CellPopulationActorGenerator.cpp

/*

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 All rights reserved.

 University of Oxford means the Chancellor, Masters and Scholars of the
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 This file is CellPopulation of Chaste.

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 * Redistributions of source code must retain the above copyright notice,
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 * Redistributions in binary form must reproduce the above copyright notice,
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 software without specific prior written permission.

 THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
 AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
 IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A CellPopulationICULAR PURPOSE
 ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE
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 */

#include <boost/filesystem.hpp>
#include <boost/lexical_cast.hpp>
#define _BACKWARD_BACKWARD_WARNING_H 1 //Cut out the vtk deprecated warning
#include <vtkPoints.h>
#include <vtkPolyData.h>
#include <vtkPolyDataMapper.h>
#include <vtkActor.h>
#include <vtkProperty.h>
#include <vtkUnsignedCharArray.h>
#if VTK_MAJOR_VERSION > 5
    #include <vtkNamedColors.h>
#endif
#include <vtkSphereSource.h>
#include <vtkGlyph3D.h>
#include <vtkGlyph2D.h>
#include <vtkCubeAxesActor2D.h>
#include <vtkImageData.h>
#include <vtkGeometryFilter.h>
#include <vtkTubeFilter.h>
#include <vtkExtractEdges.h>
#include <vtkUnstructuredGrid.h>
#include <vtkCell.h>
#include <vtkPolygon.h>
#include <vtkIdList.h>
#include <vtkFeatureEdges.h>
#include "UblasIncludes.hpp"
#include "UblasVectorInclude.hpp"
#include "Exception.hpp"
#include "BaseUnits.hpp"
#include "VesselNetworkWriter.hpp"

#include "CellPopulationActorGenerator.hpp"


template<unsigned DIM>
CellPopulationActorGenerator<DIM>::CellPopulationActorGenerator()
    : AbstractActorGenerator<DIM>(),
      mpCellPopulation()
{

}

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

}

template<unsigned DIM>
void CellPopulationActorGenerator<DIM>::AddActor(vtkSmartPointer<vtkRenderer> pRenderer)
{
    if(mpCellPopulation)
    {
        // Check the cell population type
        if(boost::dynamic_pointer_cast<MeshBasedCellPopulation<DIM> >(mpCellPopulation))
        {
            AddMeshBasedCellPopulationActor(pRenderer);
        }
        else
        {
            // Fall back to a centre based default
            vtkSmartPointer<vtkPoints> p_points = vtkSmartPointer<vtkPoints>::New();
            vtkSmartPointer<vtkPolyData> p_polydata = vtkSmartPointer<vtkPolyData>::New();

            for (typename AbstractCellPopulation<DIM>::Iterator cell_iter = mpCellPopulation->Begin();
                 cell_iter != mpCellPopulation->End(); ++cell_iter)
            {
                c_vector<double, DIM> centre = mpCellPopulation->GetLocationOfCellCentre(*cell_iter);
                if(DIM==3)
                {
                    p_points->InsertNextPoint(centre[0], centre[1], centre[2]);
                }
                else
                {
                    p_points->InsertNextPoint(centre[0], centre[1], 0.0);
                }
            }
            p_polydata->SetPoints(p_points);

            vtkSmartPointer<vtkSphereSource> p_spheres = vtkSmartPointer<vtkSphereSource>::New();
            p_spheres->SetRadius(0.5);
            p_spheres->SetPhiResolution(16);
            p_spheres->SetThetaResolution(16);

            vtkSmartPointer<vtkGlyph3D> p_glyph = vtkSmartPointer<vtkGlyph3D>::New();
            #if VTK_MAJOR_VERSION <= 5
                p_glyph->SetInput(p_polydata);
                p_glyph->SetSource(p_spheres->GetOutput());
            #else
                p_glyph->SetInputData(p_polydata);
                p_glyph->SetSourceConnection(p_spheres->GetOutputPort());
            #endif
            p_glyph->ClampingOff();
            p_glyph->SetScaleModeToScaleByScalar();
            p_glyph->SetScaleFactor(1.0);
            p_glyph->Update();

