VesselSurfaceGenerator.cpp

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#define _BACKWARD_BACKWARD_WARNING_H 1 //Cut out the vtk deprecated warning for now (gcc4.3)
#include <vtkPolygon.h>
#include <stdlib.h>
#include "Exception.hpp"
#include "Vessel.hpp"
#include "VesselNode.hpp"
#include "VesselSegment.hpp"
#include "UblasCustomFunctions.hpp"
#include "UblasIncludes.hpp"
#include "DimensionalChastePoint.hpp"
#include "Part.hpp"
#include "BaseUnits.hpp"

#include "VesselSurfaceGenerator.hpp"

template<unsigned DIM>
VesselSurfaceGenerator<DIM>::VesselSurfaceGenerator(boost::shared_ptr<VesselNetwork<DIM> > pVesselNetwork) :
        mpVesselNetwork(pVesselNetwork),
        mpSurface(vtkSmartPointer<vtkPolyData>::New()),
        mReferenceLength(BaseUnits::Instance()->GetReferenceLengthScale())
{
}

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

template<unsigned DIM>
std::vector<DimensionalChastePoint<DIM> > VesselSurfaceGenerator<DIM>::GetHoles()
{
    std::vector<DimensionalChastePoint<DIM> > hole_locations;
    std::vector<boost::shared_ptr<VesselSegment<DIM> > > segments = mpVesselNetwork->GetVesselSegments();
    for (unsigned idx = 0; idx < segments.size(); idx++)
    {
        hole_locations.push_back(segments[idx]->GetMidPoint());
    }
    return hole_locations;
}

template<unsigned DIM>
std::vector<std::vector<boost::shared_ptr<Polygon<DIM> > > > VesselSurfaceGenerator<DIM>::GetSurface()
{
    if(DIM==2)
    {
        EXCEPTION("The surface generator currently only works in 3D");
    }
    // Define the global axes
    c_vector<double, DIM> z_axis = unit_vector<double>(DIM,2);
    c_vector<double, DIM> y_axis = unit_vector<double>(DIM,1);

    // Generate a surface for each segment
    std::vector<std::vector<boost::shared_ptr<Polygon<DIM> > > > segment_polygons;
    std::vector<boost::shared_ptr<VesselSegment<DIM> > > segments = mpVesselNetwork->GetVesselSegments();

    for (unsigned idx = 0; idx < segments.size(); idx++)
    {
        boost::shared_ptr<VesselNode<DIM> > p_start_node = segments[idx]->GetNode(0);
        boost::shared_ptr<VesselNode<DIM> > p_end_node = segments[idx]->GetNode(1);
        c_vector<double, DIM> segment_tangent = segments[idx]->GetUnitTangent();

        // Create the precursor points
        std::vector<c_vector<double, DIM> > start_points = MakeCircle(p_start_node->GetRadius()/mReferenceLength);
        std::vector<c_vector<double, DIM> > end_points = MakeCircle(p_end_node->GetRadius()/mReferenceLength);

        double angle = std::acos(inner_prod(z_axis, segment_tangent));
        if (std::abs(inner_prod(z_axis, segment_tangent)) < 1.0 - 1.e-6)
        {
            c_vector<double, DIM> axis = VectorProduct(z_axis, segment_tangent);
            RotateAboutAxis(start_points, axis, angle);
            RotateAboutAxis(end_points, axis, angle);
        }

        // Get the bisection planes at the nodes
        std::vector<vtkSmartPointer<vtkPlane> > start_planes;
        std::vector<vtkSmartPointer<vtkPlane> > end_planes;
        c_vector<double, DIM> average_start_normal;
        c_vector<double, DIM> average_end_normal;

