FIX/TEST: MGHImages must be 3D or 4D

Author: effigies

nibabel/freesurfer/mghformat.py

@@ -17,7 +17,7 @@
 from ..volumeutils import (array_to_file, array_from_file, Recoder)
 from ..spatialimages import HeaderDataError, SpatialImage
 from ..fileholders import FileHolder
-from ..arrayproxy import ArrayProxy
+from ..arrayproxy import ArrayProxy, reshape_dataobj
 from ..keywordonly import kw_only_meth
 from ..openers import ImageOpener
 from ..wrapstruct import LabeledWrapStruct
@@ -390,6 +390,14 @@ class MGHImage(SpatialImage):
 
     ImageArrayProxy = ArrayProxy
 
+    def __init__(self, dataobj, affine, header=None,
+                 extra=None, file_map=None):
+        shape = dataobj.shape
+        if len(shape) < 3:
+            dataobj = reshape_dataobj(dataobj, shape + (1,) * (3 - len(shape)))
+        super(MGHImage, self).__init__(dataobj, affine, header=header,
+                                       extra=extra, file_map=file_map)
+
     @classmethod
     def filespec_to_file_map(klass, filespec):
         """ Check for compressed .mgz format, then .mgh format """

nibabel/spatialimages.py

@@ -354,7 +354,7 @@ def __init__(self, dataobj, affine, header=None,
         '''
         super(SpatialImage, self).__init__(dataobj, header=header, extra=extra,
                                            file_map=file_map)
-        if not affine is None:
+        if affine is not None:
             # Check that affine is array-like 4,4.  Maybe this is too strict at
             # this abstract level, but so far I think all image formats we know
             # do need 4,4.

nibabel/tests/test_spatialimages.py

@@ -195,7 +195,7 @@ class DataLike(object):
     shape = (3,)
 
     def __array__(self):
-        return np.arange(3)
+        return np.arange(3, dtype=np.int16)
 
 
 class TestSpatialImage(TestCase):
@@ -249,8 +249,11 @@ def test_default_header(self):
     def test_data_api(self):
         # Test minimal api data object can initialize
         img = self.image_class(DataLike(), None)
-        assert_array_equal(img.get_data(), np.arange(3))
-        assert_equal(img.shape, (3,))
+        # Shape may be promoted to higher dimension, but may not reorder or
+        # change size
+        assert_array_equal(img.get_data().flatten(), np.arange(3))
+        assert_equal(img.get_shape()[:1], (3,))
+        assert_equal(np.prod(img.get_shape()), 3)
 
     def check_dtypes(self, expected, actual):
         # Some images will want dtypes to be equal including endianness,
@@ -278,7 +281,10 @@ def test_data_shape(self):
         # See https://github.com/nipy/nibabel/issues/58
         arr = np.arange(4, dtype=np.int16)
         img = img_klass(arr, np.eye(4))
-        assert_equal(img.shape, (4,))
+        # Shape may be promoted to higher dimension, but may not reorder or
+        # change size
+        assert_equal(img.get_shape()[:1], (4,))
+        assert_equal(np.prod(img.get_shape()), 4)
         img = img_klass(np.zeros((2, 3, 4), dtype=np.float32), np.eye(4))
         assert_equal(img.shape, (2, 3, 4))
 
@@ -290,7 +296,10 @@ def test_str(self):
         arr = np.arange(5, dtype=np.int16)
         img = img_klass(arr, np.eye(4))
         assert_true(len(str(img)) > 0)
-        assert_equal(img.shape, (5,))
+        # Shape may be promoted to higher dimension, but may not reorder or
+        # change size
+        assert_equal(img.shape[:1], (5,))
+        assert_equal(np.prod(img.shape), 5)
         img = img_klass(np.zeros((2, 3, 4), dtype=np.int16), np.eye(4))
         assert_true(len(str(img)) > 0)
 
@@ -302,7 +311,10 @@ def test_get_shape(self):
         # See https://github.com/nipy/nibabel/issues/58
         img = img_klass(np.arange(1, dtype=np.int16), np.eye(4))
         with suppress_warnings():
-            assert_equal(img.get_shape(), (1,))
+            # Shape may be promoted to higher dimension, but may not reorder or
+            # change size
+            assert_equal(img.get_shape()[:1], (1,))
+            assert_equal(np.prod(img.get_shape()), 1)
             img = img_klass(np.zeros((2, 3, 4), np.int16), np.eye(4))
             assert_equal(img.get_shape(), (2, 3, 4))