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