ImageRegistrationMethodBSpline2/ImageRegistrationMethodBSpline2.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 ImageRegistrationMethodBSpline2.R fixedImageFilter movingImageFile outputTransformFile
#

library(SimpleITK)

commandIteration <- function(method)
{
    msg <- paste(method$GetOptimizerIteration(), "=",
                 method$GetMetricValue(), "\n\t#:",
                 method$GetOptimizerPosition(), '\n')
    cat(msg)
}

commandMultiIteration <- function(method)
{
    msg <- paste("--------- Resolution Changing ---------\n")
    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')

transformDomainMeshSize <- rep(10, moving$GetDimension())
tx <- BSplineTransformInitializer(fixed, transformDomainMeshSize)

cat("Initial Parameters:\n", tx$GetParameters())

R <- ImageRegistrationMethod()
R$SetMetricAsMattesMutualInformation(50)
R$SetOptimizerAsGradientDescentLineSearch(5.0, 100,
                                          convergenceMinimumValue=1e-4,
                                          convergenceWindowSize=5)
R$SetOptimizerScalesFromPhysicalShift()
R$SetInitialTransform(tx)
R$SetInterpolator('sitkLinear')

R$SetShrinkFactorsPerLevel(c(6,2,1))
R$SetSmoothingSigmasPerLevel(c(6,2,1))

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')

WriteTransform(outTx, args[[3]])