Merge pull request #1072 from matthew-brett/allow-gifti-gz

MRG: Allow compressed Gifti images

Author: effigies

nibabel/gifti/gifti.py

@@ -565,6 +565,7 @@ class GiftiImage(xml.XmlSerializable, SerializableImage):
     """
     valid_exts = ('.gii',)
     files_types = (('image', '.gii'),)
+    _compressed_suffixes = ('.gz', '.bz2')
 
     # The parser will in due course be a GiftiImageParser, but we can't set
     # that now, because it would result in a circular import.  We set it after
@@ -909,7 +910,8 @@ def from_file_map(klass, file_map, buffer_size=35000000, mmap=True):
         img : GiftiImage
         """
         parser = klass.parser(buffer_size=buffer_size, mmap=mmap)
-        parser.parse(fptr=file_map['image'].get_prepare_fileobj('rb'))
+        with file_map['image'].get_prepare_fileobj('rb') as fptr:
+            parser.parse(fptr=fptr)
         return parser.img
 
     @classmethod

nibabel/gifti/tests/data/external.gii.bz2

@@ -447,9 +447,8 @@ def test_darray_dtype_coercion_failures():
         assert_array_equal(da_copy.data, da.data)
 
 
-def test_gifti_file_close():
+def test_gifti_file_close(recwarn):
     gii = load(test_data('gifti', 'ascii.gii'))
-    with pytest.WarningsRecorder() as record:
-        with InTemporaryDirectory():
-            gii.to_filename('test.gii')
-    assert not any(isinstance(r.message, ResourceWarning) for r in record.list)
+    with InTemporaryDirectory():
+        gii.to_filename('test.gii')
+    assert not any(isinstance(r.message, ResourceWarning) for r in recwarn)

nibabel/gifti/tests/data/external.gii.gz

@@ -462,3 +462,11 @@ def test_external_file_failure_cases():
     parser = GiftiImageParser()
     with pytest.raises(GiftiParseError):
         img = parser.parse(xmldata)
+
+
+def test_load_compressed():
+    for ext in ('', '.gz', '.bz2'):
+        fn = pjoin(IO_DATA_PATH, 'external.gii' + ext)
+        img7 = load(fn)
+        assert_array_almost_equal(img7.darrays[0].data, DATA_FILE7_darr1)
+        assert_array_almost_equal(img7.darrays[1].data, DATA_FILE7_darr2)