score_micrograph.h

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/***************************************************************************
 * Authors:     AUTHOR_NAME (jvargas@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 SCORE_MICROGRAPH_H_
#define SCORE_MICROGRAPH_H_

#include <core/xmipp_program.h>
#include "ctf_estimate_from_micrograph.h"
#include "ctf_estimate_from_psd.h"
#include "ctf_sort_psds.h"



/* Score Micrograph Program Parameters ------------------------------------------ */
class ProgScoreMicrograph: public XmippProgram
{
public:

    //First we assume that the particle size is the same for the X and Y axis
    int particleSize;

    ProgCTFEstimateFromMicrograph prmEstimateCTFFromMicrograph;

    ProgCTFEstimateFromPSD  prmEstimateCTFFromPSD;

    FileName                fn_micrograph;
    int                     pieceDim;
    double                  overlap;
    int                     skipBorders;
    int                     Nsubpiece;
    int                     bootstrapN;
    bool                    estimate_ctf;
    double               defocus_range;

    ProgCTFEstimateFromMicrograph::TPSD_mode PSDEstimator_mode;

    ProgCTFEstimateFromMicrograph::TPSD_mode psd_mode;

    ProgPSDSort prmPSDSort;



public:
    void readParams();

    void defineParams();

    void run();
    //void processImage(const FileName &fnImg, const FileName &fnImgOut, const MDRow &rowIn, MDRow &rowOut);

};



#endif /* SCORE_MICROGRAPH_H_ */