ionHit.h

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/*
 * ionhit.h - Ion event data class
 * Copyright (C) 2014  D Haley
 * 
 * This program is free software: you can redistribute it and/or modify
 * it under the terms of the GNU General Public License as published by
 * the Free Software Foundation, either version 3 of the License, or
 * (at your option) any later version.
 * 
 * This program is distributed in the hope that it will be useful,
 * but WITHOUT ANY WARRANTY; without even the implied warranty of
 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 * GNU General Public License for more details.
 * 
 * You should have received a copy of the GNU General Public License
 * along with this program.  If not, see <http://www.gnu.org/licenses/>.
 */

#ifndef ATOMPROBE_IONHIT_H
#define ATOMPROBE_IONHIT_H

#include <vector>

#include "atomprobe/helper/endianTest.h"

#include "point3D.h"
#include "boundcube.h"

namespace AtomProbe {


/* Pos ions are typically obtained via reconstructed apt detector hits
 * and are of form (x,y,z mass/charge)
 */
class IonHit
{
    private:
        float massToCharge; // mass to charge ratio in Atomic Mass Units per (charge on electron)
        Point3D pos; //position (xyz) in nm
    public:
        IonHit();
        IonHit(float *);
        //copy constructor
        IonHit(const IonHit &);
        IonHit(const Point3D &p, float massToCharge);
        IonHit(float x, float y, float z, float mass);

        //Set the data from a 4 byte float array. 
        void setHit(float *arr) { pos.setValueArr(arr); massToCharge=arr[3];};
        //Set only the mass/charge value
        void setMassToCharge(float newMassToCharge);
        //Set the position of the event
        void setPos(const Point3D &pos);

        //Set the xth (0,1,2) coordinate of the data
        void setPos(unsigned int idx, float pos);
        //Set the XYZ coords of the data
        void setPos(float fX, float fY, float fZ)
            { pos.setValue(fX,fY,fZ);};

        //Retrieve  the XYZ coordinate for this data
        Point3D getPos() const;
        //obtain the XYZ coordinates as a constant ref.
        inline const Point3D &getPosRef() const {return pos;};
        //returns true if any of the 4 data pts are NaN
        bool hasNaN();

#ifdef __LITTLE_ENDIAN__        
        void switchEndian();
#endif

        //obtain the mass-to-charge for the event
        float getMassToCharge() const;


        //Helper functions
        //--
        //get the points from a vector of of ionhits
        static void getPoints(const std::vector<IonHit> &ions, std::vector<Point3D> &pts);

        //Get the bounding cube from a vector of ionhits
        static void getBoundCube(const std::vector<IonHit> &p, BoundCube &b);

        //Get the centroid from a vector of ion hits
        static void getCentroid(const std::vector<IonHit> &points, Point3D &centroid);
        
        //---

        //assignment operator
        const IonHit &operator=(const IonHit &obj);
        //equality operator
        bool operator==(const IonHit &obj) const;
        //array get operator (0,1,2,3 valid -> x/y/z/m)
        float operator[](unsigned int ui) const ;   

        //array get operator (0,1,2,3 valid -> x/y/z/m)
        float &operator[](unsigned int ui) ;       
        IonHit operator+(const Point3D &obj);

        friend std::ostream &operator<<(std::ostream &stream, const IonHit &);

        static BoundCube getIonDataLimits(const std::vector<IonHit> &points);


};


//This is an entry in the epos "format".
// There is, to best knowledge, no official specification
// There are unofficial specifications
class EPOS_ENTRY
{
    public:
        float x,y,z,massToCharge;

        float timeOfFlight,voltDC,voltPulse;
        float xDetector,yDetector;
        // !Hit multiplicity is the number of hits, for the *FIRST MULTIPLE ONLY*
        int32_t deltaPulse, hitMultiplicity;

    IonHit getIonHit() const ; 
    void getIonHit(IonHit &h) const ;

        int getDeltaPulse() { return deltaPulse;}
        int getHitMultiplicity() { return hitMultiplicity;}

    //equality operator
    bool operator==(const EPOS_ENTRY &obj) const;
};

const size_t EPOS_RECORD_SIZE = 11*4;

#ifdef DEBUG
bool testIonHit();
#endif

};

#endif