nma_alignment.h

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/***************************************************************************
 *
 * Authors:    Slavica Jonic            slavica.jonic@impmc.upmc.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_NMA_ALIGNMENT
#define _PROG_NMA_ALIGNMENT

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

class ProgPdbConverter;

class ProgNmaAlignment: public XmippMetadataProgram, public Rerunable
{
public:
    bool MPIversion;
    
    bool resume;

    FileName fnPDB;

    FileName fnOutDir;

    FileName fnModeList;

    double trustradius_scale;
    
    double sampling_rate;
    
    FileName fnmask;

    bool do_centerPDB;

    bool projMatch;

    double discrAngStep;

    double gaussian_DFT_sigma;

    double gaussian_Real_sigma;

    double weight_zero_freq;

    bool do_FilterPDBVol;

    double cutoff_LPfilter;

    bool useFixedGaussian;

    double sigmaGaussian;
 
public:

    // 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;
    
    // Best fitness
    Matrix1D<double> fitness_min;
    
    // 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];

    // Volume from PDB
    ProgPdbConverter* progVolumeFromPDB;

public:
    ProgNmaAlignment();

    ~ProgNmaAlignment();

    void defineParams();

    void readParams();

    void show();

    FileName createDeformedPDB(int pyramidLevel) const;

    void performCompleteSearch(const FileName &fnRandom,
        int pyramidLevel) const;

    double performContinuousAssignment(const FileName &fnRandom, int pyramidLevel) const;

    double computeFitness(Matrix1D<double> &trial) const;

    void updateBestFit(double fitness);

    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};
    }
};

class ObjFunc_nma_alignment: public UnconstrainedObjectiveFunction
{
  public:
    ObjFunc_nma_alignment(int _t, int _n=0);
    ~ObjFunc_nma_alignment(){};
    double eval(Vector v, int *nerror=nullptr);
};

#endif