itkscalarimagetogreylevelcooccurrencematrixgenerator.h

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/*=========================================================================

  Program:   Insight Segmentation & Registration Toolkit
  Module:    $RCSfile: itkScalarImageToGreyLevelCooccurrenceMatrixGenerator.h,v $
  Language:  C++
  Date:      $Date: 2005-08-24 15:16:54 $
  Version:   $Revision: 1.8 $

  Copyright (c) Insight Software Consortium. All rights reserved.
  See ITKCopyright.txt or http://www.itk.org/HTML/Copyright.htm 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 __itkScalarImageToGreyLevelCooccurrenceMatrixGenerator_h
#define __itkScalarImageToGreyLevelCooccurrenceMatrixGenerator_h

#include "itkImage.h"
#include "itkHistogram.h"
#include "itkDenseFrequencyContainer.h"
#include "itkVectorContainer.h"
#include "itkObject.h"
#include "itkNumericTraits.h"
#include "itkMacro.h"

namespace itk {
  namespace Statistics {

/** \class ScalarImageToGreyLevelCooccurrenceMatrixGenerator 
*  \brief This class computes a grey-level co-occurence matrix (histogram) from
* a given image. GLCM's are used for image texture description.
*
* This generator creates a grey-level co-occurence matrix from a N-D scalar
* image. This is the first step in texture description a la Haralick. (See
* Haralick, R.M., K. Shanmugam and I. Dinstein. 1973. Textural Features for
* Image Classification. IEEE Transactions on Systems, Man and Cybernetics. 
* SMC-3(6):610-620. See also Haralick, R.M. 1979. Statistical and Structural
* Approaches to Texture. Proceedings of the IEEE, 67:786-804.)
*
* The basic idea is as follows:
* Given an image and an offset (e.g. (1, -1) for a 2-d image), grey-level
* co-occurences are pairs of intensity values for a specific pixel and the
* pixel at that offset from the specified pixel. These co-occurences can provide
* information about the visual texture of an image region -- for example, an
* eight-bit image of alternating pixel-wide white and black vertical lines
* would have a large number of (0, 255) and (255, 0) co-occurences for offset
* (1, 0).
*
* The offset (or offsets) along which the co-occurences are calculated can be
* set by the user. Traditionally, only one offset is used per histogram, and
* offset components in the range [-1, 1] are used. For rotation-invariant features,
* averages of features computed over several histograms with different offsets
* are generally used, instead of computing features from one histogram created
* with several offsets. Additionally, instead of using offsets of two or more
* pixels in any direction, multy-resulution techniques (e.g. image pyramids)
* are generally used to deal with texture at different spatial resolutions.
*
* This class calculates a 2-d histogram of all the co-occurence pairs in the
* given image's requested region, for a given set of offsets. That is, if a given
* offset falls outside of the requested region at a particular point, that
* co-occurrence pair will not be added to the matrix.
* 
* The number of histogram bins on each axis can be set (defaults to 256). Also,
* by default the histogram min and max corresponds to the largest and smallest
* possible pixel value of that pixel type. To customize the histogram bounds
* for a given image, the max and min pixel values that will be placed in the
* histogram can be set manually. NB: The min and max are INCLUSIVE.
*
* Further, the type of histogram frequency container used is an optional template 
* parameter. By default, a dense container is used, but for images with little
* texture or in cases where the user wants more histogram bins, a sparse container
* can be used for the histogram instead. 
*
* WARNING: This probably won't work for pixels of double or long-double type
* unless you set the histogram min and max manually. This is because the largest
* histogram bin by default has max value of the largest possible pixel value 
* plus 1. For double and long-double types, whose "RealType" as defined by the
* NumericTraits class is the same, and thus cannot hold any larger values,
* this would cause a float overflow.
* 
* \sa MaskedScalarImageToGreyLevelCooccurrenceMatrixGenerator
* \sa GreyLevelCooccurrenceMatrixTextureCoefficientsCalculator
* \sa ScalarImageTextureCalculator
*
* Authors: Zachary Pincus and Glenn Pierce
*/
    
template< class TImageType,
          class THistogramFrequencyContainer = DenseFrequencyContainer >
class ScalarImageToGreyLevelCooccurrenceMatrixGenerator : public Object
  {
  public:
    /** Standard typedefs */
    typedef ScalarImageToGreyLevelCooccurrenceMatrixGenerator Self;
    typedef Object Superclass;
    typedef SmartPointer<Self> Pointer;
    typedef SmartPointer<const Self> ConstPointer;
    
