Image Registration Method 4

If you are not familiar with the SimpleITK registration framework we recommend that you read the registration overview before continuing with the example.

Overview

Code

#!/usr/bin/env python

from __future__ import print_function

import SimpleITK as sitk
import sys
import os


if len ( sys.argv ) < 4:
    print( "Usage: {0} <fixedImageFilter> <movingImageFile> <outputTransformFile> <numberOfBins> <samplingPercentage>".format(sys.argv[0]))
    sys.exit ( 1 )

def command_iteration(method) :
    print("{0:3} = {1:10.5f} : {2}".format(method.GetOptimizerIteration(),
                                           method.GetMetricValue(),
                                           method.GetOptimizerPosition()))


fixed = sitk.ReadImage(sys.argv[1], sitk.sitkFloat32)
moving = sitk.ReadImage(sys.argv[2], sitk.sitkFloat32)


numberOfBins = 24
samplingPercentage = 0.10

if len ( sys.argv ) > 4:
    numberOfBins = int(sys.argv[4])
if len ( sys.argv ) > 5:
    samplingPercentage = float(sys.argv[5])

R = sitk.ImageRegistrationMethod()
R.SetMetricAsMattesMutualInformation(numberOfBins)
R.SetMetricSamplingPercentage(samplingPercentage,sitk.sitkWallClock)
R.SetMetricSamplingStrategy(R.RANDOM)
R.SetOptimizerAsRegularStepGradientDescent(1.0,.001,200)
R.SetInitialTransform(sitk.TranslationTransform(fixed.GetDimension()))
R.SetInterpolator(sitk.sitkLinear)

R.AddCommand( sitk.sitkIterationEvent, lambda: command_iteration(R) )

outTx = R.Execute(fixed, moving)


print("-------")
print(outTx)
print("Optimizer stop condition: {0}".format(R.GetOptimizerStopConditionDescription()))
print(" Iteration: {0}".format(R.GetOptimizerIteration()))
print(" Metric value: {0}".format(R.GetMetricValue()))

sitk.WriteTransform(outTx,  sys.argv[3])


if ( not "SITK_NOSHOW" in os.environ ):
    resampler = sitk.ResampleImageFilter()
    resampler.SetReferenceImage(fixed);
    resampler.SetInterpolator(sitk.sitkLinear)
    resampler.SetDefaultPixelValue(100)
    resampler.SetTransform(outTx)

    out = resampler.Execute(moving)
    simg1 = sitk.Cast(sitk.RescaleIntensity(fixed), sitk.sitkUInt8)
    simg2 = sitk.Cast(sitk.RescaleIntensity(out), sitk.sitkUInt8)
    cimg = sitk.Compose(simg1, simg2, simg1//2.+simg2//2.)
    sitk.Show( cimg, "ImageRegistration4 Composition" )
# Run with:
#
# Rscript --vanilla ImageRegistrationMethod4.R fixedImageFilter movingImageFile outputTransformFile numberOfBins samplingPercentage
#

library(SimpleITK)

commandIteration <- function(method)
{
    msg <- paste(method$GetOptimizerIteration(), "=",
                 method$GetMetricValue(), ":",
                 method$GetOptimizerPosition(), "\n" )
    cat(msg)
}

args <- commandArgs( TRUE )

if (length(args) < 3) {
    stop("3, 4, or 5 arguments expected - fixedImageFilter, movingImageFile, outputTransformFile [numberOfBins] [samplingPercentage]")
}

fixed <- ReadImage(args[[1]], 'sitkFloat32')
moving <- ReadImage(args[[2]], 'sitkFloat32')

numberOfBins <- 24
samplingPercentage <- 0.10

if (length(args) > 4) {
    numberOfBins <- strtoi(args[[4]])
}
if (length(args) > 5) {
    samplingPercentage <- as.numeric(args[[5]])
}

R <- ImageRegistrationMethod()
R$SetMetricAsMattesMutualInformation(numberOfBins)
R$SetMetricSamplingPercentage(samplingPercentage)
R$SetMetricSamplingStrategy('RANDOM')
R$SetOptimizerAsRegularStepGradientDescent(1.0,.001,200)
R$SetInitialTransform(TranslationTransform(fixed$GetDimension()))
R$SetInterpolator('sitkLinear')

R$AddCommand( 'sitkIterationEvent', function() commandIteration(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]])