PhysicalModel.h

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

//pmlschema forward declaration
namespace physicalModel {
class PhysicalModel;
class Atoms;
class ExclusiveComponent;
class InformativeComponent;
class MultiComponent;
}

#include "PhysicalModelIO.h"
#include <string>
#include <memory>
#include <algorithm>
#include "PMLAbortException.h"
#include "StructuralComponent.h" // so we can put the optimized getAtom method inline
#include "Atom.h" // so we can put the optimized getAtom method inline
#include "Cell.h" // so we can put the optimized getCell method inline


class MultiComponent;
class Component;
class Cell;
class Structure;


// Hide warning for Exception + declspec(nothrow)
#if defined(_WIN32) && !defined(__MINGW32__) // MSVC only
#pragma warning( disable : 4290 )
#endif // MSVC only

using PtrToSetProgressFunction = void (*)(const float donePercentage);

namespace std {
using GlobalIndexStructurePair = std::pair<unsigned int, Structure*>;
using GlobalIndexStructureMap = std::map <unsigned int, Structure*>;
using GlobalIndexStructureMapIterator = std::map <unsigned int, Structure*> ::iterator;
}


class PhysicalModel {

public:
    PhysicalModel() noexcept;

    PhysicalModel(const char* fileName, PtrToSetProgressFunction pspf = nullptr);

    virtual ~PhysicalModel();
    static const char* VERSION;

    const std::string getName() const;
    void setName(const std::string);
    Properties* getProperties();
    bool isModified();
    void setModified();

    void xmlPrint(std::ostream& o, bool opt = false);

    void exportPatran(std::string filename);

    void exportAnsysMesh(std::string filename);

    unsigned int getNumberOfExclusiveComponents() const;

    unsigned int getNumberOfInformativeComponents() const;

    unsigned int getNumberOfAtoms() const;

    unsigned int getNumberOfCells() const;

    Component* getExclusiveComponent(const unsigned int) const;

    void setExclusiveComponents(MultiComponent*);

    MultiComponent* getExclusiveComponents() const;

    MultiComponent* getInformativeComponents() const;

    StructuralComponent* getAtoms() const;

    Component* getInformativeComponent(const unsigned int) const;

    void setInformativeComponents(MultiComponent*);

    void setAtoms(StructuralComponent*, bool deleteOld = true);

    bool addAtom(Atom*);

    Atom* getAtom(const unsigned int id);

    bool addGlobalIndexAtomPair(std::GlobalIndexStructurePair);

    bool addGlobalIndexCellPair(std::GlobalIndexStructurePair);

    Cell* getCell(const unsigned int id);

    Structure* getStructureByName(const std::string n);

    Component* getComponentByName(const std::string n);

    virtual void setProgress(const float donePercentage);

    virtual void setAtomPosition(Atom* atom, const double pos[3]);

    double* getPositionPointer() const;

    double* getPositionPointer(const unsigned int index) const;

    double* getPositionPointer(const Atom* a) const;


private:
    void xmlRead(const char* n);

    bool parseTree(std::unique_ptr<physicalModel::PhysicalModel> root, std::string defaultName);
    bool parseAtoms(physicalModel::Atoms atomsRoot);
    bool parseComponents(physicalModel::MultiComponent mcFather, Component* father, bool isExclusive);

    Properties* properties;

    bool isModifiedFlag;

    MultiComponent* exclusiveComponents;

    MultiComponent* informativeComponents;

    StructuralComponent* atoms;

    void clear();

    std::GlobalIndexStructureMap cellMap;

    std::vector <Cell*> optimizedCellList;

    bool cellIndexOptimized;

    void optimizeIndexes();

    void optimizeIndexes(MultiComponent*, unsigned int*);

    std::GlobalIndexStructureMap atomMap;

    void init();

    PtrToSetProgressFunction setProgressFunction;

    double* positionPtr;
};


// ------------------ simple inline functions ------------------
inline Properties* PhysicalModel::getProperties() {
    return properties;
}

inline const std::string PhysicalModel::getName() const {
    return properties->getName();
}

inline void PhysicalModel::setName(const std::string n) {
    properties->setName(n);
}

inline bool PhysicalModel::isModified() {
    return isModifiedFlag;
}

inline void PhysicalModel::setModified() {
    isModifiedFlag = true;
}

inline MultiComponent* PhysicalModel::getExclusiveComponents() const {
    return exclusiveComponents;
}
inline MultiComponent* PhysicalModel::getInformativeComponents() const {
    return informativeComponents;
}
inline StructuralComponent* PhysicalModel::getAtoms() const {
    return atoms;
}

// ------------------ getAtom ------------------
inline Atom* PhysicalModel::getAtom(const unsigned int id) {

    // optimization: first check if the order is the structure is not the same
    // as the atom index (which is the case very often)
    Atom* quickAccessed = dynamic_cast<Atom*>(atoms->getStructure(id));

    if (quickAccessed && quickAccessed->getIndex() == id) {
        return quickAccessed;
    }
    else {
        // if not then check if it could be found in the map
        std::GlobalIndexStructureMapIterator mapIt; // a representation map iterator
        mapIt = atomMap.find(id);

        // search in the map, and return the correct result
        return ((mapIt == atomMap.end()) ? nullptr : (Atom*) mapIt->second);
    }
}

// ------------------ getCell ------------------
inline Cell* PhysicalModel::getCell(const unsigned int cellIndex) {
    if (cellIndexOptimized) {
        return optimizedCellList[cellIndex];
    }
    else {
        std::GlobalIndexStructureMapIterator mapIt; // a representation map iterator

        // check if it was find in the list
        mapIt = cellMap.find(cellIndex);

        // search in the map, and return the correct result
        return ((mapIt == cellMap.end()) ? nullptr : (Cell*) mapIt->second);
    }
}

// ------------------ getStructureByName ------------------
inline Structure* PhysicalModel::getStructureByName(const std::string n) {
    // look for structures into the global maps

    // look for a cell with this name
    auto mapIt = cellMap.begin();

    while (mapIt != cellMap.end() && mapIt->second->getName() != n) {
        mapIt++;
    }

    // if found returns it
    if (mapIt != cellMap.end()) {
        return mapIt->second;
    }

    // look now in the atoms
    mapIt = atomMap.begin();

    while (mapIt != atomMap.end() && mapIt->second->getName() != n) {
        mapIt++;
    }

    // if found returns it
    if (mapIt != atomMap.end()) {
        return mapIt->second;
    }

    return nullptr;
}

#endif