ml_refine3d.h

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/***************************************************************************
 *
 * Authors:    Sjors Scheres           scheres@cnb.csic.es (2004)
 *
 * 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 _ML_REFINE3D_H
#define _ML_REFINE3D_H

#include "core/metadata_vec.h"
#include "core/xmipp_program.h"
#include "data/sampling.h"

class ProgReconsBase;
class ML2DBaseProgram;

//types of reconstructions to be used
#define RECONS_ART 0
#define RECONS_FOURIER 1

#define EMPTY_PROJECTIONS 0
#define EMPTY_VOLUMES 1

#define FN_ITER_VOLMD() getIterExtraPath(fn_root, iter) + "volumes.xmd"


class ProgMLRefine3D: public XmippProgram
{
public:
    // Filenames for input images, reference volumes, symmetry file and output rootname
    FileName fn_sel, fn_ref, fn_sym, fn_root, fn_solv, fn_iter, fn_symmask;
    // Metadata with reference volumes
    MetaDataVec mdVol;
    // Number of volumes to refine
    size_t Nvols;
    // Iteration numbers
    size_t iter, istart, Niter;
    // Convergence check
    double eps;
    // Angular sampling interval (degree)
    double angular;
    // Type of reconstruction to use
    int recons_type;
    // Low-pass filter digital frequency
    double lowpass;
    // For user-provided tilt range
    double tilt_range0, tilt_rangeF;
    // Parameters of wlsart reconstruction
    double wlsart_lambda, wlsart_kappa;
    int wlsart_Niter;
    // Do not use a starting volume in wlsART reconstruction
    bool wlsart_no_start;
    // Threshold for flooding-like solvent mask
    double threshold_solvent;
    // Do Wang/Terwilliger-like probabilistic solvent flattening
    bool do_prob_solvent;
    // Do separate_object-like selection of largest connected volume in
    // binarized solvent mask
    bool do_deblob_solvent;
    // Dilate (binarized) solvent mask?
    int dilate_solvent;
    // Use MLF mode
    bool fourier_mode;
    // Flag to skip reconstruction
    bool skip_reconstruction;
    // Perturb angles of reference projections
    bool do_perturb;
    // sampling object
    Sampling mysampling;
    // Symmetry setup
    int symmetry, sym_order;
    // Number of reference projections per 3D model
    int nr_projections;

    //MPI related stuff
    size_t rank, size;

    //This is the list of output filename base for
    //reconstruction of volumes
    StringVector reconsOutFnBase, reconsMdFn;
    // A pointer to the 2D alignment and classification program
    ML2DBaseProgram * ml2d;

private:
    void showToStream(std::ostream &out);

public:
    ProgMLRefine3D(bool fourier = false);
    ~ProgMLRefine3D();
    void defineParams();
    void readParams();
    void show();

    void createSampling();
    //Call produceSideInfo of ML2D and
    // Fill sampling and create DFlib
    virtual void produceSideInfo();
    virtual void produceSideInfo2();

    void run();

    virtual void createEmptyFiles(int type);

    virtual void projectVolumes(MetaData &mdProj) ;

    virtual void makeNoiseImages() ;

    virtual ProgReconsBase * createReconsProgram(FileName &input, FileName &output);

    virtual void reconstructVolumes();

    virtual void calculate3DSSNR(MultidimArray<double> &spectral_signal);

    virtual void copyVolumes();
    void updateVolumesMetadata();

    virtual void postProcessVolumes();

    virtual bool checkConvergence() ;

}; // class ProgMLRefine3D
#endif