cxAirwaysFromCenterline.h

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

Copyright (c) SINTEF Department of Medical Technology.
All rights reserved.

CustusX is released under a BSD 3-Clause license.

See Lisence.txt (https://github.com/SINTEFMedtek/CustusX/blob/master/License.txt) for details.
=========================================================================*/

#ifndef CXAIRWAYSFROMCENTERLINE_H
#define CXAIRWAYSFROMCENTERLINE_H

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

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_airwaysfromcenterline_EXPORT AirwaysFromCenterline
{
public:
    AirwaysFromCenterline();
    virtual ~AirwaysFromCenterline();
    void setTypeToBloodVessel(bool bloodVessel);
    Eigen::MatrixXd getCenterlinePositions(vtkPolyDataPtr centerline_r);
    void setBranches(BranchListPtr branches);
    void setSegmentedVolume(vtkImageDataPtr segmentedVolume);
    void processCenterline(vtkPolyDataPtr centerline_r);
    BranchListPtr getBranchList();
    vtkPolyDataPtr generateTubes(double staticRadius = 0, bool mergeWithOriginalAirways = false);
    vtkImageDataPtr initializeEmptyAirwaysVolume();
    vtkImageDataPtr initializeAirwaysVolumeFromOriginalSegmentation();
    vtkImageDataPtr addSpheresAlongCenterlines(vtkImageDataPtr airwaysVolumePtr, double staticRadius = 0);
    vtkImageDataPtr addSphereToImage(vtkImageDataPtr airwaysVolumePtr, double position[3], double radius);
    void smoothAllBranchesForVB();
    vtkPolyDataPtr addVTKPoints(std::vector< Eigen::Vector3d > positions);
    vtkPolyDataPtr getVTKPoints();

private:
        Eigen::MatrixXd mCLpoints;
        BranchListPtr mBranchListPtr;
    vtkImageDataPtr mOriginalSegmentedVolume;
    double mOrigin[3];
    Vector3D mSpacing;
    double mBounds[6];
    Eigen::Array3i mDim;
    double mAirwaysVolumeBoundaryExtention;
    double mAirwaysVolumeBoundaryExtentionTracheaStart;
    double mAirwaysVolumeSpacing;
    bool mBloodVessel = false;
    bool mMergeWithOriginalAirways = false;

};

std::pair<int, double> findDistanceToLine(Eigen::Vector3d point, Eigen::MatrixXd line);
double findDistance(Eigen::MatrixXd p1, Eigen::MatrixXd p2);

typedef boost::shared_ptr<AirwaysFromCenterline> AirwaysFromCenterlinePtr;

} /* namespace cx */

#endif // CXAIRWAYSFROMCENTERLINE_H