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#==========================================================================
#
# Copyright Insight Software Consortium
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
# http://www.apache.org/licenses/LICENSE-2.0.txt
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#
#==========================================================================*/
import itk
from sys import argv
#
# Check input parameters
# INPUTS(fixedImage): {BrainProtonDensitySliceBorder20.png}
# INPUTS(movingImage): {BrainProtonDensitySliceRotated10.png}
#
if len(argv) < 4:
print 'Missing Parameters'
print 'Usage: ImageRegistration5.py fixedImageFile movingImageFile outputImagefile'
exit()
#
# Define data types
#
FixedImageType = itk.Image[itk.F, 2]
MovingImageType = itk.Image[itk.F, 2]
OutputImageType = itk.Image[itk.UC, 2]
TransformType = itk.CenteredRigid2DTransform
#
# Read the fixed and moving images using filenames
# from the command line arguments
#
fixedImageReader = itk.ImageFileReader[FixedImageType].New()
movingImageReader = itk.ImageFileReader[MovingImageType].New()
fixedImageReader.SetFileName( argv[1] )
movingImageReader.SetFileName( argv[2] )
fixedImageReader.Update()
movingImageReader.Update()
fixedImage = fixedImageReader.GetOutput()
movingImage = movingImageReader.GetOutput()
#
# Instantiate the classes for the registration framework
#
registration = itk.ImageRegistrationMethod[FixedImageType, MovingImageType].New()
imageMetric = itk.MeanSquaresImageToImageMetric[FixedImageType, MovingImageType].New()
transform = TransformType.New()
optimizer = itk.RegularStepGradientDescentOptimizer.New()
interpolator = itk.LinearInterpolateImageFunction[FixedImageType, itk.D].New()
registration.SetOptimizer( optimizer )
registration.SetTransform( transform )
registration.SetInterpolator( interpolator)
registration.SetMetric( imageMetric )
registration.SetFixedImage( fixedImage )
registration.SetMovingImage( movingImage )
registration.SetFixedImageRegion( fixedImage.GetBufferedRegion() )
#
# Initial transform parameters
#
transform.SetAngle( 0.0 );
# center of the fixed image
fixedSpacing = fixedImage.GetSpacing()
fixedOrigin = fixedImage.GetOrigin()
fixedSize = fixedImage.GetLargestPossibleRegion().GetSize()
centerFixed = ( fixedOrigin.GetElement(0) + fixedSpacing.GetElement(0) * fixedSize.GetElement(0) / 2.0,
fixedOrigin.GetElement(1) + fixedSpacing.GetElement(1) * fixedSize.GetElement(1) / 2.0 )
# center of the moving image
movingSpacing= movingImage.GetSpacing()
movingOrigin = movingImage.GetOrigin()
movingSize = movingImage.GetLargestPossibleRegion().GetSize()
centerMoving = ( movingOrigin.GetElement(0) + movingSpacing.GetElement(0) * movingSize.GetElement(0) / 2.0,
movingOrigin.GetElement(1) + movingSpacing.GetElement(1) * movingSize.GetElement(1) / 2.0 )
# transform center
center = transform.GetCenter()
center.SetElement( 0, centerFixed[0] )
center.SetElement( 1, centerFixed[1] )
# transform translation
translation = transform.GetTranslation()
translation.SetElement( 0, centerMoving[0] - centerFixed[0] )
translation.SetElement( 1, centerMoving[1] - centerFixed[1] )
initialParameters = transform.GetParameters()
print "Initial Parameters: "
print "Angle: %f" % (initialParameters.GetElement(0), )
print "Center: %f, %f" % ( initialParameters.GetElement(1), initialParameters.GetElement(2) )
print "Translation: %f, %f" % (initialParameters.GetElement(3), initialParameters.GetElement(4))
registration.SetInitialTransformParameters( initialParameters )
#
# Define optimizer parameters
#
# optimizer scale
translationScale = 1.0 / 1000.0
optimizerScales = itk.Array[itk.D](transform.GetNumberOfParameters())
optimizerScales.SetElement(0, 1.0)
optimizerScales.SetElement(1, translationScale)
optimizerScales.SetElement(2, translationScale)
optimizerScales.SetElement(3, translationScale)
optimizerScales.SetElement(4, translationScale)
optimizer.SetScales( optimizerScales )
optimizer.SetMaximumStepLength( 0.1 )
optimizer.SetMinimumStepLength( 0.001 )
optimizer.SetNumberOfIterations( 200 )
#
# Iteration Observer
#
def iterationUpdate():
currentParameter = transform.GetParameters()
print "M: %f P: %f %f %f %f %f " % ( optimizer.GetValue(),
currentParameter.GetElement(0),
currentParameter.GetElement(1),
currentParameter.GetElement(2),
currentParameter.GetElement(3),
currentParameter.GetElement(4) )
iterationCommand = itk.PyCommand.New()
iterationCommand.SetCommandCallable( iterationUpdate )
optimizer.AddObserver( itk.IterationEvent(), iterationCommand )
print "Starting registration"
#
# Start the registration process
#
registration.Update()
#
# Get the final parameters of the transformation
#
finalParameters = registration.GetLastTransformParameters()
print "Final Registration Parameters "
print "Angle in radians = %f" % finalParameters.GetElement(0)
print "Rotation Center X = %f" % finalParameters.GetElement(1)
print "Rotation Center Y = %f" % finalParameters.GetElement(2)
print "Translation in X = %f" % finalParameters.GetElement(3)
print "Translation in Y = %f" % finalParameters.GetElement(4)
# Now, we use the final transform for resampling the moving image.
resampler = itk.ResampleImageFilter[MovingImageType, FixedImageType].New()
resampler.SetTransform( transform )
resampler.SetInput( movingImage )
region = fixedImage.GetLargestPossibleRegion()
resampler.SetSize( region.GetSize() )
resampler.SetOutputSpacing( fixedImage.GetSpacing() )
resampler.SetOutputOrigin( fixedImage.GetOrigin() )
resampler.SetOutputDirection( fixedImage.GetDirection() )
resampler.SetDefaultPixelValue( 100 )
#
# Cast for output
#
outputCast = itk.RescaleIntensityImageFilter[FixedImageType, OutputImageType].New()
outputCast.SetInput(resampler.GetOutput())
#
# Write the resampled image
#
writer = itk.ImageFileWriter[OutputImageType].New()
writer.SetFileName( argv[3] )
writer.SetInput( outputCast.GetOutput() )
writer.Update()
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