coordinates_noisy_zones_filter.cpp

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/***************************************************************************
 *
 * Authors:     David Maluenda (dmaluenda@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'
 ***************************************************************************/

#include "coordinates_noisy_zones_filter.h"

void ProgCoordinatesNoisyZonesFilter::defineParams()
{
    // Parameters
    addParamsLine(" --pos <coordinates> : Input coordinates");
    addParamsLine(" --mic <micrograph> : Reference volume");
    addParamsLine(" [--patchSize <n=50>] : Patch size for the variance filter");
    addParamsLine(" [-o <coordinates>] : Output coordinates (if not passed, "
                                                   "the input is overwritten)");
}

void ProgCoordinatesNoisyZonesFilter::readParams()
{
    fnInCoord = getParam("--pos");
    fnInMic = getParam("--mic");
    if (checkParam("-o"))
        fnOut = getParam("-o");
    else
        fnOut = fnInCoord;
    patchSize = getIntParam("--patchSize");
}

void ProgCoordinatesNoisyZonesFilter::show()
{
    if (verbose)
        std::cout
        << "Input Coordinates:     " << fnInCoord  << std::endl
        << "Input Micrograph:      " << fnInMic  << std::endl
        << "Output coordinates:    " << fnOut << std::endl
        << "Patch size:            " << patchSize << std::endl
        ;
}

//#define DEBUG
void ProgCoordinatesNoisyZonesFilter::run()
{
    show();

    Micrograph mic;
    mic.open_micrograph(fnInMic);
    mic.read_coordinates(0, (String)"particles@"+fnInCoord);
    mic.add_label("");

    Image<double> im;
    im.read(fnInMic);

    // std::cout << " - Starting normalization " << std::endl;
    MultidimArray<double> &matrixMic = im();
    matrixMic.selfNormalizeInterval();

    if (verbose>1)
    {
        Image<double> aux(matrixMic);
        aux.write(fnInCoord.withoutExtension()+"_normalized.mrc");
    }

    // giniCoeff(Image, patchSize) returns the giniCoeff of the Image and
    //   applies a variance filter to the Image with a patchSize 
    double giniV = giniCoeff(matrixMic, patchSize);

    if (verbose>1)
    {
        Image<double> aux(matrixMic);
        aux.write(fnInCoord.withoutExtension()+"_varianceFilter.mrc");
        std::cout << " Gini Coeff: " << giniV << std::endl
                  << "(" << fnInMic << ")" << std::endl;
    }
    
    // adding the variance value of the zone to every coordinate
    std::vector<Particle_coords> &allCoords=mic.coords;
    std::vector<double> varValue;
    for (size_t i=0; i<allCoords.size(); ++i)
    {
        Particle_coords &coord=allCoords[i];
        varValue.push_back(DIRECT_A2D_ELEM(matrixMic,coord.Y,coord.X));
    }

    // creating a MetaData with the coordinates and the Scores VAR and GINI
    MetaDataVec MD;
    int imax = allCoords.size();
    size_t id;
    for (int i = 0; i < imax; i++)
        if (allCoords[i].valid && allCoords[i].cost > 0
            && allCoords[i].label == 0)
        {
            id = MD.addObject();
            MD.setValue(MDL_XCOOR, allCoords[i].X, id);
            MD.setValue(MDL_YCOOR, allCoords[i].Y, id);
            MD.setValue(MDL_SCORE_BY_VAR, varValue[i], id);
            MD.setValue(MDL_SCORE_BY_GINI, giniV, id);            
        }
    MD.write((String)"particles@"+fnOut);
}
#undef DEBUG