From f89f2c677dd25a86b13a7b351c556dd589c4504b Mon Sep 17 00:00:00 2001
From: Paul McCarthy <pauldmccarthy@gmail.com>
Date: Sun, 14 Jul 2019 13:42:29 +0100
Subject: [PATCH] TEST: Tests for x5 module
---
tests/test_transform/test_x5.py | 156 ++++++++++++++++++++++++++++++++
1 file changed, 156 insertions(+)
create mode 100644 tests/test_transform/test_x5.py
diff --git a/tests/test_transform/test_x5.py b/tests/test_transform/test_x5.py
new file mode 100644
index 000000000..ec9667203
--- /dev/null
+++ b/tests/test_transform/test_x5.py
@@ -0,0 +1,156 @@
+#!/usr/bin/env python
+#
+# test_x5.py -
+#
+# Author: Paul McCarthy <pauldmccarthy@gmail.com>
+#
+
+
+import os.path as op
+import numpy as np
+
+import h5py
+
+import fsl.data.image as fslimage
+import fsl.utils.tempdir as tempdir
+import fsl.transform.affine as affine
+import fsl.transform.fnirt as fnirt
+import fsl.transform.nonlinear as nonlinear
+import fsl.transform.x5 as x5
+
+from .. import make_random_image
+
+
+def _check_metadata(group):
+ assert group.attrs['Format'] == x5.X5_FORMAT
+ assert group.attrs['Version'] == x5.X5_VERSION
+
+
+def _check_affine(group, xform):
+ assert group.attrs['Type'] == 'linear'
+ gotxform = np.array(group['Transform'])
+ assert np.all(np.isclose(gotxform, xform))
+
+
+def _check_space(group, img):
+ assert group.attrs['Type'] == 'image'
+ assert np.all(np.isclose(group.attrs['Size'], img.shape[ :3]))
+ assert np.all(np.isclose(group.attrs['Scales'], img.pixdim[:3]))
+ _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 test_readWriteLinearX5():
+ with tempdir.tempdir():
+ make_random_image('src.nii')
+ make_random_image('ref.nii')
+ xform = affine.compose(
+ np.random.randint(1, 5, 3),
+ np.random.randint(-10, 10, 3),
+ -np.pi / 4 + np.random.random(3) * np.pi / 2)
+
+ src = fslimage.Image('src.nii')
+ ref = fslimage.Image('ref.nii')
+
+ x5.writeLinearX5('linear.x5', xform, src, ref)
+
+ gotxform, gotsrc, gotref = x5.readLinearX5('linear.x5')
+ assert np.all(np.isclose(gotxform, xform))
+ assert gotsrc.sameSpace(src)
+ assert gotref.sameSpace(ref)
+
+ 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)
+
+
+def test_readWriteNonLinearX5_DisplacementField():
+ 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)
+
+ with tempdir.tempdir():
+ x5.writeNonLinearX5('nonlinear.x5', dfield)
+
+ 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))
+
+ with h5py.File('nonlinear.x5', 'r') as f:
+ _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))
--
GitLab