GoImageProcessor.h

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/*=========================================================================
 Authors: The GoFigure Dev. Team.
 at Megason Lab, Systems biology, Harvard Medical school, 2009-11

 Copyright (c) 2009-11, President and Fellows of Harvard College.
 All rights reserved.

 Redistribution and use in source and binary forms, with or without
 modification, are permitted provided that the following conditions are met:

 Redistributions of source code must retain the above copyright notice,
 this list of conditions and the following disclaimer.
 Redistributions in binary form must reproduce the above copyright notice,
 this list of conditions and the following disclaimer in the documentation
 and/or other materials provided with the distribution.
 Neither the name of the  President and Fellows of Harvard College
 nor the names of its contributors may be used to endorse or promote
 products derived from this software without specific prior written
 permission.

 THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
 "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO,
 THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
 PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS
 BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY,
 OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT
 OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
 OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
 WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE
 OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
 ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

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

#ifndef GoImageProcessor_H
#define GoImageProcessor_H

// Required for dynamic libs on Windows (QGoIOExport)
#include "QGoIOConfigure.h"

// external library include
// VTK
#include "vtkSmartPointer.h"
// ITK
#include "itkInvertIntensityImageFilter.h"
// BOOST
#include <boost/multi_index_container.hpp>
#include <boost/multi_index/member.hpp>
#include <boost/multi_index/ordered_index.hpp>
#include <boost/multi_index/hashed_index.hpp>

// include project
#include "GoMegaImageStructure.h"

// external include
class vtkLookupTable;
class vtkImageData;
class vtkImageAccumulate;

class QString;

//-----------------------------------------------------------------------------

//-----------------------------------------------------------------------------
struct set_visibility
{
  set_visibility(bool iVisibility):visibility(iVisibility){}

  void operator()(GoMegaImageStructure& iStructure)
  {
    iStructure.setVisibility(visibility);
  }

private:
  bool visibility;
};
//-----------------------------------------------------------------------------

//-----------------------------------------------------------------------------
struct set_color
{
  set_color(std::vector<double> iColor):color(iColor){}

  void operator()(GoMegaImageStructure& iStructure)
  {
    iStructure.setColor(color);
  }

private:
  std::vector<double> color;
};
//-----------------------------------------------------------------------------

//-----------------------------------------------------------------------------
struct set_LUT_Parameters
{
  set_LUT_Parameters(int iGamma, int iMin, int iMax):
      gamma(iGamma), min(iMin), max(iMax){}

  void operator()(GoMegaImageStructure& iStructure)
  {
    iStructure.setLUTParameters(gamma, min, max);
  }

private:
  int gamma;
  int min;
  int max;
};
//-----------------------------------------------------------------------------

//-----------------------------------------------------------------------------
struct set_image
{
  set_image(vtkImageData* iImage):image(iImage){}

  void operator()(GoMegaImageStructure& iStructure)
  {
    iStructure.setImage(image);
  }

private:
  vtkImageData* image;
};
//-----------------------------------------------------------------------------

//-----------------------------------------------------------------------------
struct set_PointsAlpha
{
  set_PointsAlpha(std::map< unsigned int, unsigned int> iPoints):points(iPoints){}

  void operator()(GoMegaImageStructure& iStructure)
  {
    iStructure.set_PointsAlpha(points);
  }

private:
  std::map< unsigned int, unsigned int> points;
};
//-----------------------------------------------------------------------------

//-----------------------------------------------------------------------------
/* tags for accessing the corresponding indices of GoMegaImageStructure */

struct Index{};
struct Visibility{};
struct Name{};

