SimpleITK  1.3.0.dev466
DemonsRegistration1/DemonsRegistration1.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 DemonsRegistration1.R fixedImageFilter movingImageFile 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 arguments expected - fixedImageFilter, movingImageFile, outputTransformFile")
}
fixed <- ReadImage(args[[1]], 'sitkFloat32')
moving <- ReadImage(args[[2]], 'sitkFloat32')
matcher <- HistogramMatchingImageFilter()
matcher$SetNumberOfHistogramLevels(1024)
matcher$SetNumberOfMatchPoints(7)
matcher$ThresholdAtMeanIntensityOn()
moving <- matcher$Execute(moving, fixed)
# The basic Demons Registration Filter
# Note there is a whole family of Demons Registration algorithms included in SimpleITK
demons <- DemonsRegistrationFilter()
demons$SetNumberOfIterations( 50 )
# Standard deviation for Gaussian smoothing of displacement field
demons$SetStandardDeviations( 1.0 )
demons$AddCommand( 'sitkIterationEvent', function() commandIteration(demons) )
displacementField <- demons$Execute( fixed, moving )
cat("-------\n")
cat("Number Of Iterations: ", demons$GetElapsedIterations(), "\n")
cat("RMS: ", demons$GetRMSChange(), "\n")
outTx <- DisplacementFieldTransform( displacementField )
WriteTransform(outTx, args[[3]])