def _prepare_openers(self):
# Saved openers
self._opener = dict()
# Locks (still unsure why I need that)
self._lock = dict()
for key, val in self._image.file_map.items():
mode = self.mode + 'b' # everything is binary in nibabel (?)
file_like = val.file_like
self._lock[key] = RLock()
if hasattr(file_like, 'read') and hasattr(file_like, 'seek'):
# file object -> keep stuff irrelevant
if not file_like.readable() or not file_like.seekable():
raise ValueError('File must be readable and seekable')
if '+' in self.mode and not file_like.writable():
raise ValueError('File must be writable in mode "r+"')
self._opener[(key, self.mode)] = file_like
continue
if self.keep_open:
try:
self._opener[(key, mode)] = open(file_like,
mode,
keep_open=True)
except ValueError:
self._opener[(key, mode)] = open(file_like,
'rb',
keep_open=True)
else:
self._opener[(key, 'r')] = open(file_like,
'rb',
keep_open=False)
if not self._opener[(key, 'r')].is_indexed:
del self._opener[(key, 'r')]
def to_filename(self, fname):
"""Write to file"""
with open(fname, 'wt') as f:
return self.to_file_like(f)
def from_filename(cls, fname):
"""Build from path to LTA file"""
with open(fname, 'r') as f:
return cls.from_lines(f)
def fileobj(self, key='image', mode='', seek=None):
"""Return an `Opener`.
It can be used with:
>> nii = BabelArray('/path/to/file')
>> with nii.fileobj('image') as f:
>> f.seek(pos)
>> ...
Parameters
----------
key : str, default='image'
Key of the file to open
mode : {'r', 'r+', 'w', 'w+', 'a', 'a+'}, default='r'
Opening mode. The file type ('b' or 't') should be omitted.
seek : int, optional
Position to seek.
"""
if key not in self._image.file_map:
key = 'image'
if not mode:
mode = 'r'
opener = None
# check if we have the right opener
if (key, mode) in self._opener:
opener = self._opener[(key, mode)]
# otherwise, check if we have one with more permissions than needed
if opener is None and (key, mode + '+') in self._opener:
opener = self._opener[(key, mode + '+')]
# otherwise, check if we can hack a liberal one
# (e.g., 'r+' -> 'w(+)' or 'a(+)')
if opener is None:
for (key0, mode0), opener0 in self._opener.items():
if key0 != key:
continue
try:
opener = transform_opener(opener0, mode)
break
except ValueError:
pass
# we found one -> perform a few sanity checks
if opener is not None:
check = True
if 'r' in mode or '+' in mode:
check = check and opener.readable()
if 'w' in mode or 'a' in mode:
check = check and opener.writable()
if check:
if seek is not None:
opener.seek(seek)
yield opener
return
# everything failed -> create one from scratch
file_map = self._image.file_map[key]
with open(file_map.file_like, mode=mode, keep_open=False) as opener:
check = True
if 'r' in mode or '+' in mode:
check = check and opener.readable()
if 'w' in mode or 'a' in mode:
check = check and opener.writable()
if check:
if seek is not None:
opener.seek(seek)
yield opener
return
raise RuntimeError('Could not yield an appropriate file object')