QGoMeshLevelSetAlgo.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.

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 nor the names of its contributors may be used to endorse or promote
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#ifndef __QGoMeshLevelSetAlgo_h
#define __QGoMeshLevelSetAlgo_h

#include "QGoLevelSetAlgo.h"
#include "QGoFilterChanAndVese.h"
#include "QGoAlgorithmWidget.h"
#include "QGoAlgoParameter.h"
#include "QGoGUILibConfigure.h"
#include "vtkSmartPointer.h"
#include "vtkPolyData.h"
#include "vtkImageData.h"
#include "vtkTransform.h"
#include "vtkTransformPolyDataFilter.h"

#include "GoImageProcessor.h"


class QGoMeshLevelSetAlgo: public QGoLevelSetAlgo
{
public:
  QGoMeshLevelSetAlgo(std::vector< vtkPoints* >* iSeeds, QWidget *iParent = 0);
  ~QGoMeshLevelSetAlgo();

  std::vector<vtkPolyData*> ApplyAlgo(
    GoImageProcessor* iImages,
    std::string iChannel,
    bool iIsInvertedOn = false);

protected:

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

    const unsigned int ImageDimension = 3;

    typedef TPixel PixelType;

    typedef itk::Image< PixelType, ImageDimension >  ImageType;
    typedef typename ImageType::Pointer               ImagePointer;

    // 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;
      }

    // then let's extract the Region of Interest
    ImagePointer ITK_ROI_Image =
        this->ITKExtractROI< PixelType, ImageDimension >( bounds, iImages );

    // Compute the segmentation in 3D
    // why no call to the filter itself...?
    QGoFilterChanAndVese Filter;
    Filter.Apply3DFilter< PixelType >( ITK_ROI_Image,
          iCenter,
          0, // we dont want to extract ROI from input since we already did
          this->m_Iterations->GetValue(),
          this->m_Curvature->GetValue());

    typename QGoFilterChanAndVese::Output3DPointer
        ItkOutPut = Filter.GetOutput3D();

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

    vtkPolyData* temp_output = this->ExtractPolyData(FilterOutPutToVTK, 0);
    FilterOutPutToVTK->Delete();

    double temp_bounds[6];
    temp_output->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 > translation =
        vtkSmartPointer< vtkTransform >::New();

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

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

    // MIGHT LEAK! CHECK IT  IS DELETED!
    vtkPolyData* mesh = vtkPolyData::New();
    mesh->DeepCopy( mesh_transform->GetOutput() );

    return mesh;
    }
};

#endif