##
# \file registration_method.py
# \brief Abstract class to define a registration method
#
# \author Michael Ebner (michael.ebner.14@ucl.ac.uk)
# \date Aug 2017
#
# Import libraries
import numpy as np
import SimpleITK as sitk
from abc import ABCMeta, abstractmethod
import pysitk.python_helper as ph
import niftymic.base.stack as st
import niftymic.base.slice as sl
##
# Abstract class for registration methods
# \date 2017-08-09 11:22:51+0100
#
class RegistrationMethod(object):
__metaclass__ = ABCMeta
##
# Store information for registration methods and initialize additional
# variables
# \date 2017-08-09 11:23:14+0100
#
# \param self The object
# \param fixed Fixed image as Stack/Slice object
# \param moving The moving
# \param use_fixed_mask The use fixed mask
# \param use_moving_mask The use moving mask
# \param use_verbose The use_verbose
#
def __init__(self,
fixed,
moving,
use_fixed_mask,
use_moving_mask,
use_verbose):
self._fixed = fixed
self._moving = moving
self._use_fixed_mask = use_fixed_mask
self._use_moving_mask = use_moving_mask
self._use_verbose = use_verbose
self._computational_time = ph.get_zero_time()
self._registration_method = None
##
# Sets the fixed image
# \date 2017-08-08 16:45:45+0100
#
# \param self The object
# \param fixed The fixed image as Stack/Slice object
#
def set_fixed(self, fixed):
self._fixed = fixed
##
# Gets the fixed image
# \date 2017-08-08 16:45:58+0100
#
# \param self The object
#
# \return The fixed image as Stack/Slice object.
#
def get_fixed(self):
return self._fixed
##
# Sets the moving image
# \date 2017-08-08 16:45:45+0100
#
# \param self The object
# \param moving The moving image as Stack/Slice object
#
#
def set_moving(self, moving):
self._moving = moving
##
# Gets the moving image
# \date 2017-08-08 16:45:58+0100
#
# \param self The object
#
# \return The moving image as Stack/Slice object.
#
def get_moving(self):
return self._moving
##
# Specify whether fixed mask shall be used for registration
# \date 2017-08-08 16:48:03+0100
#
# \param self The object
# \param use_fixed_mask Turn on/off use of fixed mask; bool
#
def use_fixed_mask(self, use_fixed_mask):
self._use_fixed_mask = use_fixed_mask
##
# Specify whether moving mask shall be used for registration
# \date 2017-08-08 16:48:03+0100
#
# \param self The object
# \param use_moving_mask Turn on/off use of moving mask; bool
#
def use_moving_mask(self, use_moving_mask):
self._use_moving_mask = use_moving_mask
##
# Sets the use_verbose.
# \date 2017-08-08 16:50:13+0100
#
# \param self The object
# \param use_verbose Turn on/off use_verbose output; bool
#
def use_verbose(self, use_verbose):
self._use_verbose = use_verbose
##
# Gets the computational time it took to perform the registration
# \date 2017-08-08 16:59:45+0100
#
# \param self The object
#
# \return The computational time.
#
def get_computational_time(self):
return self._computational_time
##
# Gets the obtained registration transform.
# \date 2017-08-08 16:52:36+0100
#
# \param self The object
#
# \return The registration transform as sitk object.
#
def get_registration_transform_sitk(self):
return self._registration_transform_sitk
##
# Run the registration method
# \date 2017-08-08 17:01:01+0100
#
# \param self The object
#
def run(self):
if not isinstance(self._fixed, st.Stack) and \
not isinstance(self._fixed, sl.Slice):
raise TypeError("Fixed image must be of type 'Stack' or 'Slice'")
if not isinstance(self._moving, st.Stack) and \
not isinstance(self._moving, sl.Slice):
raise TypeError("Moving image must be of type 'Stack' or 'Slice'")
time_start = ph.start_timing()
# Execute registration method
self._run()
# Get computational time
self._computational_time = ph.stop_timing(time_start)
if self._use_verbose:
ph.print_info("Required computational time: %s" %
(self.get_computational_time()))
@abstractmethod
def _run(self):
pass
##
# Gets the warped moving image, i.e. moving image warped and resampled to
# the fixed grid
# \date 2017-08-08 16:58:30+0100
#
# \param self The object
#
# \return The warped moving image as Stack/Slice object
#
@abstractmethod
def get_warped_moving(self):
pass
##
# Abstract class for affine registration methods
# \date 2017-08-09 11:22:51+0100
#
class AffineRegistrationMethod(RegistrationMethod):
__metaclass__ = ABCMeta
##
# Store information for registration methods and initialize additional
# variables
# \date 2017-08-09 11:23:14+0100
#
# \param self The object
# \param fixed Fixed image as Stack/Slice object
# \param moving The moving
# \param use_fixed_mask The use fixed mask
# \param use_moving_mask The use moving mask
# \param use_verbose The use_verbose
#
def __init__(self,
fixed,
moving,
use_fixed_mask,
use_moving_mask,
use_verbose,
registration_type,
):
RegistrationMethod.__init__(self,
fixed=fixed,
moving=moving,
use_fixed_mask=use_fixed_mask,
use_moving_mask=use_moving_mask,
use_verbose=use_verbose,
)
self._registration_type = registration_type
##
# Sets the registration type.
# \date 2017-02-02 16:42:13+0000
#
# \param self The object
# \param registration_type The registration type
#
def set_registration_type(self, registration_type):
if registration_type not in self._REGISTRATION_TYPES:
raise ValueError("Possible registration types: " +
str(self._REGISTRATION_TYPES))
self._registration_type = registration_type
##
# Gets the registration type.
# \date 2017-08-08 19:58:30+0100
#
# \param self The object
#
# \return The registration type as string.
#
def get_registration_type(self):
return self._registration_type
##
# Gets the warped moving image, i.e. moving image warped and resampled to
# the fixed grid
# \date 2017-08-08 16:58:30+0100
#
# \param self The object
#
# \return The warped moving image as Stack/Slice object
#
def get_warped_moving(self):
warped_moving_sitk_mask = sitk.Resample(
self._moving.sitk_mask,
self._fixed.sitk,
self.get_registration_transform_sitk(),
sitk.sitkNearestNeighbor,
0,
self._moving.sitk_mask.GetPixelIDValue(),
)
if isinstance(self._moving, st.Stack):
warped_moving = st.Stack.from_sitk_image(
image_sitk=self._get_warped_moving_sitk(),
filename=self._moving.get_filename(),
image_sitk_mask=warped_moving_sitk_mask,
slice_thickness=self._fixed.get_slice_thickness(),
)
else:
warped_moving = sl.Slice.from_sitk_image(
image_sitk=self._get_warped_moving_sitk(),
filename=self._moving.get_filename(),
image_sitk_mask=warped_moving_sitk_mask,
slice_thickness=self._fixed.get_slice_thickness(),
)
return warped_moving
##
# Gets the fixed image transformed by the obtained registration transform.
#
# The returned image will align the fixed image with the moving image as
# found during the registration.
# \date 2017-08-08 16:53:21+0100
#
# \param self The object
#
# \return The transformed fixed as Stack/Slice object
#
def get_transformed_fixed(self):
fixed = st.Stack.from_stack(self._fixed)
fixed.update_motion_correction(self.get_registration_transform_sitk())
return fixed
@abstractmethod
def _get_warped_moving_sitk(self):
pass
