image_peak_high_contrast.h

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/***************************************************************************
 *
 * Authors:    Federico P. de Isidro Gomez            fp.deisidro@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'
 ***************************************************************************/

#ifndef __IMAGE_PEAK_HIGH_CONTRAST
#define __IMAGE_PEAK_HIGH_CONTRAST

#include <iostream>
#include <core/xmipp_program.h>
#include <core/xmipp_image.h>
#include <core/metadata_vec.h>
#include <core/xmipp_fft.h>
#include <core/xmipp_fftw.h>
#include <math.h>
#include <limits>
#include <complex>
#include <data/fourier_filter.h>
#include <data/filters.h>
#include <string>
#include "symmetrize.h"
#include <data/morphology.h>
#include <data/point3D.h>
#include <data/point2D.h>
#include <data/basic_pca.h>

#define VERBOSE_OUTPUT
// #define DEBUG_OUTPUT_FILES
// #define DEBUG_DIM
// #define DEBUG_PREPROCESS
// #define DEBUG_HCC
// #define DEBUG_FILTERLABEL
// #define DEBUG_CLUSTER
// #define DEBUG_COORDS_IN_SLICE
// #define DEBUG_DIST
// #define DEBUG_CENTER_COORDINATES
// #define DEBUG_REMOVE_DUPLICATES
// #define DEBUG_FILTER_COORDINATES
// #define DEBUG_RADIAL_AVERAGE
// #define DEBUG_MAHALANOBIS_DISTANCE

class ProgImagePeakHighContrast : public XmippProgram
{

public:
    FileName fnVol;
    FileName fnOut;

    double fiducialSize;

    double samplingRate;

    int boxSize;

    int numberSampSlices;

    double sdThr;                       // Number of SD over the mean to consider a coordinate value as an outlier
    int numberOfCoordinatesThr;         // Minimum number of coordinates to keep a label
    double mirrorCorrelationThr;        // Minimum correlation between a fiducial and its mirror
    double mahalanobisDistanceThr;      // Maximum mahalanobis distance (empirical value)

    bool relaxedMode;               // Relaxed mode keeps coordinates when none of them pass the mirror correlation filter
    int relaxedModeThr = 0;             // Number of coordinates to run relaxed mode

     double fiducialSizePx;

    FourierTransformer transformer;

    Image<double> V;

    
private:
    size_t xSize;
    size_t ySize;
    size_t zSize;
    size_t nSize;

    size_t normDim;

    std::vector<int> centerOfMassX;
    std::vector<int> centerOfMassY;
    std::vector<int> centerOfMassZ;

    std::vector<Point3D<double>> coordinates3D;

public:

    // --------------------- IN/OUT FUNCTIONS -----------------------------

    void readParams();

    void defineParams();

    void writeOutputCoordinates();


    // ---------------------- MAIN FUNCTIONS -----------------------------

    void preprocessVolume(MultidimArray<double> &inputTomo);

    void getHighContrastCoordinates(MultidimArray<double> &volFiltered);

    void clusterHCC();

    void centerCoordinates(MultidimArray<double> volFiltered);

    void removeDuplicatedCoordinates();

    void filterCoordinatesByCorrelation(MultidimArray<double> volFiltered);


    // --------------------------- UTILS functions ----------------------------

    void generateSideInfo();

    bool filterLabeledRegions(std::vector<int> coordinatesPerLabelX, std::vector<int> coordinatesPerLabelY, double centroX, double centroY) const;

    std::vector<size_t> getCoordinatesInSliceIndex(size_t slice);

    void radialAverage(MultidimArray<float> &feature, MultidimArray<float> &radialAverage, size_t numSlices) const;
    
    void mahalanobisDistance(std::vector<MultidimArray<float>> &setOfFeatures_RA, MultidimArray<double> &mahalanobisDistance_List) const;

    // --------------------------- MAIN ----------------------------------

    void run();
};

#endif