            vtkSmartPointer<vtkPolyDataMapper> p_mapper = vtkSmartPointer<vtkPolyDataMapper>::New();
            #if VTK_MAJOR_VERSION <= 5
                p_mapper->SetInput(p_glyph->GetOutput());
            #else
                p_mapper->SetInputData(p_glyph->GetOutput());
            #endif
            p_mapper->ScalarVisibilityOff();

            vtkSmartPointer<vtkActor> p_actor = vtkSmartPointer<vtkActor>::New();
            p_actor->SetMapper(p_mapper);
            p_actor->GetProperty()->SetColor(0,1,0);
            pRenderer->AddActor(p_actor);
        }
    }
}

template<unsigned DIM>
void CellPopulationActorGenerator<DIM>::AddMeshBasedCellPopulationActor(vtkSmartPointer<vtkRenderer> pRenderer)
{
    boost::shared_ptr<MeshBasedCellPopulation<DIM> > p_cell_population = boost::dynamic_pointer_cast<MeshBasedCellPopulation<DIM> >(mpCellPopulation);

    if(!p_cell_population)
    {
        EXCEPTION("Could not cast mesh to MeshBased type.");
    }

    // Add the voronoi mesh
    p_cell_population->CreateVoronoiTessellation();
    vtkSmartPointer<vtkUnstructuredGrid> p_voronoi_grid = vtkSmartPointer<vtkUnstructuredGrid>::New();

    if(p_cell_population->GetVoronoiTessellation() != NULL)
    {
        vtkSmartPointer<vtkPoints> p_points = vtkSmartPointer<vtkPoints>::New();
        p_points->GetData()->SetName("Vertex positions");
        for (unsigned node_num=0; node_num<p_cell_population->GetVoronoiTessellation()->GetNumNodes(); node_num++)
        {
            c_vector<double, DIM> position = p_cell_population->GetVoronoiTessellation()->GetNode(node_num)->rGetLocation();
            if (DIM==2)
            {
                p_points->InsertPoint(node_num, position[0], position[1], 0.0);
            }
            else
            {
                p_points->InsertPoint(node_num, position[0], position[1], position[2]);
            }
        }
        p_voronoi_grid->SetPoints(p_points);

        for (typename VertexMesh<DIM,DIM>::VertexElementIterator iter = p_cell_population->GetVoronoiTessellation()->GetElementIteratorBegin();
             iter != p_cell_population->GetVoronoiTessellation()->GetElementIteratorEnd(); ++iter)
        {
            vtkSmartPointer<vtkCell> p_cell;
            if (DIM == 2)
            {
                p_cell = vtkSmartPointer<vtkPolygon>::New();
            }
            else
            {
                p_cell = vtkSmartPointer<vtkConvexPointSet>::New();
            }
            vtkSmartPointer<vtkIdList> p_cell_id_list = p_cell->GetPointIds();
            p_cell_id_list->SetNumberOfIds(iter->GetNumNodes());
            for (unsigned j=0; j<iter->GetNumNodes(); ++j)
            {
                p_cell_id_list->SetId(j, iter->GetNodeGlobalIndex(j));
            }
            p_voronoi_grid->InsertNextCell(p_cell->GetCellType(), p_cell_id_list);
        }
    }

    vtkSmartPointer<vtkGeometryFilter> p_geom_filter = vtkSmartPointer<vtkGeometryFilter>::New();
    #if VTK_MAJOR_VERSION <= 5
        p_geom_filter->SetInput(p_voronoi_grid);
    #else
        p_geom_filter->SetInputData(p_voronoi_grid);
    #endif

    vtkSmartPointer<vtkPolyDataMapper> p_mapper = vtkSmartPointer<vtkPolyDataMapper>::New();
    p_mapper->SetInputConnection(p_geom_filter->GetOutputPort());
    p_mapper->ScalarVisibilityOff();

    vtkSmartPointer<vtkActor> p_actor = vtkSmartPointer<vtkActor>::New();
    p_actor->SetMapper(p_mapper);
    p_actor->GetProperty()->SetColor(1,1,0);
    p_actor->GetProperty()->SetOpacity(0.8);
    pRenderer->AddActor(p_actor);

