Merge pull request #89 from matthew-brett/mgh-mgz-refactor

RF - refactor ability to load compressed .mgz file

Author: matthew-brett

nibabel/freesurfer/mghformat.py

@@ -10,6 +10,7 @@
 
 Author: Krish Subramaniam
 '''
+from os.path import splitext
 import numpy as np
 
 from nibabel.volumeutils import allopen, array_to_file, array_from_file,  \
@@ -427,7 +428,7 @@ def writeftr_to(self, fileobj):
 class MGHImage(SpatialImage):
     header_class = MGHHeader
     files_types = (('image', '.mgh'),)
-    _compressed_exts = ('.mgz',)
+    _compressed_exts = (('.gz',))
 
     ImageArrayProxy = ArrayProxy
 
@@ -437,24 +438,10 @@ def get_header(self):
 
     @classmethod
     def filespec_to_file_map(klass, filespec):
-        ''' Method reimplemented from nibabel.spatialimages because it does not
-        allow enforce_extensions in types_filenames() to be False.
-        This is needed because MGH's compressed format is not filename.mgh.gz,
-        but it is filename.mgz.. types_filenames() removes the .mgz and gives
-        an error because it then doesn't find the file 'filename' in the system
-        '''
-        try:
-            filenames = types_filenames(filespec,
-                                    klass.files_types,
-                                    trailing_suffixes=klass._compressed_exts,
-                                    enforce_extensions=False)
-        except TypesFilenamesError:
-            raise ImageFileError('Filespec "%s" does not look right for '
-                             'class %s ' % (filespec, klass))
-        file_map = {}
-        for key, fname in filenames.items():
-            file_map[key] = FileHolder(filename=fname)
-        return file_map
+        """ Check for compressed .mgz format, then .mgh format """
+        if splitext(filespec)[1] == '.mgz':
+            return dict(image=FileHolder(filename=filespec))
+        return super(MGHImage, klass).filespec_to_file_map(filespec)
 
     @classmethod
     def from_file_map(klass, file_map):

nibabel/freesurfer/tests/test_mghformat.py

@@ -122,3 +122,20 @@ def bad_dtype_mgh():
 def test_bad_dtype_mgh():
     # Now test the above function
     assert_raises(MGHError, bad_dtype_mgh)
+
+
+def test_filename_exts():
+    # Test acceptable filename extensions
+    v = np.ones((7, 13, 3, 22)).astype(np.uint8)
+    # form a MGHImage object using data
+    # and the default affine matrix (Note the "None")
+    img = MGHImage(v, None)
+    # Check if these extensions allow round trip
+    for ext in ('.mgh', '.mgz', '.mgh.gz'):
+        with InTemporaryDirectory():
+            fname = 'tmpname' + ext
+            save(img, fname)
+            # read from the tmp file and see if it checks out
+            img_back = load(fname)
+            assert_array_equal(img_back.get_data(), v)
+            del img_back