def _read_data_raw_full(self, fileobj=None, lock=None, mmap=None):
"""Read the full data from disk
Parameters
----------
fileobj : Opener, default=`self.fileobj('image')`
lock : Lock, default=`self._lock['image']`
mmap : bool, default=`self._image.dataobj._mmap`
Returns
-------
dat : np.ndarray
"""
if fileobj is None:
with self.fileobj('image') as fileobj:
return self._read_data_raw_full(fileobj, lock)
if lock is None:
with self._lock['image'] as lock:
return self._read_data_raw_full(fileobj, lock)
if mmap is None:
mmap = self._image.dataobj._mmap
return array_from_file(self._shape,
self.dtype,
fileobj,
offset=self._image.dataobj._offset,
order=self._image.dataobj.order,
mmap=mmap)
def raw_data_from_fileobj(self, frame=0):
dtype = self._get_data_dtype(frame)
if not self._header.endianness is native_code:
dtype=dtype.newbyteorder(self._header.endianness)
shape = self.get_shape(frame)
offset = self._get_frame_offset(frame)
fid_obj = self.fileobj
raw_data = array_from_file(shape, dtype, fid_obj, offset=offset)
## put data into neurologic orientation
### ASSUME Patient orientation is HFS as patient orientation
### is not always set in header
raw_data = raw_data[::-1,::-1,::-1]
return raw_data
def data_from_fileobj(self, fileobj):
''' Read data array from `fileobj`
Parameters
----------
fileobj : file-like
Must be open, and implement ``read`` and ``seek`` methods
Returns
-------
arr : ndarray
data array
'''
dtype = self.get_data_dtype()
shape = self.get_data_shape()
offset = self.get_data_offset()
return array_from_file(shape, dtype, fileobj, offset)
def data_from_fileobj(self, fileobj):
''' Read data array from `fileobj`
Parameters
----------
fileobj : file-like
Must be open, and implement ``read`` and ``seek`` methods
Returns
-------
arr : ndarray
data array
'''
dtype = self.get_data_dtype()
shape = self.get_data_shape()
offset = self.get_data_offset()
return array_from_file(shape, dtype, fileobj, offset)
def get_volume(self, volume_idx):
"""Return a specified volume belonging to a 4dim image. This
can be useful when the image is large and we want to avoid
loading the whole image into memory.
"""
from nibabel.volumeutils import allopen, array_from_file
def get_fileobj(nibimage):
fileobj = allopen(nibimage.get_filename())
return fileobj
dtype = self._base.get_data_dtype()
shape = self._base.get_header().get_data_shape()[:-1]
bytes_per_volume = np.prod(shape) * dtype.itemsize
offset = self._base.get_header().get_data_offset() + (volume_idx * bytes_per_volume)
data = array_from_file(shape, dtype, get_fileobj(self._base), offset)
return data
def get_volume(self, volume_idx):
"""Return a specified volume belonging to a 4dim image. This
can be useful when the image is large and we want to avoid
loading the whole image into memory.
"""
from nibabel.volumeutils import allopen, array_from_file
def get_fileobj(nibimage):
fileobj = allopen(nibimage.get_filename())
return fileobj
dtype = self._base.get_data_dtype()
shape = self._base.get_header().get_data_shape()[:-1]
bytes_per_volume = np.prod(shape) * dtype.itemsize
offset = self._base.get_header().get_data_offset() + (volume_idx *
bytes_per_volume)
data = array_from_file(shape, dtype, get_fileobj(self._base), offset)
return data
