ImageRegistrationMethod4/ImageRegistrationMethod4.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.
#
# =========================================================================
 
from __future__ import print_function
 
import SimpleITK as sitk
import sys
import os
 
if len(sys.argv) < 4:
    print("Usage:", sys.argv[0], "<fixedImageFilter> <movingImageFile>",
          "<outputTransformFile> <numberOfBins> <samplingPercentage>")
    sys.exit(1)
 
 
def command_iteration(method):
    print("{0:3} = {1:10.5f} : {2}".format(method.GetOptimizerIteration(),
                                           method.GetMetricValue(),
                                           method.GetOptimizerPosition()))
 
 
fixed = sitk.ReadImage(sys.argv[1], sitk.sitkFloat32)
moving = sitk.ReadImage(sys.argv[2], sitk.sitkFloat32)
 
numberOfBins = 24
samplingPercentage = 0.10
 
if len(sys.argv) > 4:
    numberOfBins = int(sys.argv[4])
if len(sys.argv) > 5:
    samplingPercentage = float(sys.argv[5])
 
R = sitk.ImageRegistrationMethod()
R.SetMetricAsMattesMutualInformation(numberOfBins)
R.SetMetricSamplingPercentage(samplingPercentage, sitk.sitkWallClock)
R.SetMetricSamplingStrategy(R.RANDOM)
R.SetOptimizerAsRegularStepGradientDescent(1.0, .001, 200)
R.SetInitialTransform(sitk.TranslationTransform(fixed.GetDimension()))
R.SetInterpolator(sitk.sitkLinear)
 
R.AddCommand(sitk.sitkIterationEvent, lambda: command_iteration(R))
 
outTx = R.Execute(fixed, moving)
 
print("-------")
print(outTx)
print("Optimizer stop condition: {0}"
      .format(R.GetOptimizerStopConditionDescription()))
print(" Iteration: {0}".format(R.GetOptimizerIteration()))
print(" Metric value: {0}".format(R.GetMetricValue()))
 
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. + simg2 // 2.)
    sitk.Show(cimg, "ImageRegistration4 Composition")