    vtkSmartPointer<vtkFeatureEdges> p_voronoi_extract_edges = vtkSmartPointer<vtkFeatureEdges>::New();
    p_voronoi_extract_edges->SetInputConnection(p_geom_filter->GetOutputPort());
    p_voronoi_extract_edges->SetFeatureEdges(false);
    p_voronoi_extract_edges->SetBoundaryEdges(true);
    p_voronoi_extract_edges->SetManifoldEdges(true);
    p_voronoi_extract_edges->SetNonManifoldEdges(false);

    vtkSmartPointer<vtkTubeFilter> p_voronoi_tubes = vtkSmartPointer<vtkTubeFilter>::New();
    p_voronoi_tubes->SetInputConnection(p_voronoi_extract_edges->GetOutputPort());
    p_voronoi_tubes->SetRadius(0.006);
    p_voronoi_tubes->SetNumberOfSides(12);

    vtkSmartPointer<vtkPolyDataMapper> p_voronoi_tube_mapper = vtkSmartPointer<vtkPolyDataMapper>::New();
    p_voronoi_tube_mapper->SetInputConnection(p_voronoi_tubes->GetOutputPort());
    p_voronoi_tube_mapper->ScalarVisibilityOff();

    vtkSmartPointer<vtkActor> p_voronoi_tube_actor = vtkSmartPointer<vtkActor>::New();
    p_voronoi_tube_actor->SetMapper(p_voronoi_tube_mapper);
    p_voronoi_tube_actor->GetProperty()->SetColor(0,0,0);
    pRenderer->AddActor(p_voronoi_tube_actor);

//    // Do the mutable mesh
//    //Make the local mesh into a VtkMesh
//    vtkSmartPointer<vtkUnstructuredGrid> p_mutable_grid = vtkSmartPointer<vtkUnstructuredGrid>::New();
//    vtkSmartPointer<vtkPoints> p_points = vtkSmartPointer<vtkPoints>::New();
//    p_points->GetData()->SetName("Vertex positions");
//
//    for (typename AbstractMesh<DIM,DIM>::NodeIterator node_iter = p_cell_population->rGetMesh().GetNodeIteratorBegin();
//         node_iter != p_cell_population->rGetMesh().GetNodeIteratorEnd();
//         ++node_iter)
//    {
//        c_vector<double, DIM> current_item = node_iter->rGetLocation();
//        if (DIM == 3)
//        {
//            p_points->InsertNextPoint(current_item[0], current_item[1], current_item[2]);
//        }
//        else if (DIM == 2)
//        {
//            p_points->InsertNextPoint(current_item[0], current_item[1], 0.0);
//        }
//        else // (DIM == 1)
//        {
//            p_points->InsertNextPoint(current_item[0], 0.0, 0.0);
//        }
//    }
//
//    p_mutable_grid->SetPoints(p_points);
//
//    for (typename AbstractTetrahedralMesh<DIM,DIM>::ElementIterator elem_iter = p_cell_population->rGetMesh().GetElementIteratorBegin();
//         elem_iter != p_cell_population->rGetMesh().GetElementIteratorEnd();
//         ++elem_iter)
//    {
//
//        vtkSmartPointer<vtkCell> p_cell;
//        ///\todo This ought to look exactly like the other MakeVtkMesh
//        if (DIM == 3)
//        {
//            p_cell = vtkSmartPointer<vtkTetra>::New();
//        }
//        else if (DIM == 2)
//        {
//            p_cell = vtkSmartPointer<vtkTriangle>::New();
//        }
//        else //(DIM == 1)
//        {
//            p_cell = vtkSmartPointer<vtkLine>::New();
//        }
//        vtkSmartPointer<vtkIdList> p_cell_id_list = p_cell->GetPointIds();
//        for (unsigned j = 0; j < DIM+1; ++j)
//        {
//            unsigned global_node_index = elem_iter->GetNodeGlobalIndex(j);
//            p_cell_id_list->SetId(j, global_node_index);
//        }
//        p_mutable_grid->InsertNextCell(p_cell->GetCellType(), p_cell_id_list);
//    }
//
//    vtkSmartPointer<vtkGeometryFilter> p_mutable_geom_filter = vtkSmartPointer<vtkGeometryFilter>::New();
//    #if VTK_MAJOR_VERSION <= 5
//    p_mutable_geom_filter->SetInput(p_mutable_grid);
//    #else
//    p_mutable_geom_filter->SetInputData(p_mutable_grid);
//    #endif
//
//    vtkSmartPointer<vtkFeatureEdges> p_extract_edges = vtkSmartPointer<vtkFeatureEdges>::New();
//    p_extract_edges->SetInputConnection(p_mutable_geom_filter->GetOutputPort());
//    p_extract_edges->SetFeatureEdges(false);
//    p_extract_edges->SetBoundaryEdges(true);
//    p_extract_edges->SetManifoldEdges(true);
//    p_extract_edges->SetNonManifoldEdges(false);
//
//    vtkSmartPointer<vtkTubeFilter> p_mutable_tubes = vtkSmartPointer<vtkTubeFilter>::New();
//    p_mutable_tubes->SetInputConnection(p_extract_edges->GetOutputPort());
//    p_mutable_tubes->SetRadius(0.02);
//    p_mutable_tubes->SetNumberOfSides(12);
//
//    vtkSmartPointer<vtkPolyDataMapper> p_mutable_mapper = vtkSmartPointer<vtkPolyDataMapper>::New();
//    p_mutable_mapper->SetInputConnection(p_mutable_tubes->GetOutputPort());
//
//    vtkSmartPointer<vtkActor> p_mutable_actor = vtkSmartPointer<vtkActor>::New();
//    p_mutable_actor->SetMapper(p_mutable_mapper);
//    p_mutable_actor->GetProperty()->SetColor(1,1,1);
//    mpRenderer->AddActor(p_mutable_actor);

