map.h

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/***************************************************************************
 *
 * Authors:     Alberto Pascual Montano (pascual@cnb.csic.es)
 *
 * Unidad de  Bioinformatica of Centro Nacional de Biotecnologia , CSIC
 *
 * 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 2 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, write to the Free Software
 * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA
 * 02111-1307  USA
 *
 *  All comments concerning this program package may be sent to the
 *  e-mail address 'xmipp@cnb.csic.es'
 ***************************************************************************/

//-----------------------------------------------------------------------------
// ClassificationMap.hh
// Implements a Map of the type used by Kohonen algorithms.
//-----------------------------------------------------------------------------

#ifndef XMIPPMAP_H
#define XMIPPMAP_H

// STL includes
#include <algorithm>
#include <vector>
#include <sstream>

// xmipp includes
#include "code_book.h"
#include "fuzzy_code_book.h"
#include "vector_ops.h"

typedef FeatureVector SomIn;
typedef std::pair<long, long> SomPos;

// Forward declarations

class Layout;

class ClassificationMap : public CodeBook
{
public:


    //---------------------------------------------------------------------------

   explicit  ClassificationMap(const ClassificationMap &op1);

    ClassificationMap(const std::string& _layout,  unsigned _width,
             const unsigned& _height, const unsigned& _size);


    ClassificationMap(const std::string& _layout,  unsigned _width,
             const unsigned& _height, const unsigned& _size, const double& _lower,
             const double& _upper);


    ClassificationMap(const std::string& _layout,  unsigned _width,
             const unsigned& _height, const ClassicTrainingVectors& _ts,
             const bool _use_rand_cvs = false);

    ClassificationMap(std::istream& _is, bool _cv = true);

    virtual ~ClassificationMap()
    {};

    virtual void add(const FeatureVector& _v, const Label& _l = Label());

    const std::string& layout() const;

    std::vector<unsigned> neighborhood(const SomPos& _center, double _radius) const;

    double neighDist(const SomPos& _center, const SomPos& _v) const;


    unsigned width() const;

    unsigned height() const;

#ifdef UNUSED // detected as unused 29.6.2018

    SomIn& itemAtPos(const SomPos& _pos);
#endif

    const SomIn& itemAtPos(const SomPos& _pos) const;

#ifdef UNUSED // detected as unused 29.6.2018

    Label& targetAtPos(const SomPos& _pos);
#endif

    const Label& targetAtPos(const SomPos& _pos) const;


    void clear();

    SomPos indexToPos(const unsigned& _i) const;


    unsigned PosToIndex(const SomPos& _pos) const;

    SomPos codVecPos(SomIn& _v);

#ifdef UNUSED // detected as unused 29.6.2018

    SomPos applyPos(const SomIn& _in);
#endif

    /*
     * Standard output for a som
     * Parameter: _os   The output stream
     * Parameter: _som  The som to be printed
     */
    friend std::ostream& operator << (std::ostream& _os, const ClassificationMap& _som)
    {
        _som.printSelf(_os);
        return _os;
    };

    /*
     * Standard input for a som
     * Parameter: _is The input stream
     * Parameter: _som The code book to be read
     * @exception  runtime_error  If there are problems with the stream
     */
    friend std::istream& operator >> (std::istream& _is, ClassificationMap& _som)
    {
        _som.readSelf(_is);
        return _is;
    };

    ClassificationMap& operator= (const ClassificationMap &op1);

    virtual void printSelf(std::ostream& _os) const;


    virtual void readSelf(std::istream& _is);

    virtual void saveObject(std::ostream& _os) const;


    virtual void loadObject(std::istream& _is);


    virtual const Layout& getLayout()  const
    {
        return (Layout&) *somLayout;
    };


protected:

    const Layout* somLayout;   // type of layout
    unsigned somWidth;         // SOM's width
    unsigned somHeight;        // SOM's height

};


class FuzzyMap : public FuzzyCodeBook
{
public:


    //---------------------------------------------------------------------------

    FuzzyMap(const std::string& _layout,  unsigned _width,
                  const unsigned& _height, const unsigned& _size, const double& _lower,
                  const double& _upper);


    FuzzyMap(const std::string& _layout,  unsigned _width,
                  const unsigned& _height, const ClassicTrainingVectors& _ts,
                  const bool _use_rand_cvs = false);

