libcamitk3-dev 3.3.2-2 / usr / include / camitk-3.3 / libraries / pml / BasicAtomProperties.h

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 * CamiTK - Computer Assisted Medical Intervention ToolKit
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#ifndef BASICATOMPROPERTIES_H
#define BASICATOMPROPERTIES_H


#include "PhysicalModelIO.h"
#include "StructureProperties.h"
/**
  * @ingroup group_cepmodeling_libraries_pml
  * 
  * @brief
  * This class is the basic Atom Properties class.
  * You should derive from this class a AtomProperties class and use it to implement your own custom stuff.
  * This is a pure virtual class.
  *  
 **/
class BasicAtomProperties : public StructureProperties {
public:
    /** Default constructor : set the position to the origin, and generate an unique index 
     *  @param myPM the physical model the atom belongs to
     */
    BasicAtomProperties(PhysicalModel *myPM);

	/** constructor from xml node: try to read and get the properties from xml
     *  @param myPM the physical model the atom belongs to
     *  @param n the xml node to read to get the information
     */
    BasicAtomProperties(PhysicalModel *myPM, xmlNodePtr n);

    /** set the position to the origin
     *  @param myPM the physical model the atom belongs to
     *  @param ind an unique index
     */
    BasicAtomProperties(PhysicalModel *myPM, const unsigned int ind);

    /** generate an unique index.
     *  @param myPM the physical model the atom belongs to
     *  @param pos the initial position
     */
    BasicAtomProperties(PhysicalModel *myPM, const double pos[3]);

    /** everything is given here
     *  @param myPM the physical model the atom belongs to
     *  @param pos the initial position
     *  @param ind an unique index
     */
    BasicAtomProperties(PhysicalModel *myPM, const unsigned int ind, const double pos[3]);

    /// the destructor...
    virtual ~BasicAtomProperties();

    /// print to an output stream in "pseudo" XML format.
    virtual void xmlPrint(std::ostream &) =0;

    /** Reinitialize the unique index to zero (usually that what you want to do when you
        * start to load a new PhysicalModel
        */
    static void resetUniqueIndex();

    /// get the position of the atom (array of 3 doubles)
    void getPosition(double pos[3]) const;

    /// set the position of the atom
    void setPosition(const double [3]);
    
    /// set the position of the atom
    void setPosition(const double, const double, const double);
        
    /** change the position pointer.
      * This is useful to allocate a big bunch of memory with all the position 
      * in order to improve memory cache usage.
      * \note this memory is not deleted/cleaned in ~BasicAtomProperties (the destructor)
      * 
      * @param ptr the pointer to the memory (should have enough space for storing double[3]
      * @param update update the new memory space using the previously stored position 
      */
    void setPositionPointer(double *ptr, bool update = true);

protected:
    /// write the default xml properties (beginning)
    void beginXML(std::ostream &);
    
    /// write the default xml properties (end)
    void endXML(std::ostream &);

private:
    /// unique number (used to generate unique index for atoms if not given at the instanciation)
    static unsigned int maxUniqueIndex;
    
    /** allocate the memory needed for the position (double[3]).
      * This place in memory is a default, it can be changed using setPositionPointer(..).
      * This method is called in all the constructors, and only there.
      */
    void allocate();
    
    /// Pointer to the memory triplet that stores the atom's position
    double *X;
    
    /// true only if the memory used for the position was allocated in the constructor and not changed afterwards
    bool allocated;
};

// --------------- inlines ---------------
inline void BasicAtomProperties::getPosition(double pos[3]) const {
    pos[0]=X[0]; pos[1]=X[1]; pos[2]=X[2];
}

inline void BasicAtomProperties::setPosition(const double pos[3]) {
    X[0]=pos[0]; X[1]=pos[1]; X[2]=pos[2];
}

inline void BasicAtomProperties::setPosition(const double x,const double y,const double z) {
    X[0]=x; X[1]=y; X[2]=z;
}

#endif //BasicAtomProperties_H