Merge pull request #1237 from petsuter/patch-1

ENH: Warn on invalid MINC2 spacing declarations, treat as missing

Author: effigies

.zenodo.json

@@ -377,6 +377,9 @@
     },
     {
       "name": "freec84"
+    },
+    {
+      "name": "Suter, Peter"
     }
   ],
   "keywords": [

nibabel/minc2.py

@@ -25,6 +25,7 @@
 
     mincstats my_funny.mnc
 """
+import warnings
 import numpy as np
 
 from .minc1 import Minc1File, Minc1Image, MincError, MincHeader
@@ -58,8 +59,13 @@ def __init__(self, mincfile):
         # We don't currently support irregular spacing
         # https://en.wikibooks.org/wiki/MINC/Reference/MINC2.0_File_Format_Reference#Dimension_variable_attributes
         for dim in self._dims:
-            if dim.spacing != b'regular__':
+            # "If this attribute is absent, a value of regular__ should be assumed."
+            spacing = getattr(dim, 'spacing', b'regular__')
+            if spacing == b'irregular':
                 raise ValueError('Irregular spacing not supported')
+            elif spacing != b'regular__':
+                warnings.warn(f'Invalid spacing declaration: {spacing}; assuming regular')
+
         self._spatial_dims = [name for name in self._dim_names if name.endswith('space')]
         self._image_max = image['image-max']
         self._image_min = image['image-min']

nibabel/tests/data/minc2_baddim.mnc

@@ -10,6 +10,7 @@
 from os.path import join as pjoin
 
 import numpy as np
+import pytest
 
 from .. import minc2
 from ..minc2 import Minc2File, Minc2Image
@@ -121,3 +122,12 @@ class TestMinc2Image(tm2.TestMinc1Image):
         image_class = Minc2Image
         eg_images = (pjoin(data_path, 'small.mnc'),)
         module = minc2
+
+
+def test_bad_diminfo():
+    fname = pjoin(data_path, 'minc2_baddim.mnc')
+    # File has a bad spacing field 'xspace' when it should be
+    # `irregular`, `regular__` or absent (default to regular__).
+    # We interpret an invalid spacing as absent, but warn.
+    with pytest.warns(UserWarning) as w:
+        Minc2Image.from_filename(fname)