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/*
//
// Copyright 1997-2012 Torsten Rohlfing
//
// Copyright 2004-2012 SRI International
//
// This file is part of the Computational Morphometry Toolkit.
//
// http://www.nitrc.org/projects/cmtk/
//
// The Computational Morphometry Toolkit is free software: you can
// redistribute it and/or modify it under the terms of the GNU General Public
// License as published by the Free Software Foundation, either version 3 of
// the License, or (at your option) any later version.
//
// The Computational Morphometry Toolkit is distributed in the hope that it
// will be useful, but WITHOUT ANY WARRANTY; without even the implied
// warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
// GNU General Public License for more details.
//
// You should have received a copy of the GNU General Public License along
// with the Computational Morphometry Toolkit. If not, see
// <http://www.gnu.org/licenses/>.
//
// $Revision: 3517 $
//
// $LastChangedDate: 2011-10-27 12:42:15 -0700 (Thu, 27 Oct 2011) $
//
// $LastChangedBy: torstenrohlfing $
//
*/
#ifndef __cmtkMultiChannelEntropyMinimizationIntensityCorrectionFunctional_h_included_
#define __cmtkMultiChannelEntropyMinimizationIntensityCorrectionFunctional_h_included_
#include <cmtkconfig.h>
#include <Segmentation/cmtkEntropyMinimizationIntensityCorrectionFunctional.h>
#include <Base/cmtkUniformVolume.h>
#include <Base/cmtkDataGrid.h>
#include <System/cmtkSmartPtr.h>
#include <vector>
namespace
cmtk
{
/** \addtogroup Segmentation */
//@{
/** Functional to correct MR intensity bias by miniming image entropy.
*/
template<unsigned int NOrderAdd,unsigned int NOrderMul>
class MultiChannelEntropyMinimizationIntensityCorrectionFunctional :
/// Inherit from base class.
public Functional
{
public:
/// This class type.
typedef MultiChannelEntropyMinimizationIntensityCorrectionFunctional<NOrderAdd,NOrderMul> Self;
/// Class for single-channel functional type.
typedef EntropyMinimizationIntensityCorrectionFunctional<NOrderAdd,NOrderMul> SingleChannelFunctionalType;
/// Pointer to this class.
typedef SmartPointer<Self> SmartPtr;
/// Superclass type.
typedef Functional Superclass;
/// Constructor.
MultiChannelEntropyMinimizationIntensityCorrectionFunctional( std::vector<UniformVolume::SmartConstPointer>& inputImages )
: m_InputImages( inputImages )
{
this->m_SingleChannelFunctionals.resize( this->m_InputImages.size() );
for ( size_t idx = 0; idx < this->m_SingleChannelFunctionals.size(); ++idx )
{
this->m_SingleChannelFunctionals[idx] = SingleChannelFunctionalType::SmartPtr( new SingleChannelFunctionalType );
this->m_SingleChannelFunctionals[idx]->SetInputImage( this->m_InputImages[idx] );
}
}
/// Set foreground mask for all input images.
virtual void SetForegroundMask( const UniformVolume& foregroundMask )
{
for ( size_t idx = 0; idx < this->m_SingleChannelFunctionals.size(); ++idx )
{
this->m_SingleChannelFunctionals[idx]->SetForegroundMask( foregroundMask );
}
}
/// Virtual destructor.
virtual ~MultiChannelEntropyMinimizationIntensityCorrectionFunctional() {}
/// Return parameter vector length.
virtual size_t ParamVectorDim() const
{
return SingleChannelFunctionalType::NumberOfParameters * this->m_InputImages.size();
}
/// Return parameter stepping.
#pragma GCC diagnostic ignored "-Wtype-limits"
virtual Types::Coordinate GetParamStep( const size_t idx, const Types::Coordinate mmStep = 1 ) const
{
// delegate to corresponding single-channel functional, although they are really all the same.
return this->m_SingleChannelFunctionals[idx / SingleChannelFunctionalType::NumberOfParameters]->GetParamStep( idx % SingleChannelFunctionalType::NumberOfParameters );
}
/// Copy parameters to the two correction polynomials.
virtual void SetParamVector( CoordinateVector& v )
{
this->m_ParameterVector = v;
for ( size_t idx = 0; idx < this->m_SingleChannelFunctionals.size(); ++idx )
{
}
}
/// Extract parameter vector from the two correction polynomials.
virtual void GetParamVector( CoordinateVector& v )
{
v = this->m_ParameterVector;
}
/** Fast implementation of gradient evaluation.
* This function only updates either the additive of the multiplicative bias
* field, depending on which gradient component is being determined.
*/
virtual typename Self::ReturnType EvaluateWithGradient( CoordinateVector& v, CoordinateVector& g, const Types::Coordinate step );
private:
/// Keep a copy of the current parameter vector.
CoordinateVector m_ParameterVector;
/// Vector of input images.
std::vector<UniformVolume::SmartConstPtr> m_InputImages;
/// Vector of single-channel functionals.
std::vector<typename SingleChannelFunctionalType::SmartPtr> m_SingleChannelFunctionals;
};
/// Create functional templated over polynomial degrees.
template<unsigned int NDegreeMul>
MultiChannelEntropyMinimizationIntensityCorrectionFunctionalBase::SmartPtr
CreateMultiChannelEntropyMinimizationIntensityCorrectionFunctional
( const unsigned int polynomialDegreeAdd );
/// Create functional templated over polynomial degrees.
MultiChannelEntropyMinimizationIntensityCorrectionFunctionalBase::SmartPtr
CreateMultiChannelEntropyMinimizationIntensityCorrectionFunctional
( const unsigned int polynomialDegreeAdd, const unsigned int polynomialDegreeMul );
/** Create functional templated over polynomial degrees with initialization from old functional.
* This function creates a new functional and copies the polynomial coefficients from an existing
* functional of equal or lower polynomial degrees into the correct locations of the new functional's
* parameter vector. This is for incremental computation.
*/
MultiChannelEntropyMinimizationIntensityCorrectionFunctionalBase::SmartPtr
CreateMultiChannelEntropyMinimizationIntensityCorrectionFunctional
( const unsigned int polynomialDegreeAdd, const unsigned int polynomialDegreeMul,
MultiChannelEntropyMinimizationIntensityCorrectionFunctionalBase::SmartPtr oldFunctional );
//@}
} // namespace cmtk
#include "cmtkMultiChannelEntropyMinimizationIntensityCorrectionFunctional.txx"
#endif // #ifndef __cmtkMultiChannelEntropyMinimizationIntensityCorrectionFunctional_h_included_
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