TEST: Tests for x5 module

tests/test_transform/test_x5.py

+#!/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))