    /** Run-time type information (and related methods). */
    itkTypeMacro(ScalarImageToGreyLevelCooccurrenceMatrixGenerator, Object);
    
    /** standard New() method support */
    itkNewMacro(Self) ;
    
    typedef TImageType                                      ImageType;
    typedef typename ImageType::Pointer                     ImagePointer;
    typedef typename ImageType::ConstPointer                ImageConstPointer;
    typedef typename ImageType::PixelType                   PixelType;
    typedef typename ImageType::RegionType                  RegionType;
    typedef typename ImageType::SizeType                    RadiusType;
    typedef typename ImageType::OffsetType                  OffsetType;
    typedef VectorContainer<unsigned char, OffsetType>      OffsetVector;
    typedef typename OffsetVector::Pointer                  OffsetVectorPointer;
    typedef typename OffsetVector::ConstPointer             OffsetVectorConstPointer;
    
    typedef typename NumericTraits<PixelType>::RealType     MeasurementType;
    
    typedef Histogram< MeasurementType, 2, THistogramFrequencyContainer >
                                                            HistogramType;
    typedef typename HistogramType::Pointer                 HistogramPointer;
    typedef typename HistogramType::ConstPointer            HistogramConstPointer;
    typedef typename HistogramType::MeasurementVectorType   MeasurementVectorType;
    
    
    itkStaticConstMacro(DefaultBinsPerAxis, unsigned int, 256);
    
    /** Triggers the Computation of the histogram */
    void Compute( void );
    
    /** Connects the input image for which the histogram is going to be computed */
    itkSetConstObjectMacro( Input, ImageType );
    itkGetConstObjectMacro( Input, ImageType );

    /** Set the offset or offsets over which the co-occurrence pairs will be computed.
        Calling either of these methods clears the previous offsets.*/
    itkSetConstObjectMacro( Offsets, OffsetVector );
    itkGetConstObjectMacro( Offsets, OffsetVector );
    void SetOffset( const OffsetType offset )
      {
      OffsetVectorPointer offsetVector = OffsetVector::New();
      offsetVector->push_back(offset);
      this->SetOffsets(offsetVector);
      }
        
    /** Return the histogram.
      \warning This output is only valid after the Compute() method has been invoked 
      \sa Compute */
    itkGetObjectMacro( Output, HistogramType );
    
    /** Set number of histogram bins along each axis */
    itkSetMacro( NumberOfBinsPerAxis, unsigned int );
    itkGetMacro( NumberOfBinsPerAxis, unsigned int );

    /** Set the min and max (inclusive) pixel value that will be placed in the histogram */
    void SetPixelValueMinMax( PixelType min, PixelType max );
    itkGetMacro(Min, PixelType);
    itkGetMacro(Max, PixelType);
    
    /** Set the calculator to normalize the histogram (divide all bins by the 
      total frequency). Normalization is off by default.*/
    itkSetMacro(Normalize, bool);
    itkGetMacro(Normalize, bool);
    itkBooleanMacro(Normalize);
    
  protected:
    ScalarImageToGreyLevelCooccurrenceMatrixGenerator();
    virtual ~ScalarImageToGreyLevelCooccurrenceMatrixGenerator() {};
    void PrintSelf(std::ostream& os, Indent indent) const;
    virtual void FillHistogram( RadiusType radius, RegionType region );
        
   private:
    void NormalizeHistogram( void );
  
    ImageConstPointer        m_Input;
    HistogramPointer         m_Output;
    OffsetVectorConstPointer m_Offsets;
    PixelType                m_Min, m_Max;

    unsigned int            m_NumberOfBinsPerAxis;
    MeasurementVectorType   m_LowerBound, m_UpperBound;
    bool                    m_Normalize;

  };
    
    
  } // end of namespace Statistics 
} // end of namespace itk 

#ifndef ITK_MANUAL_INSTANTIATION
#include "itkScalarImageToGreyLevelCooccurrenceMatrixGenerator.txx"
#endif

#endif