Image Registration Method 3¶
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
import SimpleITK as sitk
import sys
import os
def command_iteration(method):
if method.GetOptimizerIteration() == 0:
print("Estimated Scales: ", method.GetOptimizerScales())
print(
f"{method.GetOptimizerIteration():3} "
+ f"= {method.GetMetricValue():7.5f} "
+ f": {method.GetOptimizerPosition()}"
)
if len(sys.argv) < 4:
print(
"Usage:",
sys.argv[0],
"<fixedImageFilter> <movingImageFile> <outputTransformFile>",
)
sys.exit(1)
pixelType = sitk.sitkFloat32
fixed = sitk.ReadImage(sys.argv[1], sitk.sitkFloat32)
moving = sitk.ReadImage(sys.argv[2], sitk.sitkFloat32)
R = sitk.ImageRegistrationMethod()
R.SetMetricAsCorrelation()
R.SetOptimizerAsRegularStepGradientDescent(
learningRate=2.0,
minStep=1e-4,
numberOfIterations=500,
gradientMagnitudeTolerance=1e-8,
)
R.SetOptimizerScalesFromIndexShift()
tx = sitk.CenteredTransformInitializer(
fixed, moving, sitk.Similarity2DTransform()
)
R.SetInitialTransform(tx)
R.SetInterpolator(sitk.sitkLinear)
R.AddCommand(sitk.sitkIterationEvent, lambda: command_iteration(R))
outTx = R.Execute(fixed, moving)
print("-------")
print(outTx)
print(f"Optimizer stop condition: {R.GetOptimizerStopConditionDescription()}")
print(f" Iteration: {R.GetOptimizerIteration()}")
print(f" Metric value: {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(1)
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 // 2.0 + simg2 // 2.0)
sitk.Show(cimg, "ImageRegistration2 Composition")
# Run with:
#
# Rscript --vanilla ImageRegistrationMethod3.R fixedImageFilter movingImageFile outputTransformFile
#
library(SimpleITK)
commandIteration <- function(method)
{
if (method$GetOptimizerIteration()==0) {
cat("Estimated Scales:", method$GetOptimizerScales())
}
msg <- paste(method$GetOptimizerIteration(), "=",
method$GetMetricValue(), ":",
method$GetOptimizerPosition(), "\n" )
cat(msg)
}
args <- commandArgs( TRUE )
if (length(args) != 3) {
stop("3 arguments expected - fixedImageFilter, movingImageFile, outputTransformFile")
}
pixelType <- 'sitkFloat32'
fixed <- ReadImage(args[[1]], 'sitkFloat32')
moving <- ReadImage(args[[2]], 'sitkFloat32')
R <- ImageRegistrationMethod()
R$SetMetricAsCorrelation()
R$SetOptimizerAsRegularStepGradientDescent(learningRate=2.0,
minStep=1e-4,
numberOfIterations=500,
relaxationFactor=0.5,
gradientMagnitudeTolerance=1e-8 )
R$SetOptimizerScalesFromIndexShift()
tx <- CenteredTransformInitializer(fixed, moving, Similarity2DTransform())
R$SetInitialTransform(tx)
R$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]])