        if (p_start_node->GetNumberOfSegments() == 1)
        {
            c_vector<double, DIM> node_location = p_start_node->rGetLocation().GetLocation(mReferenceLength);
            vtkSmartPointer<vtkPlane> p_plane = vtkSmartPointer<vtkPlane>::New();
            if(DIM==2)
            {
                p_plane->SetOrigin(node_location[0], node_location[1], node_location[2]);
                p_plane->SetNormal(segment_tangent[0], segment_tangent[1], segment_tangent[2]);
            }
            else
            {
                p_plane->SetOrigin(node_location[0], node_location[1], 0.0);
                p_plane->SetNormal(segment_tangent[0], segment_tangent[1], 0.0);
            }
            start_planes.push_back(p_plane);
        }
        else
        {
            std::vector<boost::shared_ptr<VesselSegment<DIM> > > node_segments = p_start_node->GetSegments();
            for (unsigned jdx = 0; jdx < node_segments.size(); jdx++)
            {
                if (node_segments[jdx] != segments[idx])
                {
                    c_vector<double, DIM> other_segment_tangent = node_segments[jdx]->GetUnitTangent();
                    if (node_segments[jdx]->GetNode(0) == p_start_node)
                    {
                        other_segment_tangent = -other_segment_tangent;
                    }

                    average_start_normal += VectorProduct(segment_tangent, other_segment_tangent);
                    c_vector<double, DIM> node_location = p_start_node->rGetLocation().GetLocation(mReferenceLength);
                    vtkSmartPointer<vtkPlane> p_plane = vtkSmartPointer<vtkPlane>::New();
                    if(DIM==2)
                    {
                        p_plane->SetOrigin(node_location[0], node_location[1], 0.0);
                    }
                    else
                    {
                        p_plane->SetOrigin(node_location[0], node_location[1], node_location[2]);
                    }

                    c_vector<double, DIM> bisection_vector = segment_tangent + other_segment_tangent;
                    bisection_vector /= norm_2(bisection_vector);
                    if(DIM==2)
                    {
                        p_plane->SetNormal(bisection_vector[0], bisection_vector[1], 0.0);
                    }
                    else
                    {
                        p_plane->SetNormal(bisection_vector[0], bisection_vector[1], bisection_vector[2]);
                    }
                    start_planes.push_back(p_plane);
                }
            }
        }

        if (p_end_node->GetNumberOfSegments() == 1)
        {
            c_vector<double, DIM> node_location = p_end_node->rGetLocation().GetLocation(mReferenceLength);
            vtkSmartPointer<vtkPlane> p_plane = vtkSmartPointer<vtkPlane>::New();
            p_plane->SetOrigin(node_location[0], node_location[1], node_location[2]);
            p_plane->SetNormal(segment_tangent[0], segment_tangent[1], segment_tangent[2]);
            end_planes.push_back(p_plane);
        }
        else
        {
            std::vector<boost::shared_ptr<VesselSegment<DIM> > > node_segments = p_end_node->GetSegments();
            for (unsigned jdx = 0; jdx < node_segments.size(); jdx++)
            {
                if (node_segments[jdx] != segments[idx])
                {
                    c_vector<double, DIM> other_segment_tangent = node_segments[jdx]->GetUnitTangent();
                    if (node_segments[jdx]->GetNode(1) == p_end_node)
                    {
                        other_segment_tangent = -other_segment_tangent;
                    }
                    average_end_normal += VectorProduct(segment_tangent, other_segment_tangent);

                    c_vector<double, DIM> node_location = p_end_node->rGetLocation().GetLocation(mReferenceLength);
                    vtkSmartPointer<vtkPlane> p_plane = vtkSmartPointer<vtkPlane>::New();
                    if(DIM==2)
                    {
                        p_plane->SetOrigin(node_location[0], node_location[1], 0.0);
                    }
                    else
                    {
                        p_plane->SetOrigin(node_location[0], node_location[1], node_location[2]);
                    }

                    c_vector<double, DIM> bisection_vector = segment_tangent + other_segment_tangent;
                    bisection_vector /= norm_2(bisection_vector);
                    if(DIM==2)
                    {
                        p_plane->SetNormal(bisection_vector[0], bisection_vector[1], 0.0);
                    }
                    else
                    {
                        p_plane->SetNormal(bisection_vector[0], bisection_vector[1], bisection_vector[2]);
                    }
                    end_planes.push_back(p_plane);
                }
            }
        }

