NetworkToSurface.cpp

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#include "NetworkToSurface.hpp"
#include "NetworkToImage.hpp"
#include <vtkMarchingSquares.h>
#include <vtkMarchingCubes.h>
#include <vtkCleanPolyData.h>
#include <vtkStripper.h>
#include <vtkSplineFilter.h>
#include <vtkTriangleFilter.h>
#include <vtkTransform.h>
#include <vtkClipPolyData.h>
#include <vtkPolyData.h>
#include <vtkIdList.h>
#include <vtkLine.h>
#include <vtkCellArray.h>
#include <vtkBox.h>
#include <vtkVersion.h>
#include <vtkProbeFilter.h>
#include <vtkPolyDataNormals.h>
#include <vtkWindowedSincPolyDataFilter.h>
//#include <vtkvmtkSimpleCapPolyData.h>
//#include <vtkvmtkPolyDataSizingFunction.h>
//#include <vtkvmtkPolyDataToUnstructuredGridFilter.h>
#include "UblasCustomFunctions.hpp"
#include "UblasIncludes.hpp"
#include "UnitCollection.hpp"

template<unsigned DIM>
NetworkToSurface<DIM>::NetworkToSurface() :
    mpNetwork(),
    mSamplingGridSpacing(2.0 * 1.e-6 * unit::metres),
    mSplineResamplingLength(10.0 * 1.e-6 * unit::metres),
    mpSurface(),
    mpImage(),
    mReferenceLength(BaseUnits::Instance()->GetReferenceLengthScale())
{

}

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

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

}

template<unsigned DIM>
vtkSmartPointer<vtkPolyData> NetworkToSurface<DIM>::GetSurface()
{
    return mpSurface;
}

template<unsigned DIM>
vtkSmartPointer<vtkImageData> NetworkToSurface<DIM>::GetSamplingImage()
{
    return mpImage;
}

template<unsigned DIM>
void NetworkToSurface<DIM>::SetVesselNetwork(boost::shared_ptr<VesselNetwork<DIM> > pNetwork)
{
    mpNetwork = pNetwork;
}

template<unsigned DIM>
void NetworkToSurface<DIM>::SetResamplingSplineSize(units::quantity<unit::length> splineResampleSize)
{
    mSplineResamplingLength = splineResampleSize;
}

template<unsigned DIM>
void NetworkToSurface<DIM>::SetResamplingGridSize(units::quantity<unit::length> sampleGridSize)
{
    mSamplingGridSpacing = sampleGridSize;
}

template<unsigned DIM>
void NetworkToSurface<DIM>::Update()
{
    if(DIM==2)
    {
        // Interpolate the network onto a regular grid
        boost::shared_ptr<NetworkToImage<DIM> > p_net_to_image = NetworkToImage<DIM>::Create();
        p_net_to_image->SetNetwork(mpNetwork);
        p_net_to_image->SetGridSpacing(mSamplingGridSpacing);
        p_net_to_image->SetPaddingFactors(0.1, 0.1, 0.0);
        p_net_to_image->SetImageDimension(2);
        p_net_to_image->Update();
        mpImage = p_net_to_image->GetOutput();

        // Get the outer boundaries of the network
        vtkSmartPointer<vtkMarchingSquares> p_squares = vtkSmartPointer<vtkMarchingSquares>::New();
        #if VTK_MAJOR_VERSION <= 5
            p_squares->SetInput(mpImage);
        #else
            p_squares->SetInputData(mpImage);
        #endif
        p_squares->SetValue(0, 1);

        // Remove duplicate points and join up lines to form polylines
        vtkSmartPointer<vtkCleanPolyData> p_cleaner = vtkSmartPointer<vtkCleanPolyData>::New();
        p_cleaner->SetInputConnection(p_squares->GetOutputPort());

        vtkSmartPointer<vtkStripper> p_stripper = vtkSmartPointer<vtkStripper>::New();
        p_stripper->SetInputConnection(p_cleaner->GetOutputPort());

        // Downsample and smooth the polyline
        vtkSmartPointer<vtkSplineFilter> p_spline= vtkSmartPointer<vtkSplineFilter>::New();
        p_spline->SetLength(mSplineResamplingLength/mReferenceLength);
        p_spline->SetSubdivideToLength();
        p_spline->SetInputConnection(p_stripper->GetOutputPort());

        vtkSmartPointer<vtkTriangleFilter> p_triangle = vtkSmartPointer<vtkTriangleFilter>::New();
        p_triangle->SetInputConnection(p_spline->GetOutputPort());
        p_triangle->Update();

        vtkSmartPointer<vtkPolyData> p_cleaned = p_triangle->GetOutput();

