incorrect datatype in GIFTI output (INT64 instead of INT32)

[hyperbolicTom]

Having an issue with NODE_INDEX. To reproduce:

#! /usr/bin/env python

import sys
import numpy as np
import nibabel

print("nibabel.__version__ =", nibabel.__version__)

idx = np.arange(10)

da = nibabel.gifti.GiftiDataArray(idx,
                                  intent = 'NIFTI_INTENT_NODE_INDEX',
                                  datatype = 'NIFTI_TYPE_INT32')

gim = nibabel.gifti.gifti.GiftiImage(darrays = [da])
nibabel.save(gim, "idx.gii")

gim = nibabel.load("idx.gii")
print(gim.darrays[0].data)

da = nibabel.gifti.GiftiDataArray(idx, encoding = 'GIFTI_ENCODING_ASCII',
                                  intent = 'NIFTI_INTENT_NODE_INDEX',
                                  datatype = 'NIFTI_TYPE_INT32')

gim = nibabel.gifti.gifti.GiftiImage(darrays = [da])
nibabel.save(gim, "idx.gii")

gim = nibabel.load("idx.gii")
print(gim.darrays[0].data)

What I get here, on a 64-bit machine:

nibabel.__version__ = 3.0.0dev
[0 0 1 0 2 0 3 0 4 0 5 0 6 0 7 0 8 0 9 0]
[0 1 2 3 4 5 6 7 8 9]

The problem is that internally, the node index is stored as an int64 array, and although the output is specified as being INT32, it isn't converted before .tostring() is called.

Here's a fix:

diff --git a/nibabel/gifti/gifti.py b/nibabel/gifti/gifti.py
index 22d6449e..e1149647 100644
--- a/nibabel/gifti/gifti.py
+++ b/nibabel/gifti/gifti.py
@@ -464,7 +464,7 @@ class GiftiDataArray(xml.XmlSerializable):
         # write data array depending on the encoding
         dt_kind = data_type_codes.dtype[self.datatype].kind
         data_array.append(
-            _data_tag_element(self.data,
+            _data_tag_element(self.data.astype(dt_kind),
                               gifti_encoding_codes.specs[self.encoding],
                               KIND2FMT[dt_kind],
                               self.ind_ord))

Perhaps the bug is that self.data is int64 already, but I'm not sure about that.
Anyway with this change the output is the same as with ASCII encoding.

[effigies]

Hi @hyperbolicTom. Thanks for the report. Would you be interested in submitting a PR?

It would be nice to start out with some tests that attempt to create some DataArrays whose inputs match and don't match their datatype, and making sure that writing either raises an exception (e.g., if you have floats that can't be safely coerced to int) or produces a file that reads consistently with the datatype code.

Once the tests are in place, and the failures are where we expect, then we can apply a fix. I think (but it's better to use tests to verify this) that probably the better way to make this fix is to adjust the datatype parameter to take the actual datatype, as opposed to KIND2FMT[data_type_codes[self.datatype].kind]. Then, if enclabel is ASCII, it uses the format string, and if it's B64BIN or B64GZ, then it uses astype(data_type_codes[self.datatype]).tostring() to coerce into an appropriately serializable form.

nibabel/nibabel/gifti/gifti.py

Lines 273 to 293 in 10ad38a

	def _data_tag_element(dataarray, encoding, datatype, ordering):
	""" Creates data tag with given `encoding`, returns as XML element
	"""
	import zlib
	ord = array_index_order_codes.npcode[ordering]
	enclabel = gifti_encoding_codes.label[encoding]
	if enclabel == 'ASCII':
	da = _arr2txt(dataarray, datatype)
	elif enclabel in ('B64BIN', 'B64GZ'):
	out = dataarray.tostring(ord)
	if enclabel == 'B64GZ':
	out = zlib.compress(out)
	da = base64.b64encode(out).decode()
	elif enclabel == 'External':
	raise NotImplementedError("In what format are the external files?")
	else:
	da = ''
	data = xml.Element('Data')
	data.text = da
	return data

[effigies]

Closed in #806.