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/*=========================================================================
Program: Advanced Normalization Tools
Module: $RCSfile: itkPICSLAdvancedNormalizationToolKit.h,v $
Language: C++
Date: $Date: 2008/11/15 23:46:06 $
Version: $Revision: 1.18 $
Copyright (c) ConsortiumOfANTS. All rights reserved.
See accompanying COPYING.txt or
http://sourceforge.net/projects/advants/files/ANTS/ANTSCopyright.txt for details.
This software is distributed WITHOUT ANY WARRANTY; without even
the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
PURPOSE. See the above copyright notices for more information.
=========================================================================*/
#ifndef __itkPICSLAdvancedNormalizationToolKit_h
#define __itkPICSLAdvancedNormalizationToolKit_h
#include "itkObject.h"
#include "itkObjectFactory.h"
#include "itkANTSImageTransformation.h"
#include "itkANTSImageRegistrationOptimizer.h"
#include "itkANTSSimilarityMetric.h"
#include "antsCommandLineParser.h"
#include "itkImage.h"
#include "itkMacro.h"
#include "itkANTSLabeledPointSet.h"
namespace itk
{
template <unsigned int TDimension = 3, class TReal = float>
class PICSLAdvancedNormalizationToolKit
: public Object
{
public:
/** Standard class typedefs. */
typedef PICSLAdvancedNormalizationToolKit Self;
typedef Object Superclass;
typedef SmartPointer<Self> Pointer;
typedef SmartPointer<const Self> ConstPointer;
/** Method for creation through the object factory. */
itkNewMacro( Self );
/** Run-time type information (and related methods). */
itkTypeMacro( PICSLAdvancedNormalizationToolKit, Object );
itkStaticConstMacro( Dimension, unsigned int, TDimension );
typedef double TComp;
typedef TReal RealType;
typedef Image<RealType,
itkGetStaticConstMacro( Dimension )> ImageType;
typedef typename ImageType::Pointer ImagePointer;
typedef typename ImageType::PixelType PixelType;
typedef itk::ANTSImageTransformation<Dimension, TReal> TransformationModelType;
typedef typename TransformationModelType::Pointer TransformationModelPointer;
typedef itk::ANTSImageRegistrationOptimizer<Dimension, TReal> RegistrationOptimizerType;
typedef typename RegistrationOptimizerType::Pointer RegistrationOptimizerPointer;
typedef typename TransformationModelType::DisplacementFieldType DisplacementFieldType;
typedef typename TransformationModelType::AffineTransformType AffineTransformType;
typedef typename RegistrationOptimizerType::OptAffineType OptAffineType;
/** Point Set Type */
typedef itk::ANTSLabeledPointSet<Dimension> LabeledPointSetType;
typedef typename LabeledPointSetType::Pointer LabeledPointSetPointer;
typedef typename LabeledPointSetType::PointSetType PointSetType;
/** Typedefs for similarity metrics */
typedef ANTSSimilarityMetric<itkGetStaticConstMacro( Dimension ), TReal> SimilarityMetricType;
typedef typename SimilarityMetricType::Pointer SimilarityMetricPointer;
typedef std::vector<SimilarityMetricPointer> SimilarityMetricListType;
typedef typename SimilarityMetricType::MetricType MetricBaseType;
typedef ants::CommandLineParser ParserType;
typedef typename ParserType::OptionType OptionType;
void ParseCommandLine( int argc, char * *argv );
TransformationModelPointer GetTransformationModel()
{
return this->m_TransformationModel;
}
RegistrationOptimizerPointer SetRegistrationOptimizer()
{
return this->m_RegistrationOptimizer;
}
void SetTransformationModel( TransformationModelPointer T )
{
this->m_TransformationModel = T;
}
void SetRegistrationOptimizer( RegistrationOptimizerPointer T )
{
this->m_RegistrationOptimizer = T;
}
void InitializeTransformAndOptimizer();
void RunRegistration();
protected:
PICSLAdvancedNormalizationToolKit();
virtual ~PICSLAdvancedNormalizationToolKit()
{
}
void PrintSelf( std::ostream& os, Indent indent ) const ITK_OVERRIDE;
private:
PICSLAdvancedNormalizationToolKit( const Self & ); // purposely not implemented
void operator=( const Self & ); // purposely not implemented
ImagePointer SubsampleImage( ImagePointer, RealType );
ImagePointer PreprocessImage( ImagePointer );
ImagePointer ReplaceProblematicPixelValues( ImagePointer, PixelType );
void InitializeCommandLineOptions();
void ReadImagesAndMetrics();
typename ParserType::Pointer m_Parser;
TransformationModelPointer m_TransformationModel;
RegistrationOptimizerPointer m_RegistrationOptimizer;
SimilarityMetricListType m_SimilarityMetrics;
};
} // end namespace itk
#ifndef ITK_MANUAL_INSTANTIATION
#include "itkPICSLAdvancedNormalizationToolKit.hxx"
#endif
#endif
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