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 *
 *  Copyright Insight Software Consortium
 *
 *  Licensed under the Apache License, Version 2.0 (the "License");
 *  you may not use this file except in compliance with the License.
 *  You may obtain a copy of the License at
 *
 *         http://www.apache.org/licenses/LICENSE-2.0.txt
 *
 *  Unless required by applicable law or agreed to in writing, software
 *  distributed under the License is distributed on an "AS IS" BASIS,
 *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 *  See the License for the specific language governing permissions and
 *  limitations under the License.
 *
 *=========================================================================*/
#ifndef itkScalarImageToTextureFeaturesFilter_h
#define itkScalarImageToTextureFeaturesFilter_h

#include "itkDataObjectDecorator.h"

#include "itkHistogramToTextureFeaturesFilter.h"
#include "itkScalarImageToCooccurrenceMatrixFilter.h"

namespace itk
{
namespace Statistics
{
/** \class ScalarImageToTextureFeaturesFilter
 *  \brief This class computes texture descriptions from an image.
 *
 * This class computes features that summarize the texture of a given image.
 * The texture features are computed a la Haralick, and have proven to be useful
 * in image classification for biological and medical imaging.
 * This class computes the texture features of an image (optionally in a
 * masked region), averaged across several spatial directions so that they are
 * invariant to rotation.
 *
 * By default, texure features are computed for each spatial
 * direction and then averaged afterward, so it is possible to access the standard
 * deviations of the texture features. These values give a clue as to texture
 * anisotropy. However, doing this is much more work, because it involved computing
 * one GLCM for each offset given. To compute a single GLCM using the first offset ,
 * call FastCalculationsOn(). If this is called, then the texture standard deviations
 * will not be computed (and will be set to zero), but texture computation will
 * be much faster.
 *
 * This class is templated over the input image type.
 *
 * Template Parameters:
 * The image type, and the type of histogram frequency container. If you are using
 * a large number of bins per axis, a sparse frequency container may be advisable.
 * The default is to use a dense frequency container.
 *
 * Inputs and parameters:
 * -# An image
 * -# A mask defining the region over which texture features will be
 *    calculated. (Optional)
 * -# The pixel value that defines the "inside" of the mask. (Optional, defaults
 *    to 1 if a mask is set.)
 * -# The set of features to be calculated. These features are defined
 *    in the GreyLevelCooccurrenceMatrixTextureCoefficientsCalculator class. (Optional,
 *    defaults to {Energy, Entropy, InverseDifferenceMoment, Inertia, ClusterShade,
 *    ClusterProminence}, as in Conners, Trivedi and Harlow.)
 * -# The number of intensity bins. (Optional, defaults to 256.)
 * -# The set of directions (offsets) to average across. (Optional, defaults to
 *    {(-1, 0), (-1, -1), (0, -1), (1, -1)} for 2D images and scales analogously for ND
 *    images.)
 * -# The pixel intensity range over which the features will be calculated.
 *    (Optional, defaults to the full dynamic range of the pixel type.)
 *
 * In general, the default parameter values should be sufficient.
 *
 * Outputs:
 * (1) The average value of each feature.
 * (2) The standard deviation in the values of each feature.
 *
 * Web reference:
 * http://www.fp.ucalgary.ca/mhallbey/tutorial.htm
 *
 * Print references:
 * 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.
 *
 * Haralick, R.M. 1979. Statistical and Structural Approaches to Texture.
 * Proceedings of the IEEE, 67:786-804.
 *
 * R.W. Conners and C.A. Harlow. A Theoretical Comaprison of Texture Algorithms.
 * IEEE Transactions on Pattern Analysis and Machine Intelligence,  2:204-222, 1980.
 *
 * R.W. Conners, M.M. Trivedi, and C.A. Harlow. Segmentation of a High-Resolution
 * Urban Scene using Texture  Operators. Computer Vision, Graphics and Image
 * Processing, 25:273-310,  1984.
 *
 * \sa ScalarImageToCooccurrenceMatrixFilter
 * \sa HistogramToTextureFeaturesFilter
 *
 * Author: Zachary Pincus
 * \ingroup ITKStatistics
 */

template< typename TImageType,
          typename THistogramFrequencyContainer = DenseFrequencyContainer2 >
class ITK_TEMPLATE_EXPORT ScalarImageToTextureFeaturesFilter:public ProcessObject
{
public:
  /** Standard typedefs */
  typedef ScalarImageToTextureFeaturesFilter Self;
  typedef ProcessObject                      Superclass;
  typedef SmartPointer< Self >               Pointer;
  typedef SmartPointer< const Self >         ConstPointer;

  /** Run-time type information (and related methods). */
  itkTypeMacro(ScalarImageToTextureFeaturesFilter, ProcessObject);

