niftkGeneralSegmentorPipeline.h

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

  NifTK: A software platform for medical image computing.

  Copyright (c) University College London (UCL). All rights reserved.

  This software is distributed WITHOUT ANY WARRANTY; without even
  the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  PURPOSE.

  See LICENSE.txt in the top level directory for details.

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

#ifndef niftkGeneralSegmentorPipeline_h
#define niftkGeneralSegmentorPipeline_h

#include "niftkMIDASExports.h"

#include <itkCastImageFilter.h>
#include <itkContinuousIndex.h>
#include <itkExtractImageFilter.h>
#include <itkImage.h>
#include <itkIndex.h>
#include <itkPasteImageFilter.h>

#include <mitkContourModelSet.h>
#include <mitkPointSet.h>
#include <mitkTool.h>

#include <itkMIDASRegionGrowingImageFilter.h>

namespace niftk
{

typedef itk::PolyLineParametricPath<3>     ParametricPathType;
typedef std::vector<ParametricPathType::Pointer> ParametricPathVectorType;
typedef ParametricPathType::VertexListType ParametricPathVertexListType;
typedef ParametricPathType::VertexType     ParametricPathVertexType;


void NIFTKMIDAS_EXPORT ConvertMITKSeedsAndAppendToITKSeeds(const mitk::PointSet* seeds, itk::PointSet<float, 3>* points);


void NIFTKMIDAS_EXPORT ConvertMITKContoursAndAppendToITKContours(mitk::ContourModelSet* mitkContours, ParametricPathVectorType& itkContours, const mitk::Vector3D& spacing);


struct NIFTKMIDAS_EXPORT GeneralSegmentorPipelineParams
{
  bool m_EraseFullSlice;
  int m_SliceAxis;
  int m_SliceIndex;
  double m_LowerThreshold;
  double m_UpperThreshold;
  const mitk::PointSet* m_Seeds;
  mitk::ContourModelSet* m_SegmentationContours;
  mitk::ContourModelSet* m_DrawContours;
  mitk::ContourModelSet* m_PolyContours;
};

class NIFTKMIDAS_EXPORT GeneralSegmentorPipelineInterface
{
public:
  typedef itk::PointSet<float, 3>      PointSetType;
  typedef PointSetType::Pointer        PointSetPointer;
  typedef PointSetType::PointType      PointSetPointType;

  typedef itk::PolyLineParametricPath<3>     ParametricPathType;
  typedef std::vector<ParametricPathType::Pointer> ParametricPathVectorType;
  typedef ParametricPathType::VertexListType ParametricPathVertexListType;
  typedef ParametricPathType::VertexType     ParametricPathVertexType;

  virtual ~GeneralSegmentorPipelineInterface();

protected:
  GeneralSegmentorPipelineInterface();

public:
  virtual void Update(GeneralSegmentorPipelineParams& params) = 0;

};

template<typename TPixel, unsigned int VImageDimension>
class GeneralSegmentorPipeline : public GeneralSegmentorPipelineInterface
{
public:

  typedef itk::Index<VImageDimension>                                      IndexType;
  typedef itk::ContinuousIndex<double, VImageDimension>                    ContinuousIndexType;
  typedef itk::Image<TPixel, VImageDimension>                              GreyScaleImageType;
  typedef itk::Image<mitk::Tool::DefaultSegmentationDataType,
                     VImageDimension>                                      SegmentationImageType;
  typedef typename SegmentationImageType::PixelType                        SegmentationImagePixelType;
  typedef typename GreyScaleImageType::RegionType                          RegionType;
  typedef typename GreyScaleImageType::SizeType                            SizeType;
  typedef typename GreyScaleImageType::PointType                           PointType;
  typedef itk::ExtractImageFilter<GreyScaleImageType, GreyScaleImageType>  ExtractGreySliceFromGreyImageFilterType;
  typedef typename ExtractGreySliceFromGreyImageFilterType::Pointer        ExtractGreySliceFromGreyImageFilterPointer;
  typedef itk::ExtractImageFilter<SegmentationImageType,
                                  SegmentationImageType>                   ExtractBinarySliceFromBinaryImageFilterType;
  typedef typename ExtractBinarySliceFromBinaryImageFilterType::Pointer    ExtractBinarySliceFromBinaryImageFilterPointer;

  typedef itk::CastImageFilter<GreyScaleImageType, SegmentationImageType>  CastGreySliceToSegmentationSliceFilterType;
  typedef typename CastGreySliceToSegmentationSliceFilterType::Pointer     CastGreySliceToSegmentationSliceFilterPointer;
  typedef itk::MIDASRegionGrowingImageFilter<GreyScaleImageType,
                                             SegmentationImageType,
                                             itk::PointSet<float, 3> >     MIDASRegionGrowingFilterType;
  typedef typename MIDASRegionGrowingFilterType::Pointer                   MIDASRegionGrowingFilterPointer;

  GeneralSegmentorPipeline();

  virtual ~GeneralSegmentorPipeline();

  void SetParam(const GreyScaleImageType* referenceImage, SegmentationImageType* segmentationImage, GeneralSegmentorPipelineParams& params);

  void Update(GeneralSegmentorPipelineParams &params);

  void DisconnectPipeline();

private:

  void SetPaintingRegion(const ContinuousIndexType& voxel, RegionType& paintingRegion);

public:

  // Member variables.
  int m_SliceAxis;
  int m_SliceIndex;
  TPixel m_LowerThreshold;
  TPixel m_UpperThreshold;
  PointSetPointer m_AllSeeds;
  ParametricPathVectorType m_SegmentationContours;
  ParametricPathVectorType m_ManualContours;

  // Controls whether we write to output. Default = true. If false, we can directly look at m_RegionGrowingFilter->GetOutput().
  bool m_UseOutput;
  bool m_EraseFullSlice;

  // The main filters.
  ExtractGreySliceFromGreyImageFilterPointer     m_ExtractGreyRegionOfInterestFilter;
  ExtractBinarySliceFromBinaryImageFilterPointer m_ExtractBinaryRegionOfInterestFilter;
  CastGreySliceToSegmentationSliceFilterPointer  m_CastToSegmentationContourFilter;
  CastGreySliceToSegmentationSliceFilterPointer  m_CastToManualContourFilter;
  MIDASRegionGrowingFilterPointer                m_RegionGrowingFilter;
  SegmentationImageType*                         m_OutputImage;
};

}

#include "niftkGeneralSegmentorPipeline.txx"

#endif