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

PythonR

#!/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} = {method.GetMetricValue():7.5f} : {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. + simg2 // 2.)
    sitk.Show(cimg, "ImageRegistration2 Composition")