RF+TST: check/error for bad axcodes codes/labels

As Kesshi Jordan pointed out, TRK files can have lower-case axis codes,
and this causes unexpected output from axcodes2ornt.  Extend
axcodes2ornt to

a) Check whether the axis codes do in fact correspond to the labels.
b) Check for duplicate labels.

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/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'))