SimpleITK  2.0.0rc1.post255
N4BiasFieldCorrection/N4BiasFieldCorrection.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 N4BiasFieldCorrection.R inputImage, outputImage, shrinkFactor, maskImage, numberOfIterations, numberOfFittingLevels
#
library(SimpleITK)
args <- commandArgs( TRUE )
if (length(args) < 2) {
stop("At least 2 arguments expected - inputImage, outputImage, [shrinkFactor], ",
"[maskImage], [numberOfIterations], [numberOfFittingLevels]")
}
inputImage <- ReadImage(args[[1]])
if (length( args ) > 4) {
maskImage <- ReadImage( args[[4]], 'sitkUint8' )
} else {
maskImage <- OtsuThreshold( inputImage, 0, 1, 200 )
}
if (length( args ) > 3) {
inputImage <- Shrink( inputImage, rep(strtoi(args[3]), inputImage$GetDimension()) )
maskImage <- Shrink( maskImage, rep(strtoi(args[3]), inputImage$GetDimension()) )
}
inputImage <- Cast( inputImage, 'sitkFloat32' )
corrector <- N4BiasFieldCorrectionImageFilter()
numberFittingLevels <- 4
if (length ( args ) > 6) {
numberFittingLevels <- strtoi( args[[6]] )
}
if (length ( args ) > 5) {
corrector$SetMaximumNumberOfIterations( rep(strtoi( args[[5]], numberFittingLevels)) )
}
output <- corrector$Execute( inputImage, maskImage )
WriteImage(output, args[[2]])