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/*
//
// Copyright 1997-2009 Torsten Rohlfing
//
// Copyright 2004-2011 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 $
//
*/
#include "cmtkLabelCombinationLocalWeighting.h"
#include <System/cmtkConsole.h>
#include <System/cmtkDebugOutput.h>
#include <System/cmtkExitException.h>
#include <Base/cmtkRegionIndexIterator.h>
#include <Registration/cmtkTypedArraySimilarity.h>
#include <vector>
#include <algorithm>
#ifdef _OPENMP
# include <omp.h>
#endif
void
cmtk::LabelCombinationLocalWeighting::AddAtlasImage
( const UniformVolume::SmartConstPtr image )
{
if ( !this->m_TargetImage->GridMatches( *image ) )
{
StdErr << "Atlas intensity image grid does not match target image.\n";
throw ExitException( 1 );
}
this->m_AtlasImages.push_back( image );
}
void
cmtk::LabelCombinationLocalWeighting::ExcludeGlobalOutliers()
{
std::vector<Types::DataItem> ncc( this->m_AtlasImages.size() );
for ( size_t i = 0; i < this->m_AtlasImages.size(); ++i )
{
ncc[i] = TypedArraySimilarity::GetCrossCorrelation( this->m_TargetImage->GetData(), this->m_AtlasImages[i]->GetData() );
}
std::vector<Types::DataItem> nccSort = ncc;
std::sort( nccSort.begin(), nccSort.end() );
// determine 1st and 3rd quartile values
const Types::DataItem Q1 = nccSort[static_cast<size_t>( 0.25 * nccSort.size() )];
const Types::DataItem Q3 = nccSort[static_cast<size_t>( 0.75 * nccSort.size() )];
// compute threshold from 1st quartile and inter-quartile range
const Types::DataItem lThresh = Q1 - 1.5 * (Q3-Q1);
size_t iAtlas = 0;
for ( size_t i = 0; i < this->m_AtlasImages.size(); ++i )
{
if ( ncc[i] < lThresh )
{
DebugOutput( 2 ) << "INFO: atlas #" << i << " excluded as outlier based on low NCC with target image (" << ncc[i] << ", thresh=" << lThresh << ")\n";
this->DeleteAtlas( iAtlas );
}
else
{
++iAtlas;
}
}
}
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