ImageRegistrationMethod1/ImageRegistrationMethod1.R

#=========================================================================
#
#  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.
#
#=========================================================================
# Run with:
#
# Rscript --vanilla ImageRegistrationMethod1.R fixedImage movingImage outputTransform
#
 
 
library(SimpleITK)
 
 
commandIteration <- function(method)
{
    msg <- paste("Optimizer iteration number ", method$GetOptimizerIteration(),
                 " = ", method$GetMetricValue(), " : ", method$GetOptimizerPosition(),
                 "\n" )
    cat(msg)
}
 
args <- commandArgs( TRUE )
 
if (length(args) != 3) {
    stop("3 arguments expected - FixedImage, MovingImage, TransformFilename")
}
 
fixed <- ReadImage(args[[1]], 'sitkFloat32')
 
moving <- ReadImage(args[[2]], 'sitkFloat32')
 
 
Reg = ImageRegistrationMethod()
Reg$SetMetricAsMeanSquares()
Reg$SetOptimizerAsRegularStepGradientDescent(4.0, .01, 200 )
Reg$SetInitialTransform(TranslationTransform(fixed$GetDimension()))
Reg$SetInterpolator('sitkLinear')
 
Reg$AddCommand('sitkIterationEvent', function() commandIteration(Reg))
 
outTx = Reg$Execute(fixed, moving)
 
WriteTransform(outTx, args[[3]])