def set_data(self, dat, casting='unsafe'):
if '+' not in self.mode:
raise RuntimeError('Cannot write into read-only volume. '
'Re-map in mode "r+" to allow in-place '
'writing.')
# --- convert to numpy ---
if torch.is_tensor(dat):
dat = dat.detach().cpu()
dat = np.asanyarray(dat)
# --- sanity check ---
if dat.shape != self.shape:
raise ValueError(
'Expected an array of shape {} but got {}.'.format(
self.shape, dat.shape))
# --- special case if empty view ---
if dat.size == 0:
# nothing to write
return self
# --- cast ---
dat = volutils.cast(dat, self.dtype, casting)
# --- unpermute ---
drop, perm, slicer = split_operation(self.permutation, self.slicer,
'w')
dat = dat[drop].transpose(perm)
# --- dispatch ---
if self.is_compressed('image'):
if not all(is_fullslice(slicer, self._shape)):
# read-and-write
slice = dat
with self.fileobj('image', 'r') as f:
dat = self._read_data_raw(fileobj=f, mmap=False)
dat[slicer] = slice
with self.fileobj('image', 'w', seek=0) as f:
if self.same_file('image', 'header'):
self._set_header_raw(fileobj=f)
self._write_data_raw_full(dat, fileobj=f)
if self.same_file('image', 'footer'):
self._set_footer_raw(fileobj=f)
elif all(is_fullslice(slicer, self._shape)):
with self.fileobj('image', 'r+') as f:
self._write_data_raw_full(dat, fileobj=f)
else:
with self.fileobj('image', 'r+') as f:
self._write_data_raw_partial(dat, slicer, fileobj=f)
return self
def _read_data_raw(self, slicer=None, tiffobj=None):
"""Read native data
Dispatch to `_read_data_raw_full` or `_read_data_raw_partial`.
Parameters
----------
slicer : tuple[index_like], optional
A tuple of indices that describe the chunk of data to read.
If None, read everything.
tiffobj : file object, default=`self.fileobj('image', 'r')`
A file object (with `seek`, `read`) from which to read
Returns
-------
dat : np.ndarray
"""
if tiffobj is None:
with self.tiffobj() as tiffobj:
return self._read_data_raw(slicer, tiffobj)
# load sub-array
if slicer is None or all(is_fullslice(slicer, self._shape)):
dat = self._read_data_raw_full(tiffobj)
else:
dat = self._read_data_raw_partial(slicer, tiffobj)
return dat
def _read_data_raw(self, slicer=None, fileobj=None, mmap=None):
"""Read native data
Dispatch to `_read_data_raw_full` or `_read_data_raw_partial`.
Parameters
----------
slicer : tuple[index_like], optional
A tuple of indices that describe the chunk of data to read.
If None, read everything.
fileobj : file object, default=`self.fileobj('image', 'r')`
A file object (with `seek`, `read`) from which to read
mmap : bool, default=`self._image.dataobj.mmap`
If True, try to memory map the data.
Returns
-------
dat : np.ndarray
"""
# load sub-array
if slicer is None or all(is_fullslice(slicer, self._shape)):
dat = self._read_data_raw_full(fileobj, mmap=mmap)
if slicer is not None:
dat = dat[slicer]
else:
dat = self._read_data_raw_partial(slicer, fileobj)
return dat
def _write_data_raw_partial(self, dat, slicer, fileobj=None):
"""Write native data
Parameters
----------
dat : np.ndarray
Should already have the on-disk data type, including byte-order
slicer : tuple[index_like]
Unpermuted slicer, without new axes.
fileobj : nibabel.Opener, optional
File object
"""
if fileobj is None:
# Create our own context
with self.fileobj('image', 'r+') as fileobj:
return self._write_data_raw_partial(dat, slicer, fileobj)
# sanity checks for developers
# (asserts because proper conversion/dispatch should happen before)
assert isinstance(dat, np.ndarray), "Data should already be numpy"
assert dat.dtype == self.dtype, "Data should already have correct type"
assert not self.is_compressed('image'), "Data cannot be compressed"
assert not all(is_fullslice(
slicer, self._shape)), "No need for partial writing"
if not fileobj.readable():
raise RuntimeError('File object not readable')
if not fileobj.writable():
raise RuntimeError('File object not writable')
# write data chunk
writeslice(dat,
fileobj,
tuple(slicer),
self._shape,
self.dtype,
offset=self._image.dataobj.offset,
order=self._image.dataobj.order,
lock=self._lock['image'])
def level(self, val):
if val != self.level and not all(is_fullslice(self.slicer)):
raise RuntimeError("Cannot change resolution level in a view")
self._level = val
self._cache = {}
def series(self, val):
if val != self.series and not all(is_fullslice(self.slicer)):
raise RuntimeError("Cannot change series in a view")
self._series = val
self._cache = {}