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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.
*
*=========================================================================*/
#ifndef elxPCAMetric_hxx
#define elxPCAMetric_hxx
#include "elxPCAMetric.h"
#include "itkTimeProbe.h"
#include <itkDeref.h>
namespace elastix
{
/**
* ******************* Initialize ***********************
*/
template <class TElastix>
void
PCAMetric<TElastix>::Initialize()
{
itk::TimeProbe timer;
timer.Start();
this->Superclass1::Initialize();
const Configuration & configuration = itk::Deref(Superclass2::GetConfiguration());
if (configuration.HasParameter("SubtractMean"))
{
log::warn(std::string("WARNING: From elastix version 5.2, the ") + elxGetClassNameStatic() +
" parameter `SubtractMean` (default \"false\") is "
"replaced with `UseZeroAverageDisplacementConstraint` "
"(default \"true\").");
}
timer.Stop();
log::info(std::ostringstream{} << "Initialization of PCAMetric metric took: "
<< static_cast<long>(timer.GetMean() * 1000) << " ms.");
} // end Initialize()
/**
* ***************** BeforeRegistration ***********************
*/
template <class TElastix>
void
PCAMetric<TElastix>::BeforeRegistration()
{
/** Check if this elastix object has a transform. (If so, it must be a combination transform.) */
if (CombinationTransformType * const combinationTransform{
BaseComponent::AsITKBaseType(this->GetElastix()->GetElxTransformBase()) })
{
auto * const currentTransform = combinationTransform->GetModifiableCurrentTransform();
/** Check for B-spline transform. */
if (const auto bsplineTransform = dynamic_cast<BSplineTransformBaseType *>(currentTransform))
{
this->SetGridSize(bsplineTransform->GetGridRegion().GetSize());
}
else
{
/** Check for stack transform. */
if (const auto stackTransform = dynamic_cast<StackTransformType *>(currentTransform))
{
/** Set itk member variable. */
this->SetTransformIsStackTransform(true);
// Return early, now that the current transform is a stack transform.
return;
}
}
}
// If the current transform would have been a stack transform, the function would have returned earlier.
this->SetTransformIsStackTransform(false);
}
/**
* ***************** BeforeEachResolution ***********************
*/
template <class TElastix>
void
PCAMetric<TElastix>::BeforeEachResolution()
{
const Configuration & configuration = itk::Deref(Superclass2::GetConfiguration());
const std::string componentLabel = BaseComponent::GetComponentLabel();
/** Get the current resolution level. */
unsigned int level = (this->m_Registration->GetAsITKBaseType())->GetCurrentLevel();
unsigned int NumEigenValues = 6;
configuration.ReadParameter(NumEigenValues, "NumEigenValues", componentLabel, level, 0);
this->SetNumEigenValues(NumEigenValues);
/** Get and set if we want to subtract the mean from the derivative. */
bool useZeroAverageDisplacementConstraint = true;
// The parameter name "SubtractMean" is obsolete, so just use it as initial value, for backward compatibility.
configuration.ReadParameter(useZeroAverageDisplacementConstraint, "SubtractMean", componentLabel, 0, 0);
configuration.ReadParameter(
useZeroAverageDisplacementConstraint, "UseZeroAverageDisplacementConstraint", componentLabel, 0, 0);
this->SetUseZeroAverageDisplacementConstraint(useZeroAverageDisplacementConstraint);
/** Get and set the number of additional samples sampled at the fixed timepoint. */
// unsigned int numAdditionalSamplesFixed = 0;
// configuration.ReadParameter( numAdditionalSamplesFixed,
// "NumAdditionalSamplesFixed", componentLabel, level, 0 );
// this->SetNumAdditionalSamplesFixed( numAdditionalSamplesFixed );
/** Get and set the fixed timepoint number. */
// unsigned int reducedDimensionIndex = 0;
// configuration.ReadParameter(
// reducedDimensionIndex, "ReducedDimensionIndex",
// componentLabel, 0, 0 );
// this->SetReducedDimensionIndex( reducedDimensionIndex );
/** Set moving image derivative scales. */
this->SetUseMovingImageDerivativeScales(false);
MovingImageDerivativeScalesType movingImageDerivativeScales;
bool usescales = true;
for (unsigned int i = 0; i < MovingImageDimension; ++i)
{
usescales =
usescales && configuration.ReadParameter(
movingImageDerivativeScales[i], "MovingImageDerivativeScales", componentLabel, i, -1, true);
}
if (usescales)
{
this->SetUseMovingImageDerivativeScales(true);
this->SetMovingImageDerivativeScales(movingImageDerivativeScales);
log::info(std::ostringstream{} << "Multiplying moving image derivatives by: " << movingImageDerivativeScales);
}
log::info("end BeforeEachResolution");
} // end BeforeEachResolution()
} // end namespace elastix
#endif // end #ifndef elxPCAMetric_hxx
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