Merge pull request #462 from MarcCote/fix_tractogram_slicing

MRG: Copy affine_to_rasmm when slicing a Tractogram object

Set the affine_to_rasmm when creating a new Tractogram object that is the result of advanced indexing or slicing. Add a test to check it is working properly.

Author: matthew-brett

nibabel/streamlines/tests/test_tractogram.py

@@ -18,6 +18,7 @@
 
 def setup():
     global DATA
+    DATA['rng'] = np.random.RandomState(1234)
     DATA['streamlines'] = [np.arange(1*3, dtype="f4").reshape((1, 3)),
                            np.arange(2*3, dtype="f4").reshape((2, 3)),
                            np.arange(5*3, dtype="f4").reshape((5, 3))]
@@ -373,6 +374,13 @@ def test_tractogram_getitem(self):
                          DATA['tractogram'].data_per_streamline[::-1],
                          DATA['tractogram'].data_per_point[::-1])
 
+        # Make sure slicing conserves the affine_to_rasmm property.
+        tractogram = DATA['tractogram'].copy()
+        tractogram.affine_to_rasmm = DATA['rng'].rand(4, 4)
+        tractogram_view = tractogram[::2]
+        assert_array_equal(tractogram_view.affine_to_rasmm,
+                           tractogram.affine_to_rasmm)
+
     def test_tractogram_add_new_data(self):
         # Tractogram with only streamlines
         t = DATA['simple_tractogram'].copy()

nibabel/streamlines/tractogram.py

@@ -335,7 +335,8 @@ def __getitem__(self, idx):
         if isinstance(idx, (numbers.Integral, np.integer)):
             return TractogramItem(pts, data_per_streamline, data_per_point)
 
-        return Tractogram(pts, data_per_streamline, data_per_point)
+        return Tractogram(pts, data_per_streamline, data_per_point,
+                          affine_to_rasmm=self.affine_to_rasmm)
 
     def __len__(self):
         return len(self.streamlines)