ctf_sort_psds.h

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/***************************************************************************
 *
 * Authors:     Carlos Oscar S. Sorzano (coss@cnb.csic.es)
 *              Slavica Jonic (slavica.jonic@impmc.jussieu.fr)
 *
 * 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 _PROG_CTF_SORT_PSDS_HH
#define _PROG_CTF_SORT_PSDS_HH

#include "core/xmipp_metadata_program.h"


class PSDEvaluation {
public:
    double defocusU;
    double defocusV;
    double PSDcorrelation90;
    double firstZeroRatio;
    double firstZeroAvg;
    double firstMinimumStddev_ZeroStddev; // sigma(firstMinimum)/sigma(firstZero)
    double firstMinimumDiffStddev_ZeroStddev; // sigma(firstMinimum-firstZero)/sigma(firstZero)
    double maxFreq;
    double firstZeroDisagreement;
    double beating;
    double maxDampingAtBorder;
    double PSDradialIntegral;
    double fittingScore;
    double fittingCorr13;
    double PSDVariance;
    double PSDPC1Variance;
    double PSDPCRunsTest;
    double histogramNormality;
    FileName ctf_envelope_ssnr;
};

/* Sort PSD Program Parameters ------------------------------------------ */
class ProgPSDSort: public XmippMetadataProgram
{
public:
    double filter_w1;

    double filter_w2;

    double decay_width;

    double mask_w1;

    double mask_w2;

    // COSS: double downsampling; // This is already in the CTF file
public:
    ProgPSDSort();

    void defineLabelParam();

    void readParams();

    void defineParams();

    void show();

    void processImage(const FileName &fnImg, const FileName &fnImgOut, const MDRow &rowIn, MDRow &rowOut);
};
#endif