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/*
//
// Copyright 1997-2009 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: 5436 $
//
// $LastChangedDate: 2018-12-10 19:01:20 -0800 (Mon, 10 Dec 2018) $
//
// $LastChangedBy: torstenrohlfing $
//
*/
#ifndef __cmtkLabelCombinationLocalWeighting_h_included_
#define __cmtkLabelCombinationLocalWeighting_h_included_
#include <cmtkconfig.h>
#include <System/cmtkSmartPtr.h>
#include <System/cmtkSmartConstPtr.h>
#include <Base/cmtkUniformVolume.h>
#include <vector>
namespace
cmtk
{
/** \addtogroup Segmentation */
//@{
/** Base class for segmentation combination using local weighting.
*/
class LabelCombinationLocalWeighting
{
public:
/// This class.
typedef LabelCombinationLocalWeighting Self;
/// Smart pointer to this class.
typedef SmartPointer<Self> SmartPtr;
/// Smart pointer to const to this class.
typedef SmartConstPointer<Self> SmartConstPtr;
/// Constructor: compute label combination.
LabelCombinationLocalWeighting( const UniformVolume::SmartConstPtr targetImage ) :
m_TargetImage( targetImage ),
m_PatchRadius( 1 ),
m_PatchRadiusPlusOne( 2 ),
m_SearchRegion( UniformVolume::IndexType( 0 ), UniformVolume::IndexType( 1 ) )
{}
/// Add an atlas image (reformatted, target-matched intensity image).
void AddAtlasImage( const UniformVolume::SmartConstPtr image );
/** Exclude global outliers.
* Detect atlases with abnormally low correlation between reformatted atlas and target image,
* then delete these atlases. Outliers are defined as NCC below Q1-1.5*(Q3-Q1), where Q1 is
* the 25th percentile of NCC between atlas and target over all atlases, Q3 is the 75th
* percentile.
*/
void ExcludeGlobalOutliers();
/// Set patch radius.
void SetPatchRadius( const int radius )
{
this->m_PatchRadius = UniformVolume::IndexType( radius );
this->m_PatchRadiusPlusOne = UniformVolume::IndexType( radius+1 );
}
/// Set patch radius.
void SetSearchRadius( const int radius )
{
this->m_SearchRegion.From() = UniformVolume::IndexType( -radius );
this->m_SearchRegion.To() = UniformVolume::IndexType( radius+1 );
}
/// Get resulting combined segmentation.
virtual TypedArray::SmartPtr GetResult() const = 0;
protected:
/// Target image region type.
typedef UniformVolume::RegionType TargetRegionType;
/// The target image.
UniformVolume::SmartConstPtr m_TargetImage;
/// Vector of target-matched atlas images.
std::vector<UniformVolume::SmartConstPtr> m_AtlasImages;
/// Image patch radius in pixels (x,y,z).
UniformVolume::IndexType m_PatchRadius;
/// Image patch radius in pixels (x,y,z) plus one added to each dimension.
UniformVolume::IndexType m_PatchRadiusPlusOne;
/// Patch search region in pixels (x,y,z).
UniformVolume::RegionType m_SearchRegion;
/** Delete atlas with given index.
* Derived classes may need to overload this to make sure additional atlas components (e.g.,
* distance map, label map) are also properly deleted.
*/
virtual void DeleteAtlas( const size_t i )
{
this->m_AtlasImages.erase( this->m_AtlasImages.begin() + i );
}
};
} // namespace cmtk
#endif // #ifndef __cmtkLabelCombinationLocalWeighting_h_included_
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