    FuzzyMap(std::istream& _is, const unsigned _size = 0, bool _cv = true);

    explicit FuzzyMap(const FuzzyMap& other);

    virtual ~FuzzyMap()
    {};

    virtual void add(const FeatureVector& _v, const Label& _l = Label());

    const std::string& layout() const;

    std::vector<unsigned> neighborhood(const SomPos& _center, double _radius) const;

    void neighborhood(const SomPos& _center, double _radius, std::vector<unsigned>& _neig) const;


    void localAve(const SomPos& _center, std::vector<double>& _aveVector) const;


    double neighDist(const SomPos& _center, const SomPos& _v) const;


    unsigned width() const;

    unsigned height() const;

    SomIn& itemAtPos(const SomPos& _pos);

    const SomIn& itemAtPos(const SomPos& _pos) const;


    Label& targetAtPos(const SomPos& _pos);

    const Label& targetAtPos(const SomPos& _pos) const;


    void clear();

    SomPos indexToPos(const unsigned& _i) const;

    unsigned PosToIndex(const SomPos& _pos) const;

    SomPos codVecPos(SomIn& _v);

    SomPos applyPos(const unsigned& _in);

    /*
     * Standard output for a fuzzy som
     * Parameter: _os   The output stream
     * Parameter: _som  The som to be printed
     */
    friend std::ostream& operator << (std::ostream& _os, const FuzzyMap& _fsom)
    {
        _fsom.printSelf(_os);
        return _os;
    };

    /*
     * Standard input for a som
     * Parameter: _is The input stream
     * Parameter: _som The code book to be read
     * @exception  runtime_error  If there are problems with the stream
     */
    friend std::istream& operator >> (std::istream& _is, FuzzyMap& _fsom)
    {
        _fsom.readSelf(_is);
        return _is;
    };


    FuzzyMap& operator= (const FuzzyMap &op1);



    virtual void printSelf(std::ostream& _os) const;


    virtual void readSelf(std::istream& _is, const unsigned _size = 0);

    virtual void saveObject(std::ostream& _os) const;


    virtual void loadObject(std::istream& _is);


    virtual const Layout& getLayout()  const
    {
        return (Layout&) *somLayout;
    };


protected:

    const Layout* somLayout;   // type of layout
    unsigned somWidth;         // SOM's width
    unsigned somHeight;        // SOM's height

};



//-----------------------------------------------------------------------------
// Different layout managers
//-----------------------------------------------------------------------------



//---------------------------------------------------------------------------
// Class to manage different Layouts
//---------------------------------------------------------------------------

class Layout
{
public:

    Layout(const std::string& _id = "") : theId(_id)
    {};

    virtual ~Layout()
    {};


    std::vector<unsigned> neighborhood(const ClassificationMap* _som, const SomPos& _center,
                                  double _radius) const;


    std::vector<unsigned> neighborhood(const FuzzyMap* _som, const SomPos& _center,
                                  double _radius) const;



    virtual void localAve(const FuzzyMap* _som, const SomPos& _center, std::vector<double>& _aveVector) const = 0;


    virtual double numNeig(const FuzzyMap* _som, const SomPos& _center) const = 0;


    virtual bool isIn(const SomPos& _center, const SomPos& _v,
                      double _radius) const;


    virtual double dist(const SomPos& _center, const SomPos& _v) const = 0;


    const std::string& id() const;

private:

    std::string theId;
};

class RECTLayout : public Layout
{
public:

    RECTLayout() : Layout("rect")
    {};


    virtual double dist(const SomPos& _center, const SomPos& _v) const;

    virtual void localAve(const FuzzyMap* _som, const SomPos& _center, std::vector<double>& _aveVector) const;

    virtual double numNeig(const FuzzyMap* _som, const SomPos& _center) const;


protected:

    RECTLayout(const std::string& _id) : Layout(_id)
    {};
};

class HEXALayout : public Layout
{
public:

    HEXALayout() : Layout("hexa")
    {};

    virtual double dist(const SomPos& _center, const SomPos& _v) const;

    virtual void localAve(const FuzzyMap* _som, const SomPos& _center, std::vector<double>& _aveVector) const;

    virtual double numNeig(const FuzzyMap* _som, const SomPos& _center) const;

protected:

    HEXALayout(const std::string& _id) : Layout(_id)
    {};
};


#endif