From 6f1d7c2aba8e40603517fd8be9b32b441b6bd81f Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Mon, 22 Jul 2019 10:12:04 +0100
Subject: [PATCH] TEST: Unit tests for apply_x5
---
tests/test_scripts/test_fsl_apply_x5.py | 130 +++++++++++++++++++++++-
1 file changed, 129 insertions(+), 1 deletion(-)
diff --git a/tests/test_scripts/test_fsl_apply_x5.py b/tests/test_scripts/test_fsl_apply_x5.py
index 939fa7d47..57a56959f 100644
--- a/tests/test_scripts/test_fsl_apply_x5.py
+++ b/tests/test_scripts/test_fsl_apply_x5.py
@@ -1,3 +1,131 @@
#!/usr/bin/env python
-# TODO
+
+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.transform.x5 as x5
+import fsl.transform.affine as affine
+import fsl.utils.tempdir as tempdir
+
+from ..test_transform.test_nonlinear import _affine_field
+
+
+def _random_affine():
+ return affine.compose(
+ np.random.randint(2, 5, 3),
+ np.random.randint(1, 10, 3),
+ 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
+ return fslimage.Image(data, xform=aff)
+
+
+def test_linear():
+ with tempdir.tempdir():
+
+ src2ref = _random_affine()
+ src = _random_image(np.eye(4))
+ ref = _random_image(src2ref)
+
+ x5.writeLinearX5('xform.x5', src2ref, src, ref)
+
+ src.save('src')
+ ref.save('ref')
+
+ fsl_apply_x5.main('src xform.x5 out'.split())
+
+ result = fslimage.Image('out')
+ expect = resample.resampleToReference(src, ref, matrix=src2ref)[0]
+
+ assert result.sameSpace(ref)
+ assert np.all(np.isclose(result.data, expect))
+
+
+def test_nonlinear():
+ with tempdir.tempdir():
+
+ src2ref = _random_affine()
+ ref2src = affine.invert(src2ref)
+ src = _random_image(np.eye(4))
+ ref = _random_image(src2ref)
+ field = _affine_field(src, ref, ref2src, 'world', 'world')
+
+ x5.writeNonLinearX5('xform.x5', field)
+
+ src.save('src')
+
+ fsl_apply_x5.main('src xform.x5 out'.split())
+
+ result = fslimage.Image('out')
+ expect = resample.resampleToReference(src, ref, matrix=src2ref)[0]
+
+ assert result.sameSpace(ref)
+
+ # We might get truncation on the edges
+ result = result.data[1:-1, 1:-1, 1:-1]
+ expect = expect[ 1:-1, 1:-1, 1:-1]
+
+ assert np.all(np.isclose(result, expect))
+
+
+def test_linear_altref():
+ with tempdir.tempdir():
+
+ src2ref = affine.scaleOffsetXform([1, 1, 1], [5, 5, 5])
+ altv2w = affine.scaleOffsetXform([1, 1, 1], [10, 10, 10])
+
+ srcdata = np.random.randint(1, 65536, (10, 10, 10))
+ src = fslimage.Image(srcdata, xform=np.eye(4))
+ ref = fslimage.Image(src.data, xform=src2ref)
+ altref = fslimage.Image(src.data, xform=altv2w)
+
+ src .save('src')
+ ref .save('ref')
+ altref.save('altref')
+
+ x5.writeLinearX5('xform.x5', src2ref, src, ref)
+
+ fsl_apply_x5.main('src xform.x5 out -r altref'.split())
+
+ result = fslimage.Image('out')
+ expect = np.zeros(srcdata.shape)
+ expect[:5, :5, :5] = srcdata[5:, 5:, 5:]
+
+ assert result.sameSpace(altref)
+ assert np.all(result.data == expect)
+
+
+def test_nonlinear_altref():
+ with tempdir.tempdir():
+
+ src2ref = affine.scaleOffsetXform([1, 1, 1], [5, 5, 5])
+ ref2src = affine.invert(src2ref)
+ altv2w = affine.scaleOffsetXform([1, 1, 1], [10, 10, 10])
+
+ srcdata = np.random.randint(1, 65536, (10, 10, 10))
+ src = fslimage.Image(srcdata, xform=np.eye(4))
+ ref = fslimage.Image(src.data, xform=src2ref)
+ altref = fslimage.Image(src.data, xform=altv2w)
+
+ field = _affine_field(src, ref, ref2src, 'world', 'world')
+
+ src .save('src')
+ ref .save('ref')
+ altref.save('altref')
+
+ x5.writeNonLinearX5('xform.x5', field)
+
+ fsl_apply_x5.main('src xform.x5 out -r altref'.split())
+
+ result = fslimage.Image('out')
+ expect = np.zeros(srcdata.shape)
+ expect[:5, :5, :5] = srcdata[5:, 5:, 5:]
+
+ assert result.sameSpace(altref)
+ assert np.all(result.data == expect)
--
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