/* Define a multi_index_container of images with following indices:
 *   - a non-unique index sorted by GoMegaImageStructure::Index,
 *   - a non-unique index sorted by GoMegaImageStructure::Visibility,
 *   - a non-unique index sorted by GoMegaImageStructure::Channel,
 */

typedef boost::multi_index_container<
  GoMegaImageStructure,
  boost::multi_index::indexed_by<
    boost::multi_index::ordered_non_unique<
      boost::multi_index::tag<Index>,
      BOOST_MULTI_INDEX_MEMBER(GoMegaImageStructure,unsigned int,Index)>,
    boost::multi_index::ordered_non_unique<
      boost::multi_index::tag<Visibility>,
      BOOST_MULTI_INDEX_MEMBER(GoMegaImageStructure,bool,Visibility)>,
    boost::multi_index::hashed_non_unique<
      boost::multi_index::tag<Name>,
      BOOST_MULTI_INDEX_MEMBER(GoMegaImageStructure,std::string,Name)> >
> GoMegaImageStructureMultiIndexContainer;

//-----------------------------------------------------------------------------

class QGOIO_EXPORT GoImageProcessor
{
public:

  GoImageProcessor();

  GoImageProcessor( const GoImageProcessor& iE );

  virtual ~GoImageProcessor();

  friend std::ostream & operator<<
    (std::ostream & os, const GoImageProcessor & c)
  {
    //os << "TraceID " << c.TraceID << std::endl;
    return os;
  }

  // LUT
  //---------------------------------------------------------------------------

  vtkSmartPointer<vtkLookupTable> createLUT(const double& iRed,
                                            const double& iGreen,
                                            const double& iBlue,
                                            const double& iAlpha);

  vtkSmartPointer<vtkLookupTable> getLookuptable(const std::string& iName) const;

  vtkSmartPointer<vtkLookupTable> getLookuptable() const;

  // opacity transfer functions
  //---------------------------------------------------------------------------
  vtkSmartPointer<vtkPiecewiseFunction>
  getOpacityTransferFunction(const std::string& iName) const;

  std::vector<vtkPiecewiseFunction*> getOpacityTransferFunctions();

  // colors
  //---------------------------------------------------------------------------
  std::vector<double> getColor(const std::string& iName) const;

  void setColor(const std::string& iName, std::vector<double>& iColor);

  void setLUTParameters(const std::string& iName, int iGamma, int iMin, int iMax);

  std::vector<int> getLUTParameters(const std::string& iName);

  std::map<unsigned int, unsigned int> getAlpha(
    const std::string& iName) const;

  void updatePoints(std::string iChannel,
                    std::map< unsigned int, unsigned int> iPointsAlpha);

  vtkSmartPointer< vtkImageAccumulate>
      getHistogram(const std::string& iName) const;

  virtual void initTimePoint(const unsigned int& iTime) = 0;

  virtual void setTimePoint(const unsigned int& iTime) = 0;

  virtual void setDoppler(const unsigned int& iTime,
                          const unsigned int& iPrevious) = 0;

  // images
  //---------------------------------------------------------------------------

  vtkSmartPointer<vtkImageData> getImageBW(const std::string& iName);
  vtkSmartPointer<vtkImageData> getImageBW(const unsigned int& iIndex);

  vtkSmartPointer<vtkImageData> getImageBW();

  std::string getChannelName(const unsigned int& iIndex);

  std::vector<vtkImageData*> getColoredImages();

  template< class PixelType, const unsigned int VImageDimension >
  typename itk::Image< PixelType, VImageDimension >::Pointer
  getImageITK(std::string iIndex, bool iIsInverted = false)
  {
  GoMegaImageStructureMultiIndexContainer::index<Name>::type::iterator it =
      m_MegaImageContainer.get< Name >().find(iIndex);

  assert(it!=m_MegaImageContainer.get< Name >().end());

  if(iIsInverted)
    {
    //get image and invert it
    typedef itk::Image<PixelType, VImageDimension> ImageType;
    typedef itk::InvertIntensityImageFilter <ImageType> InvertFilterType;
    typename InvertFilterType::Pointer invertFilter = InvertFilterType::New();
    invertFilter->SetInput( it->Convert2ITK<PixelType, VImageDimension>() );
    invertFilter->Update();

    typename ImageType::Pointer itkImage = invertFilter->GetOutput();
    itkImage->DisconnectPipeline();

    return itkImage;
    }
  else
    {
    return it->Convert2ITK<PixelType, VImageDimension>();
    }
    return NULL;
  }

  vtkSmartPointer<vtkImageData> getVisibleImages();

