phantom_simulate_microscope.h

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/***************************************************************************
 *
 * Authors:     Carlos Oscar S. Sorzano (coss@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 _PROG_MICROSCOPE_HH
#define _PROG_MICROSCOPE_HH

#include "core/xmipp_metadata_program.h"
#include "data/fourier_filter.h"

/* Microscope Program Parameters ------------------------------------------- */
class ProgSimulateMicroscope: public XmippMetadataProgram
{
public:
    FileName fn_ctf;
    double   sigma;
    double   low_pass_before_CTF;
    bool     after_ctf_noise;
    double   defocus_change;
    double targetSNR;
    bool estimateSNR;
    bool CTFpresent;
    FourierFilter ctf;
    FourierFilter lowpass;
    FourierFilter after_ctf;
    double   sigma_before_CTF;
    double   sigma_after_CTF;
    size_t   Xdim;
    size_t   Ydim;
    MetaDataVec *pmdIn;
    double downsampling;
    /* save U defocus in case we randomize it */
    double defocusU;
    /* save V defocus in case we randomize it */
    double defocusV;

public:
    void readParams();

    void defineParams();

    void show();

    void estimateSigma();

    void setupFourierFilter(FourierFilter &filter, bool isBackground, double &power);

    void updateCtfs();

    void preProcess();


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

    void apply(MultidimArray<double> &I);

};
#endif