mitkPhotoacousticMotionCorrectionFilter.h

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

The Medical Imaging Interaction Toolkit (MITK)

Copyright (c) German Cancer Research Center (DKFZ)
All rights reserved.

Use of this source code is governed by a 3-clause BSD license that can be
found in the LICENSE file.

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

#ifndef _MITKPHOTOACOUSTICSMOTIONCORRECTIONFILTER_H_
#define _MITKPHOTOACOUSTICSMOTIONCORRECTIONFILTER_H_

#include "mitkImageToImageFilter.h"
#include <itkObject.h>

#include "opencv2/imgproc.hpp"
// TODO: Find out why build fails with this option or replace with something
// else
/* #include "opencv2/opencv.hpp" */
#include "opencv2/video/tracking.hpp"

#include "itkOpenCVImageBridge.h"

#include <MitkPhotoacousticsAlgorithmsExports.h>

#include "mitkImageCast.h"
#include <mitkImageToOpenCVImageFilter.h>
#include <mitkOpenCVToMitkImageFilter.h>
#include <mitkImageStatisticsHolder.h>

#define IMAGE_DIMENSION 3 
#define MAX_MATRIX 255.0 
namespace mitk
{
  class MITKPHOTOACOUSTICSALGORITHMS_EXPORT PhotoacousticMotionCorrectionFilter : public ImageToImageFilter
  {
  public:
    mitkClassMacro(PhotoacousticMotionCorrectionFilter, ImageToImageFilter);

    itkFactorylessNewMacro(Self);

    // Setters and Getters for the class variables
    itkSetMacro(BatchSize, unsigned int);
    itkSetMacro(PyrScale, double);
    itkSetMacro(Levels, unsigned int);
    itkSetMacro(WinSize, unsigned int);
    itkSetMacro(Iterations, unsigned int);
    itkSetMacro(PolyN, unsigned int);
    itkSetMacro(PolySigma, double);
    itkSetMacro(Flags, unsigned int);
    itkGetConstMacro(BatchSize, unsigned int);
    itkGetConstMacro(PyrScale, double);
    itkGetConstMacro(Levels, unsigned int);
    itkGetConstMacro(WinSize, unsigned int);
    itkGetConstMacro(Iterations, unsigned int);
    itkGetConstMacro(PolyN, unsigned int);
    itkGetConstMacro(PolySigma, double);
    itkGetConstMacro(Flags, unsigned int);

    // Wrapper for SetInput, GetInput and GetOutput
    void SetPaInput(mitk::Image::Pointer);
    mitk::Image::Pointer GetPaInput();
    void SetUsInput(mitk::Image::Pointer);
    mitk::Image::Pointer GetUsInput();
    mitk::Image::Pointer GetPaOutput();
    mitk::Image::Pointer GetUsOutput();

  protected:
    PhotoacousticMotionCorrectionFilter();

    ~PhotoacousticMotionCorrectionFilter() override;

    void GenerateData() override;
    void CheckInput(mitk::Image::Pointer paImage, mitk::Image::Pointer usImage);
    void InitializeOutputIfNecessary(mitk::Image::Pointer paInput,
                                     mitk::Image::Pointer usInput,
                                     mitk::Image::Pointer paOutput,
                                     mitk::Image::Pointer usOutput);
    void InitializeOutput(mitk::Image::Pointer input, mitk::Image::Pointer output);
    void PerformCorrection(mitk::Image::Pointer paInput,
                           mitk::Image::Pointer usInput,
                           mitk::Image::Pointer paOutput,
                           mitk::Image::Pointer usOutput);
    cv::Mat GetMatrix(const mitk::Image::Pointer input, unsigned int i);

    cv::Mat FitMatrixToChar(cv::Mat mat);

    void InsertMatrixAsSlice(cv::Mat mat, mitk::Image::Pointer output, unsigned int i);

    cv::Mat ComputeFlowMap(cv::Mat);

  private:
    // Parameters
    double m_PyrScale;         
    double m_PolySigma;        
    unsigned int m_Levels;     
    unsigned int m_WinSize;    
    unsigned int m_Iterations; 
    unsigned int m_PolyN;      
    unsigned int m_Flags;      
    unsigned int m_BatchSize;  
    float m_MaxValue; 
    float m_MinValue; 
    // Stuff that OpenCV needs
    cv::Mat m_UsRef; 
    cv::Mat m_Flow;  
    cv::Mat m_PaRes; 
    cv::Mat m_UsRes; 
    cv::Mat m_PaMat; 
    cv::Mat m_UsMat; 
    cv::Mat m_Map; 
    mitk::OpenCVToMitkImageFilter::Pointer m_OpenCVToImageFilter =
      mitk::OpenCVToMitkImageFilter::New(); 
    mitk::ImageToOpenCVImageFilter::Pointer m_ImageToOpenCVFilter =
      mitk::ImageToOpenCVImageFilter::New(); 
  };
}
#endif