double GlobalAdaptation::getInitialValue()
{
unsigned int numberOfParameters;
if (mode_ == "rotation")
numberOfParameters = 3;
else if (mode_ == "rotation+scaling")
numberOfParameters = 4;
else if (mode_ == "rotation+translation")
numberOfParameters = 6;
else numberOfParameters = 3;
ParametersType pInit;
double* init = new double[numberOfParameters];
for (int i=0; i<numberOfParameters; i++) init[i] = 0.0;
if (mode_ == "rotation+scaling")
init[3] = 1.0;
pInit.SetData(init,numberOfParameters,false);
SCRegion* region = new SCRegion();
int *sizeDesired = new int[3];
double *spacingDesired = new double[3];
sizeDesired[0] = 61; sizeDesired[1] = 61; sizeDesired[2] = 81;
spacingDesired[0] = 1; spacingDesired[1] = 1; spacingDesired[2] = 1;
region->setSize(sizeDesired);
region->setSpacing(spacingDesired);
region->setOrigin(pointRotation_[0],pointRotation_[1],pointRotation_[2]);
region->setNormal(normal_mesh_[0],normal_mesh_[1],normal_mesh_[2]);
region->setFactor(image_->getTypeImageFactor());
region->build2DGaussian(5);
FoncteurGlobalAdaptation* f = new FoncteurGlobalAdaptation(image_,mesh_->getListTrianglesBarycentre(),numberOfParameters);
f->setGaussianRegion(region);
return f->GetValue(pInit);
}
mitk::NumericTwoCompartmentExchangeModelParameterizer::ParametersType
mitk::NumericTwoCompartmentExchangeModelParameterizer::GetDefaultInitialParameterization() const
{
ParametersType initialParameters;
initialParameters.SetSize(4);
initialParameters[mitk::NumericTwoCompartmentExchangeModel::POSITION_PARAMETER_PS] = 5.0;
initialParameters[mitk::NumericTwoCompartmentExchangeModel::POSITION_PARAMETER_F] = 20.0;
initialParameters[mitk::NumericTwoCompartmentExchangeModel::POSITION_PARAMETER_ve] = 0.1;
initialParameters[mitk::NumericTwoCompartmentExchangeModel::POSITION_PARAMETER_vp] = 0.04;
return initialParameters;
};
mitk::NumericTwoTissueCompartmentModelParameterizer::ParametersType
mitk::NumericTwoTissueCompartmentModelParameterizer::GetDefaultInitialParameterization() const
{
ParametersType initialParameters;
initialParameters.SetSize(5);
initialParameters[mitk::NumericTwoTissueCompartmentModel::POSITION_PARAMETER_K1] = 0.23;
initialParameters[mitk::NumericTwoTissueCompartmentModel::POSITION_PARAMETER_k2] = 0.4;
initialParameters[mitk::NumericTwoTissueCompartmentModel::POSITION_PARAMETER_k3] = 0.13;
initialParameters[mitk::NumericTwoTissueCompartmentModel::POSITION_PARAMETER_k4] = 0.15;
initialParameters[mitk::NumericTwoTissueCompartmentModel::POSITION_PARAMETER_VB] = 0.03;
return initialParameters;
};
void MutualInformationRegistration::serialize(XmlSerializer& s) const {
VolumeProcessor::serialize(s);
ParametersType parameters = transform_->GetParameters();
ParametersType fixedParameters = transform_->GetFixedParameters();
std::vector<double> params;
std::vector<double> fixedParams;
for(size_t i=0; i<parameters.GetSize(); i++)
params.push_back(parameters[i]);
for(size_t i=0; i<fixedParameters.GetSize(); i++)
fixedParams.push_back(fixedParameters[i]);
s.serialize("parameters", params);
s.serialize("fixedParameters", fixedParams);
}
void
copyFromNonVirtual ( const AnyParametersModifierTemplate & copy_from )
{
if( copy_from.parameters.debug >= DEBUG_All ) {
cout << "[debug] GALOSH::ParametersModifierTemplate::copyFromNonVirtual( copy_from )" << endl;
}
isModified_copyFromNonVirtual( copy_from );
parameters.copyFromNonVirtual( copy_from.parameters );
} // copyFromNonVirtual( AnyParametersModifierTemplate const & )
// set up optimization routine
void PatchTracking::beginTracking() {
_transform = TransformType::New();
ParametersType initialParams;
initialParams.SetSize(_transform->GetNumberOfParameters());
initialParams.Fill(0);
_costFunc = CostFunctionType::New();
_costFunc->SetFixedImage(_patches[0]);
_costFunc->SetFixedInterpolator(LinearImageInterpolatorType::New());
_costFunc->SetMovingImage(_images[1]);
_costFunc->SetMovingInterpolator(LinearImageInterpolatorType::New());
_costFunc->SetMovingTransform(_transform);
_costFunc->SetParameters(initialParams);
setupMetric(_costFunc);
_costFunc->Initialize();
OptimizerType::ScalesType scales;
scales.SetSize(initialParams.Size());
scales.Fill(1);
OptimizerProgress<OptimizerType>::Pointer progress = OptimizerProgress<OptimizerType>::New();
_optimizer = OptimizerType::New();
_optimizer->SetScales(scales);
_optimizer->SetScalesEstimator(_estimator);
_optimizer->SetMetric(_costFunc);
// _optimizer->AddObserver(itk::IterationEvent(), progress);
setupOptimizer(_optimizer);
_optimizer->StartOptimization();
cout << "Iterations: " << _optimizer->GetCurrentIteration() << endl;
cout << "Stop Reason: " << _optimizer->GetStopConditionDescription() << endl;
const ParametersType& params = _optimizer->GetCurrentPosition();
_transform->SetParameters(params);
resamplePatch();
transformPatchRegion();
}
void MutualInformationRegistration::deserialize(XmlDeserializer& s) {
VolumeProcessor::deserialize(s);
ParametersType parameters = transform_->GetParameters();
ParametersType fixedParameters = transform_->GetFixedParameters();
std::vector<double> params;
std::vector<double> fixedParams;
s.deserialize("parameters", params);
s.deserialize("fixedParameters", fixedParams);
for(size_t i=0; i<parameters.GetSize(); i++)
parameters[i] = params[i];
for(size_t i=0; i<fixedParameters.GetSize(); i++)
fixedParameters[i] = fixedParams[i];
transform_->SetParameters(parameters);
transform_->SetFixedParameters(fixedParameters);
}
void reset ()
{
isModified_reset();
parameters.resetToDefaults();
} // reset()
