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/*
//
// Copyright 2010-2014 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 "cmtkSimpleLevelset.h"
#include <Base/cmtkMathUtil.h>
#include <Base/cmtkUniformVolume.h>
#include <Base/cmtkUniformVolumePainter.h>
#include <Base/cmtkUniformVolumeGaussianFilter.h>
#include <Base/cmtkUnits.h>
#include <System/cmtkProgress.h>
#include <System/cmtkDebugOutput.h>
#ifdef CMTK_BUILD_DEMO
# include <IO/cmtkVolumeIO.h>
#endif // #ifdef CMTK_BUILD_DEMO
void
cmtk::SimpleLevelset
::InitializeCenteredSphere()
{
this->m_Levelset = this->m_Volume->CloneGrid();
this->m_Levelset->CreateDataArray( TYPE_FLOAT );
this->m_Levelset->GetData()->Fill( -1.0 );
FixedVector<3,int> center( this->m_Volume->GetDims() );
center /= 2;
UniformVolumePainter painter( this->m_Levelset );
painter.DrawSphere( center, this->m_ScaleInitialSphere * ((this->m_Levelset->GetDims()[0]+this->m_Levelset->GetDims()[1]+this->m_Levelset->GetDims()[2])/6), 1.0 );
}
void
cmtk::SimpleLevelset
::Evolve( const int numberOfIterations, const bool forceIterations )
{
const size_t numberOfPixels = this->m_Volume->GetNumberOfPixels();
size_t nInsideOld = 0, nInside = 1;
Progress::Begin( 0, numberOfIterations, 1, "Levelset Evolution" );
for ( int it = 0; (it < numberOfIterations) && ((nInside!=nInsideOld) || forceIterations); ++it )
{
Progress::SetProgress( it );
nInsideOld = nInside;
nInside = 0;
Types::DataItem insideSum = 0, outsideSum = 0;
this->m_Levelset->SetData( UniformVolumeGaussianFilter( this->m_Levelset ).GetFiltered3D( this->m_FilterSigma ) );
#pragma omp parallel for reduction(+:nInside) reduction(+:insideSum) reduction(+:outsideSum)
for ( int n = 0; n < static_cast<int>( numberOfPixels ); ++n )
{
if ( this->m_Levelset->GetDataAt( n ) > 0 )
{
insideSum += this->m_Volume->GetDataAt( n );
++nInside;
}
else
outsideSum += this->m_Volume->GetDataAt( n );
}
if ( nInside == 0 )
throw Self::DegenerateLevelsetException();
const size_t nOutside = numberOfPixels - nInside;
if ( nOutside == 0 )
throw Self::DegenerateLevelsetException();
const Types::DataItem ratioInOut = 1.0 * nInside / nOutside;
const Types::DataItem mInside = insideSum / nInside;
const Types::DataItem mOutside = outsideSum / nOutside;
DebugOutput( 1 ) << it << " IN: " << nInside << " " << mInside << " OUT: " << nOutside << " " << mOutside << "\r";
#pragma omp parallel for
for ( int n = 0; n < static_cast<int>( numberOfPixels ); ++n )
{
const Types::DataItem data = this->m_Volume->GetDataAt( n );
const Types::DataItem zInside = fabs( mInside - data );
const Types::DataItem zOutside = fabs( mOutside - data );
Types::DataItem newLevel = this->m_Levelset->GetDataAt( n );
if ( zInside>zOutside )
{
newLevel -= this->m_TimeDelta * ratioInOut;
}
else
{
newLevel += this->m_TimeDelta / ratioInOut;
}
this->m_Levelset->SetDataAt( std::min<Types::DataItem>( this->m_LevelsetThreshold, std::max<Types::DataItem>( -this->m_LevelsetThreshold, newLevel ) ), n );
}
#ifdef CMTK_BUILD_DEMO
UniformVolume::SmartConstPtr slice = this->m_Levelset->ExtractSlice( AXIS_Z, this->m_Levelset->m_Dims[2] / 2 );
char path[PATH_MAX];
snprintf( path, PATH_MAX, "levelset-%03d.nii", it );
VolumeIO::Write( *slice, path );
#endif
}
Progress::Done();
}
cmtk::UniformVolume::SmartPtr&
cmtk::SimpleLevelset
::GetLevelset( const bool binarize, const float threshold )
{
if ( binarize )
{
this->m_Levelset->GetData()->Binarize( threshold );
this->m_Levelset->SetData( TypedArray::SmartPtr( this->m_Levelset->GetData()->Convert( TYPE_BYTE ) ) );
this->m_Levelset->GetData()->SetDataClass( DATACLASS_LABEL );
}
return this->m_Levelset;
}
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