TEST: Rename modules/functions in tests, new test for fsl_convert_x5

tests/test_fsl_convert_x5.py

+#!/usr/bin/env python
+
+
+import numpy as np
+
+import fsl.utils.tempdir   as tempdir
+import fsl.utils.transform as transform
+import fsl.data.image      as fslimage
+
+import fsl.scripts.fsl_convert_x5 as fsl_convert_x5
+
+
+def random_image():
+    vx, vy, vz = np.random.randint(10, 50, 3)
+    dx, dy, dz = np.random.randint( 1, 10, 3)
+    data       = (np.random.random((vx, vy, vz)) - 0.5) * 10
+    aff        = transform.compose(
+        (dx, dy, dz),
+        np.random.randint(1, 100, 3),
+        np.random.random(3) * np.pi / 2)
+
+    return fslimage.Image(data, xform=aff)
+
+
+
+def test_convert_flirt():
+    with tempdir.tempdir():
+        src = random_image()
+        ref = random_image()
+        src.save('src')
+        ref.save('ref')
+
+        xform = transform.compose(
+            np.random.randint(1, 10, 3),
+            np.random.randint(-100, 100, 3),
+            (np.random.random(3) - 0.5) * np.pi)
+
+        np.savetxt('src2ref.mat', xform)
+
+        fsl_convert_x5.main('flirt -s src -r ref '
+                            'src2ref.mat src2ref.x5'.split())
+        expxform = transform.concat(
+            ref.getAffine('fsl', 'world'),
+            xform,
+            src.getAffine('world', 'fsl'))
+        gotxform, gotsrc, gotref = transform.readFlirtX5('src2ref.x5')
+        assert np.all(np.isclose(gotxform, expxform))
+        assert src.sameSpace(gotsrc)
+        assert ref.sameSpace(gotref)
+
+        fsl_convert_x5.main('flirt -s src -r ref src2ref.x5 '
+                            'src2ref_copy.mat'.split())
+
+        gotxform = transform.readFlirt('src2ref_copy.mat')
+        assert np.all(np.isclose(gotxform, xform))

tests/test_transform_nonlinear.py

@@ -6,7 +6,7 @@ import nibabel as nib
 
 import fsl.data.image                as fslimage
 import fsl.utils.transform           as transform
-import fsl.utils.transform.dispfield as dispfield
+import fsl.utils.transform.nonlinear as nonlinear
 
 
 def _random_field():
@@ -19,7 +19,7 @@ def _random_field():
         np.random.randint(1, 100, 3),
         np.random.random(3) * np.pi / 2)
 
-    return dispfield.DisplacementField(field, xform=aff)
+    return nonlinear.DisplacementField(field, xform=aff)
 
 
 def _field_coords(field):
@@ -33,29 +33,29 @@ def _field_coords(field):
         field.getAffine('voxel', 'fsl')).reshape(field.shape)
 
 
-def test_detectType():
+def test_detectDisplacementType():
     relfield = _random_field()
     coords   = _field_coords(relfield)
-    absfield = dispfield.DisplacementField(
+    absfield = nonlinear.DisplacementField(
         relfield.data + coords, xform=relfield.voxToWorldMat)
 
-    assert dispfield.detectType(relfield) == 'relative'
-    assert dispfield.detectType(absfield) == 'absolute'
+    assert nonlinear.detectDisplacementType(relfield) == 'relative'
+    assert nonlinear.detectDisplacementType(absfield) == 'absolute'
 
 
-def test_convertType():
-    relfield = dispfield.DisplacementField(_random_field())
+def test_convertDisplacemenyType():
+    relfield = nonlinear.DisplacementField(_random_field())
     coords   = _field_coords(relfield)
     absfield = fslimage.Image(
         relfield.data + coords, xform=relfield.voxToWorldMat)
 
-    relfield = dispfield.DisplacementField(relfield)
-    absfield = dispfield.DisplacementField(absfield)
+    relfield = nonlinear.DisplacementField(relfield)
+    absfield = nonlinear.DisplacementField(absfield)
 
-    gotconvrel1 = dispfield.convertType(relfield)
-    gotconvabs1 = dispfield.convertType(absfield)
-    gotconvrel2 = dispfield.convertType(relfield, 'absolute')
-    gotconvabs2 = dispfield.convertType(absfield, 'relative')
+    gotconvrel1 = nonlinear.convertDisplacementType(relfield)
+    gotconvabs1 = nonlinear.convertDisplacementType(absfield)
+    gotconvrel2 = nonlinear.convertDisplacementType(relfield, 'absolute')
+    gotconvabs2 = nonlinear.convertDisplacementType(absfield, 'relative')
 
     assert np.all(np.isclose(gotconvrel1, absfield.data))
     assert np.all(np.isclose(gotconvabs1, relfield.data))