##
# \file joint_image_mask_builder.py
# \brief Build common mask from multiple, individual ones
#
# \author Michael Ebner (michael.ebner.14@ucl.ac.uk)
# \date November 2017
#
import SimpleITK as sitk
import numpy as np
import pysitk.simple_itk_helper as sitkh
import niftymic.base.stack as st
class JointImageMaskBuilder(object):
def __init__(self,
stacks,
target,
dilation_radius=1,
dilation_kernel="Ball",
max_distance=50):
self._stacks = stacks
self._target = target
self._dilation_radius = dilation_radius
self._dilation_kernel = dilation_kernel
self._max_distance = max_distance
self._joint_image_mask = None
def run(self):
recon_space = self._target.get_isotropically_resampled_stack(
extra_frame=self._max_distance,
)
mask_sitk = 0 * recon_space.sitk_mask
dim = mask_sitk.GetDimension()
for stack in self._stacks:
stack_mask_sitk = sitk.Resample(
stack.sitk_mask,
mask_sitk,
eval("sitk.Euler%dDTransform()" % dim),
sitk.sitkNearestNeighbor,
0,
mask_sitk.GetPixelIDValue())
mask_sitk += stack_mask_sitk
thresholder = sitk.BinaryThresholdImageFilter()
mask_sitk = thresholder.Execute(mask_sitk, 0, 0.5, 0, 1)
if self._dilation_radius > 0:
dilater = sitk.BinaryDilateImageFilter()
dilater.SetKernelType(eval("sitk.sitk" + self._dilation_kernel))
dilater.SetKernelRadius(self._dilation_radius)
mask_sitk = dilater.Execute(mask_sitk)
self._joint_image_mask = st.Stack.from_sitk_image(
image_sitk=recon_space.sitk,
image_sitk_mask=mask_sitk,
filename=self._target.get_filename(),
slice_thickness=recon_space.get_slice_thickness(),
)
def get_stack(self):
return st.Stack.from_stack(self._joint_image_mask)
