Image Registration Method BSpline 2

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

Python

R

#!/usr/bin/env python

from __future__ import print_function

import SimpleITK as sitk
import sys
import os


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


def command_multi_iteration(method):
    print("--------- Resolution Changing ---------")


if len(sys.argv) < 4:
    print("Usage:", sys.argv[0], "<fixedImageFilter> <movingImageFile>",
          "<outputTransformFile>")
    sys.exit(1)

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

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

transformDomainMeshSize = [10] * moving.GetDimension()
tx = sitk.BSplineTransformInitializer(fixed,
                                      transformDomainMeshSize)

print("Initial Parameters:")
print(tx.GetParameters())

R = sitk.ImageRegistrationMethod()
R.SetMetricAsMattesMutualInformation(50)
R.SetOptimizerAsGradientDescentLineSearch(5.0, 100,
                                          convergenceMinimumValue=1e-4,
                                          convergenceWindowSize=5)
R.SetOptimizerScalesFromPhysicalShift()
R.SetInitialTransform(tx)
R.SetInterpolator(sitk.sitkLinear)

R.SetShrinkFactorsPerLevel([6, 2, 1])
R.SetSmoothingSigmasPerLevel([6, 2, 1])

R.AddCommand(sitk.sitkIterationEvent, lambda: command_iteration(R))
R.AddCommand(sitk.sitkMultiResolutionIterationEvent,
             lambda: command_multi_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 ("SITK_NOSHOW" not 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, "ImageRegistration1 Composition")

# Run with:
#
# Rscript --vanilla ImageRegistrationMethodBSpline2.R fixedImageFilter movingImageFile outputTransformFile
#

library(SimpleITK)

commandIteration <- function(method)
{
    msg <- paste(method$GetOptimizerIteration(), "=",
                 method$GetMetricValue(), "\n\t#:",
                 method$GetOptimizerPosition(), '\n')
    cat(msg)
}

commandMultiIteration <- function(method)
{
    msg <- paste("--------- Resolution Changing ---------\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')

transformDomainMeshSize <- rep(10, moving$GetDimension())
tx <- BSplineTransformInitializer(fixed, transformDomainMeshSize)

cat("Initial Parameters:\n", tx$GetParameters())

R <- ImageRegistrationMethod()
R$SetMetricAsMattesMutualInformation(50)
R$SetOptimizerAsGradientDescentLineSearch(5.0, 100,
                                          convergenceMinimumValue=1e-4,
                                          convergenceWindowSize=5)
R$SetOptimizerScalesFromPhysicalShift()
R$SetInitialTransform(tx)
R$SetInterpolator('sitkLinear')

R$SetShrinkFactorsPerLevel(c(6,2,1))
R$SetSmoothingSigmasPerLevel(c(6,2,1))

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