    // Render the centres
    vtkSmartPointer<vtkPoints> p_centres_points = vtkSmartPointer<vtkPoints>::New();
    vtkSmartPointer<vtkPolyData> p_polydata = vtkSmartPointer<vtkPolyData>::New();

    for (typename AbstractCellPopulation<DIM>::Iterator cell_iter = mpCellPopulation->Begin();
         cell_iter != mpCellPopulation->End(); ++cell_iter)
    {
        c_vector<double, DIM> centre = mpCellPopulation->GetLocationOfCellCentre(*cell_iter);
        if(DIM==3)
        {
            p_centres_points->InsertNextPoint(centre[0], centre[1], centre[2]);
        }
        else
        {
            p_centres_points->InsertNextPoint(centre[0], centre[1], 0.0);
        }
    }
    p_polydata->SetPoints(p_centres_points);

    vtkSmartPointer<vtkSphereSource> p_spheres = vtkSmartPointer<vtkSphereSource>::New();
    p_spheres->SetRadius(0.1);
    p_spheres->SetPhiResolution(16);
    p_spheres->SetThetaResolution(16);

    vtkSmartPointer<vtkGlyph3D> p_glyph = vtkSmartPointer<vtkGlyph3D>::New();
    #if VTK_MAJOR_VERSION <= 5
        p_glyph->SetInput(p_polydata);
        p_glyph->SetSource(p_spheres->GetOutput());
    #else
        p_glyph->SetInputData(p_polydata);
        p_glyph->SetSourceConnection(p_spheres->GetOutputPort());
    #endif
    p_glyph->ClampingOff();
    p_glyph->SetScaleModeToScaleByScalar();
    p_glyph->SetScaleFactor(1.0);
    p_glyph->Update();

    vtkSmartPointer<vtkPolyDataMapper> p_centres_mapper = vtkSmartPointer<vtkPolyDataMapper>::New();
    #if VTK_MAJOR_VERSION <= 5
        p_centres_mapper->SetInput(p_glyph->GetOutput());
    #else
        p_centres_mapper->SetInputData(p_glyph->GetOutput());
    #endif
    p_centres_mapper->ScalarVisibilityOff();

    vtkSmartPointer<vtkActor> p_centres_actor = vtkSmartPointer<vtkActor>::New();
    p_centres_actor->SetMapper(p_centres_mapper);
    p_centres_actor->GetProperty()->SetColor(0.6,0.0,0.0);
    pRenderer->AddActor(p_centres_actor);

}

template<unsigned DIM>
void CellPopulationActorGenerator<DIM>::SetCellPopulation(boost::shared_ptr<AbstractCellPopulation<DIM> > pCellPopulation)
{
    this->mpCellPopulation = pCellPopulation;
}

template class CellPopulationActorGenerator<2>;
template class CellPopulationActorGenerator<3>;