ctf_estimate_from_psd_fast.h

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/***************************************************************************
 *
 * Authors:      Javier Mota Garcia    jmota@cnb.csic.es
 *               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 _ADJUST_CTF_FAST_HH
#define _ADJUST_CTF_FAST_HH

#include "ctf_estimate_from_psd_base.h"
#include "data/ctf.h"

class ProgCTFEstimateFromPSDFast: public ProgCTFBasicParams
{
public:

    CTFDescription1D    initial_ctfmodel, current_ctfmodel, ctfmodel_defoci;
    CTFDescription      initial_ctfmodel2D;

    ProgCTFEstimateFromPSDFast(){};

public:

    void readBasicParams(XmippProgram *program);

    void readParams();
    static void defineBasicParams(XmippProgram * program);

    void defineParams();

    void produceSideInfo();

    void run();

    /* Assign ctfmodel from a vector and viceversa ----------------------------- */
    void assignCTFfromParameters_fast(double *p, CTFDescription1D &ctf1Dmodel, int ia, int l);

    void assignParametersFromCTF_fast(const CTFDescription1D &ctfmodel, double *p, int ia, int l);

    /* Center focus ----------------------------------------------------------- */
    void center_optimization_focus_fast(bool adjust_th, double margin);

    /* The model is taken from global_adjust and global_ctfmodel is modified */
    void generateModelSoFar_fast(MultidimArray<double> &I, bool apply_log);

    /* Compute central region -------------------------------------------------- */
    void compute_central_region_fast(double &w1, double &w2, double ang);

    /* Save intermediate results ----------------------------------------------- */
    /* First call to generate model so far and then save the image, and a couple
     of cuts along X and Y.
     This function returns the fitting error.*/
    void saveIntermediateResults_fast(const FileName &fn_root, bool generate_profiles);

    double CTF_fitness_object_fast(double *p);

    // Estimate sqrt parameters
    void estimate_background_sqrt_parameters_fast();

    // Estimate first gaussian parameters ------------------------------------- */
    void estimate_background_gauss_parameters_fast();

    // Estimate second gaussian parameters ------------------------------------- */
    void estimate_background_gauss_parameters2_fast();

    // Estimate envelope parameters -------------------------------------------- */
    void estimate_envelope_parameters_fast();

    // Estimate defoci --------------------------------------------------------- */
    void showFirstDefoci_fast();
    void estimate_defoci_fast();

};

double ROUT_Adjust_CTFFast(ProgCTFEstimateFromPSDFast &prm, CTFDescription1D &output_ctfmodel,
    bool standalone = true);
#endif