        // Project the precursor points onto the first plane they hit
        Translate(start_points, segments[idx]->GetMidPoint().GetLocation(mReferenceLength));
        Translate(end_points, segments[idx]->GetMidPoint().GetLocation(mReferenceLength));

        std::vector<c_vector<double, DIM> > projected_start_points = start_points;
        std::vector<c_vector<double, DIM> > projected_end_points = end_points;

        for (unsigned jdx = 0; jdx < start_planes.size(); jdx++)
        {
            if (jdx == 0)
            {
                ProjectOnPlane(projected_start_points, -segment_tangent, 2.0 * (segments[idx]->GetLength()/mReferenceLength), start_planes[jdx]);
            }
            else
            {
                std::vector<c_vector<double, DIM> > candidate_points = start_points;
                ProjectOnPlane(candidate_points, -segment_tangent, 2.0 * (segments[idx]->GetLength()/mReferenceLength), start_planes[jdx]);
                for (unsigned mdx = 0; mdx < projected_start_points.size(); mdx++)
                {
                    if (norm_2(candidate_points[mdx] - start_points[mdx])
                            < norm_2(projected_start_points[mdx] - start_points[mdx]))
                    {
                        projected_start_points[mdx] = candidate_points[mdx];
                    }
                }
            }
        }

        for (unsigned jdx = 0; jdx < end_planes.size(); jdx++)
        {
            if (jdx == 0)
            {
                ProjectOnPlane(projected_end_points, -segment_tangent, 2.0 * (segments[idx]->GetLength()/mReferenceLength),end_planes[jdx]);
            }
            else
            {
                std::vector<c_vector<double, DIM> > candidate_points = end_points;
                ProjectOnPlane(candidate_points, -segment_tangent, 2.0 * (segments[idx]->GetLength()/mReferenceLength), end_planes[jdx]);
                for (unsigned mdx = 0; mdx < projected_end_points.size(); mdx++)
                {
                    if (norm_2(candidate_points[mdx] - end_points[mdx])
                            < norm_2(projected_end_points[mdx] - end_points[mdx]))
                    {
                        projected_end_points[mdx] = candidate_points[mdx];
                    }
                }
            }
        }

        // Create the vertices and polygons
        std::vector<boost::shared_ptr<DimensionalChastePoint<DIM> > > start_vertices;
        std::vector<boost::shared_ptr<DimensionalChastePoint<DIM> > > end_vertices;

        for (unsigned jdx = 0; jdx < projected_start_points.size(); jdx++)
        {
            start_vertices.push_back(DimensionalChastePoint<DIM>::Create(projected_start_points[jdx], mReferenceLength));
        }
        for (unsigned jdx = 0; jdx < projected_end_points.size(); jdx++)
        {
            end_vertices.push_back(DimensionalChastePoint<DIM>::Create(projected_end_points[jdx], mReferenceLength));
        }

        //
        std::vector<boost::shared_ptr<Polygon<DIM> > > polygons;
        for (unsigned jdx = 0; jdx < start_vertices.size(); jdx++)
        {
            unsigned index2;
            if (jdx != start_vertices.size() - 1)
            {
                index2 = jdx + 1;
            }
            else
            {
                index2 = 0;
            }
            boost::shared_ptr<Polygon<DIM> > p_polygon = Polygon<DIM>::Create(start_vertices[jdx]);
            p_polygon->AddVertex(start_vertices[index2]);
            p_polygon->AddVertex(end_vertices[index2]);
            p_polygon->AddVertex(end_vertices[jdx]);
            polygons.push_back(p_polygon);
        }
        // If a node has connectivity one add an end-cap
        if (segments[idx]->GetNode(0)->GetNumberOfSegments() == 1)
        {
            polygons.push_back(Polygon<DIM>::Create(start_vertices));
        }

        if (segments[idx]->GetNode(1)->GetNumberOfSegments() == 1)
        {
            polygons.push_back(Polygon<DIM>::Create(end_vertices));
        }
        segment_polygons.push_back(polygons);
    }
    return segment_polygons;
}

template<unsigned DIM>
std::vector<boost::shared_ptr<Polygon<DIM> > > VesselSurfaceGenerator<DIM>::GetSurfacePolygons()
{
    std::vector<std::vector<boost::shared_ptr<Polygon<DIM> > > > segment_polygons = GetSurface();
    std::vector<boost::shared_ptr<Polygon<DIM> > > polygons;
    for (unsigned idx = 0; idx < segment_polygons.size(); idx++)
    {
        for (unsigned jdx = 0; jdx < segment_polygons[idx].size(); jdx++)
        {
            polygons.push_back(segment_polygons[idx][jdx]);
        }
    }
    return polygons;
}

template<unsigned DIM>
vtkSmartPointer<vtkPolyData> VesselSurfaceGenerator<DIM>::GetVtkSurface()
{
    std::vector<std::vector<boost::shared_ptr<Polygon<DIM> > > > segment_polygons = GetSurface();

