def __save_nibabel(arr, hdr, filename):
"""
Image saver using the third-party module nibabel.
@param arr the image data
@param hdr the image header with met-information
@param filename the target location
"""
import nibabel
from ..utilities import nibabelu
logger = Logger.getInstance()
logger.debug('Saving image as {} with NiBabel...'.format(filename))
# convert type bool to int8
if scipy.bool_ == arr.dtype:
arr = arr.astype(scipy.uint8)
# if original image object was provided with hdr, try to use it for creating the image object
if hdr and __is_header_nibabel(hdr):
__update_header_from_array_nibabel(hdr, arr)
image = nibabelu.image_like(arr, hdr)
# if not, create new image object and copy meta data as far as possible
else:
image = nibabelu.image_new(arr, filename)
if hdr: copy_meta_data(image, hdr)
# save image
nibabel.save(image, filename)
def __save_itk(arr, hdr, filename):
"""
Image saver using the third-party module itk.
@param arr the image data
@param hdr the image header with met-information
@param filename the target location
"""
import itk
from medpy.itkvtk.utilities import itku
logger = Logger.getInstance()
logger.debug('Saving image as {} with Itk...'.format(filename))
# determine image type from array
image_type = itku.getImageTypeFromArray(arr)
# convert array to itk image
try:
img = itku.getImageFromArray(arr)
except KeyError:
raise DependencyError('The itk python PyBuffer transition object was compiled without support for image of type {}.'.format(image_type))
# if original image object was provided with hdr, try to use it for creating the image object
if __is_header_itk(hdr):
# save original image shape / largest possible region
shape = []
for i in range(img.GetLargestPossibleRegion().GetImageDimension()):
shape.append(img.GetLargestPossibleRegion().GetSize().GetElement(i))
# copy meta data
try:
img.CopyInformation(hdr.GetPointer())
# reset largest possible region / shape to original value
for i in range(len(shape)):
img.GetLargestPossibleRegion().GetSize().SetElement(i, shape[i])
except RuntimeError as e: # raised when the meta data information could not be copied (e.g. when the two images ndims differ)
logger.debug('The meta-information could not be copied form the old header. CopyInformation signaled: {}.'.format(e))
pass
elif hdr: # otherwise copy meta-data information as far as possible
copy_meta_data(img, hdr)
# save the image
writer = itk.ImageFileWriter[image_type].New()
writer.SetFileName(filename)
writer.SetInput(img.GetPointer())
writer.Update()
