DemonsRegistration2/DemonsRegistration2.py

#!/usr/bin/env python
# =========================================================================
#
#  Copyright NumFOCUS
#
#  Licensed under the Apache License, Version 2.0 (the "License");
#  you may not use this file except in compliance with the License.
#  You may obtain a copy of the License at
#
#         http://www.apache.org/licenses/LICENSE-2.0.txt
#
#  Unless required by applicable law or agreed to in writing, software
#  distributed under the License is distributed on an "AS IS" BASIS,
#  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
#  See the License for the specific language governing permissions and
#  limitations under the License.
#
# =========================================================================
 
import SimpleITK as sitk
import sys
import os
 
 
def command_iteration(filter):
    print(f"{filter.GetElapsedIterations():3} = {filter.GetMetric():10.5f}")
 
 
if len(sys.argv) < 4:
    print(
        "Usage:",
        sys.argv[0],
        "<fixedImageFilter> <movingImageFile>",
        "[initialTransformFile] <outputTransformFile>",
    )
    sys.exit(1)
 
fixed = sitk.ReadImage(sys.argv[1])
 
moving = sitk.ReadImage(sys.argv[2])
 
matcher = sitk.HistogramMatchingImageFilter()
if fixed.GetPixelID() in (sitk.sitkUInt8, sitk.sitkInt8):
    matcher.SetNumberOfHistogramLevels(128)
else:
    matcher.SetNumberOfHistogramLevels(1024)
matcher.SetNumberOfMatchPoints(7)
matcher.ThresholdAtMeanIntensityOn()
moving = matcher.Execute(moving, fixed)
 
# The fast symmetric forces Demons Registration Filter
# Note there is a whole family of Demons Registration algorithms included in
# SimpleITK
demons = sitk.FastSymmetricForcesDemonsRegistrationFilter()
demons.SetNumberOfIterations(200)
# Standard deviation for Gaussian smoothing of displacement field
demons.SetStandardDeviations(1.0)
 
demons.AddCommand(sitk.sitkIterationEvent, lambda: command_iteration(demons))
 
if len(sys.argv) > 4:
    initialTransform = sitk.ReadTransform(sys.argv[3])
    sys.argv[-1] = sys.argv.pop()
 
    toDisplacementFilter = sitk.TransformToDisplacementFieldFilter()
    toDisplacementFilter.SetReferenceImage(fixed)
 
    displacementField = toDisplacementFilter.Execute(initialTransform)
 
    displacementField = demons.Execute(fixed, moving, displacementField)
 
else:
 
    displacementField = demons.Execute(fixed, moving)
 
print("-------")
print(f"Number Of Iterations: {demons.GetElapsedIterations()}")
print(f" RMS: {demons.GetRMSChange()}")
 
outTx = sitk.DisplacementFieldTransform(displacementField)
 
sitk.WriteTransform(outTx, sys.argv[3])
 
if "SITK_NOSHOW" not in os.environ:
    resampler = sitk.ResampleImageFilter()
    resampler.SetReferenceImage(fixed)
    resampler.SetInterpolator(sitk.sitkLinear)
    resampler.SetDefaultPixelValue(100)
    resampler.SetTransform(outTx)
 
    out = resampler.Execute(moving)
    simg1 = sitk.Cast(sitk.RescaleIntensity(fixed), sitk.sitkUInt8)
    simg2 = sitk.Cast(sitk.RescaleIntensity(out), sitk.sitkUInt8)
    cimg = sitk.Compose(simg1, simg2, simg1 // 2.0 + simg2 // 2.0)
    sitk.Show(cimg, "DeformableRegistration1 Composition")