    // Add the polygons to a part
    Part<DIM> part;
    for (unsigned idx = 0; idx < segment_polygons.size(); idx++)
    {
        for (unsigned jdx = 0; jdx < segment_polygons[idx].size(); jdx++)
        {
            part.AddPolygon(segment_polygons[idx][jdx]->GetVertices(), true);
        }
    }

    mpSurface = part.GetVtk();
    return mpSurface;
}

template<unsigned DIM>
std::vector<c_vector<double, DIM> > VesselSurfaceGenerator<DIM>::MakeCircle(double radius, unsigned numberOfSegments)
{

    double increment = 2.0 * M_PI / double(numberOfSegments);
    double angle = 0.0;
    std::vector<c_vector<double, DIM> > points;

    for (unsigned idx = 0; idx < numberOfSegments; idx++)
    {
        c_vector<double, DIM> point;
        point[0] = radius * std::cos(angle);
        point[1] = radius * std::sin(angle);
        point[2] = 0.0;
        points.push_back(point);
        angle += increment;
    }
    return points;
}

template<unsigned DIM>
void VesselSurfaceGenerator<DIM>::ProjectOnPlane(std::vector<c_vector<double, DIM> >& rPoints,
                                                 c_vector<double, DIM> directionVector, double length,
                                                 vtkSmartPointer<vtkPlane> plane)
{
    for (unsigned idx = 0; idx < rPoints.size(); idx++)
    {
        c_vector<double, DIM> point_on_line = rPoints[idx] + length * directionVector;
        c_vector<double, DIM> projected_point;
        double parametric_distance;
        plane->IntersectWithLine(&rPoints[idx][0], &point_on_line[0], parametric_distance, &projected_point[0]);
        rPoints[idx] = projected_point;
    }
}

template<unsigned DIM>
void VesselSurfaceGenerator<DIM>::RotateAboutAxis(std::vector<c_vector<double, DIM> >& rPoints, c_vector<double, DIM> axis,
                                                  double angle)
{
    double sin_a = std::sin(angle);
    double cos_a = std::cos(angle);
    c_vector<double, DIM> unit_axis = axis / norm_2(axis);

    for (unsigned idx = 0; idx < rPoints.size(); idx++)
    {
        double dot_product = inner_prod(rPoints[idx], unit_axis);
        c_vector<double, DIM> new_point;
        new_point[0] = (unit_axis[0] * dot_product * (1.0 - cos_a) + rPoints[idx][0] * cos_a
                + (-unit_axis[2] * rPoints[idx][1] + unit_axis[1] * rPoints[idx][2]) * sin_a);
        new_point[1] = (unit_axis[1] * dot_product * (1.0 - cos_a) + rPoints[idx][1] * cos_a
                + (unit_axis[2] * rPoints[idx][0] - unit_axis[0] * rPoints[idx][2]) * sin_a);
        new_point[2] = (unit_axis[2] * dot_product * (1.0 - cos_a) + rPoints[idx][2] * cos_a
                + (-unit_axis[1] * rPoints[idx][0] + unit_axis[0] * rPoints[idx][1]) * sin_a);

        rPoints[idx] = new_point;
    }
}

template<unsigned DIM>
void VesselSurfaceGenerator<DIM>::Translate(std::vector<c_vector<double, DIM> >& rPoints,
                                            c_vector<double, DIM> translationVector)
{
    for (unsigned idx = 0; idx < rPoints.size(); idx++)
    {
        rPoints[idx] += translationVector;
    }
}

template class VesselSurfaceGenerator<2> ;
template class VesselSurfaceGenerator<3> ;