ImageRegistrationMethod1/ImageRegistrationMethod1.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 ImageRegistrationMethod1.R fixedImage movingImage outputTransform
#


library(SimpleITK)


commandIteration <- function(method)
{
     res <- function() {
     msg <- paste("Optimizer iteration number ", method$GetOptimizerIteration(),
                  " = ", method$GetMetricValue(), " : ", method$GetOptimizerPosition(),
                  "\n" )
     cat(msg)
    }
    return(res)
}

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', commandIteration(Reg))

outTx = Reg$Execute(fixed, moving)

WriteTransform(outTx, args[[3]])