def load(self):
"""Load the image data into memory, if it is not already accessible.
It is save to call this method several times successively.
"""
# do nothing if there already is data
# which included memory mapped arrays not just data in memory
if self._haveImageData():
return
if ncl.nifti_image_load(self.raw_nimg) < 0:
raise RuntimeError, "Unable to load image data."
self._data = ncl.wrapImageDataWithArray(self.raw_nimg)
# take data pointer away from nifticlibs so we can let Python manage
# the memory
ncl.detachDataFromImage(self.raw_nimg)
def save(self, filename=None, filetype="NIFTI", update_minmax=True):
"""Save the image to a file.
If the image was created using array data (i.e., not loaded from a file)
a filename has to be specified.
If not yet done already, the image data will be loaded into memory
before saving the file.
:Parameters:
filename: str | None
The name of the target file (typically including its extension).
Filenames might be provided as unicode strings. However, as the
underlying library does not support unicode, they must be
ascii-encodable, i.e. must not contain pure unicode characters.
Usually setting the filename also determines the filetype
(NIfTI/ANALYZE). Please see
:meth:`~nifti.image.NiftiImage.setFilename` for some more
details. If None, an image loaded from a file will cause the
original image to be overwritten.
filetype: str
Provide intented filetype. Please see the documentation of the
`setFilename()` method for some more details.
update_minmax: bool
Whether the image header's min and max values should be updated
according to the current image data.
.. warning::
There will be no exception if writing fails for any reason, as the
underlying function nifti_write_hdr_img() from libniftiio does not
provide any feedback. Suggestions for improvements are appreciated.
"""
if not filename is None:
# make sure filename is not unicode
try:
filename = str(filename)
except UnicodeEncodeError:
raise UnicodeError, "The filename must not contain unicode characters, since " "the NIfTI library cannot handle them."
# If image data is not yet loaded, do it now.
# It is important to do it already here, because nifti_image_load
# depends on the correct filename set in the nifti_image struct
# and this will be modified in this function!
self.load()
# set a default description if there is none
if not self.description:
self.description = "Written by PyNIfTI version %s" % nifti.__version__
# update header information
if update_minmax:
self.updateCalMinMax()
# saving for the first time?
if not self.filename or filename:
if not filename:
raise ValueError, "When saving an image for the first time a filename " + "has to be specified."
self.setFilename(filename, filetype)
# if still no data is present data source has been an array
# -> allocate memory in nifti struct and assign data to it
if not self.raw_nimg.data:
if not ncl.allocateImageMemory(self.raw_nimg):
raise RuntimeError, "Could not allocate memory for image data."
else:
raise RuntimeError, "This should never happen! Please report me!"
# This assumes that the nimg struct knows about the correct datatype and
# dimensions of the array
a = ncl.wrapImageDataWithArray(self.raw_nimg)
a[:] = self._data[:]
#
# embed meta data
#
if len(self.meta.keys()):
self.extensions += ("pypickle", cPickle.dumps(self.meta, protocol=0))
# now save it
ncl.nifti_image_write_hdr_img(self.raw_nimg, 1, "wb")
# yoh comment: unfortunately return value of nifti_image_write_hdr_img
# can't be used to track the successful completion of save
# raise IOError, 'An error occured while attempting to save the image
# file.'
# take data pointer away from nifticlibs so we can let Python manage
# the memory
ncl.detachDataFromImage(self.raw_nimg)
# and finally clean 'pypickle' extension again, since its data is in
# 'meta'
self._removePickleExtension()