SimpleITK  1.3.0.dev466
ImageRegistrationMethodDisplacement1/ImageRegistrationMethodDisplacement1.R
#=========================================================================
#
# Copyright Insight Software Consortium
#
# 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.
#
#=========================================================================
# Run with:
#
# Rscript --vanilla ImageRegistrationMethodDisplacement1.R fixedImageFilter movingImageFile outputTransformFile
#
library(SimpleITK)
commandIteration <- function(method)
{
if (method$GetOptimizerIteration()==0) {
cat("\tLevel:", method$GetCurrentLevel(),
"\n\tScales:", method$GetOptimizerScales(), "\n")
}
msg <- paste("#", method$GetOptimizerIteration(),
"\n\tMetric Value: ", method$GetMetricValue(),
"\n\tLearning Rate: ", method$GetOptimizerLearningRate(),
'\n', sep="")
cat(msg)
}
commandMultiIteration <- function(method)
{
msg <- paste("\tStop Condition: ", method$GetOptimizerStopConditionDescription(),
"\n============= Resolution Change =============\n", sep="")
cat(msg)
}
args <- commandArgs( TRUE )
if (length(args) != 3) {
stop("3 arguments expected - fixedImageFilter, movingImageFile, outputTransformFile")
}
fixed <- ReadImage(args[[1]], 'sitkFloat32')
moving <- ReadImage(args[[2]], 'sitkFloat32')
initialTx <- CenteredTransformInitializer(fixed, moving, AffineTransform(fixed$GetDimension()))
R <- ImageRegistrationMethod()
R$SetShrinkFactorsPerLevel(c(3,2,1))
R$SetSmoothingSigmasPerLevel(c(2,1,1))
R$SetMetricAsJointHistogramMutualInformation(20)
R$MetricUseFixedImageGradientFilterOff()
R$SetOptimizerAsGradientDescent(learningRate=1.0,
numberOfIterations=100,
convergenceMinimumValue=1e-6,
convergenceWindowSize=10,
estimateLearningRate = 'EachIteration')
R$SetOptimizerScalesFromPhysicalShift()
R$SetInitialTransform(initialTx, inPlace=TRUE)
R$SetInterpolator('sitkLinear')
R$AddCommand( 'sitkIterationEvent', function() commandIteration(R) )
R$AddCommand( 'sitkMultiResolutionIterationEvent', function() commandMultiIteration(R) )
outTx <- R$Execute(fixed, moving)
cat("-------\n")
outTx
cat("Optimizer stop condition:", R$GetOptimizerStopConditionDescription(), '\n')
cat("Iteration:", R$GetOptimizerIteration(), '\n')
cat("Metric value:", R$GetMetricValue(), '\n')
displacementField <- Image(fixed$GetSize(), 'sitkVectorFloat64')
displacementField$CopyInformation(fixed)
displacementTx <- DisplacementFieldTransform(displacementField)
rm(displacementField)
displacementTx$SetSmoothingGaussianOnUpdate(varianceForUpdateField=0.0,
varianceForTotalField=1.5)
R$SetMovingInitialTransform(outTx)
R$SetInitialTransform(displacementTx, inPlace=TRUE)
R$SetMetricAsANTSNeighborhoodCorrelation(4)
R$MetricUseFixedImageGradientFilterOff()
R$SetShrinkFactorsPerLevel(c(3,2,1))
R$SetSmoothingSigmasPerLevel(c(2,1,1))
R$SetOptimizerScalesFromPhysicalShift()
R$SetOptimizerAsGradientDescent(learningRate=1,
numberOfIterations=300,
convergenceMinimumValue=1e-6,
convergenceWindowSize=10,
estimateLearningRate = 'EachIteration')
outTx$AddTransform( R$Execute(fixed, moving) )
cat("-------\n")
outTx
cat("Optimizer stop condition:", R$GetOptimizerStopConditionDescription(), '\n')
cat("Iteration:", R$GetOptimizerIteration(), '\n')
cat("Metric value:", R$GetMetricValue(), '\n')
WriteTransform(outTx, args[[3]])