From 7fee93d6ab0bd66313bf2478b84e9fc23c97d33d Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Sun, 21 Jul 2019 19:36:58 +0100
Subject: [PATCH] TEST: Tests for new resample/nonlinear things. Empty apply_x5
test module
---
tests/test_image_resample.py | 25 +++++++
tests/test_scripts/test_fsl_apply_x5.py | 3 +
tests/test_transform/test_nonlinear.py | 88 +++++++++++++++++++++++--
3 files changed, 112 insertions(+), 4 deletions(-)
create mode 100644 tests/test_scripts/test_fsl_apply_x5.py
diff --git a/tests/test_image_resample.py b/tests/test_image_resample.py
index d9f474bf4..8fb488760 100644
--- a/tests/test_image_resample.py
+++ b/tests/test_image_resample.py
@@ -263,3 +263,28 @@ def test_resampleToReference3():
exp = np.array([refdata[..., 0]] * 15).transpose((1, 2, 3, 0))
resampled, xform = resample.resampleToReference(img, ref, order=0, mode='nearest')
assert np.all(resampled == exp)
+
+
+def test_resampleToReference4():
+
+ # the image and ref are out of
+ # alignment, but this affine
+ # will bring them into alignment
+ img2ref = transform.scaleOffsetXform([2, 2, 2], [10, 10, 10])
+
+ imgdata = np.random.randint(0, 65536, (5, 5, 5))
+ refdata = np.zeros((5, 5, 5))
+ img = fslimage.Image(imgdata)
+ ref = fslimage.Image(refdata, xform=img2ref)
+
+ # Without the affine, the image
+ # will be out of the FOV of the
+ # reference
+ resampled, xform = resample.resampleToReference(img, ref)
+ assert np.all(resampled == 0)
+
+ # But applying the affine will
+ # cause them to overlap
+ # perfectly in world coordinates
+ resampled, xform = resample.resampleToReference(img, ref, matrix=img2ref)
+ assert np.all(resampled == imgdata)
diff --git a/tests/test_scripts/test_fsl_apply_x5.py b/tests/test_scripts/test_fsl_apply_x5.py
new file mode 100644
index 000000000..939fa7d47
--- /dev/null
+++ b/tests/test_scripts/test_fsl_apply_x5.py
@@ -0,0 +1,3 @@
+#!/usr/bin/env python
+
+# TODO
diff --git a/tests/test_transform/test_nonlinear.py b/tests/test_transform/test_nonlinear.py
index 2da07f386..c32e7f06f 100644
--- a/tests/test_transform/test_nonlinear.py
+++ b/tests/test_transform/test_nonlinear.py
@@ -5,10 +5,11 @@ import os.path as op
import numpy as np
-import fsl.data.image as fslimage
-import fsl.transform.affine as affine
-import fsl.transform.nonlinear as nonlinear
-import fsl.transform.fnirt as fnirt
+import fsl.data.image as fslimage
+import fsl.utils.image.resample as resample
+import fsl.transform.affine as affine
+import fsl.transform.nonlinear as nonlinear
+import fsl.transform.fnirt as fnirt
datadir = op.join(op.dirname(__file__), 'testdata')
@@ -40,6 +41,26 @@ def _random_field():
return nonlinear.DeformationField(field, src=src, xform=aff)
+
+def _affine_field(src, ref, xform, srcSpace, refSpace):
+ 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
+ rcoords = affine.transform(rvoxels, ref.getAffine('voxel', refSpace))
+ scoords = affine.transform(rcoords, xform)
+
+ field = np.zeros(list(ref.shape[:3]) + [3])
+ field[:] = (scoords - rcoords).reshape(*it.chain(ref.shape, [3]))
+ field = nonlinear.DeformationField(field, src, ref,
+ srcSpace=srcSpace,
+ refSpace=refSpace,
+ header=ref.header,
+ defType='relative')
+ return field
+
+
def _random_affine_field():
src = _random_image()
@@ -310,3 +331,62 @@ def test_coefficientFieldToDeformationField():
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_applyDeformation():
+
+ src2ref = affine.compose(
+ np.random.randint(2, 5, 3),
+ np.random.randint(1, 10, 3),
+ np.random.random(3))
+ 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')
+
+ expect, xf = resample.resampleToReference(
+ src, ref, matrix=src2ref, order=1, mode='nearest')
+ result = nonlinear.applyDeformation(
+ src, field, order=1, mode='nearest')
+
+ assert np.all(np.isclose(expect, result))
+
+
+
+def test_applyDeformation_altref():
+ src2ref = affine.compose(
+ np.random.randint(2, 5, 3),
+ np.random.randint(1, 10, 3),
+ np.random.random(3))
+ 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')
+
+ altrefxform = affine.concat(
+ src2ref,
+ affine.scaleOffsetXform([1, 1, 1], [5, 0, 0]))
+
+ altref = fslimage.Image(refdata, xform=altrefxform)
+
+ expect, xf = resample.resampleToReference(
+ src, altref, matrix=src2ref, order=1, mode='constant', cval=0)
+ result = nonlinear.applyDeformation(
+ src, field, ref=altref, order=1, mode='constant', cval=0)
+
+ # We can get imprecision/rounding errors
+ # which may cause affine_transform and
+ # map_coordinates to determine that
+ # boundary voxels are out of bounds
+ expect = expect[1:-1, 1:-1, 1:-1]
+ result = result[1:-1, 1:-1, 1:-1]
+
+ assert np.all(np.isclose(expect, result))
--
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