void RunRigid() {
_initialTransform = InitialTransform::New();
_initialTransform->SetFixedParameters(_centerOfRotation);
OptiReporter::Pointer optiReporter = OptiReporter::New();
Metric::Pointer metric = Metric::New();
metric->SetFixedImage(_dst);
metric->SetMovingImage(_src);
metric->SetInterpolator(Interpolator::New());
metric->SetTransform(_initialTransform);
//metric->SetFixedImageRegion(_dst->GetBufferedRegion());
metric->SetFixedImageIndexes(_labelIndexes);
// metric->SetUseAllPixels(true);
metric->Initialize();
Optimizer::Pointer opti = Optimizer::New();
opti->SetCostFunction(metric);
Optimizer::ScalesType scales;
scales.SetSize(InitialTransform::ParametersDimension);
scales.Fill(1);
//scales[0] = scales[1] = scales[2] = .1;
opti->SetUseUnitLengthGradient(true);
opti->SetScales(scales);
opti->SetInitialPosition(_initialTransform->GetParameters());
opti->AddObserver(itk::StartEvent(), optiReporter);
opti->AddObserver(itk::IterationEvent(), optiReporter);
opti->StartOptimization();
cout << "Current Cost: " << opti->GetCurrentCost() << endl;
_initialResult = opti->GetCurrentPosition();
_initialTransform->SetParameters(opti->GetCurrentPosition());
}
void RunNine() {
_finalTransform = NineTransform::New();
// NineTransform::OutputVectorType initialTranslation;
// initialTranslation[0] = _initialResult[0];
// initialTranslation[1] = _initialResult[1];
// initialTranslation[2] = _initialResult[2];
// _finalTransform->SetTranslation(initialTranslation);
_finalTransform->SetFixedParameters(_centerOfRotation);
OptiReporter::Pointer optiReporter = OptiReporter::New();
Metric::Pointer metric = Metric::New();
metric->SetFixedImage(_dst);
metric->SetMovingImage(_src);
metric->SetInterpolator(InterpolatorNN::New());
metric->SetTransform(_finalTransform);
metric->SetFixedImageIndexes(_labelIndexes);
// metric->SetUseAllPixels(true);
metric->Initialize();
Optimizer::Pointer opti = Optimizer::New();
opti->SetCostFunction(metric);
Optimizer::ScalesType scales;
scales.SetSize(NineTransform::ParametersDimension);
scales.Fill(1);
scales[0] = scales[1] = scales[2] = 10;
scales[6] = scales[7] = scales[8] = 100;
opti->SetMaximumIteration(500);
opti->SetUseUnitLengthGradient(true);
opti->SetStepLength(0.5);
opti->SetScales(scales);
opti->SetInitialPosition(_finalTransform->GetParameters());
opti->AddObserver(itk::StartEvent(), optiReporter);
opti->AddObserver(itk::IterationEvent(), optiReporter);
opti->StartOptimization();
cout << "Current Cost: " << opti->GetCurrentCost() << endl;
_finalResult = opti->GetCurrentPosition();
_finalTransform->SetParameters(opti->GetCurrentPosition());
}
void GammaVariate::optimize() {
Optimizer::Pointer optimizer = Optimizer::New();
itk::GammaCostFunction::Pointer myCostFunction = itk::GammaCostFunction::New();
myCostFunction->SetData( samples );
optimizer->SetCostFunction( myCostFunction );
Optimizer::ParametersType p(5);
p[0] = t0;
p[1] = t0 + t0max;
p[2] = y0;
p[3] = y0 + y0max;
p[4] = findAlpha();
optimizer->SetInitialPosition( p );
optimizer->SetMaximumIteration( MaximumNumberOfIterations );
optimizer->SetValueTolerance(1.0);
try {
optimizer->StartOptimization();
