libgofigure-dev 0.9.0-3+b1 / usr / include / gofigure2 / itkvtkPolyDataToGoFigureMeshAttributes.txx

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

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#ifndef __itkvtkPolyDataToGoFigureMeshAttributes_txx
#define __itkvtkPolyDataToGoFigureMeshAttributes_txx

#include "itkvtkPolyDataToGoFigureMeshAttributes.h"

#include "vtkTriangle.h"

namespace itk
{
template< class TImage >
vtkPolyDataToGoFigureMeshAttributes< TImage >::vtkPolyDataToGoFigureMeshAttributes() : m_Mesh(NULL), m_Image(NULL)
{
  m_IntensityComputation = true;
  m_Binarizer = PolyDataToBinaryMaskImageFilterType::New();
  m_AttributeCalculator = BinaryMaskImageToGoFigureMeshAttributesType::New();
  m_ROIFilter = ROIFilterType::New();
}

template< class TImage >
vtkPolyDataToGoFigureMeshAttributes< TImage >::
~vtkPolyDataToGoFigureMeshAttributes()
{
}

template< class TImage >
void
vtkPolyDataToGoFigureMeshAttributes< TImage >::SetIntensityBasedComputation(const bool & iComputation)
{
  this->m_IntensityComputation = iComputation;
}

template< class TImage >
void
vtkPolyDataToGoFigureMeshAttributes< TImage >::SetPolyData(vtkPolyData *iMesh)
{
  m_Mesh = iMesh;

  if ( m_Mesh && m_Image.IsNotNull() )
    {
    m_Binarizer->SetInput(m_Image);
    m_Binarizer->SetPolyData(m_Mesh);
    try
      {
      m_Binarizer->Update();
      }
    catch(itk::ExceptionObject & e)
      {
      std::cerr << "Exception: " << e << std::endl;
      }
    }
}

template< class TImage >
void
vtkPolyDataToGoFigureMeshAttributes< TImage >::SetImage(ImageType *iImage)
{
  m_Image = iImage;
  m_ROIFilter->SetInput(m_Image);

  if ( m_Mesh && m_Image.IsNotNull() )
    {
    m_Binarizer->SetInput(m_Image);
    m_Binarizer->SetPolyData(m_Mesh);
    try
      {
      m_Binarizer->Update();
      }
    catch(itk::ExceptionObject & e)
      {
      std::cerr << "Exception: " << e << std::endl;
      }
    }
}

template< class TImage >
void
vtkPolyDataToGoFigureMeshAttributes< TImage >::Update()
{
  GenerateData();
}

template< class TImage >
unsigned int
vtkPolyDataToGoFigureMeshAttributes< TImage >::GetSize()
{
  return m_Size;
}

template< class TImage >
double
vtkPolyDataToGoFigureMeshAttributes< TImage >::GetPhysicalSize()
{
  return m_PhysicalSize;
}

template< class TImage >
double vtkPolyDataToGoFigureMeshAttributes< TImage >::GetMeanIntensity()
{
  return m_Mean;
}

template< class TImage >
double vtkPolyDataToGoFigureMeshAttributes< TImage >::GetSumIntensity()
{
  return m_Sum;
}

template< class TImage >
double vtkPolyDataToGoFigureMeshAttributes< TImage >::GetArea()
{
  return m_Area;
}

template< class TImage >
void
vtkPolyDataToGoFigureMeshAttributes< TImage >::GenerateData()
{
  m_AttributeCalculator->SetMaskImage( m_Binarizer->GetOutput() );
  m_AttributeCalculator->SetIntensityBasedComputation(m_IntensityComputation);

  if ( m_IntensityComputation )
    {
    double bounds[6];
    m_Mesh->GetBounds(bounds);

    typename ImageType::PointType org;
    org[0] = bounds[0];
    org[1] = bounds[2];
    org[2] = bounds[4];

    typename ImageType::IndexType start_idx;
    m_Image->TransformPhysicalPointToIndex(org, start_idx);

    typename ImageType::SizeType size =
      m_Binarizer->GetOutput()->GetLargestPossibleRegion().GetSize();

    typename ImageType::SizeType image_size = m_Image->GetLargestPossibleRegion().GetSize();

    // make sure we will stay inside the bounding box while iterating
    for(int i = 0; i<3; i++)
      {
      if(size[i] + start_idx[i] > image_size[i])
        {
        size[i] = image_size[i] - start_idx[i];
        }
      }

    typename ImageType::RegionType region;
    region.SetSize(size);
    region.SetIndex(start_idx);

    m_ROIFilter->SetRegionOfInterest(region);

    try
      {
      m_ROIFilter->Update();
      }
    catch(itk::ExceptionObject & e)
      {
      std::cerr << "Exception: " << e << std::endl;
      }

    m_AttributeCalculator->SetImage( m_ROIFilter->GetOutput() );
    }

  try
    {
    m_AttributeCalculator->Update();
    }
  catch(itk::ExceptionObject & e)
    {
    std::cerr << "Exception: " << e << std::endl;
    }

  m_Size = m_AttributeCalculator->GetSize();
  m_PhysicalSize = m_AttributeCalculator->GetPhysicalSize();
  m_Mean = m_AttributeCalculator->GetMeanIntensity();
  m_Sum = m_AttributeCalculator->GetSumIntensity();

  ComputeArea();
}

template< class TImage >
void
vtkPolyDataToGoFigureMeshAttributes< TImage >::ComputeArea()
{
  vtkIdType NbOfCells = m_Mesh->GetNumberOfCells();

  m_Area = 0.;

  for ( vtkIdType i = 0; i < NbOfCells; ++i )
    {
    vtkTriangle *t = dynamic_cast< vtkTriangle * >( m_Mesh->GetCell(i) );
    m_Area += t->ComputeArea();
    }
}

}

#endif