsl.transform.nonlinear as nonlinear
import fsl.transform.fnirt as fnirt
@@ -362,6 +363,53 @@ def test_applyDeformation():
assert np.all(np.isclose(expect, result))
+def test_applyDeformation_altsrc():
+
+ src2ref = affine.compose(
+ np.random.randint(2, 5, 3),
+ np.random.randint(1, 10, 3),
+ [0, 0, 0])
+ ref2src = affine.invert(src2ref)
+
+ srcdata = np.random.randint(1, 65536, (10, 10, 10))
+ refdata = np.random.randint(1, 65536, (10, 10, 10))
+
+ src = fslimage.Image(srcdata)
+ ref = fslimage.Image(refdata, xform=src2ref)
+ field = _affine_field(src, ref, ref2src, 'world', 'world')
+
+ # First try a down-sampled version
+ # of the original source image
+ altsrc, xf = resample.resample(src, (5, 5, 5), origin='corner')
+ altsrc = fslimage.Image(altsrc, xform=xf, header=src.header)
+ expect, xf = resample.resampleToReference(
+ altsrc, ref, matrix=src2ref, order=1, mode='nearest')
+ result = nonlinear.applyDeformation(
+ altsrc, field, order=1, mode='nearest')
+ assert np.all(np.isclose(expect, result))
+
+ # Now try a down-sampled ROI
+ # of the original source image
+ altsrc = roi.roi(src, [(2, 9), (2, 9), (2, 9)])
+ altsrc, xf = resample.resample(altsrc, (4, 4, 4))
+ altsrc = fslimage.Image(altsrc, xform=xf, header=src.header)
+ expect, xf = resample.resampleToReference(
+ altsrc, ref, matrix=src2ref, order=1, mode='nearest')
+ result = nonlinear.applyDeformation(
+ altsrc, field, order=1, mode='nearest')
+ assert np.all(np.isclose(expect, result))
+
+ # down-sampled and offset ROI
+ # of the original source image
+ altsrc = roi.roi(src, [(-5, 8), (-5, 8), (-5, 8)])
+ altsrc, xf = resample.resample(altsrc, (6, 6, 6))
+ altsrc = fslimage.Image(altsrc, xform=xf, header=src.header)
+ expect, xf = resample.resampleToReference(
+ altsrc, ref, matrix=src2ref, order=1, mode='nearest')
+ result = nonlinear.applyDeformation(
+ altsrc, field, order=1, mode='nearest')
+ assert np.all(np.isclose(expect, result))
+
def test_applyDeformation_altref():
src2ref = affine.compose(
@@ -427,8 +475,6 @@ def test_applyDeformation_worldAligned():
result = nonlinear.applyDeformation(
src, field, order=1, mode='constant', cval=0)
- fslimage.Image(result, xform=ref.voxToWorldMat).save('result')
-
expect = expect[1:-1, 1:-1, 1:-1]
result = result[1:-1, 1:-1, 1:-1]