} catch( itk::ExceptionObject & err ) {
std::cerr << "ExceptionObject caught !" << std::endl;
std::cerr << err << std::endl;
}
p = optimizer->GetCurrentPosition();
setParameters( p[0], p[1], p[2], p[3], p[4]);
}
void RunRegistration() {
_transform = TransformType::New();
OptiReporter::Pointer optiReporter = OptiReporter::New();
Metric::Pointer metric = Metric::New();
metric->SetFixedImage(_dst);
bool useIndexes = false;
if (useIndexes) {
_centerOfRotation.SetSize(ImageType::ImageDimension);
for (int i = 0; i < ImageType::ImageDimension; i++) {
_centerOfRotation[i] = i;
}
itk::ImageRegionConstIteratorWithIndex<LabelType> labelIter(_dstLabel, _dstLabel->GetBufferedRegion());
int nPixels = 0;
for (labelIter.GoToBegin(); !labelIter.IsAtEnd(); ++labelIter) {
LabelType::PixelType label = labelIter.Get();
if (label > 0) {
_labelIndexes.push_back(labelIter.GetIndex());
for (int i = 0; i < ImageType::ImageDimension; i++) {
_centerOfRotation[i] += labelIter.GetIndex()[i];
}
nPixels ++;
}
}
for (int i = 0; i < ImageType::ImageDimension; i++) {
_centerOfRotation[i] /= nPixels;
}
metric->SetFixedImageIndexes(_labelIndexes);
_transform->SetFixedParameters(_centerOfRotation);
} else {
metric->SetFixedImageRegion(_dst->GetBufferedRegion());
metric->SetUseAllPixels(true);
_centerOfRotation.SetSize(ImageType::ImageDimension);
for (int i = 0; i < 3; i++) {
_centerOfRotation[i] = _dstCenter[i];
}
_transform->SetFixedParameters(_centerOfRotation);
}
cout << "Fixed Parameters: " << _centerOfRotation << endl;
metric->SetMovingImage(_src);
metric->SetInterpolator(Interpolator::New());
metric->SetTransform(_transform);
metric->Initialize();
Optimizer::Pointer opti = Optimizer::New();
opti->SetCostFunction(metric);
Optimizer::ScalesType scales;
scales.SetSize(TransformType::ParametersDimension);
scales.Fill(1);
if (_method == "affine") {
cout << "apply affine scaling ..." << endl;
for (int i = 0; i < 3; i++) {
for (int j = 0; j < 3; j++) {
if (i == j) {
scales[3*i+j] = 160;
} else {
scales[3*i+j] = 30;
}
}
}
scales[9] = scales[10] = scales[11] = 0.1;
} else if (_method == "scale") {
scales[0] = scales[1] = scales[2] = 30;
scales[3] = scales[4] = scales[5] = .5;
scales[6] = scales[7] = scales[8] = 100;
} else if (_method == "similar") {
scales[0] = scales[1] = scales[2] = 10;
scales[3] = scales[4] = scales[5] = 0.5;
scales[6] = 100;
}
opti->SetScales(scales);
const int maxIters = 100;
#ifdef USE_CG_OPTIMIZER
opti->SetMaximumIteration(maxIters);
opti->SetMaximumLineIteration(10);
opti->SetUseUnitLengthGradient(true);
opti->SetStepLength(1);
opti->SetToFletchReeves();
#endif
#ifdef USE_GD_OPTIMIZER
opti->SetNumberOfIterations(maxIters);
opti->SetMinimumStepLength(1e-4);
opti->SetMaximumStepLength(3);
opti->SetRelaxationFactor(.5);
opti->SetGradientMagnitudeTolerance(1e-4);
#endif
opti->SetInitialPosition(_transform->GetParameters());
opti->AddObserver(itk::StartEvent(), optiReporter);
opti->AddObserver(itk::IterationEvent(), optiReporter);
opti->StartOptimization();
cout << "Current Cost: " << opti->GetValue() << endl;
_transformResult = opti->GetCurrentPosition();
_transform->SetParameters(opti->GetCurrentPosition());
}