def apply_transformation_workflow(moving_file, output_file, output_transform_file=None):
"""
"""
moving_image = pos_itk_transforms.read_itk_image(moving_file)
translation, rotation = get_random_rigid_3d_tranform_parameters(
tmean=CONFIG['tmean'], tsigma=CONFIG['tsigma'],
rmean=CONFIG['rmean'], rsigma=CONFIG['rsigma'])
vol_transform = itk.Euler3DTransform.D.New()
vol_transform.SetTranslation([0, 0, 0])
vol_transform.SetRotation(*list(rotation))
center = [0, 0, 0]
center[0] = moving_image.GetLargestPossibleRegion().GetSize()[0]/2
center[1] = moving_image.GetLargestPossibleRegion().GetSize()[1]/2
center[2] = moving_image.GetLargestPossibleRegion().GetSize()[2]/2
center = map(int, center) # Sometimes the indexes are returned as long ints
phisycal_center = moving_image.TransformIndexToPhysicalPoint(center)
vol_transform.SetCenter(phisycal_center)
resliced_image = pos_itk_transforms.reslice_image([vol_transform],
moving_image, default_pixel_value=CONFIG['default_pixel_value'])
pos_itk_transforms.write_itk_image(resliced_image, output_file)
if output_transform_file:
write_itk_matrix_transformation_to_file(vol_transform, output_transform_file)
def _load_single_image(self, attr_base, filename):
"""
Load itk image and store the image itself and its type
as a class attribute. The image is stored as
`<prefix>_image` attribute and the type of the image
is stored under the `<prefix> type` attribute.
:param attr_base: The base for the class attribute name.
:type attr_base: str
:return: None
:rtype: None
"""
# Generating the attributes names based on
# the image type.
image_attr_name = "_" + attr_base + "_image"
type_attr_name = "_" + attr_base + "_type"
setattr(self, image_attr_name,
pos_itk_transforms.read_itk_image(filename))
setattr(self, type_attr_name,
pos_itk_core.autodetect_file_type(filename))
# We read and report the number of components of the image.
numbers_of_components = \
getattr(self, image_attr_name).GetNumberOfComponentsPerPixel()
self._logger.info("Number of components of the image %s is: %d.",
filename, numbers_of_components)