TEST: Unit tests for apply_x5

tests/test_scripts/test_fsl_apply_x5.py

 #!/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)