ENH: Adding co-occurrence indexed list to seperate class

Code/FeatureExtraction/otbGreyLevelCooccurrenceIndexedList.h

+/*=========================================================================
+
+Program:   ORFEO Toolbox
+Language:  C++
+Date:      $Date$
+Version:   $Revision$
+
+
+Copyright (c) Centre National d'Etudes Spatiales. All rights reserved.
+See OTBCopyright.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 __otbGreyLevelCooccurrenceIndexedList_h
+#define __otbGreyLevelCooccurrenceIndexedList_h
+
+#include "itkLightObject.h"
+#include "itkArray.h"
+#include "itkHistogram.h"
+#include <vector>
+
+namespace otb
+{
+
+/** \class GreyLevelCooccurrenceIndexedList
+* \brief This class holds unique non-zero co-occurrence pairs called
+* CooccurrenceIndexedList (GLCIL) instead of GLCM.
+* GreyLevelCooccurrenceIndexedList instance is created for every neighborhood
+* iteration over the given input image. This class keep an internal itk::Array
+* as a lookup array with the same size of the histogram created in the Filter
+* which uses it. The lookup array stores the position of each pixel pair in an
+* std::vector. A pixel pair is a combination of (Center, Offset)
+* Pixels. A -1 value in the lookup array indicates zero existance of pixel
+* pair. Index stored in the CooccurrencePairType is the index of the pixel pair
+* calculated from the histogram. Histogram instance is created outside this
+* class.
+*
+* Print references:
+* David A. Clausi and Yongping Zhao. 2002. Rapid extraction of image texture by
+* co-occurrence using a hybrid data structure. Comput. Geosci. 28, 6 (July
+* 2002), 763-774. DOI=10.1016/S0098-3004(01)00108-X
+* http://dx.doi.org/10.1016/S0098-3004(01)00108-X
+*
+* de O.Bastos, L.; Liatsis, P.; Conci, A., Automatic texture segmentation based
+* on k-means clustering and efficient calculation of co-occurrence
+* features. Systems, Signals and Image Processing, 2008. IWSSIP 2008. 15th
+* International Conference on , vol., no., pp.141,144, 25-28 June 2008
+* doi: 10.1109/IWSSIP.2008.4604387
+*/
+
+template <class THistogram >
+class ITK_EXPORT GreyLevelCooccurrenceIndexedList : public itk::LightObject
+{
+public:
+
+  /** Standard typedefs */
+  typedef GreyLevelCooccurrenceIndexedList Self;
+  typedef itk::LightObject                 Superclass;
+  typedef itk::SmartPointer<Self>          Pointer;
+  typedef itk::SmartPointer<const Self>    ConstPointer;
+
+  /** Creation through the object factory */
+  itkNewMacro(Self);
+
+  /** RTTI */
+  itkTypeMacro(GreyLevelCooccurrenceIndexedList, itk::LightObject);
+
+  typedef THistogram                                          HistogramType;
+  typedef typename HistogramType::RelativeFrequencyType       RelativeFrequencyType;
+  typedef typename HistogramType::TotalAbsoluteFrequencyType  TotalAbsoluteFrequencyType;
+  typedef typename HistogramType::IndexType                   IndexType;
+  typedef typename HistogramType::SizeType                    SizeType;
+  typedef typename IndexType::ValueType                       IndexValueType;
+  typedef typename HistogramType::InstanceIdentifier          InstanceIdentifier;
+
+  /** struct to hold non-zero frequency and its index in the histogram */
+  struct CooccurrencePairType
+  {
+    IndexType index;
+    RelativeFrequencyType frequency;
+  };
+
+  /** Lookup array used to store the index of the given pixel pair. Size of
+    * LookupAray is equal to the nbins * nbins. Values in the array represents 1D
+    * index of the elements in the Histogram */
+  typedef itk::Array<int> LookupArrayType;
+
+  /** std::vector to hold CooccurrencePairType. Index of the array where the
+    * cooccurrence is stored is saved in the LookupArrayType.*/
+  typedef std::vector<CooccurrencePairType> VectorType;
+
+  /** Get the total frequency of Co-occurrence pairs. */
+  itkGetMacro(TotalFrequency, TotalAbsoluteFrequencyType);
+
+  GreyLevelCooccurrenceIndexedList();
+
+  ~GreyLevelCooccurrenceIndexedList() { }
+
+  /** Fill m_LookupArray with -1 and set m_TotalFreqency to zero */
+  void Initialize(SizeType size, bool symmetry = true);
+
+  /** Get std::vector containing non-zero co-occurrence pairs */
+  VectorType GetVector();
+
+  /** Add the CooccurrencePairType to list. Next occurrence of same index is
+    * checked via m_LookupArray value and the correspoding frequency value is
+    * incremented. If m_Symmetry is true the co-occurrence pair is added again */
+  void AddPairToList(IndexType index);
+
+  /** Update frequency of the pair with given index */
+  void AddIndex(IndexType index);
+
+  /* Get the frequency value from Vector with index =[j,i] */
+  RelativeFrequencyType GetFrequency(IndexValueType i, IndexValueType j);
+
+  /* Get the frequency value from Vector with index =[j,i] from given
+   * vector. This is used if we have a copy of m_Vector normalized. */
+  RelativeFrequencyType GetFrequency(IndexValueType i, IndexValueType j, const VectorType& vect) const;
+
+private:
+
+  /* Store the total frequency of co-occurrence pairs in GreyLevelCooccureneIndexedList class */
+  TotalAbsoluteFrequencyType m_TotalFrequency;
+
+  /** LookupArray instance */
+  LookupArrayType m_LookupArray;
+
+  /* std::vector holding actual co-occurrence pairs */
+  VectorType m_Vector;
+
+  /* Size instance */
+  SizeType m_Size;
+
+  bool m_Symmetry;
+};
+
+} // End namespace otb
+
+#ifndef OTB_MANUAL_INSTANTIATION
+#include "otbGreyLevelCooccurrenceIndexedList.txx"
+#endif
+
+#endif

