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/*
//
// Copyright 1997-2009 Torsten Rohlfing
//
// Copyright 2004-2013 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 "cmtkAtlasSegmentation.h"
#include <Registration/cmtkRegistrationCallback.h>
#include <Registration/cmtkAffineRegistration.h>
#include <Registration/cmtkElasticRegistration.h>
#include <Registration/cmtkReformatVolume.h>
#include <System/cmtkDebugOutput.h>
#include <System/cmtkExitException.h>
cmtk::AtlasSegmentation::AtlasSegmentation
( UniformVolume::SmartPtr& targetImage, UniformVolume::SmartPtr& atlasImage, UniformVolume::SmartPtr& atlasLabels ) :
m_Fast( false ),
m_TargetImage( targetImage ),
m_AtlasImage( atlasImage ),
m_AtlasLabels( atlasLabels ),
m_LabelMap( NULL )
{
}
void
cmtk::AtlasSegmentation
::RegisterAffine()
{
AffineRegistration ar;
ar.SetVolume_1( this->m_TargetImage );
ar.SetVolume_2( this->m_AtlasImage );
// run 6 DOFs first, then 9 at each level.
ar.AddNumberDOFs( 6 );
ar.AddNumberDOFs( 9 );
ar.SetInitialAlignCenters( true );
ar.SetExploration( 4 * this->m_TargetImage->GetMaxDelta() );
ar.SetAccuracy( .1 * this->m_TargetImage->GetMaxDelta() );
ar.SetSampling( 2 * this->m_TargetImage->GetMaxDelta() );
ar.SetUseOriginalData( !this->m_Fast );
(DebugOutput( 1 ) << "Affine registration...").flush();
ar.Register();
DebugOutput( 1 ) << " done.\n";
try
{
this->m_AffineXform = ar.GetTransformation();
}
catch ( const AffineXform::MatrixType::SingularMatrixException& )
{
StdErr << "ERROR: singular matrix in AffineRegistration::GetTransformation()\n";
throw ExitException( 1 );
}
}
void
cmtk::AtlasSegmentation
::RegisterSpline()
{
ElasticRegistration er;
er.SetVolume_1( this->m_TargetImage );
er.SetVolume_2( this->m_AtlasImage );
er.SetInitialTransformation( this->GetAffineXform() );
er.SetUseOriginalData( !this->m_Fast );
er.SetFastMode( this->m_Fast );
const Types::Coordinate minSize = std::min( std::min( this->m_TargetImage->m_Size[0], this->m_TargetImage->m_Size[1] ), this->m_TargetImage->m_Size[2] );
er.SetGridSpacing( minSize / 2 );
er.SetRefineGrid( std::max<int>( 0, static_cast<int>( (log( minSize / this->m_TargetImage->GetMaxDelta() ) / log(2.0)) - 3 ) ) );
er.SetDelayRefineGrid( !this->m_Fast );
er.SetGridEnergyWeight( 1e-1f );
er.SetAdaptiveFixParameters( true );
er.SetAlgorithm( 3 );
er.SetExploration( minSize / 8 );
er.SetAccuracy( .1 * this->m_TargetImage->GetMinDelta() );
er.SetSampling( 2 * this->m_TargetImage->GetMaxDelta() );
(DebugOutput( 1 ) << "Nonrigid registration...").flush();
er.Register();
DebugOutput( 1 ) << " done.\n";
this->m_WarpXform = er.GetTransformation();
}
void
cmtk::AtlasSegmentation
::ReformatLabels()
{
ReformatVolume reformat;
reformat.SetInterpolation( Interpolators::PARTIALVOLUME );
reformat.SetPaddingValue( 0 );
reformat.SetUsePaddingValue( true );
reformat.SetReferenceVolume( this->m_TargetImage );
reformat.SetFloatingVolume( this->m_AtlasLabels );
WarpXform::SmartPtr warpXform = this->GetWarpXform();
reformat.SetWarpXform( warpXform );
this->m_LabelMap = UniformVolume::SmartPtr( reformat.PlainReformat() );
}
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