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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;
using ScalarType = double; // 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. */
using TransformType = itk::ThinPlateSplineKernelTransform2<ScalarType, Dimension>;
using JacobianType = TransformType::JacobianType;
using NonZeroJacobianIndicesType = TransformType::NonZeroJacobianIndicesType;
using PointSetType = TransformType::PointSetType;
using InputPointType = TransformType::InputPointType;
using PointsContainerType = PointSetType::PointsContainer;
using PointsContainerPointer = PointsContainerType::Pointer;
using PointType = PointSetType::PointType;
using MersenneTwisterType = itk::Statistics::MersenneTwisterRandomVariateGenerator;
/** Create the kernel transform. */
auto kernelTransform = TransformType::New();
/** Read landmarks. */
auto landmarkReader = itk::TransformixInputPointFileReader<PointSetType>::New();
landmarkReader->SetFileName(argv[1]);
try
{
landmarkReader->Update();
}
catch (const 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();
auto 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();
auto 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);
}
auto 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 inputPoint;
inputPoint[0] = 10.0;
inputPoint[1] = 20.0;
inputPoint[2] = 30.0;
/** Test TransformPoint(). */
startClock = clock();
kernelTransform->TransformPoint(inputPoint);
std::cerr << "TransformPoint() computation took: " << clock() - startClock << " ms." << std::endl;
/** Test GetJacobian(). */
startClock = clock();
JacobianType jac;
NonZeroJacobianIndicesType nzji;
kernelTransform->GetJacobian(inputPoint, 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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