BF+TST: fix XML output from in-memory Gifti array

GiftiDataArrays created in memory (rather than loaded from disk) had
ExternalFileOffset attribute value as an integer, but for valid XML, the
values have to be strings.

Closes gh-469.

Author: matthew-brett

nibabel/gifti/gifti.py

@@ -436,6 +436,7 @@ def _to_xml_element(self):
         # fix endianness to machine endianness
         self.endian = gifti_endian_codes.code[sys.byteorder]
 
+        # All attribute values must be strings
         data_array = xml.Element('DataArray', attrib={
             'Intent': intent_codes.niistring[self.intent],
             'DataType': data_type_codes.niistring[self.datatype],
@@ -444,7 +445,7 @@ def _to_xml_element(self):
             'Encoding': gifti_encoding_codes.specs[self.encoding],
             'Endian': gifti_endian_codes.specs[self.endian],
             'ExternalFileName': self.ext_fname,
-            'ExternalFileOffset': self.ext_offset})
+            'ExternalFileOffset': str(self.ext_offset)})
         for di, dn in enumerate(self.dims):
             data_array.attrib['Dim%d' % di] = str(dn)
 

nibabel/gifti/tests/test_gifti.py

@@ -2,6 +2,7 @@
 """
 import warnings
 import sys
+from io import BytesIO
 
 import numpy as np
 
@@ -12,6 +13,7 @@
                            GiftiCoordSystem)
 from nibabel.gifti.gifti import data_tag
 from nibabel.nifti1 import data_type_codes
+from nibabel.fileholders import FileHolder
 
 from numpy.testing import (assert_array_almost_equal,
                            assert_array_equal)
@@ -275,3 +277,114 @@ def test_data_tag_deprecated():
         warnings.filterwarnings('once', category=DeprecationWarning)
         data_tag(np.array([]), 'ASCII', '%i', 1)
         assert_equal(len(w), 1)
+
+
+def test_gifti_round_trip():
+    # From section 14.4 in GIFTI Surface Data Format Version 1.0
+    # (with some adaptations)
+
+    test_data = b'''<?xml version="1.0" encoding="UTF-8"?>
+<!DOCTYPE GIFTI SYSTEM "http://www.nitrc.org/frs/download.php/1594/gifti.dtd">
+<GIFTI
+xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+xsi:noNamespaceSchemaLocation="http://www.nitrc.org/frs/download.php/1303/GIFTI_Caret.xsd"
+Version="1.0"
+NumberOfDataArrays="2">
+<MetaData>
+<MD>
+<Name><![CDATA[date]]></Name>
+<Value><![CDATA[Thu Nov 15 09:05:22 2007]]></Value>
+</MD>
+</MetaData>
+<LabelTable/>
+<DataArray Intent="NIFTI_INTENT_POINTSET"
+DataType="NIFTI_TYPE_FLOAT32"
+ArrayIndexingOrder="RowMajorOrder"
+Dimensionality="2"
+Dim0="4"
+Dim1="3"
+Encoding="ASCII"
+Endian="LittleEndian"
+ExternalFileName=""
+ExternalFileOffset="">
+<CoordinateSystemTransformMatrix>
+<DataSpace><![CDATA[NIFTI_XFORM_TALAIRACH]]></DataSpace>
+<TransformedSpace><![CDATA[NIFTI_XFORM_TALAIRACH]]></TransformedSpace>
+<MatrixData>
+1.000000 0.000000 0.000000 0.000000
+0.000000 1.000000 0.000000 0.000000
+0.000000 0.000000 1.000000 0.000000
+0.000000 0.000000 0.000000 1.000000
+</MatrixData>
+</CoordinateSystemTransformMatrix>
+<Data>
+10.5 0 0
+0 20.5 0
+0 0 30.5
+0 0 0
+</Data>
+</DataArray>
+<DataArray Intent="NIFTI_INTENT_TRIANGLE"
+DataType="NIFTI_TYPE_INT32"
+ArrayIndexingOrder="RowMajorOrder"
+Dimensionality="2"
+Dim0="4"
+Dim1="3"
+Encoding="ASCII"
+Endian="LittleEndian"
+ExternalFileName="" ExternalFileOffset="">
+<Data>
+0 1 2
+1 2 3
+0 1 3
+0 2 3
+</Data>
+</DataArray>
+</GIFTI>'''
+
+    exp_verts = np.zeros((4, 3))
+    exp_verts[0, 0] = 10.5
+    exp_verts[1, 1] = 20.5
+    exp_verts[2, 2] = 30.5
+    exp_faces = np.asarray([[0, 1, 2], [1, 2, 3], [0, 1, 3], [0, 2, 3]],
+                           dtype=np.int32)
+
+    def _check_gifti(gio):
+        vertices = gio.get_arrays_from_intent('NIFTI_INTENT_POINTSET')[0].data
+        faces = gio.get_arrays_from_intent('NIFTI_INTENT_TRIANGLE')[0].data
+        assert_array_equal(vertices, exp_verts)
+        assert_array_equal(faces, exp_faces)
+
+    bio = BytesIO()
+    fmap = dict(image=FileHolder(fileobj=bio))
+
+    bio.write(test_data)
+    bio.seek(0)
+    gio = GiftiImage.from_file_map(fmap)
+    _check_gifti(gio)
+    # Write and read again
+    bio.seek(0)
+    gio.to_file_map(fmap)
+    bio.seek(0)
+    gio2 = GiftiImage.from_file_map(fmap)
+    _check_gifti(gio2)
+
+
+def test_data_array_round_trip():
+    # Test valid XML generated from new in-memory array
+    # See: https://github.com/nipy/nibabel/issues/469
+    verts = np.zeros((4, 3), np.float32)
+    verts[0, 0] = 10.5
+    verts[1, 1] = 20.5
+    verts[2, 2] = 30.5
+
+    vertices = GiftiDataArray(verts)
+    img = GiftiImage()
+    img.add_gifti_data_array(vertices)
+    bio = BytesIO()
+    fmap = dict(image=FileHolder(fileobj=bio))
+    bio.write(img.to_xml())
+    bio.seek(0)
+    gio = GiftiImage.from_file_map(fmap)
+    vertices = gio.darrays[0].data
+    assert_array_equal(vertices, verts)