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/*
//
// Copyright 1997-2009 Torsten Rohlfing
//
// Copyright 2004-2010 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 <Segmentation/cmtkEntropyMinimizationIntensityCorrectionFunctionalBase.h>
#include <System/cmtkThreadPool.h>
#include <System/cmtkException.h>
#include <algorithm>
#ifdef CMTK_BUILD_DEMO
# include <IO/cmtkVolumeIO.h>
#endif // #ifdef CMTK_BUILD_DEMO
namespace cmtk
{
/** \addtogroup Segmentation */
//@{
void
EntropyMinimizationIntensityCorrectionFunctionalBase
::SetInputImage( UniformVolume::SmartConstPtr& inputImage )
{
this->m_InputImage = inputImage;
this->m_NumberOfPixels = this->m_InputImage->GetNumberOfPixels();
const Types::DataItemRange range = this->m_InputImage->GetData()->GetRange();
this->m_InputImageRange = range.Width();
if ( this->m_UseLogIntensities )
{
this->m_EntropyHistogram = HistogramType::SmartPtr( new LogHistogramType( this->m_NumberOfHistogramBins ) );
}
else
{
this->m_EntropyHistogram = HistogramType::SmartPtr( new HistogramType( this->m_NumberOfHistogramBins ) );
}
// extend value range to accomodate corrected intensities without overflows
this->m_EntropyHistogram->SetRange( Types::DataItemRange( range.m_LowerBound - this->m_InputImageRange, range.m_UpperBound + this->m_InputImageRange ) );
if ( this->m_ForegroundMask.size() )
this->UpdateCorrectionFactors();
this->m_BiasFieldAdd = FloatArray::Create( this->m_NumberOfPixels );
this->m_BiasFieldAdd->Fill( 0.0 );
this->m_BiasFieldMul = FloatArray::Create( this->m_NumberOfPixels );
this->m_BiasFieldAdd->Fill( 1.0 );
this->m_OutputImage = UniformVolume::SmartPtr( this->m_InputImage->CloneGrid() );
this->m_OutputImage->CreateDataArray( TYPE_FLOAT );
}
void
EntropyMinimizationIntensityCorrectionFunctionalBase
::SetForegroundMask( const UniformVolume& foregroundMask )
{
const size_t maskPixels = foregroundMask.GetNumberOfPixels();
if ( maskPixels != this->m_NumberOfPixels )
{
throw Exception( "Number of mask pixels does not match number of input image pixels." );
}
this->m_ForegroundMask.resize( maskPixels );
if ( (this->m_SamplingDensity > 0) && (this->m_SamplingDensity < 1) )
{
for ( size_t i = 0; i < maskPixels; ++i )
{
this->m_ForegroundMask[i] = (foregroundMask.GetDataAt( i ) > 0) && (MathUtil::UniformRandom() <= this->m_SamplingDensity);
}
}
else
{
for ( size_t i = 0; i < maskPixels; ++i )
{
this->m_ForegroundMask[i] = (foregroundMask.GetDataAt( i ) > 0);
}
}
if ( this->m_InputImage )
this->UpdateCorrectionFactors();
}
UniformVolume::SmartPtr&
EntropyMinimizationIntensityCorrectionFunctionalBase
::GetOutputImage( CoordinateVector& v, const bool foregroundOnly )
{
this->SetParamVector( v );
this->UpdateBiasFields( foregroundOnly );
this->UpdateOutputImage( foregroundOnly );
return this->m_OutputImage;
}
EntropyMinimizationIntensityCorrectionFunctionalBase::ReturnType
EntropyMinimizationIntensityCorrectionFunctionalBase
::EvaluateAt( CoordinateVector& v )
{
this->SetParamVector( v );
this->UpdateBiasFields();
this->UpdateOutputImage();
return this->Evaluate();
}
#ifdef CMTK_BUILD_DEMO
void
EntropyMinimizationIntensityCorrectionFunctionalBase
::SnapshotAt( CoordinateVector& v )
{
this->SetParamVector( v );
this->UpdateBiasFields();
static int it = 0;
this->UpdateOutputImage( false /*foregroundOnly*/ );
UniformVolume::SmartConstPtr slice = this->m_OutputImage->ExtractSlice( AXIS_Z, this->m_OutputImage->m_Dims[2] / 2 );
char path[PATH_MAX];
snprintf( path, PATH_MAX, "mrbias-%03d.nii", it++ );
VolumeIO::Write( *slice, path );
}
#endif
void
EntropyMinimizationIntensityCorrectionFunctionalBase
::UpdateOutputImage( const bool foregroundOnly )
{
ThreadPool& threadPool = ThreadPool::GetGlobalThreadPool();
const size_t numberOfTasks = 4 * threadPool.GetNumberOfThreads() - 3;
std::vector<UpdateOutputImageThreadParameters> taskParameters( numberOfTasks );
for ( size_t task = 0; task < numberOfTasks; ++task )
{
taskParameters[task].thisObject = this;
taskParameters[task].m_ForegroundOnly = foregroundOnly;
}
threadPool.Run( UpdateOutputImageThreadFunc, taskParameters );
}
void
EntropyMinimizationIntensityCorrectionFunctionalBase
::UpdateOutputImageThreadFunc( void *args, const size_t taskIdx, const size_t taskCnt, const size_t, const size_t )
{
UpdateOutputImageThreadParameters* threadParameters = static_cast<UpdateOutputImageThreadParameters*>( args );
Self* This = threadParameters->thisObject;
const Self* ThisConst = threadParameters->thisObject;
const UniformVolume* inputImage = ThisConst->m_InputImage;
TypedArray::SmartPtr outputData = This->m_OutputImage->GetData();
const size_t numberOfPixels = inputImage->GetNumberOfPixels();
const float* biasFieldPtrAdd = ThisConst->m_BiasFieldAdd->GetDataPtrTemplate();
const float* biasFieldPtrMul = ThisConst->m_BiasFieldMul->GetDataPtrTemplate();
Types::DataItem value;
for ( size_t ofs = taskIdx; ofs < numberOfPixels; ofs += taskCnt )
{
if ( !threadParameters->m_ForegroundOnly || ThisConst->m_ForegroundMask[ofs] )
{
if ( inputImage->GetDataAt( value, ofs ) )
{
outputData->Set( value * biasFieldPtrMul[ofs] + biasFieldPtrAdd[ofs], ofs );
}
else
{
outputData->SetPaddingAt( ofs );
}
}
else
{
outputData->SetPaddingAt( ofs );
}
}
}
} // namespace cmtk
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