ITK  4.9.0
Insight Segmentation and Registration Toolkit
Examples/RegistrationITKv4/DeformableRegistration17.cxx
/*=========================================================================
*
* 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.
*
*=========================================================================*/
/*******************************************************************************
Abstract: - Multiresolution symmetric forces demons registration - 4 multiresolution levels
Created: July 8 2008
Last Revision 7/9/2008
by Vidya Rajagopalan on 7/9/2008
Copyright (c) 2008, Bioimaging Systems Lab, Virginia Tech
All rights reserved.
Redistribution and use in source and binary forms, with or without modification,
are permitted provided that the following conditions are met:
* Redistributions of source code must retain the above copyright notice, this
list of conditions and the following disclaimer.
* Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
* Neither the name of Virgina Tech nor the names of its contributors may
be used to endorse or promote products derived from this software without
specific prior written permission.
THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE
LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING
IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY
OF SUCH DAMAGE.
*******************************************************************************/
// Software Guide : BeginLatex
//
// This example illustrates the use of the
// \doxygen{MultiResolutionPDEDeformableRegistration} class for performing
// deformable registration of two $2D$ images using multiple resolution levels.
//
// The MultiResolution filter drives a SymmetricForcesDemonsRegistrationFilter
// at every level of resolution in the pyramid.
//
// \index{itk::MultiResolutionPDEDeformableRegistration}
// \index{itk::SymmetricForcesDemonsRegistrationFilter}
//
// Software Guide : EndLatex
//
// CREDITS:
//
// This example was contributed to ITK by
//
// Vidya Rajagopalan, Bioimaging Systems Lab, Virginia Tech
//
// The example was improved during the NAMIC programming week on July 2008
// http://wiki.na-mic.org/Wiki/index.php/2008_Summer_Project_Week
//
// National Alliance for Medical Image Computing (NAMIC),
// funded by the National Institutes of Health
// through the NIH Roadmap for Medical Research,
// Grant U54 EB005149.
//
// Data for these examples have been contributed by
//
// Paul Laurienti, Wake Forest University School of Medicine,
// Data acquired under NIH grant number NS042568
//
//
#include <iostream>
#include <cstdlib>
// ITK IO includes
// ITK Registration includes
unsigned int RmsCounter = 0;
double MaxRmsE[4] = {0.8, 0.75, 0.4, 0.2};
// The following section of code implements a Command observer
// that will monitor the evolution of the registration process.
// This observer has a layer of intelligence, for deciding what
// MaximumRMS convergence criteria to use at every resolution level.
//
class CommandIterationUpdate : public itk::Command
{
public:
typedef CommandIterationUpdate Self;
itkNewMacro( Self );
protected:
CommandIterationUpdate() {};
// define ITK short-hand types
typedef short PixelType;
typedef float InternalPixelType;
typedef itk::Image< PixelType, 2 > ImageType;
typedef itk::Image< InternalPixelType, 2 > InternalImageType;
typedef itk::Vector< float, 2 > VectorPixelType;
typedef itk::Image< VectorPixelType, 2 > DisplacementFieldType;
InternalImageType, DisplacementFieldType> RegistrationFilterType;
public:
void Execute(const itk::Object *, const itk::EventObject & ) ITK_OVERRIDE
{
std::cout << "Warning: The const Execute method shouldn't be called" << std::endl;
}
void Execute(itk::Object *caller, const itk::EventObject & event) ITK_OVERRIDE
{
RegistrationFilterType * filter = static_cast< RegistrationFilterType * >( caller );
if( !(itk::IterationEvent().CheckEvent( &event )) )
{
return;
}
if(filter)
{
filter->SetMaximumRMSError(MaxRmsE[RmsCounter]);
std::cout << filter->GetMetric() << " RMS Change: " << filter->GetRMSChange() << std::endl;
std::cout << "Level Tolerance= "<<filter->GetMaximumRMSError ()<<std::endl;
}
}
};
//
// The following command observer reports the progress of the registration
// inside a given resolution level.
