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

PythonR

#!/usr/bin/env python

import SimpleITK as sitk
import sys
import os


def command_iteration(method):
    print(
        f"{method.GetOptimizerIteration():3} "
        + f"= {method.GetMetricValue():10.5f}"
    )
    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(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(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 // 2.0 + simg2 // 2.0)
    sitk.Show(cimg, "ImageRegistration1 Composition")