Merge pull request #806 from effigies/fix/gifti_types

FIX: Coerce data types on writing GIFTI DataArrays

Author: effigies

nibabel/gifti/gifti.py

@@ -270,16 +270,21 @@ def _to_xml_element(self):
     return DataTag(dataarray, encoding, datatype, ordering).to_xml()
 
 
-def _data_tag_element(dataarray, encoding, datatype, ordering):
+def _data_tag_element(dataarray, encoding, dtype, ordering):
     """ Creates data tag with given `encoding`, returns as XML element
     """
     import zlib
-    ord = array_index_order_codes.npcode[ordering]
+    order = array_index_order_codes.npcode[ordering]
     enclabel = gifti_encoding_codes.label[encoding]
     if enclabel == 'ASCII':
-        da = _arr2txt(dataarray, datatype)
+        # XXX Accommodating data_tag API
+        # On removal (nibabel 4.0) drop str case
+        da = _arr2txt(dataarray, dtype if isinstance(dtype, str) else KIND2FMT[dtype.kind])
     elif enclabel in ('B64BIN', 'B64GZ'):
-        out = dataarray.tostring(ord)
+        # XXX Accommodating data_tag API - don't try to fix dtype
+        if isinstance(dtype, str):
+            dtype = dataarray.dtype
+        out = np.asanyarray(dataarray, dtype).tostring(order)
         if enclabel == 'B64GZ':
             out = zlib.compress(out)
         da = base64.b64encode(out).decode()
@@ -462,11 +467,10 @@ def _to_xml_element(self):
         if self.coordsys is not None:
             data_array.append(self.coordsys._to_xml_element())
         # write data array depending on the encoding
-        dt_kind = data_type_codes.dtype[self.datatype].kind
         data_array.append(
             _data_tag_element(self.data,
                               gifti_encoding_codes.specs[self.encoding],
-                              KIND2FMT[dt_kind],
+                              data_type_codes.dtype[self.datatype],
                               self.ind_ord))
 
         return data_array

nibabel/gifti/tests/test_gifti.py

@@ -21,6 +21,7 @@
 from nibabel.testing import clear_and_catch_warnings
 from .test_parse_gifti_fast import (DATA_FILE1, DATA_FILE2, DATA_FILE3,
                                     DATA_FILE4, DATA_FILE5, DATA_FILE6)
+import itertools
 
 
 def test_gifti_image():
@@ -400,3 +401,20 @@ def test_data_array_round_trip():
     gio = GiftiImage.from_file_map(fmap)
     vertices = gio.darrays[0].data
     assert_array_equal(vertices, verts)
+
+
+def test_darray_dtype_coercion_failures():
+    dtypes = (np.uint8, np.int32, np.int64, np.float32, np.float64)
+    encodings = ('ASCII', 'B64BIN', 'B64GZ')
+    for data_dtype, darray_dtype, encoding in itertools.product(dtypes,
+                                                                dtypes,
+                                                                encodings):
+        da = GiftiDataArray(np.arange(10).astype(data_dtype),
+                            encoding=encoding,
+                            intent='NIFTI_INTENT_NODE_INDEX',
+                            datatype=darray_dtype)
+        gii = GiftiImage(darrays=[da])
+        gii_copy = GiftiImage.from_bytes(gii.to_bytes())
+        da_copy = gii_copy.darrays[0]
+        assert_equal(np.dtype(da_copy.data.dtype), np.dtype(darray_dtype))
+        assert_array_equal(da_copy.data, da.data)