//
class CommandResolutionLevelUpdate : public itk::Command
{
public:
typedef CommandResolutionLevelUpdate Self;
itkNewMacro( Self );
protected:
CommandResolutionLevelUpdate() {};
public:
void Execute(itk::Object *caller, const itk::EventObject & event) ITK_OVERRIDE
{
Execute( (const itk::Object *)caller, event);
}
void Execute(const itk::Object *, const itk::EventObject & ) ITK_OVERRIDE
{
std::cout << "----------------------------------" << std::endl;
RmsCounter = RmsCounter + 1;
std::cout << "----------------------------------" << std::endl;
}
};
int main( int argc, char * argv [] )
{
// Verify the number of parameters in the command line
if( argc != 5 )
{
std::cerr << "usage: " << std::endl;
std::cerr << argv[0] << " fixedImage movingImage registeredImage deformationField" << std::endl;
return EXIT_FAILURE;
}
// define ITK short-hand types
const unsigned int Dimension = 2;
typedef short PixelType;
typedef float InternalPixelType;
typedef itk::Image< InternalPixelType, Dimension > InternalImageType;
// setup input file readers
ReaderType::Pointer targetReader = ReaderType::New();
targetReader->SetFileName( argv[1] );
targetReader->Update();
ReaderType::Pointer sourceReader = ReaderType::New();
sourceReader->SetFileName( argv[2] );
sourceReader->Update();
// cast target and source to float
ImageCasterType::Pointer targetImageCaster = ImageCasterType::New();
ImageCasterType::Pointer sourceImageCaster = ImageCasterType::New();
targetImageCaster->SetInput( targetReader->GetOutput() );
sourceImageCaster->SetInput( sourceReader->GetOutput() );
// match the histograms between source and target
InternalImageType, InternalImageType > MatchingFilterType;
MatchingFilterType::Pointer matcher = MatchingFilterType::New();
matcher->SetInput( sourceImageCaster->GetOutput() );
matcher->SetReferenceImage( targetImageCaster->GetOutput() );
matcher->SetNumberOfHistogramLevels( 1024 );
matcher->SetNumberOfMatchPoints( 7 );
matcher->ThresholdAtMeanIntensityOn();
// setup the deformation field and filter
typedef itk::Vector< float, Dimension > VectorPixelType;
typedef itk::Image< VectorPixelType, Dimension > DisplacementFieldType;
InternalImageType,
InternalImageType,
DisplacementFieldType> RegistrationFilterType;
RegistrationFilterType::Pointer filter = RegistrationFilterType::New();
filter->SetStandardDeviations( 1.0 );
//
// Create the Command observer and register it with the registration filter.
//
CommandIterationUpdate::Pointer observer = CommandIterationUpdate::New();
filter->AddObserver( itk::IterationEvent(), observer );
// use multiresolution scheme
InternalImageType,
InternalImageType,
DisplacementFieldType > MultiResRegistrationFilterType;
MultiResRegistrationFilterType::Pointer multires =
MultiResRegistrationFilterType::New();
multires->SetRegistrationFilter( filter );
multires->SetNumberOfLevels( 4 );
multires->SetFixedImage( targetImageCaster->GetOutput() );
multires->SetMovingImage( matcher->GetOutput() );
unsigned int nIterations[4] = {40, 40, 32, 32 };
multires->SetNumberOfIterations( nIterations );
//
// Create the Command observer and register it with the registration filter.
//
CommandResolutionLevelUpdate::Pointer levelobserver = CommandResolutionLevelUpdate::New();
multires->AddObserver( itk::IterationEvent(), levelobserver );
// apply the registration filter
try
{
multires->Update();
}
catch( itk::ExceptionObject & excp )
{
std::cerr << excp << std::endl;
return EXIT_FAILURE;
}
// compute the output (warped) image
WarperType::Pointer warper = WarperType::New();
InterpolatorType::Pointer interpolator = InterpolatorType::New();
ImageType::Pointer targetImage = targetReader->GetOutput();
warper->SetInput( sourceReader->GetOutput() );
warper->SetInterpolator( interpolator );
warper->SetOutputSpacing( targetImage->GetSpacing() );
warper->SetOutputOrigin( targetImage->GetOrigin() );
warper->SetOutputDirection( targetImage->GetDirection() );
warper->SetDisplacementField( multires->GetOutput() );
WriterType::Pointer writer = WriterType::New();
writer->SetFileName( argv[3] );
writer->SetInput( warper->GetOutput() );
try
{
writer->Update();
}
catch( itk::ExceptionObject & excp )
{
std::cerr << excp << std::endl;
return EXIT_FAILURE;
}
// write the deformation field
typedef itk::ImageFileWriter< DisplacementFieldType > DeformationWriterType;
DeformationWriterType::Pointer defwriter = DeformationWriterType::New();
defwriter->SetFileName( argv[4] );
defwriter->SetInput( multires->GetOutput() );
try
{
defwriter->Update();
}
catch( itk::ExceptionObject & excp )
{
std::cerr << excp << std::endl;
return EXIT_FAILURE;
}
return EXIT_SUCCESS;
}