        // Want flat ends on input and output network nodes. It is important to do this after smoothing
        std::vector<boost::shared_ptr<VesselNode<DIM> > > nodes = mpNetwork->GetNodes();
        c_vector<double, 3> box_axis = unit_vector<double>(3,0);

        for(unsigned idx=0; idx< nodes.size(); idx++)
        {
            if(nodes[idx]->GetFlowProperties()->IsInputNode() or nodes[idx]->GetFlowProperties()->IsOutputNode())
            {
                double radius = nodes[idx]->GetRadius()/mReferenceLength;
                vtkSmartPointer<vtkBox> p_box = vtkSmartPointer<vtkBox>::New();
                p_box->SetBounds(-1.1*radius, 0.0, -1.1*radius, 1.1*radius, - 1.1*radius, 1.1*radius);

                c_vector<double, 3> loc;
                loc[0]= nodes[idx]->rGetLocation().GetLocation(mReferenceLength)[0];
                loc[1]= nodes[idx]->rGetLocation().GetLocation(mReferenceLength)[1];
                loc[2]=0.0;

                c_vector<double, 3> tangent;
                tangent[0]= nodes[idx]->GetSegment(0)->GetOppositeNode(nodes[idx])->rGetLocation().GetLocation(mReferenceLength)[0] - loc[0];
                tangent[1]= nodes[idx]->GetSegment(0)->GetOppositeNode(nodes[idx])->rGetLocation().GetLocation(mReferenceLength)[1] - loc[1];
                tangent[2] = 0.0;
                tangent /=norm_2(tangent);

                double rotation_angle = std::acos(inner_prod(box_axis, tangent))*(180.0/M_PI);
                c_vector<double, 3> rotation_axis = VectorProduct(box_axis, tangent);

                vtkSmartPointer<vtkTransform> p_tranform = vtkSmartPointer<vtkTransform>::New();
                if (std::abs(inner_prod(box_axis, tangent)) < 1.0 - 1.e-6)
                {
                    p_tranform->RotateWXYZ(-rotation_angle, rotation_axis[0], rotation_axis[1], rotation_axis[2]);
                }
                else
                {
                    p_tranform->RotateWXYZ(-rotation_angle, 0.0, 0.0, 1.0);
                }
                p_tranform->Translate(-loc[0],-loc[1], -loc[2]);
                p_box->SetTransform(p_tranform);

                vtkSmartPointer<vtkClipPolyData> p_clipper = vtkSmartPointer<vtkClipPolyData>::New();
                #if VTK_MAJOR_VERSION <= 5
                    p_clipper->SetInput(p_cleaned);
                #else
                    p_clipper->SetInputData(p_cleaned);
                #endif
                p_clipper->SetClipFunction(p_box);
                p_clipper->Update();

                // Assuming we have two points with connectivity 1, join them
                std::vector<unsigned> edge_ids;
                vtkSmartPointer<vtkIdList> p_cell_list = vtkSmartPointer<vtkIdList>::New();
                for (unsigned idx =0; idx< p_clipper->GetOutput()->GetNumberOfPoints(); idx++)
                {
                    p_clipper->GetOutput()->GetPointCells(idx, p_cell_list);
                    if(p_cell_list->GetNumberOfIds()==1)
                    {
                        edge_ids.push_back(idx);
                    }
                }

                vtkSmartPointer<vtkLine> p_line = vtkSmartPointer<vtkLine>::New();
                p_line->GetPointIds()->SetId(0, edge_ids[0]);
                p_line->GetPointIds()->SetId(1, edge_ids[1]);
                p_clipper->GetOutput()->GetLines()->InsertNextCell(p_line);

                p_cleaned->DeepCopy(p_clipper->GetOutput());
            }
        }
        mpSurface = p_cleaned;
    }
    else
    {
        // Interpolate the network onto a regular grid
        boost::shared_ptr<NetworkToImage<DIM> > p_net_to_image = NetworkToImage<DIM>::Create();
        p_net_to_image->SetNetwork(mpNetwork);
        p_net_to_image->SetGridSpacing(mSamplingGridSpacing);
        p_net_to_image->SetPaddingFactors(0.1, 0.1, 0.1);
        p_net_to_image->SetImageDimension(3);
        p_net_to_image->Update();
        mpImage = p_net_to_image->GetOutput();

