Elastix/Registration/elx.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
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#         http://www.apache.org/licenses/LICENSE-2.0.txt
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#=========================================================================
 
library(SimpleITK)
 
args <- commandArgs(TRUE)
 
if (length(args) < 5) {
    stop("Usage: elx <fixedImage> <movingImage> <parameterFile> <outputImage> <outputParameterFile>")
}
 
# Instantiate SimpleElastix
elastixImageFilter <- ElastixImageFilter()
 
# Read input
elastixImageFilter$SetFixedImage(ReadImage(args[1]))
elastixImageFilter$SetMovingImage(ReadImage(args[2]))
elastixImageFilter$SetParameterMap(elastixImageFilter$ReadParameterFile(args[3]))
elastixImageFilter$LogToConsoleOn()
 
# Run registration
output_image <- elastixImageFilter$Execute()
 
# Write result image
WriteImage(output_image, args[4])
 
# Write parameter file. This example only supports one parameter map and one transform parameter map.
elastixImageFilter$WriteParameterFile(elastixImageFilter$GetTransformParameterMap(0L), args[5])