cxRouteToTarget.h

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#ifndef CXROUTETOTARGET_H
#define CXROUTETOTARGET_H

#include "org_custusx_filter_routetotarget_Export.h"

#include "cxMesh.h"
#include <QDomElement>


namespace cx
{

typedef std::vector< Eigen::Matrix4d > M4Vector;
typedef boost::shared_ptr<class RouteToTarget> RouteToTargetPtr;
typedef boost::shared_ptr<class BranchList> BranchListPtr;
typedef boost::shared_ptr<class Branch> BranchPtr;


class org_custusx_filter_routetotarget_EXPORT RouteToTarget
{
public:
        RouteToTarget();
        virtual ~RouteToTarget();
        void setBloodVesselVolume(ImagePtr bloodVesselVolume);
        //void setCenterline(vtkPolyDataPtr centerline);
        Eigen::MatrixXd getCenterlinePositions(vtkPolyDataPtr centerline_r);
        void setSmoothing(bool smoothing);
        void processCenterline(MeshPtr mesh);
        void setBranchList(BranchListPtr branchList);
        void processBloodVesselCenterline(Eigen::MatrixXd positions);
        void findClosestPointInBranches(Vector3D targetCoordinate_r);
        void findClosestPointInBloodVesselBranches(Vector3D targetCoordinate_r);
        void findRoutePositions();
        void findRoutePositionsInBloodVessels();
        void searchBranchUp(BranchPtr searchBranchPtr, int startIndex);
        void searchBloodVesselBranchUp(BranchPtr searchBranchPtr, int startIndex);
        vtkPolyDataPtr findRouteToTarget(PointMetricPtr targetPoint);
        vtkPolyDataPtr findExtendedRoute(PointMetricPtr targetPoint);
        vtkPolyDataPtr findRouteToTargetAlongBloodVesselCenterlines(MeshPtr bloodVesselCenterlineMesh, PointMetricPtr targetPoint);
        vtkPolyDataPtr generateAirwaysFromBloodVesselCenterlines();
        bool makeConnectedAirwayAndBloodVesselRoute();
        vtkPolyDataPtr getConnectedAirwayAndBloodVesselRoute();
        vtkPolyDataPtr addVTKPoints(std::vector< Eigen::Vector3d > positions);
        void addRouteInformationToFile(VisServicesPtr services);
        static double calculateRouteLength(std::vector< Eigen::Vector3d > route);
        void setBloodVesselRadius();
        double calculateBloodVesselRadius(Eigen::Vector3d position, Eigen::Vector3d orientation);
        double findDistanceToSegmentationEdge(vtkImageDataPtr bloodVesselImage, Eigen::Vector3i indexVector, Eigen::Vector3d perpendicularVector, int* dim, double* spacing, int direction);
        void makeMarianaCenterlineFile(QString filename);
        QJsonArray makeMarianaCenterlineJSON();
        std::vector< Eigen::Vector3d > getRoutePositions();
        std::vector< double > getCameraRotation();

        double getTracheaLength();
        static std::vector<Eigen::Vector3d> getRoutePositions(MeshPtr route);


private:
        Eigen::MatrixXd mCLpoints;
        bool mSmoothing = true;
        BranchListPtr mBranchListPtr;
        BranchListPtr mBloodVesselBranchListPtr;
        BranchPtr mProjectedBranchPtr;
        BranchPtr mProjectedBloodVesselBranchPtr;
        int mProjectedIndex;
        int mProjectedBloodVesselIndex;
        ImagePtr mBloodVesselVolume;
        Vector3D mTargetPosition;
        std::vector< Eigen::Vector3d > mRoutePositions;
        std::vector< Eigen::Vector3d > mExtendedRoutePositions;
        std::vector< double > mCameraRotation;
    std::vector< double > mExtendedCameraRotation;
        std::vector< Eigen::Vector3d > mBloodVesselRoutePositions;
        std::vector< Eigen::Vector3d > mMergedAirwayAndBloodVesselRoutePositions;
        std::vector< int > mBranchingIndex;
        std::vector<BranchPtr> mSearchBranchPtrVector;
        std::vector<int> mSearchIndexVector;
        Eigen::MatrixXd mConnectedPointsInBVCL;
        bool checkIfRouteToTargetEndsAtEndOfLastBranch();
        bool mPathToBloodVesselsFound = false;
};

Eigen::MatrixXd findClosestBloodVesselSegments(Eigen::MatrixXd bloodVesselPositions , Eigen::MatrixXd airwayPositions, Vector3D targetPosition);
std::pair< Eigen::MatrixXd, Eigen::MatrixXd > findLocalPointsInCT(int closestCLIndex , Eigen::MatrixXd CLpoints);
std::pair<int, double> findDistanceFromPointToLine(Eigen::MatrixXd point, std::vector< Eigen::Vector3d > line);
std::vector< Eigen::Vector3d > getBranchPositions(BranchPtr branchPtr, int startIndex);
double findDistance(Eigen::MatrixXd p1, Eigen::MatrixXd p2);
Eigen::MatrixXd convertToEigenMatrix(std::vector< Eigen::Vector3d > positionsVector);
double variance(Eigen::VectorXd X);

org_custusx_filter_routetotarget_EXPORT QJsonArray makeMarianaCenterlineOfFullBranchTreeJSON(BranchListPtr branchList);

} /* namespace cx */

#endif // CXROUTETOTARGET_H