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RF/ENH: remove file prior writing in to_filename #466

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RF/ENH: remove file prior writing in to_filename #466

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RF/ENH: remove file prior writing in to_filename
yarikoptic Jul 29, 2016
cf564b6
RF: git-annex specific handling in to_filename + allow NIBABEL_REMOVE…
yarikoptic Aug 1, 2016
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20 changes: 19 additions & 1 deletion nibabel/filebasedimages.py
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Original file line number Diff line number Diff line change
Expand Up @@ -8,6 +8,7 @@
### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ### ##
''' Common interface for any image format--volume or surface, binary or xml.'''

import os
import warnings

from .externals.six import string_types
Expand All @@ -16,6 +17,14 @@
splitext_addext)
from .openers import ImageOpener

# OS-specific path
_GIT_ANNEX_OBJECTS_PATH = os.path.join('.git', 'annex', 'objects')


def _is_annex_symlink(path):
"""Return True if file is a symlink to the git-annex objects"""
return os.path.islink(path) and _GIT_ANNEX_OBJECTS_PATH in os.path.realpath(path)


class ImageFileError(Exception):
pass
Expand Down Expand Up @@ -347,7 +356,16 @@ def to_filename(self, filename):
-------
None
'''
self.file_map = self.filespec_to_file_map(filename)
self.file_map = file_map = self.filespec_to_file_map(filename)
remove_env = os.environ.get('NIBABEL_REMOVE_BEFORE_TO_FILENAME', None)
for _, fh in file_map.items():
if not isinstance(fh, FileHolder):
continue
if os.path.lexists(fh.filename) and (remove_env or _is_annex_symlink(fh.filename)):
# Remove previous file where new file would be saved
# Necessary e.g. for cases where file is a symlink pointing
# to some non-writable file (e.g. under git annex control)
os.unlink(fh.filename)
self.to_file_map()
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or @matthew-brett do you think it would remain kosher to shift this functionality even deeper into to_file_map? ;)

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Yes, to do this properly would mean going down into to_file_map, because it's possible to save images with filenames that way, but then, at the moment, you'd have to go into the implementation for each file type (to_file_map not implemented by default).


def to_filespec(self, filename):
Expand Down