VesselNetworkWriter.cpp

/*

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 */

#ifdef CHASTE_VTK
#define _BACKWARD_BACKWARD_WARNING_H 1
#include <vtkDoubleArray.h>
#include <vtkCellData.h>
#include <vtkCellArray.h>
#include <vtkPointData.h>
#include <vtkLine.h>
#include <vtkXMLPolyDataWriter.h>
#include <vtkVersion.h>
#endif // CHASTE_VTK
#include "SmartPointers.hpp"
#include "Exception.hpp"
#include "PetscTools.hpp"
#include "VesselNetworkWriter.hpp"

template <unsigned DIM>
VesselNetworkWriter<DIM>::VesselNetworkWriter() :
    mpVesselNetwork(),
    mpVtkVesselNetwork(vtkSmartPointer<vtkPolyData>::New()),
    mIsVtkNetworkUpToDate(false),
    mFilename(),
    mReferenceLength(1.e-6 * unit::metres)
{

}

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

}

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

template <unsigned DIM>
void VesselNetworkWriter<DIM>::SetVesselNetwork(boost::shared_ptr<VesselNetwork<DIM> > pNetwork)
{
    mpVesselNetwork = pNetwork;
    mIsVtkNetworkUpToDate = false;
}

template <unsigned DIM>
void VesselNetworkWriter<DIM>::SetReferenceLengthScale(units::quantity<unit::length> rReferenceLength)
{
    mReferenceLength = rReferenceLength;
}

template <unsigned DIM>
vtkSmartPointer<vtkPolyData> VesselNetworkWriter<DIM>::GetOutput()
{
    if(!mpVesselNetwork)
    {
        EXCEPTION("A vessel network is required for the vtk writer.");
    }

    if(mReferenceLength == 0.0 * unit::metres)
    {
        EXCEPTION("A non zero reference length scale is required for the vtk writer.");
    }

    mpVtkVesselNetwork = vtkSmartPointer<vtkPolyData>::New();

    if(mpVesselNetwork->GetNumberOfVessels()>0)
    {
        // Set up the vessel data arrays.
        std::vector<boost::shared_ptr<Vessel<DIM> > > vessels = mpVesselNetwork->GetVessels();
        std::vector<vtkSmartPointer<vtkDoubleArray> > pVesselInfoVector;
        std::map<std::string, double>::iterator vessel_map_iterator;
        std::map<std::string, double> vessel_data_map = vessels[0]->GetOutputData();
        for(vessel_map_iterator = vessel_data_map.begin(); vessel_map_iterator != vessel_data_map.end(); vessel_map_iterator++)
        {
            vtkSmartPointer<vtkDoubleArray> pVesselInfo = vtkSmartPointer<vtkDoubleArray>::New();
            pVesselInfo->SetNumberOfComponents(1);
            pVesselInfo->SetNumberOfTuples(vessels.size());
            pVesselInfo->SetName((*vessel_map_iterator).first.c_str());
            pVesselInfoVector.push_back(pVesselInfo);
        }

        // Set up node data arrays
        std::vector<boost::shared_ptr<VesselNode<DIM> > > nodes = mpVesselNetwork->GetNodes();
        std::vector<vtkSmartPointer<vtkDoubleArray> > pNodeInfoVector;
        std::map<std::string, double>::iterator vtk_node_map_iterator;
        std::map<std::string, double> vtk_node_map = vessels[0]->GetStartNode()->GetOutputData();
        for(vtk_node_map_iterator = vtk_node_map.begin(); vtk_node_map_iterator != vtk_node_map.end(); vtk_node_map_iterator++)
        {
            vtkSmartPointer<vtkDoubleArray> pNodeInfo = vtkSmartPointer<vtkDoubleArray>::New();
            pNodeInfo->SetNumberOfComponents(1);
            pNodeInfo->SetNumberOfTuples(nodes.size());
            pNodeInfo->SetName((*vtk_node_map_iterator).first.c_str());
            pNodeInfoVector.push_back(pNodeInfo);
        }

