VesselNetworkReader.cpp

/*

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#define _BACKWARD_BACKWARD_WARNING_H 1 //Cut out the strstream deprecated warning for now (gcc4.3)
#include <vtkDoubleArray.h>
#include <vtkCellData.h>
#include <vtkCellArray.h>
#include <vtkPointData.h>
#include <vtkPolyData.h>
#include <vtkLine.h>
#include <vtkXMLPolyDataReader.h>
#include <vtkSmartPointer.h>
#include <vtkCleanPolyData.h>
#include <vtkSplineFilter.h>
#include <vtkVersion.h>
#include "Exception.hpp"
#include "VesselNetworkReader.hpp"

template<unsigned DIM>
VesselNetworkReader<DIM>::VesselNetworkReader()
    : mFileName(),
      mRadiusLabel("Node Radius"),
      mRadiusConversionFactor(1.0),
      mMergeCoincidentPoints(false),
      mTargetSegmentLength(0.0*unit::metres),
      mReferenceLength(1.e-6 * unit::metres)
{

}

template<unsigned DIM>
VesselNetworkReader<DIM>::~VesselNetworkReader()
{
}

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

template <unsigned DIM>
void VesselNetworkReader<DIM>::SetRadiusArrayName(const std::string& rRadius)
{
    mRadiusLabel = rRadius;
}

template <unsigned DIM>
void VesselNetworkReader<DIM>::SetMergeCoincidentPoints(bool mergePoints)
{
    mMergeCoincidentPoints = mergePoints;
}

template <unsigned DIM>
void VesselNetworkReader<DIM>::SetTargetSegmentLength(units::quantity<unit::length> targetSegmentLength)
{
    mTargetSegmentLength = targetSegmentLength;
}

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

template<unsigned DIM>
boost::shared_ptr<VesselNetwork<DIM> > VesselNetworkReader<DIM>::Read()
{
    if(mFileName.empty())
    {
        EXCEPTION("File name not set in vessel network reader");
    }

    // Create an empty vessel network
    boost::shared_ptr<VesselNetwork<DIM> > p_network = VesselNetwork<DIM>::Create();

    // Create a VTK PolyData object based on the contents of the input VTK file
    vtkSmartPointer<vtkXMLPolyDataReader> p_reader = vtkSmartPointer<vtkXMLPolyDataReader>::New();
    p_reader->SetFileName(mFileName.c_str());
    p_reader->Update();

    vtkSmartPointer<vtkPolyData> p_polydata = p_reader->GetOutput();

    if(mMergeCoincidentPoints)
    {
        vtkSmartPointer<vtkCleanPolyData> p_cleaner = vtkSmartPointer<vtkCleanPolyData>::New();
        #if VTK_MAJOR_VERSION <= 5
            p_cleaner->SetInput(p_polydata);
        #else
            p_cleaner->SetInputData(p_polydata);
        #endif
        p_cleaner->Update();
        p_polydata = p_cleaner->GetOutput();
    }

    if(mTargetSegmentLength != 0.0*unit::metres)
    {
        vtkSmartPointer<vtkSplineFilter> p_spline_filter = vtkSmartPointer<vtkSplineFilter>::New();
        #if VTK_MAJOR_VERSION <= 5
            p_spline_filter->SetInput(p_polydata);
        #else
            p_spline_filter->SetInputData(p_polydata);
        #endif
        p_spline_filter->SetSubdivideToLength();
        p_spline_filter->SetLength(mTargetSegmentLength/mReferenceLength);
        p_spline_filter->Update();
        p_polydata = p_spline_filter->GetOutput();
    }

    // Create the nodes
    vtkSmartPointer<vtkPointData> p_point_data = vtkSmartPointer<vtkPointData>::New();
    std::vector<boost::shared_ptr<VesselNode<DIM> > > nodes;
    for (vtkIdType i = 0; i < p_polydata->GetNumberOfPoints(); i++)
    {
        double point_coords[3];
        p_polydata->GetPoint(i, point_coords);
        if (DIM < 3)
        {
            nodes.push_back(VesselNode<DIM>::Create(point_coords[0], point_coords[1], 0.0, mReferenceLength));
        }
        else
        {
            nodes.push_back(VesselNode<DIM>::Create(point_coords[0], point_coords[1], point_coords[2], mReferenceLength));
        }
    }

    // Extract radii corresponding to each node from the VTK Polydata and store them in a list.
    p_point_data = p_polydata->GetPointData();
    std::vector<double> radii;
    for (vtkIdType i = 0; i < p_point_data->GetNumberOfArrays(); i++)
    {
        std::string array_name = p_point_data->GetArrayName(i);
        if (array_name.compare(mRadiusLabel) == 0)
        {
            for (vtkIdType j = 0; j < p_point_data->GetArray(i)->GetNumberOfTuples(); j++)
            {
                radii.push_back(p_point_data->GetArray(i)->GetTuple1(j));
            }
        }
    }

    // Extract vessels from the VTK Polydata. This is done by iterating over a VTK CellArray object which
    // returns a 'pointList' vtkIdList object. This object contains the point IDs of the nodes which make up
    // the vessel.
    vtkSmartPointer<vtkCellArray> pCellArray = vtkSmartPointer<vtkCellArray>::New();
    pCellArray = p_polydata->GetLines();
    for (int i = 0; i < p_polydata->GetNumberOfLines(); i++)
    {
        // Make a new vessel
        vtkIdType num_segments;
        vtkIdType* pSegmentList;
        pCellArray->GetNextCell(num_segments, pSegmentList);
        std::vector<boost::shared_ptr<VesselSegment<DIM> > > segments;
        // Add segments to the vessels in order
        for (int j = 1; j < num_segments; j++)
        {
            boost::shared_ptr<VesselSegment<DIM> > p_segment = VesselSegment<DIM>::Create(nodes[pSegmentList[j - 1]],nodes[pSegmentList[j]]);
            if(unsigned(radii.size())> pSegmentList[j])
            {
                p_segment->SetRadius(radii[pSegmentList[j]] * mReferenceLength);
            }
            segments.push_back(p_segment);
        }
        // Add the resulting vessel to the network
        p_network->AddVessel(Vessel<DIM>::Create(segments));
    }
    return p_network;
}

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

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