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 launch(self):
# Execute the parents before-execution activities
super(self.__class__, self)._pre_launch()
# Just for our convenience, we make an alias
# for the direction of the computations
self.direction = self.options.direction
self._load_images()
self._load_coregistration_transformation()
# Define the single component processing type All single component data
# type will be converted to this tupe for the purpose of processing.
# It will be converted back to its initial data type upon completion of
# the processing.
self._processing_type = \
pos_itk_core.io_component_string_name_to_image_type[
C_INTERMEDIATE_SINGLE_COMPONENT_TYPEDEF]
# Determine the number of components in the image to be processed.
# Single component image is easy to process. Multichannel workflow
# is a bit more complicated
self._numbers_of_components = \
self._moving_image.GetNumberOfComponentsPerPixel()
# There are different workflows depending on the number of components,
# of the provided input image.
if self._numbers_of_components > 1:
processed_image = \
self.use_multicomponent_workflow()
else:
processed_image = \
self.use_single_component_workflow()
# This is a very important line of code. It gives us the final image!
# Yey....
pos_itk_transforms.write_itk_image(
processed_image, self.options.output_image)
# Run parent's post execution activities
super(self.__class__, self)._post_launch()
