ImageToMesh.cpp

/*

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#include "Exception.hpp"
#include "ImageToMesh.hpp"
#include <vtkThreshold.h>
#include <vtkGeometryFilter.h>
#include <vtkMarchingCubes.h>
#include <vtkTriangleFilter.h>
#include <vtkPoints.h>
#include <vtkPolyData.h>
#include <vtkProbeFilter.h>
#include "ImageToSurface.hpp"
#include "SurfaceCleaner.hpp"
#include "BoundaryExtractor.hpp"
#include "UblasIncludes.hpp"
#include "GeometryWriter.hpp"
#include "DiscreteContinuumMeshGenerator.hpp"
#include "BaseUnits.hpp"

template<unsigned DIM>
ImageToMesh<DIM>::ImageToMesh()
    : mpImage(vtkSmartPointer<vtkImageData>::New()),
      mElementSize(0.0 * unit::metres * unit::metres* unit::metres),
      mMesh(),
      mpDomain()
{

}

template<unsigned DIM>
boost::shared_ptr<ImageToMesh<DIM> > ImageToMesh<DIM>::Create()
{
    MAKE_PTR(ImageToMesh, pSelf);
    return pSelf;
}

template<unsigned DIM>
ImageToMesh<DIM>::~ImageToMesh()
{

}

template<unsigned DIM>
boost::shared_ptr<DiscreteContinuumMesh<DIM, DIM> > ImageToMesh<DIM>::GetMesh()
{
    if(mMesh)
    {
        return(mMesh);
    }
    else
    {
        EXCEPTION("No mesh set. Did you run 'Update()' ?");
    }
}

template<unsigned DIM>
void ImageToMesh<DIM>::SetTissueDomain(boost::shared_ptr<Part<DIM> > pTissueDomain)
{
    mpDomain = pTissueDomain;
}

template<unsigned DIM>
void ImageToMesh<DIM>::SetElementSize(units::quantity<unit::volume> elementSize)
{
    mElementSize = elementSize;
}

template<unsigned DIM>
void ImageToMesh<DIM>::SetInput(vtkSmartPointer<vtkImageData> pImage)
{
    mpImage = pImage;
}

template<unsigned DIM>
void ImageToMesh<DIM>::SetInputRaw(vtkImageData* pImage)
{
    mpImage.TakeReference(pImage);
//    pImage->Delete();
}

template<unsigned DIM>
void ImageToMesh<DIM>::Update()
{
    if(!mpImage)
    {
        EXCEPTION("No input set.");
    }

    ImageToSurface image_to_surface;
    image_to_surface.SetInput(mpImage);
    image_to_surface.SetThreshold(1.0, false);
    image_to_surface.Update();

    BoundaryExtractor extractor;
    extractor.SetInput(image_to_surface.GetOutput());
    extractor.SetDoSmoothing(true);
    extractor.SetSmoothingLength(10.0);
    extractor.Update();

    if(DIM==2)
    {
        DiscreteContinuumMeshGenerator<DIM, DIM> temp_mesh_generator;
        temp_mesh_generator.SetDomain(extractor.GetOutput());
        if(mpDomain)
        {
            temp_mesh_generator.SetDomain(mpDomain);
        }
        temp_mesh_generator.Update();
        boost::shared_ptr<DiscreteContinuumMesh<DIM, DIM> > p_temp_mesh = temp_mesh_generator.GetMesh();

        std::vector<DimensionalChastePoint<DIM> > mesh_points = p_temp_mesh->GetNodeLocationsAsPoints();
        std::vector<std::vector<unsigned> > mesh_connectivity = p_temp_mesh->GetConnectivity();

        units::quantity<unit::length> reference_length = p_temp_mesh->GetReferenceLengthScale();
        vtkSmartPointer<vtkPoints> p_vtk_points = vtkSmartPointer<vtkPoints>::New();
        for(unsigned idx = 0; idx<mesh_connectivity.size(); idx++)
        {
            c_vector<double, DIM> location0 = mesh_points[mesh_connectivity[idx][0]].GetLocation(reference_length);
            c_vector<double, DIM> location1 = mesh_points[mesh_connectivity[idx][1]].GetLocation(reference_length);
            c_vector<double, DIM> location2 = mesh_points[mesh_connectivity[idx][2]].GetLocation(reference_length);
            double centx = (location0[0] + location1[0] + location2[0])/3.0;
            double centy = (location0[1] + location1[1] + location2[1])/3.0;
            p_vtk_points->InsertNextPoint(centx, centy, 0.0);
        }

        // Get the value of the vessel from the image to determine if the point is inside or outside a vessel
        vtkSmartPointer<vtkPolyData> p_sampling_data = vtkSmartPointer<vtkPolyData>::New();
        p_sampling_data->SetPoints(p_vtk_points);

        vtkSmartPointer<vtkProbeFilter> p_image_probe = vtkSmartPointer<vtkProbeFilter>::New();
        #if VTK_MAJOR_VERSION <= 5
            p_image_probe->SetInput(p_sampling_data);
            p_image_probe->SetSource(mpImage);
        #else
            p_image_probe->SetInputData(p_sampling_data);
            p_image_probe->SetSourceData(mpImage);
        #endif
        p_image_probe->Update();

        std::vector<DimensionalChastePoint<DIM> > holes;
        std::vector<DimensionalChastePoint<DIM> > regions;
        for(unsigned idx=0; idx<p_image_probe->GetOutput()->GetPointData()->GetScalars()->GetNumberOfTuples(); idx++)
        {
            if(p_image_probe->GetOutput()->GetPointData()->GetScalars()->GetTuple1(idx)>5)
            {
                if(mpDomain)
                {
                    c_vector<double, DIM> loc;
                    loc[0] = p_vtk_points->GetPoint(idx)[0];
                    loc[1] = p_vtk_points->GetPoint(idx)[1];
                    if(mpDomain->GetPolygons()[0]->ContainsPoint(DimensionalChastePoint<DIM>(loc, reference_length)))
                    {
                        regions.push_back(DimensionalChastePoint<DIM>(loc, reference_length));
                    }
                    else
                    {
                        holes.push_back(DimensionalChastePoint<DIM>(loc, reference_length));
                    }
                }
                else
                {
                    c_vector<double, DIM> loc;
                    loc[0] = p_vtk_points->GetPoint(idx)[0];
                    loc[1] = p_vtk_points->GetPoint(idx)[1];
                    holes.push_back(DimensionalChastePoint<DIM>(loc, reference_length));
                }
            }
        }
        DiscreteContinuumMeshGenerator<DIM, DIM> fine_mesh_generator;
        fine_mesh_generator.SetDomain(extractor.GetOutput());
        fine_mesh_generator.SetMaxElementArea(mElementSize);
        fine_mesh_generator.SetHoles(holes);
        fine_mesh_generator.SetRegionMarkers(regions);
        if(mpDomain)
        {
            fine_mesh_generator.SetDomain(mpDomain);
        }
        fine_mesh_generator.Update();
        boost::shared_ptr<DiscreteContinuumMesh<DIM, DIM> > p_fine_mesh = fine_mesh_generator.GetMesh();
        mMesh = p_fine_mesh;
    }
    else
    {
        EXCEPTION("3d image meshing not yet implemented");
    }
}

// Explicit instantiation
template class ImageToMesh<2> ;
template class ImageToMesh<3> ;