        // Create the geometric data
        vtkSmartPointer<vtkPoints> pPoints= vtkSmartPointer<vtkPoints>::New();
        vtkSmartPointer<vtkCellArray> pLines = vtkSmartPointer<vtkCellArray>::New();
        unsigned vessel_index=0;
        for(unsigned idx=0; idx<nodes.size(); idx++)
        {
            nodes[idx]->SetId(idx);
            if(DIM == 2)
            {
                pPoints->InsertNextPoint(nodes[idx]->rGetLocation().GetLocation(mReferenceLength)[0],
                                         nodes[idx]->rGetLocation().GetLocation(mReferenceLength)[1], 0.0);
            }
            else
            {
                pPoints->InsertNextPoint(nodes[idx]->rGetLocation().GetLocation(mReferenceLength)[0],
                                         nodes[idx]->rGetLocation().GetLocation(mReferenceLength)[1],
                                         nodes[idx]->rGetLocation().GetLocation(mReferenceLength)[2]);
            }

            std::map<std::string, double> vtk_node_data = nodes[idx]->GetOutputData();
            for(unsigned jdx=0; jdx < pNodeInfoVector.size(); jdx++)
            {
                std::string key = pNodeInfoVector[jdx]->GetName();
                // check if the key exists in the data map, if yes populate the vtk node data array
                if(vtk_node_data.count(key) == 1)
                {
                    pNodeInfoVector[jdx]->SetValue(idx, vtk_node_data[key]);
                }
            }
        }

        // Create the vessels
        typename std::vector<boost::shared_ptr<Vessel<DIM> > >::iterator it;
        for(it = vessels.begin(); it < vessels.end(); it++)
        {
            vtkSmartPointer<vtkLine> pLine = vtkSmartPointer<vtkLine>::New();
            std::vector<boost::shared_ptr<VesselSegment<DIM> > > segments = (*it)->GetSegments();
            for(unsigned i = 0; i < segments.size(); i++)
            {
                pLine->GetPointIds()->InsertId(i, segments[i]->GetNode(0)->GetId());

                // Do an extra insert for the last node in the segment
                if (i == segments.size() - 1)
                {
                    pLine->GetPointIds()->InsertId(i + 1, segments[i]->GetNode(1)->GetId());
                }
            }
            pLines->InsertNextCell(pLine);

            // Add the vessel data
            std::map<std::string, double> vtk_vessel_data = (*it)->GetOutputData();
            for(unsigned idx=0; idx < pVesselInfoVector.size(); idx++)
            {
                std::string key = pVesselInfoVector[idx]->GetName();
                // If the key is in the vtk data use it
                if(vtk_vessel_data.count(key) == 1)
                {
                    pVesselInfoVector[idx]->SetValue(vessel_index, vtk_vessel_data[key]);
                }
            }
            vessel_index++;
        }
        mpVtkVesselNetwork->SetPoints(pPoints);
        mpVtkVesselNetwork->SetLines(pLines);

        for (unsigned i = 0; i < pVesselInfoVector.size(); i++)
        {
            mpVtkVesselNetwork->GetCellData()->AddArray(pVesselInfoVector[i]);
        }

        for (unsigned i = 0; i < pNodeInfoVector.size(); i++)
        {
            mpVtkVesselNetwork->GetPointData()->AddArray(pNodeInfoVector[i]);
        }
    }
    mIsVtkNetworkUpToDate = true;
    return mpVtkVesselNetwork;
}

template <unsigned DIM>
void VesselNetworkWriter<DIM>::SetFileName(const std::string& rFileName)
{
    mFilename = rFileName;
}

template <unsigned DIM>
void VesselNetworkWriter<DIM>::Write()
{
    if(mFilename.empty())
    {
        EXCEPTION("No file name set for VesselNetworkWriter");
    }

    if(PetscTools::AmMaster())
    {
        vtkSmartPointer<vtkXMLPolyDataWriter> writer = vtkSmartPointer<vtkXMLPolyDataWriter>::New();
        writer->SetFileName(mFilename.c_str());

        #if VTK_MAJOR_VERSION <= 5
            writer->SetInput(this->GetOutput());
        #else
            writer->SetInputData(this->GetOutput());
        #endif
        writer->Write();
    }
}

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