Merge pull request #600 from matthew-brett/trk-codes-with-check

MRG: fix lower-case TRK codes, add error message

* Kesshi's initial fix and test for lower-case codes in TRK header;
* Error checking in axcodes2ornt to detect unknown or duplicate codes.

Author: matthew-brett

nibabel/orientations.py

@@ -349,8 +349,13 @@ def axcodes2ornt(axcodes, labels=None):
            [ 0., -1.],
            [ 2.,  1.]])
     """
-    if labels is None:
-        labels = list(zip('LPI', 'RAS'))
+    labels = list(zip('LPI', 'RAS')) if labels is None else labels
+    allowed_labels = sum([list(L) for L in labels], []) + [None]
+    if len(allowed_labels) != len(set(allowed_labels)):
+        raise ValueError('Duplicate labels in {}'.format(allowed_labels))
+    if not set(axcodes).issubset(allowed_labels):
+        raise ValueError('Not all axis codes {} in label set {}'
+                         .format(list(axcodes), allowed_labels))
     n_axes = len(axcodes)
     ornt = np.ones((n_axes, 2), dtype=np.int8) * np.nan
     for code_idx, code in enumerate(axcodes):

nibabel/streamlines/tests/test_trk.py

@@ -17,7 +17,7 @@
 from ..tractogram_file import HeaderError, HeaderWarning
 
 from .. import trk as trk_module
-from ..trk import TrkFile, encode_value_in_name, decode_value_from_name
+from ..trk import TrkFile, encode_value_in_name, decode_value_from_name, get_affine_trackvis_to_rasmm
 from ..header import Field
 
 DATA = {}
@@ -110,6 +110,17 @@ def trk_with_bytes(self, trk_key='simple_trk_fname', endian='<'):
         return trk_struct, trk_bytes
 
     def test_load_file_with_wrong_information(self):
+        # Simulate a TRK file where `voxel_order` is lowercase.
+        trk_struct1, trk_bytes1 = self.trk_with_bytes()
+        trk_struct1[Field.VOXEL_ORDER] = b'LAS'
+        trk1 = TrkFile.load(BytesIO(trk_bytes1))
+        trk_struct2, trk_bytes2 = self.trk_with_bytes()
+        trk_struct2[Field.VOXEL_ORDER] = b'las'
+        trk2 = TrkFile.load(BytesIO(trk_bytes2))
+        trk1_aff2rasmm = get_affine_trackvis_to_rasmm(trk1.header)
+        trk2_aff2rasmm = get_affine_trackvis_to_rasmm(trk2.header)
+        assert_array_equal(trk1_aff2rasmm,trk2_aff2rasmm)
+
         # Simulate a TRK file where `count` was not provided.
         trk_struct, trk_bytes = self.trk_with_bytes()
         trk_struct[Field.NB_STREAMLINES] = 0

nibabel/streamlines/trk.py

@@ -107,7 +107,7 @@ def get_affine_trackvis_to_rasmm(header):
     if hasattr(vox_order, 'item'):  # structured array
         vox_order = header[Field.VOXEL_ORDER].item()
     affine_ornt = "".join(aff2axcodes(header[Field.VOXEL_TO_RASMM]))
-    header_ornt = axcodes2ornt(vox_order.decode('latin1'))
+    header_ornt = axcodes2ornt(vox_order.decode('latin1').upper())
     affine_ornt = axcodes2ornt(affine_ornt)
     ornt = nib.orientations.ornt_transform(header_ornt, affine_ornt)
     M = nib.orientations.inv_ornt_aff(ornt, header[Field.DIMENSIONS])

nibabel/tests/test_orientations.py

@@ -300,11 +300,8 @@ def test_axcodes2ornt():
                        )
 
     # default is RAS output directions
-    assert_array_equal(axcodes2ornt(('R', 'A', 'S')),
-                       [[0, 1],
-                        [1, 1],
-                        [2, 1]]
-                       )
+    default = np.c_[range(3), [1] * 3]
+    assert_array_equal(axcodes2ornt(('R', 'A', 'S')), default)
 
     # dropped axes produce None
     assert_array_equal(axcodes2ornt(('R', None, 'S')),
@@ -313,6 +310,28 @@ def test_axcodes2ornt():
                         [2, 1]]
                        )
 
+    # Missing axcodes raise an error
+    assert_array_equal(axcodes2ornt('RAS'), default)
+    assert_raises(ValueError, axcodes2ornt, 'rAS')
+    # None is OK as axis code
+    assert_array_equal(axcodes2ornt(('R', None, 'S')),
+                                    [[0, 1],
+                                     [np.nan, np.nan],
+                                     [2, 1]])
+    # Bad axis code with None also raises error.
+    assert_raises(ValueError, axcodes2ornt, ('R', None, 's'))
+    # Axis codes checked with custom labels
+    labels = ('SD', 'BF', 'lh')
+    assert_array_equal(axcodes2ornt('BlD', labels),
+                       [[1, -1],
+                        [2, -1],
+                        [0, 1]])
+    assert_raises(ValueError, axcodes2ornt, 'blD', labels)
+
+    # Duplicate labels
+    assert_raises(ValueError, axcodes2ornt, 'blD', ('SD', 'BF', 'lD'))
+    assert_raises(ValueError, axcodes2ornt, 'blD', ('SD', 'SF', 'lD'))
+
 
 def test_aff2axcodes():
     assert_equal(aff2axcodes(np.eye(4)), tuple('RAS'))