flexible_alignment.h

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/***************************************************************************
 *
 * Authors:    Slavica Jonic            slavica.jonic@impmc.jussieu.fr
 *             Carlos Oscar             coss@cnb.uam.es
 *
 * 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.uam.es'
 ***************************************************************************/

#ifndef _PROG_FLEXIBLE_ALIGNMENT
#define _PROG_FLEXIBLE_ALIGNMENT

#include "core/xmipp_metadata_program.h"
#include "core/rerunable_program.h"
#include "core/matrix1d.h"
#include "core/metadata_vec.h"

class ProgFlexibleAlignment: public XmippMetadataProgram, public Rerunable
{
public:
    bool MPIversion;

    bool resume;

    FileName fnPDB;

    FileName fnModeList;

    FileName fnOutDir;

    double maxdefamp;

    double defampsampling;

    double scale_defamp;

    double scdefamp;

    double translsampling;

    double maxtransl;

    double sampling_rate;

    FileName fnmask;

    bool do_centerPDB;

    bool projMatch;

    double minAngularSampling;

    double gaussian_Real_sigma;

    double weight_zero_freq;

    bool do_FilterPDBVol;

    double cutoff_LPfilter;

    bool useFixedGaussian;

    double sigmaGaussian;

    // value of cost function
    double costfunctionvalue;

    // value of cost function in angular continuous assignment
    double costfunctionvalue_cst;

    double sigma;

    int max_no_iter;

public:
    // List of modes
    std::vector<std::string> modeList;

    // Random generator seed
    int rangen;

    // All estimated parameters (with the cost)
    Matrix1D<double> parameters;

    // Trial parameters
    Matrix1D<double> trial;

    // Best trial parameters
    Matrix1D<double> trial_best;

    // Number of modes
    int numberOfModes;

    // Size of the images in the selfile
    int imgSize;

    // Current image being considered
    FileName currentImgName;

    // Current stage of optimization
    int currentStage;

    // Solution of the first stage
    Matrix1D<double> bestStage1;

    // Temporary document file
    MetaDataVec DF_out;

    // Template for temporal filename generation
    char nameTemplate[256];

    //File name of reduced image
    FileName fnDown;

public:
    ProgFlexibleAlignment();

    void defineParams();

    void readParams();

    void show();

    FileName createDeformedPDB() const;

    void performCompleteSearch(int pyramidLevel);

    double performContinuousAssignment(int pyramidLevel);

    double eval();

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

    virtual void finishProcessing();

    virtual void writeImageParameters(const FileName &fnImg);
  
  protected:
    virtual void createWorkFiles() {
      return Rerunable::createWorkFiles(resume, getInputMd());
    }

  private:
    using Rerunable::createWorkFiles;
    
    std::vector<MDLabel> getLabelsForEmpty() override {
      return std::vector<MDLabel>{MDL_IMAGE,      MDL_ENABLED,   MDL_ANGLE_ROT,
                                  MDL_ANGLE_TILT, MDL_ANGLE_PSI, MDL_SHIFT_X,
                                  MDL_SHIFT_Y,    MDL_NMA,       MDL_COST};
    }
};


#endif