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/*
//
// Copyright 1997-2009 Torsten Rohlfing
//
// Copyright 2004-2012, 2014 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 "cmtkLabelCombinationLocalVoting.h"
#include <System/cmtkConsole.h>
#include <System/cmtkExitException.h>
#include <Base/cmtkRegionIndexIterator.h>
#include <Base/cmtkTypedArray.h>
#include <Registration/cmtkTypedArraySimilarity.h>
#include <algorithm>
#ifdef _OPENMP
# include <omp.h>
#endif
void
cmtk::LabelCombinationLocalVoting::AddAtlas
( const UniformVolume::SmartConstPtr image, const UniformVolume::SmartConstPtr atlas )
{
Superclass::AddAtlasImage( image );
if ( !this->m_TargetImage->GridMatches( *atlas ) )
{
StdErr << "Atlas label image grid does not match target image.\n";
throw ExitException( 1 );
}
this->m_AtlasLabels.push_back( atlas );
}
int
cmtk::LabelCombinationLocalVoting::ComputeMaximumLabelValue() const
{
int maxLabel = 0;
for ( size_t n = 0; n < this->m_AtlasLabels.size(); ++n )
{
maxLabel = std::max( maxLabel, static_cast<int>( this->m_AtlasLabels[n]->GetData()->GetRange().m_UpperBound ) );
}
return maxLabel;
}
size_t
cmtk::LabelCombinationLocalVoting::ComputeLabelNumberOfPixels( const int label ) const
{
size_t nPixelsLabel = 0;
for ( size_t n = 0; n < this->m_AtlasLabels.size(); ++n )
{
const size_t nPixels = this->m_AtlasLabels[n]->GetNumberOfPixels();
for ( size_t px = 0; px < nPixels; ++px )
{
if ( label == static_cast<int>( this->m_AtlasLabels[n]->GetDataAt( px, -1 ) ) )
++nPixelsLabel;
}
}
return nPixelsLabel;
}
cmtk::TypedArray::SmartPtr
cmtk::LabelCombinationLocalVoting::GetResult() const
{
const UniformVolume& targetImage = *(this->m_TargetImage);
cmtk::TypedArray::SmartPtr result( TypedArray::Create( TYPE_SHORT, targetImage.GetNumberOfPixels() ) );
result->SetDataClass( DATACLASS_LABEL );
const size_t nAtlases = this->m_AtlasImages.size();
this->m_GlobalAtlasWeights.resize( nAtlases );
if ( this->m_UseGlobalAtlasWeights )
{
for ( size_t n = 0; n < nAtlases; ++n )
{
this->m_GlobalAtlasWeights[n] = 1.0 / TypedArraySimilarity::GetCrossCorrelation( targetImage.GetData(), this->m_AtlasImages[n]->GetData() );
}
}
else
{
std::fill( this->m_GlobalAtlasWeights.begin(), this->m_GlobalAtlasWeights.end(), 1.0 );
}
const TargetRegionType region = targetImage.CropRegion();
#ifdef _OPENMP
#pragma omp parallel for
for ( int slice = region.From()[2]; slice < region.To()[2]; ++slice )
{
TargetRegionType threadRegion = region;
threadRegion.From()[2] = slice;
threadRegion.To()[2] = slice+1;
this->ComputeResultForRegion( threadRegion, *result );
}
#else // _OPENMP
this->ComputeResultForRegion( region, *result );
#endif // _OPENMP
return result;
}
void
cmtk::LabelCombinationLocalVoting::ComputeResultForRegion( const Self::TargetRegionType& region, TypedArray& result ) const
{
const UniformVolume& targetImage = *(this->m_TargetImage);
const Self::TargetRegionType wholeImageRegion = targetImage.CropRegion();
const size_t nAtlases = this->m_AtlasImages.size();
std::vector<bool> valid( nAtlases );
std::vector<short> labels( nAtlases );
for ( RegionIndexIterator<TargetRegionType> it( region ); it != it.end(); ++it )
{
const size_t i = targetImage.GetOffsetFromIndex( it.Index() );
for ( size_t n = 0; n < nAtlases; ++n )
{
Types::DataItem value;
if ( (valid[n] = this->m_AtlasLabels[n]->GetData()->Get( value, i ) ) )
labels[n] = static_cast<short>( value );
}
// find first non-padding atlas label
size_t firstValid = 0;
while ( (firstValid < nAtlases) && !valid[firstValid] )
++firstValid;
// if all input atlases are undefined (padding) for this pixel, set output to padding and skip to next pixel.
if ( firstValid == nAtlases )
{
result.SetPaddingAt( i );
continue;
}
// check if all (valid) input atlas labels are the same
bool allTheSame = true;
for ( size_t n = 1; n < nAtlases; ++n )
{
if ( valid[n] )
{
if ( labels[n] != labels[firstValid] )
{
allTheSame = false;
break;
}
}
}
// no need for weighted combination if all labels are the same.
if ( allTheSame )
{
result.Set( labels[firstValid], i );
}
else
{
// Compute weights for the atlases from local image patch similarity.
const TargetRegionType patchRegion( Max( wholeImageRegion.From(), it.Index() - this->m_PatchRadius ), Min( wholeImageRegion.To(), it.Index() + this->m_PatchRadiusPlusOne ) );
TypedArray::SmartConstPtr targetDataPatch( targetImage.GetRegionData( patchRegion ) );
std::map<unsigned short,Types::DataItem> labelToTotalWeight;
for ( size_t n = 0; n < nAtlases; ++n )
{
if ( valid[n] )
{
TypedArray::SmartConstPtr atlasDataPatch( this->m_AtlasImages[n]->GetRegionData( patchRegion ) );
labelToTotalWeight[labels[n]] += TypedArraySimilarity::GetCrossCorrelation( targetDataPatch, atlasDataPatch ) * this->m_GlobalAtlasWeights[n];
}
}
short maxLabel = 0;
Types::DataItem maxWeight = 0;
for ( std::map<unsigned short,Types::DataItem>::const_iterator mapIt = labelToTotalWeight.begin(); mapIt != labelToTotalWeight.end(); ++mapIt )
{
if ( mapIt->second > maxWeight )
{
maxLabel = mapIt->first;
maxWeight = mapIt->second;
}
}
result.Set( maxLabel, i );
}
}
}
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