cxBranchList.h

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/*=========================================================================
This file is part of CustusX, an Image Guided Therapy Application.

Copyright (c) 2008-2014, SINTEF Department of Medical Technology
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   may be used to endorse or promote products derived from this software 
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#ifndef BRANCHLIST_H_
#define BRANCHLIST_H_

#include "cxBranch.h"
#include "cxMesh.h"
#include "cxVector3D.h"
#include <vtkPolyData.h>
#include "org_custusx_registration_method_bronchoscopy_Export.h"


namespace cx
{

typedef std::vector< Eigen::Matrix4d > M4Vector;
typedef boost::shared_ptr<class BranchList> BranchListPtr;

class org_custusx_registration_method_bronchoscopy_EXPORT BranchList
{
        std::vector<BranchPtr> mBranches;
public:
    BranchList();
        virtual ~BranchList();
        void addBranch(BranchPtr b);
        void deleteBranch(BranchPtr b);
        void deleteAllBranches();
        std::vector<BranchPtr> getBranches();
    void findBranchesInCenterline(Eigen::MatrixXd positions_r);
        void selectGenerations(int maxGeneration);
        void calculateOrientations();
        void smoothOrientations();
        void interpolateBranchPositions(int interpolationFactor);
        void smoothBranchPositions();
        BranchListPtr removePositionsForLocalRegistration(Eigen::MatrixXd trackingPositions, double maxDistance);

};

std::pair<Eigen::MatrixXd,Eigen::MatrixXd > findConnectedPointsInCT(int startIndex , Eigen::MatrixXd positionsNotUsed);
Eigen::MatrixXd sortMatrix(int rowNumber, Eigen::MatrixXd matrix);
Eigen::MatrixXd eraseCol(int removeIndex, Eigen::MatrixXd positions);
std::pair<Eigen::MatrixXd::Index, double> dsearch(Eigen::Vector3d p, Eigen::MatrixXd positions);
std::pair<std::vector<Eigen::MatrixXd::Index>, Eigen::VectorXd > dsearchn(Eigen::MatrixXd p1, Eigen::MatrixXd p2);

}//namespace cx

#endif /* BRANCHLIST_H_ */