Code/FeatureExtraction/otbGreyLevelCooccurrenceIndexedList.txx

+/*=========================================================================
+
+Program:   ORFEO Toolbox
+Language:  C++
+Date:      $Date$
+Version:   $Revision$
+
+
+Copyright (c) Centre National d'Etudes Spatiales. All rights reserved.
+See OTBCopyright.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 __otbGreyLevelCooccurrenceIndexedList_txx
+#define __otbGreyLevelCooccurrenceIndexedList_txx
+
+#include "otbGreyLevelCooccurrenceIndexedList.h"
+
+namespace otb
+{
+template <class THistogram >
+GreyLevelCooccurrenceIndexedList<THistogram>
+::GreyLevelCooccurrenceIndexedList()
+: m_Size(2)
+, m_Symmetry(true)
+{
+}
+
+template <class THistogram >
+void
+GreyLevelCooccurrenceIndexedList<THistogram>
+::Initialize(SizeType size, bool symmetry)
+{
+  m_Size = size;
+  m_Symmetry = symmetry;
+  m_LookupArray = LookupArrayType(size[0] * size[1]);
+  m_LookupArray.Fill(-1);
+  m_TotalFrequency = 0;
+}
+
+template <class THistogram >
+typename GreyLevelCooccurrenceIndexedList<THistogram>::RelativeFrequencyType
+GreyLevelCooccurrenceIndexedList<THistogram>::
+GetFrequency(IndexValueType i, IndexValueType j)
+{
+  double frequency = 0;
+  InstanceIdentifier instanceId = i * m_Size[0] + j;
+  if (instanceId < m_LookupArray.size())
+    {
+    int findex = m_LookupArray[instanceId];
+    if(findex > -1 )
+      frequency = m_Vector[findex].frequency / m_TotalFrequency;
+    }
+  return frequency;
+}
+
+template <class THistogram >
+typename GreyLevelCooccurrenceIndexedList<THistogram>::RelativeFrequencyType
+GreyLevelCooccurrenceIndexedList<THistogram>::
+GetFrequency(IndexValueType i, IndexValueType j, const VectorType& vect) const
+{
+  double frequency = 0;
+  InstanceIdentifier instanceId = i * m_Size[0] + j;
+  if (instanceId < m_LookupArray.size())
+    {
+    int findex = m_LookupArray[instanceId];
+    if(findex > -1 )
+      frequency = vect[findex].frequency;
+    }
+  return frequency;
+}
+
+template <class THistogram >
+typename GreyLevelCooccurrenceIndexedList<THistogram>::VectorType
+GreyLevelCooccurrenceIndexedList<THistogram>
+::GetVector()
+{
+  return m_Vector;
+}
+
+template <class THistogram >
+void
+GreyLevelCooccurrenceIndexedList<THistogram>
+::AddPairToList(IndexType index)
+{
+  AddIndex(index);
+  if( m_Symmetry )
+    {
+    typename IndexType::ValueType temp;
+    temp = index[0];
+    index[0] = index[1];
+    index[1] = temp;
+    AddIndex(index);
+    }
+}
+
+template <class THistogram >
+void
+GreyLevelCooccurrenceIndexedList<THistogram>
+::AddIndex(IndexType index)
+{
+  InstanceIdentifier instanceId = 0;
+  instanceId = index[1] * m_Size[0] + index[0];
+  int vindex = m_LookupArray[instanceId];
+  if( vindex < 0)
+    {
+    m_LookupArray[instanceId] = m_Vector.size();
+    CooccurrencePairType cooccur;
+    cooccur.index = index;
+    cooccur.frequency = 1;
+    m_Vector.push_back(cooccur);
+    }
+  else
+    {
+    m_Vector[vindex].frequency++;
+    }
+  m_TotalFrequency = m_TotalFrequency + 1;
+}
+
+} //end namespace otb
+
+#endif