SimpleITK  1.3.0.dev466
DemonsRegistration2/DemonsRegistration2.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 DemonsRegistration2.R fixedImageFilter movingImageFile [initialTransformFile] outputTransformFile
#
library(SimpleITK)
commandIteration <- function(filter)
{
msg <- paste("Iteration number ", filter$GetElapsedIterations(),
" = ", filter$GetMetric(), "\n" )
cat(msg)
}
args <- commandArgs( TRUE )
if (length(args) < 3) {
stop("3 (or 4) arguments expected - fixedImageFilter, movingImageFile, [initialTransformFile], outputTransformFile")
}
fixed <- ReadImage(args[[1]])
moving <- ReadImage(args[[2]])
matcher <- HistogramMatchingImageFilter()
if ( fixed$GetPixelID() %in% c( 'sitkUInt8', 'sitkInt8' ) ) {
matcher$SetNumberOfHistogramLevels(128)
} else {
matcher$SetNumberOfHistogramLevels(1024)
}
matcher$SetNumberOfMatchPoints(7)
matcher$ThresholdAtMeanIntensityOn()
moving <- matcher$Execute(moving, fixed)
# The fast symmetric forces Demons Registration Filter
# Note there is a whole family of Demons Registration algorithms included in SimpleITK
demons <- FastSymmetricForcesDemonsRegistrationFilter()
demons$SetNumberOfIterations(200)
# Standard deviation for Gaussian smoothing of displacement field
demons$SetStandardDeviations(1.0)
demons$AddCommand( 'sitkIterationEvent', function() commandIteration(demons) )
if (length(args) > 3) {
initialTransform <- ReadTransform(args[[3]])
toDisplacementFilter <- TransformToDisplacementFieldFilter()
toDisplacementFilter$SetReferenceImage(fixed)
displacementField <- toDisplacementFilter$Execute(initialTransform)
displacementField <- demons$Execute(fixed, moving, displacementField)
} else {
displacementField <- demons$Execute(fixed, moving)
}
cat("-------\n")
cat("Number Of Iterations: ",demons$GetElapsedIterations(), "\n")
cat(" RMS: ", demons$GetRMSChange(), "\n")
outTx <- DisplacementFieldTransform(displacementField)
WriteTransform(outTx, tail(args, n=1))