  // Image parameters
  //---------------------------------------------------------------------------
  unsigned int* getBoundsTime();
  unsigned int* getBoundsChannel();

  int*          getExtent();

  unsigned int getNumberOfTimePoints();
  unsigned int getNumberOfChannels();

  unsigned int getTimeInterval() const;

  // Doppler parameters
  //---------------------------------------------------------------------------
  unsigned int getDopplerStep();
  void setDopplerStep(unsigned int iStep);
  std::vector<int> getDopplerTime(unsigned int iTime);
  void setDopplerMode(const bool& iEnable, const unsigned int& iChannel);
  bool getDopplerMode();
  unsigned int getDopplerChannel();
  void setDopplerSize(int iSize);
  unsigned int getDopplerSize();

  void visibilityChanged(std::string iName, bool iVisibility);

  unsigned int getNumberOfVisibleChannels();

  int getMaxThreshold();

  int getMaxImage();

protected:
  /*
   * \brief Color an image given the original image and a lookuptable (LUT)
   * \param[in] iImage image to be colored
   * \param[in] iLUT LUT to be applied to the image
   * \return colored image
   */
  vtkSmartPointer<vtkImageData> colorImage(vtkSmartPointer<vtkImageData> iImage,
                                           vtkSmartPointer<vtkLookupTable> iLUT);

  GoMegaImageStructureMultiIndexContainer m_MegaImageContainer;
  vtkSmartPointer<vtkImageData>           m_Output;

  unsigned int m_CurrentTimePoint;

  // Image parameters
  //--------------------
  unsigned int m_BoundsTime[2];
  unsigned int m_BoundsChannel[2];
  int          m_Extent[6];
  unsigned int m_TimeInterval;
  int          m_MaxThreshold;
  int          m_MaxImage;
  //--------------------

  // Doppler view parameters
  //--------------------
  bool             m_DopplerMode;
  unsigned int     m_DopplerStep;
  std::vector<int> m_DopplerTime;
  unsigned int     m_DopplerChannel;
  unsigned int     m_DopplerSize;
  //--------------------

private:
  // overload "=" operator
  GoImageProcessor& operator=(const GoImageProcessor &rhs)
  {
    // Only do assignment if RHS is a different object from this.
    if (this != &rhs)
      {
      this->m_MegaImageContainer = rhs.m_MegaImageContainer;
      this->m_BoundsTime[0] = rhs.m_BoundsTime[0];
      this->m_BoundsTime[1] = rhs.m_BoundsTime[1];
      this->m_BoundsChannel[0] = rhs.m_BoundsChannel[0];
      this->m_BoundsChannel[1] = rhs.m_BoundsChannel[1];
      this->m_Extent[0] = rhs.m_Extent[0];
      this->m_Extent[1] = rhs.m_Extent[1];
      this->m_Extent[2] = rhs.m_Extent[2];
      this->m_Extent[3] = rhs.m_Extent[3];
      this->m_Extent[4] = rhs.m_Extent[4];
      this->m_Extent[5] = rhs.m_Extent[5];
      this->m_TimeInterval = rhs.m_TimeInterval;
      this->m_MaxThreshold = rhs.m_MaxThreshold;
      this->m_DopplerMode = rhs.m_DopplerMode;
      this->m_DopplerStep = rhs.m_DopplerStep;
      this->m_DopplerTime = rhs.m_DopplerTime;
      this->m_DopplerChannel = rhs.m_DopplerChannel;
      }
    return *this;
  }

};

#endif // GoImageProcessor_H