Merge branch 'enh/nonlinear' into 'master'

Enh/nonlinear

See merge request fsl/fslpy!212

CHANGELOG.rst

@@ -62,6 +62,8 @@ Fixed
   split.
 * Fixed some bugs in the :func:`.fslsub.info` and :func:`.fslinfo.wait`
   functions.
+* Fixed the :func:`.DeformationField.transform` method so it works with
+  a single set of coordinates.
 
 
 2.8.4 (Monday 2nd March 2020)

fsl/transform/nonlinear.py

@@ -251,7 +251,9 @@ class DeformationField(NonLinearTransform):
         if from_ is None: from_ = self.refSpace
         if to    is None: to    = self.srcSpace
 
-        coords = np.asanyarray(coords)
+        coords   = np.asanyarray(coords)
+        outshape = coords.shape
+        coords   = coords.reshape((-1, 3))
 
         # We may need to pre-transform the
         # coordinates so they are in the
@@ -299,7 +301,7 @@ class DeformationField(NonLinearTransform):
         outcoords          = np.full(coords.shape, np.nan)
         outcoords[voxmask] = disps
 
-        return outcoords
+        return outcoords.reshape(outshape)
 
 
 class CoefficientField(NonLinearTransform):

tests/test_transform/test_nonlinear.py

@@ -205,6 +205,10 @@ def test_DeformationField_transform():
     got = absfield.transform(rcoords)
     assert np.all(np.isclose(got, scoords))
 
+    # test single set of coords
+    got = absfield.transform(rcoords[0])
+    assert np.all(np.isclose(got, scoords[0]))
+
     got = relfield.transform(rvoxels, from_='voxel', to='voxel')
     assert np.all(np.isclose(got, svoxels))
     got = absfield.transform(rvoxels, from_='voxel', to='voxel')