QGoSetOfContoursWaterShedAlgo.h

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

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#ifndef __QGoSetOfContoursWaterShedAlgo_h
#define __QGoSetOfContoursWaterShedAlgo_h

// external files
#include "vtkSmartPointer.h"
#include "vtkPolyData.h"
#include "vtkImageData.h"
#include "vtkTransform.h"
#include "vtkTransformPolyDataFilter.h"

// project files
#include "QGoWaterShedAlgo.h"
#include "QGoAlgorithmWidget.h"
#include "QGoAlgoParameter.h"
#include "QGoGUILibConfigure.h"
#include "QGoFilterWatershed.h"

// temp for debug purpose
#include "vtkPolyDataMapper.h"
#include "vtkActor.h"
#include "vtkRenderer.h"
#include "vtkRenderWindow.h"
#include "vtkRenderWindowInteractor.h"
#include "itkImageFileWriter.h"


#include "vtkPointData.h"

class GoImageProcessor;


class QGoSetOfContoursWaterShedAlgo: public QGoWaterShedAlgo
{
public:
  QGoSetOfContoursWaterShedAlgo(std::vector< vtkPoints* >* iSeeds,
                                int iMaxThreshold,
                                QWidget* iParent = 0);
  ~QGoSetOfContoursWaterShedAlgo();

  // should not be virutal pure since we dont implement it....
  std::vector<vtkPolyData*> ApplyAlgo(
    GoImageProcessor* iImages,
    std::string iChannel,
    bool iIsInvertedOn = false);

  std::vector<std::vector<vtkPolyData*> > ApplyAlgoSeveralSeeds(
    GoImageProcessor* iImages, std::string iChannel);

protected:

  QGoAlgoParameter<int>*          m_Sampling;

  template < class TPixel >
            // note this will work only in 3D, so we can remove the template
            // parameter on the image dimension
             //unsigned int VImageDimension >
  std::vector<vtkPolyData *> ApplyWaterShedFilter(
    const std::vector<double>& iCenter,
    typename itk::Image< TPixel, 3 >::Pointer iImages,
    const unsigned int& iOrientation)
    {
    assert( iCenter.size() == 3);

    const unsigned int ImageDimension = 3;

    typedef TPixel                                  PixelType;
    typedef itk::Image< PixelType, ImageDimension > ImageType;
    typedef typename ImageType::Pointer             ImagePointer;
    typedef itk::Image< PixelType, 2 >              ImageType2D;
    typedef typename ImageType2D::Pointer           ImageType2DPointer;
    typedef typename ImageType::SpacingType         ImageSpacingType;

    std::vector<vtkPolyData*> output;

    ImageSpacingType spacing = iImages->GetSpacing();

    for(int i= 0; i<this->m_Sampling->GetValue(); ++i)
      {
      // let's compute the bounds of the region of interest
      double radius = this->m_Radius->GetValue();

      std::vector< double > bounds( 2 * ImageDimension, 0. );
      unsigned int k = 0;
      for( unsigned int dim = 0; dim < ImageDimension; dim++ )
        {
        bounds[k++] = iCenter[dim] - 2. * radius;
        bounds[k++] = iCenter[dim] + 2. * radius;
        }

      int pair = i+ i%2 -1;
      if(pair < 0)
        {
        pair = 0;
        }

      bounds[2*iOrientation]    =
          iCenter[iOrientation] + (pair*(pow(-1., static_cast<int>(i) ) )*spacing[iOrientation]);
      bounds[2*iOrientation +1] =
          iCenter[iOrientation] + (pair*(pow(-1., static_cast<int>(i) ) )*spacing[iOrientation]);

      // then let's extract the Slice of Interest
      ImageType2DPointer ITK_Slice_Image =
     this->ITKExtractSlice<PixelType>( bounds, iImages );

      // Compute the segmentation in 3D
      QGoFilterWatershed Filter;
      Filter.Apply2DFilter< PixelType >(
            ITK_Slice_Image,
            this->m_ThresMin->GetValue(),
            this->m_ThresMax->GetValue(),
            this->m_CorrThres->GetValue(),
            this->m_Alpha->GetValue(),
            this->m_Beta->GetValue());

      typename QGoFilterWatershed::Output2DPointer
          ItkOutPut = Filter.GetOutput2D();

      // Here it would be better if the mesh extraction would be performed directly
      // in ITK instead.
      vtkImageData * FilterOutPutToVTK =
          this->ConvertITK2VTK<
            typename QGoFilterWatershed::OutputPixelType,
            2>( ItkOutPut );

      // Nicolas- should be able to tune the parameter -0.5-
      vtkPolyData* temp_output = this->ExtractPolyData(FilterOutPutToVTK, 0.5);

      // translation transform -----------------------
      //------------------------------------------------------------------------
      double temp_bounds[6];
      FilterOutPutToVTK->GetBounds( temp_bounds );

      double temp_center[3];
      temp_center[0] = ( temp_bounds[0] + temp_bounds[1] ) * 0.5;
      temp_center[1] = ( temp_bounds[2] + temp_bounds[3] ) * 0.5;
      temp_center[2] = ( temp_bounds[4] + temp_bounds[5] ) * 0.5;

      vtkSmartPointer< vtkTransform > translation2 =
          vtkSmartPointer< vtkTransform >::New();

       translation2->Translate(-temp_center[0],
                               -temp_center[1],
                               -temp_center[2]);

       vtkSmartPointer< vtkTransformPolyDataFilter > mesh_transform2 =
           vtkSmartPointer< vtkTransformPolyDataFilter >::New();
       mesh_transform2->SetTransform(translation2);
       mesh_transform2->SetInput( temp_output );
       mesh_transform2->Update();

      // rotation transform -----------------------
      //------------------------------------------------------------------------
      vtkSmartPointer< vtkTransform > translation =
          vtkSmartPointer< vtkTransform >::New();
      // rotate polydata if necessary
      if(iOrientation == 0)
        {
        translation->RotateY(-90); // check if + or - 90
        }
      else if(iOrientation == 1)
        {
        translation->RotateX(-90); // check if + or - 90
        }
      else if(iOrientation == 2)
        {
        // no rotation, we are in the good plan
        }

      vtkSmartPointer< vtkTransformPolyDataFilter > mesh_transform =
          vtkSmartPointer< vtkTransformPolyDataFilter >::New();
      mesh_transform->SetTransform(translation);
      mesh_transform->SetInput( mesh_transform2->GetOutput() );
      mesh_transform->Update();

      // translate back -----------------------
      //------------------------------------------------------------------------
      double temp_center2[3];
      temp_center2[0] = ( bounds[0] + bounds[1] ) * 0.5;
      temp_center2[1] = ( bounds[2] + bounds[3] ) * 0.5;
      temp_center2[2] = ( bounds[4] + bounds[5] ) * 0.5;

      vtkSmartPointer< vtkTransform > translation23 =
          vtkSmartPointer< vtkTransform >::New();

       translation23->Translate(temp_center2[0],
                                temp_center2[1],
                                temp_center2[2]);

       vtkSmartPointer< vtkTransformPolyDataFilter > mesh_transform23 =
           vtkSmartPointer< vtkTransformPolyDataFilter >::New();
       mesh_transform23->SetTransform(translation23);
       mesh_transform23->SetInput( mesh_transform->GetOutput() );
       mesh_transform23->Update();

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

       temp_output->Delete();

      vtkPolyData* testt = vtkPolyData::New();
      testt->DeepCopy(mesh_transform23->GetOutput());

      output.push_back(testt);
      }

    return output;
    }
};

#endif