  /** standard New() method support */
  itkNewMacro(Self);

  typedef THistogramFrequencyContainer FrequencyContainerType;
  typedef TImageType                   ImageType;
  typedef typename ImageType::Pointer  ImagePointer;

  typedef typename ImageType::PixelType                PixelType;
  typedef typename ImageType::OffsetType               OffsetType;
  typedef VectorContainer< unsigned char, OffsetType > OffsetVector;
  typedef typename OffsetVector::Pointer               OffsetVectorPointer;
  typedef typename OffsetVector::ConstPointer          OffsetVectorConstPointer;

  typedef ScalarImageToCooccurrenceMatrixFilter<
    ImageType, FrequencyContainerType >               CooccurrenceMatrixFilterType;

  typedef typename CooccurrenceMatrixFilterType::HistogramType HistogramType;
  typedef HistogramToTextureFeaturesFilter< HistogramType >    TextureFeaturesFilterType;

  typedef short                                                  TextureFeatureName;
  typedef VectorContainer< unsigned char, TextureFeatureName >   FeatureNameVector;

  typedef typename FeatureNameVector::Pointer      FeatureNameVectorPointer;
  typedef typename FeatureNameVector::ConstPointer FeatureNameVectorConstPointer;
  typedef VectorContainer< unsigned char, double > FeatureValueVector;
  typedef typename FeatureValueVector::Pointer     FeatureValueVectorPointer;

  /** Smart Pointer type to a DataObject. */
  typedef DataObject::Pointer DataObjectPointer;

  /** Type of DataObjects used for scalar outputs */
  typedef DataObjectDecorator< FeatureValueVector >
  FeatureValueVectorDataObjectType;

  const FeatureValueVectorDataObjectType * GetFeatureMeansOutput() const;

  const FeatureValueVectorDataObjectType * GetFeatureStandardDeviationsOutput() const;

  /** Connects the input image for which the features are going to be computed
    */
  using Superclass::SetInput;
  void SetInput(const ImageType *);

  const ImageType * GetInput() const;

  /** Return the feature means and deviations.  */
  itkGetConstReferenceObjectMacro(FeatureMeans, FeatureValueVector);
  itkGetConstReferenceObjectMacro(FeatureStandardDeviations, FeatureValueVector);

  /** Set the desired feature set. Optional, for default value see above. */
  itkSetConstObjectMacro(RequestedFeatures, FeatureNameVector);
  itkGetConstObjectMacro(RequestedFeatures, FeatureNameVector);

  /** Set the  offsets over which the co-occurrence pairs will be computed.
      Optional; for default value see above. */
  itkSetConstObjectMacro(Offsets, OffsetVector);
  itkGetConstObjectMacro(Offsets, OffsetVector);

  /** Set number of histogram bins along each axis.
      Optional; for default value see above. */
  void SetNumberOfBinsPerAxis(unsigned int);

  /** Set the min and max (inclusive) pixel value that will be used for
      feature calculations. Optional; for default value see above. */
  void SetPixelValueMinMax(PixelType min, PixelType max);

  /** Connects the mask image for which the histogram is going to be computed.
      Optional; for default value see above. */
  void SetMaskImage(const ImageType *);

  const ImageType * GetMaskImage() const;

  /** Set the pixel value of the mask that should be considered "inside" the
      object. Optional; for default value see above. */
  void SetInsidePixelValue(PixelType InsidePixelValue);

  itkGetConstMacro(FastCalculations, bool);
  itkSetMacro(FastCalculations, bool);
  itkBooleanMacro(FastCalculations);

protected:
  ScalarImageToTextureFeaturesFilter();
  virtual ~ScalarImageToTextureFeaturesFilter() ITK_OVERRIDE {}
  virtual void PrintSelf(std::ostream & os, Indent indent) const ITK_OVERRIDE;

  void FastCompute();

  void FullCompute();

  /** This method causes the filter to generate its output. */
  virtual void GenerateData() ITK_OVERRIDE;

  /** Make a DataObject to be used for output output. */
  typedef ProcessObject::DataObjectPointerArraySizeType DataObjectPointerArraySizeType;
  using Superclass::MakeOutput;
  virtual DataObjectPointer MakeOutput(DataObjectPointerArraySizeType) ITK_OVERRIDE;

private:
  typename CooccurrenceMatrixFilterType::Pointer m_GLCMGenerator;

  typename TextureFeaturesFilterType::Pointer    m_GLCMCalculator;

  FeatureValueVectorPointer     m_FeatureMeans;
  FeatureValueVectorPointer     m_FeatureStandardDeviations;
  FeatureNameVectorConstPointer m_RequestedFeatures;
  OffsetVectorConstPointer      m_Offsets;
  bool                          m_FastCalculations;
};
} // end of namespace Statistics
} // end of namespace itk

#ifndef ITK_MANUAL_INSTANTIATION
#include "itkScalarImageToTextureFeaturesFilter.hxx"
#endif

#endif