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¶
#!/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: {0} <fixedImageFilter> <movingImageFile> <outputTransformFile>".format(sys.argv[0]))
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 ( 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, "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]])