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/*=========================================================================
*
* Copyright UMC Utrecht and contributors
*
* 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.
*
*=========================================================================*/
#include "SplineKernelTransform/itkThinPlateSplineKernelTransform2.h"
#include "itkTransformixInputPointFileReader.h"
#include "itkMersenneTwisterRandomVariateGenerator.h"
#include <ctime>
#include <fstream>
#include <iomanip>
//-------------------------------------------------------------------------------------
int
main( int argc, char * argv[] )
{
/** Some basic type definitions. */
const unsigned int Dimension = 3;
typedef double ScalarType; // ScalarType double used in elastix
/** Only perform the test with usedNumberOfLandmarks. */
const unsigned long usedNumberOfLandmarks = 100;
std::cerr << "Number of used landmarks: "
<< usedNumberOfLandmarks << std::endl;
/** Check. */
if( argc != 2 )
{
std::cerr << "ERROR: You should specify a text file with the thin plate spline "
<< "source (fixed image) landmarks." << std::endl;
return 1;
}
/** Other typedefs. */
typedef itk::ThinPlateSplineKernelTransform2<
ScalarType, Dimension > TransformType;
typedef TransformType::JacobianType JacobianType;
typedef TransformType::NonZeroJacobianIndicesType NonZeroJacobianIndicesType;
typedef TransformType::PointSetType PointSetType;
typedef TransformType::InputPointType InputPointType;
typedef itk::TransformixInputPointFileReader<
PointSetType > IPPReaderType;
typedef PointSetType::PointsContainer PointsContainerType;
typedef PointsContainerType::Pointer PointsContainerPointer;
typedef PointSetType::PointType PointType;
typedef itk::Statistics::MersenneTwisterRandomVariateGenerator MersenneTwisterType;
/** Create the kernel transform. */
TransformType::Pointer kernelTransform = TransformType::New();
/** Read landmarks. */
IPPReaderType::Pointer landmarkReader = IPPReaderType::New();
landmarkReader->SetFileName( argv[ 1 ] );
try
{
landmarkReader->Update();
}
catch( itk::ExceptionObject & excp )
{
std::cerr << " Error while opening landmark file." << std::endl;
std::cerr << excp << std::endl;
return 1;
}
PointSetType::Pointer sourceLandmarks = landmarkReader->GetOutput();
/** Check: Expect points, not indices. */
if( landmarkReader->GetPointsAreIndices() )
{
std::cerr << "ERROR: landmarks should be specified as points (not indices)"
<< std::endl;
return 1;
}
/** Get subset. */
PointsContainerPointer usedLandmarkPoints = PointsContainerType::New();
PointSetType::Pointer usedSourceLandmarks = PointSetType::New();
for( unsigned long j = 0; j < usedNumberOfLandmarks; j++ )
{
PointType tmp = ( *sourceLandmarks->GetPoints() )[ j ];
usedLandmarkPoints->push_back( tmp );
}
usedSourceLandmarks->SetPoints( usedLandmarkPoints );
/** Test 1: Time setting the source landmarks. */
clock_t startClock = clock();
kernelTransform->SetSourceLandmarks( usedSourceLandmarks );
std::cerr << "Setting source landmarks took "
<< clock() - startClock << " ms." << std::endl;
/** Further setup the kernel transform. */
kernelTransform->SetStiffness( 0.0 ); // interpolating
kernelTransform->SetMatrixInversionMethod( "QR" ); // faster
kernelTransform->SetIdentity(); // target landmarks = source landmarks
/** Create new target landmarks by adding a random vector to it. */
PointSetType::ConstPointer targetLandmarks = kernelTransform->GetTargetLandmarks();
PointsContainerPointer newTargetLandmarkPoints = PointsContainerType::New();
MersenneTwisterType::Pointer mersenneTwister = MersenneTwisterType::New();
mersenneTwister->Initialize( 140377 );
for( unsigned long j = 0; j < targetLandmarks->GetNumberOfPoints(); j++ )
{
PointType tmp = ( *targetLandmarks->GetPoints() )[ j ];
PointType randomPoint;
for( unsigned int dim = 0; dim < Dimension; dim++ )
{
randomPoint[ dim ] = tmp[ dim ] + mersenneTwister->GetNormalVariate( 1.0, 5.0 );
}
newTargetLandmarkPoints->push_back( randomPoint );
}
PointSetType::Pointer newTargetLandmarks = PointSetType::New();
newTargetLandmarks->SetPoints( newTargetLandmarkPoints );
/** Test 2: Time setting the target landmarks. */
startClock = clock();
kernelTransform->SetTargetLandmarks( newTargetLandmarks );
std::cerr << "Setting source landmarks took "
<< clock() - startClock << " ms." << std::endl;
InputPointType ipp; ipp[ 0 ] = 10.0; ipp[ 1 ] = 20.0; ipp[ 2 ] = 30.0;
/** Test TransformPoint(). */
startClock = clock();
kernelTransform->TransformPoint( ipp );
std::cerr << "TransformPoint() computation took: "
<< clock() - startClock << " ms." << std::endl;
/** Test GetJacobian(). */
startClock = clock();
JacobianType jac; NonZeroJacobianIndicesType nzji;
kernelTransform->GetJacobian( ipp, jac, nzji );
std::cerr << "GetJacobian() computation took: "
<< clock() - startClock << " ms." << std::endl;
/** Additional checks. */
if( !kernelTransform->GetHasNonZeroSpatialHessian() )
{
std::cerr << "ERROR: GetHasNonZeroSpatialHessian() should return true." << std::endl;
return 1;
}
if( !kernelTransform->GetHasNonZeroJacobianOfSpatialHessian() )
{
std::cerr << "ERROR: GetHasNonZeroJacobianOfSpatialHessian() should return true." << std::endl;
return 1;
}
if( kernelTransform->GetMatrixInversionMethod() != "QR" )
{
std::cerr << "ERROR: GetMatrixInversionMethod() should return \"QR\"." << std::endl;
return 1;
}
/** Exercise PrintSelf() method. */
kernelTransform->Print( std::cerr );
/** Return a value. */
return 0;
} // end main
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