ctf_estimate_from_psd_base.h

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/*
 * ctf_estimate_from_psd_base.h
 *
 *  Created on: Aug 29, 2017
 *      Author: javier mota <jmota@cnb.csic.es>
 */
#ifndef _ADJUST_CTF_BASIC_PARAMS
#define _ADJUST_CTF_BASIC_PARAMS

#include "core/xmipp_program.h"
#include "core/xmipp_filename.h"
#include "core/xmipp_image.h"

class ProgCTFBasicParams: public XmippProgram
{
public:
    FileName             fn_psd;
    double               downsampleFactor;
    Image<double>        ctftomodel;
    Image<double>        enhanced_ctftomodel;
    Image<double>        enhanced_ctftomodel_fullsize;
    bool                 show_optimization;
    bool                 selfEstimation;
    int                  ctfmodelSize;
    bool                 bootstrap;
    bool                 refineAmplitudeContrast;
    bool                 fastDefocusEstimate;
    bool                 noDefocusEstimate;
    double               lambdaPhase;
    int                  sizeWindowPhase;
    double               min_freq;
    double               max_freq;
    double               Tm;
    double               defocus_range;
    double               f1;
    double               f2;
    double               enhanced_weight;
    Matrix1D<double>     adjust;
    int                  modelSimplification;
    MultidimArray<double> x_contfreq;
    MultidimArray<double> y_contfreq;
    MultidimArray<double> w_contfreq;
    MultidimArray<double> x_digfreq;
    MultidimArray<double> y_digfreq;
    MultidimArray<double> w_digfreq;
    MultidimArray<double> psd_exp_radial;
    MultidimArray<double> psd_exp_enhanced_radial;
    MultidimArray<double> psd_exp_enhanced_radial_2;
    MultidimArray<double> psd_exp_enhanced_radial_derivative;
    MultidimArray<double> psd_theo_radial_derivative;
    MultidimArray<double> psd_exp_radial_derivative;
    MultidimArray<double> psd_theo_radial;
    MultidimArray<double> w_digfreq_r_iN;
    MultidimArray<double> w_digfreq_r;
    MultidimArray<std::complex<double> > psd_fft;
    std::vector<double> amplitud;
    MultidimArray<double> mask;
    MultidimArray<double> mask_between_zeroes;
    MultidimArray<double> w_count;
    //Global values
    // Autofocus
    double value_th;
    double min_freq_psd;
    double max_freq_psd;

    // Maximum of the gaussian
    double max_gauss_freq;

    int show_inf; // 0: Do not show
    // 1: Partially detailed
    // 2: Very detailed

    // Program status
    int action;
    // 0: Computing the background (sqrt)
    // 1: Computing the full background
    // 2: Computing the envelope
    // 3: Computing defoci
    // 4: Computing all CTF parameters
    // 5: Computing all CTF parameters + Gaussian2
    // 6: Computing all CTF parameters + Gaussian2
    // 7: Produce output

    double corr13;

    // Penalization factor for the background
    bool penalize;

    // Speed up factor
    int evaluation_reduction;

    // Penalization for forbidden values of the parameters
    double heavy_penalization;
    double current_penalty;
    static constexpr double penalty = 32.0; // Maximum penalization
    //Some aliases
    MultidimArray<double> *f; // The CTF to model
    Matrix1D<double> *adjust_params; // Current theoretical adjustment

    ProgCTFBasicParams()
    {
    }

public:
    void readParams();

    void readBasicParams(XmippProgram *program);

    void show();

    static void defineBasicParams(XmippProgram * program);

    void defineParams();

    void produceSideInfo();

    void generate_model_halfplane(int Ydim, int Xdim, MultidimArray<double> &model);

    void generate_model_quadrant(int Ydim, int Xdim, MultidimArray<double> &model);

};

double evaluateIceness(MultidimArray<double> &psd, double Tm);
#endif