Unclosed file warning in GiftiImage.to_file_map

[HippocampusGirl]

I get the following warning when fMRIPrep tries to write a GIfTI file

[2021-08-04 18:29:53,0633] [py.warnings     ] [WARNING  ] /usr/local/miniconda/lib/python3.7/site-packages/nibabel/filebasedimages.py:333: ResourceWarning: unclosed file <_io.BufferedWriter name='/ext/mnt/mbServerData/data/DYNAMORE/halfpipe_test-11002/nipype/fmriprep_wf/single_subject_11002_wf/func_preproc_task_stress_wf/bold_surf_wf/_target_fsaverage/update_metadata/mapflow/_update_metadata0/lh.fsaverage.gii'>
│   self.to_file_map()
│ Stack (most recent call last):
│   File "<string>", line 1, in <module>
│   File "/usr/local/miniconda/lib/python3.7/multiprocessing/forkserver.py", line 281, in main
│     old_handlers)
│   File "/usr/local/miniconda/lib/python3.7/multiprocessing/forkserver.py", line 317, in _serve_one
│     code = spawn._main(child_r)
│   File "/usr/local/miniconda/lib/python3.7/multiprocessing/spawn.py", line 118, in _main
│     return self._bootstrap()
│   File "/usr/local/miniconda/lib/python3.7/multiprocessing/process.py", line 297, in _bootstrap
│     self.run()
│   File "/usr/local/miniconda/lib/python3.7/multiprocessing/process.py", line 99, in run
│     self._target(*self._args, **self._kwargs)
│   File "/usr/local/miniconda/lib/python3.7/concurrent/futures/process.py", line 239, in _process_worker
│     r = call_item.fn(*call_item.args, **call_item.kwargs)
│   File "/usr/local/miniconda/lib/python3.7/site-packages/halfpipe/plugins/multiproc.py", line 70, in run_node
│     result["result"] = node.run(updatehash=updatehash)
│   File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 516, in run
│     result = self._run_interface(execute=True)
│   File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 635, in _run_interface
│     return self._run_command(execute)
│   File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/pipeline/engine/nodes.py", line 741, in _run_command
│     result = self._interface.run(cwd=outdir)
│   File "/usr/local/miniconda/lib/python3.7/site-packages/nipype/interfaces/base/core.py", line 428, in run
│     runtime = self._run_interface(runtime)
│   File "/usr/local/miniconda/lib/python3.7/site-packages/niworkflows/interfaces/surf.py", line 303, in _run_interface
│     img.to_filename(out_file)
│   File "/usr/local/miniconda/lib/python3.7/site-packages/nibabel/filebasedimages.py", line 333, in to_filename
│     self.to_file_map()
│   File "/usr/local/miniconda/lib/python3.7/warnings.py", line 110, in _showwarnmsg
│     msg.file, msg.line)
│   File "/usr/local/miniconda/lib/python3.7/site-packages/halfpipe/logging/base.py", line 36, in showwarning
└─    logger.warning(f"{s}", stack_info=True)

The code on the fMRIPrep side looks fine (see https://github.com/nipreps/niworkflows/blob/691436a28c10aa8f1d39cbad37610220e49f3abd/niworkflows/interfaces/surf.py#L303).

As far as I can tell, this could be resolved by adding a call to close_if_mine at the end of the function.

nibabel/nibabel/gifti/gifti.py

Lines 865 to 881 in 88e4761

	def to_file_map(self, file_map=None):
	""" Save the current image to the specified file_map
	Parameters
	----------
	file_map : dict
	Dictionary with single key ``image`` with associated value which is
	a :class:`FileHolder` instance pointing to the image file.
	Returns
	-------
	None
	"""
	if file_map is None:
	file_map = self.file_map
	f = file_map['image'].get_prepare_fileobj('wb')
	f.write(self.to_xml())

[effigies]

Yup, good catch. I think we assumed the garbage collector would clean up for us... Fortunately this is a context manager:

nibabel/nibabel/openers.py

Lines 185 to 189 in 62aea04

	def __enter__(self):
	return self
	def __exit__(self, exc_type, exc_val, exc_tb):
	self.close_if_mine()

So we should be able to write:

with file_map['image'].get_prepare_fileobj('wb') as f:
    f.write(self.to_xml())

Would you mind making the PR? And is there a minimal reproduction where we can always emit the warning? If so, it'd be good to have a test.