        // Get the outer boundaries of the network
        vtkSmartPointer<vtkMarchingCubes> p_cubes = vtkSmartPointer<vtkMarchingCubes>::New();
        #if VTK_MAJOR_VERSION <= 5
            p_cubes->SetInput(mpImage);
        #else
            p_cubes->SetInputData(mpImage);
        #endif
        p_cubes->SetValue(0, 1);

        vtkSmartPointer<vtkCleanPolyData> p_cleaner = vtkSmartPointer<vtkCleanPolyData>::New();
        p_cleaner->SetInputConnection(p_cubes->GetOutputPort());

        vtkSmartPointer<vtkWindowedSincPolyDataFilter> p_smoother = vtkSmartPointer<vtkWindowedSincPolyDataFilter>::New();
        p_smoother->SetInputConnection(p_cleaner->GetOutputPort());
        p_smoother->SetNumberOfIterations(500.0);
        p_smoother->BoundarySmoothingOn();
        p_smoother->FeatureEdgeSmoothingOn();
        p_smoother->SetFeatureAngle(30.0);
        p_smoother->SetPassBand(0.03);
        p_smoother->NonManifoldSmoothingOn();
        p_smoother->NormalizeCoordinatesOn();
        p_smoother->Update();

        vtkSmartPointer<vtkPolyData> p_cleaned = p_smoother->GetOutput();

        // Open any ends marked as inlet or outlet nodes
        std::vector<boost::shared_ptr<VesselNode<DIM> > > nodes = mpNetwork->GetNodes();
        c_vector<double, 3> box_axis = unit_vector<double>(3,0);
        for(unsigned idx=0; idx< nodes.size(); idx++)
        {
            if(nodes[idx]->GetFlowProperties()->IsInputNode() or nodes[idx]->GetFlowProperties()->IsOutputNode())
            {
                double radius = nodes[idx]->GetRadius()/nodes[idx]->GetReferenceLengthScale();
                vtkSmartPointer<vtkBox> p_box = vtkSmartPointer<vtkBox>::New();

                p_box->SetBounds(-1.1*radius, 0.0, -1.1*radius, 1.1*radius, - 1.1*radius, 1.1*radius);

                c_vector<double, 3> loc = nodes[idx]->rGetLocation().GetLocation(mReferenceLength);
                c_vector<double, 3> tangent;
                tangent = nodes[idx]->GetSegment(0)->GetOppositeNode(nodes[idx])->rGetLocation().GetLocation(mReferenceLength) - loc;
                tangent /=norm_2(tangent);

                double rotation_angle = std::acos(inner_prod(box_axis, tangent))*(180.0/M_PI);
                c_vector<double, 3> rotation_axis = VectorProduct(box_axis, tangent);

                vtkSmartPointer<vtkTransform> p_tranform = vtkSmartPointer<vtkTransform>::New();
                if (std::abs(inner_prod(box_axis, tangent)) < 1.0 - 1.e-6)
                {
                    p_tranform->RotateWXYZ(-rotation_angle, rotation_axis[0], rotation_axis[1], rotation_axis[2]);
                }
                else
                {
                    p_tranform->RotateWXYZ(-rotation_angle, 0.0, 0.0, 1.0);
                }
                p_tranform->Translate(-loc[0],-loc[1], -loc[2]);
                p_box->SetTransform(p_tranform);

                vtkSmartPointer<vtkClipPolyData> p_clipper = vtkSmartPointer<vtkClipPolyData>::New();
                #if VTK_MAJOR_VERSION <= 5
                    p_clipper->SetInput(p_cleaned);
                #else
                    p_clipper->SetInputData(p_cleaned);
                #endif
                p_clipper->SetClipFunction(p_box);
                p_clipper->Update();
                p_cleaned->DeepCopy(p_clipper->GetOutput());
            }
        }

        // Use vmtk to cap the surface
//        vtkSmartPointer<vtkvmtkSimpleCapPolyData> p_capper = vtkSmartPointer<vtkvmtkSimpleCapPolyData>::New();
//        p_capper->SetInputData(p_cleaned);
//        p_capper->SetCellEntityIdsArrayName("CellEntityIds");
//        p_capper->SetCellEntityIdOffset(1);
//        p_capper->Update();

        vtkSmartPointer<vtkPolyDataNormals> p_normals = vtkSmartPointer<vtkPolyDataNormals>::New();
//        p_normals->SetInputConnection(p_capper->GetOutputPort());
        #if VTK_MAJOR_VERSION <= 5
            p_normals->SetInput(p_cleaned);
        #else
            p_normals->SetInputData(p_cleaned);
        #endif

        p_normals->AutoOrientNormalsOn();
        p_normals->SplittingOff();
        p_normals->ConsistencyOn();
        p_normals->Update();

        mpSurface = p_normals->GetOutput();
    }
}

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