dimred_tools.h

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/***************************************************************************
 *
 * Authors:    Carlos Oscar            coss@cnb.csic.es (2013)
 *
 * 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'
 ***************************************************************************/
#ifndef _DIMRED_TOOLS
#define _DIMRED_TOOLS

#include <core/matrix2d.h>
#include <core/matrix1d.h>
#include "core/xmipp_filename.h"


enum class DatasetType { SWISS, HELIX, TWINPEAKS, CLUSTER3D, INTERSECT};
class GenerateData
{
public:
    Matrix2D<double> X;

    Matrix2D<double> t;

    Matrix1D<unsigned char> label;


public:
    void generateNewDataset(const DatasetType &type, int N=1000, double noise=0.05);
};

typedef double (*DimRedDistance2)  (const Matrix2D<double> &X, size_t i1, size_t i2);

void computeDistance(const Matrix2D<double> &X, Matrix2D<double> &distance, DimRedDistance2 f=NULL, bool computeSqrt=true);

void computeRandomPointsDistance(const Matrix2D<double> &X, Matrix1D<double> &distance, Matrix1D<int> ind1, Matrix1D<int> ind2, DimRedDistance2 f, bool computeSqrt);

void computeDistanceToNeighbours(const Matrix2D<double> &X, int K, Matrix2D<double> &distance, DimRedDistance2 f=NULL, bool computeSqrt=true);

void computeSimilarityMatrix(Matrix2D<double> &D2, double sigma, bool skipZeros=false, bool normalize=false);

void computeGraphLaplacian(const Matrix2D<double> &G, Matrix2D<double> &L);

double intrinsicDimensionality(Matrix2D<double> &X, const String &method="MLE", bool normalize=true, DimRedDistance2 f=NULL);

void kNearestNeighbours(const Matrix2D<double> &X, int K, Matrix2D<int> &idx, Matrix2D<double> &distance, DimRedDistance2 f=NULL, bool computeSqrt=true);

void extractNearestNeighbours(const Matrix2D<double> &X, Matrix2D<int> &idx, int i, Matrix2D<double> &Xi);

class DimRedAlgorithm
{
public:
    Matrix2D<double> *X;

    size_t outputDim;

    Matrix2D<double> Y;

    DimRedDistance2 distance;

    FileName fnMapping;
public:
    DimRedAlgorithm();

    void setInputData(Matrix2D<double> &X);

    void setOutputDimensionality(size_t outputDim);

    virtual void reduceDimensionality()=0;

    const Matrix2D<double> &getReducedData();
};
#endif