averager.h

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/*
 * Author: Steven Ludtke, 04/10/2003 (sludtke@bcm.edu)
 * Copyright (c) 2000-2006 Baylor College of Medicine
 *
 * This software is issued under a joint BSD/GNU license. You may use the
 * source code in this file under either license. However, note that the
 * complete EMAN2 and SPARX software packages have some GPL dependencies,
 * so you are responsible for compliance with the licenses of these packages
 * if you opt to use BSD licensing. The warranty disclaimer below holds
 * in either instance.
 *
 * This complete copyright notice must be included in any revised version of the
 * source code. Additional authorship citations may be added, but existing
 * author citations must be preserved.
 *
 * 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
 *
 * */

#ifndef eman_averager_h__
#define eman_averager_h__ 1

#include "emobject.h"
#include "emdata.h"

#include <vector>
using std::vector;

namespace EMAN
{
        class EMData;
        class XYData;

        class Averager
        {
          public:
                Averager() : result(0) {}

                virtual ~ Averager()
                {
                }

                virtual void add_image(EMData * image) = 0;

                virtual void add_image_list(const vector<EMData*> & images);

                virtual EMData * finish() = 0;

                virtual string get_name() const = 0;

                virtual string get_desc() const = 0;

                virtual void set_params(const Dict & new_params)
                {
                        params = new_params;
                }

                virtual void mult(const float& s);

                virtual TypeDict get_param_types() const
                {
                        TypeDict d;
                        return d;
                }
                
          protected:
                mutable Dict params;
                EMData *result;
        };

        class ImageAverager:public Averager
        {
          public:
                ImageAverager();

                void add_image( EMData * image);
                EMData * finish();

                string get_name() const
                {
                        return "mean";
                }

                string get_desc() const
                {
                        return "Simple mean average of images";
                }

                static Averager *NEW()
                {
                        return new ImageAverager();
                }

                TypeDict get_param_types() const
                {
                        TypeDict d;
                        d.put("sigma", EMObject::EMDATA, "sigma value");
                        d.put("ignore0", EMObject::INT, "if set, ignore zero value pixels");
                        return d;
                }

                virtual void mult(const float&) { }

        private:
                EMData *sigma_image;
                int *nimg_n0;
                int ignore0;
                int nimg;
        };

        class MinMaxAverager:public Averager
        {
          public:
                MinMaxAverager();

                void add_image( EMData * image);
                EMData * finish();

                string get_name() const
                {
                        return "minmax";
                }

                string get_desc() const
                {
                        return "Finds the minimum or maximum value in each pixel";
                }

                static Averager *NEW()
                {
                        return new MinMaxAverager();
                }

                TypeDict get_param_types() const
                {
                        TypeDict d;
                        d.put("max", EMObject::INT, "If set, will find the max value, otherwise finds min");
                        return d;
                }

                virtual void mult(const float&) { }

        private:
                int max;
                int nimg;
        };

        class IterationAverager:public Averager
        {
          public:
                IterationAverager();
                void add_image( EMData * image);
                EMData * finish();

                string get_name() const
                {
                        return "iteration";
                }

                string get_desc() const
                {
                        return "Unknown";
                }

                static Averager *NEW()
                {
                        return new IterationAverager();
                }
        private:
                EMData * sigma_image;
                int nimg;
        };

        class CtfAverager:public Averager
        {
          public:
                CtfAverager();
                void add_image( EMData * image);
                EMData * finish();

                vector < float >get_snr() const
                {
                        return snr;
                }

          protected:
                XYData *sf;
                EMData *curves;
                bool need_snr;
                const char *outfile;
          private:
                mutable vector < float >snr;
                EMData * image0_fft;
                EMData * image0_copy;

                vector<vector<float> > ctf;
                vector<vector<float> > ctfn;

                float *snri;
                float *snrn;
                float *tdr;
                float *tdi;
                float *tn;

                float filter;
                int nimg;
                int nx;
                int ny;
                int nz;
        };

        class WeightingAverager:public CtfAverager
        {
          public:
                string get_name() const
                {
                        return "snr_weight";
                }

                string get_desc() const
                {
                        return "SNR Weighted average without CTF amplitude correction";
                }

                static Averager *NEW()
                {
                        return new WeightingAverager();
                }

                void set_params(const Dict & new_params)
                {
                        params = new_params;
                        curves = params["curves"];
                        sf = params["sf"];
                }

                TypeDict get_param_types() const
                {
                        TypeDict d;
                        d.put("curves", EMObject::EMDATA);
                        d.put("sf", EMObject::XYDATA);
                        return d;
                }
        };

        class CtfCAverager:public CtfAverager
        {
          public:
                string get_name() const
                {
                        return "ctfc";
                }

                string get_desc() const
                {
                        return "CTF amplitude corrected average, including SNR weight, but result is unprocessed.";
                }

                static Averager *NEW()
                {
                        return new CtfCAverager();
                }
        };

        class CtfCWAverager:public CtfAverager
        {
          public:
                string get_name() const
                {
                        return "ctfcw";
                }

                string get_desc() const
                {
                        return "CTF amplitude corrected average, including SNR weight and Wiener filtration";
                }

                static Averager *NEW()
                {
                        return new CtfCWAverager();
                }

                void set_params(const Dict & new_params)
                {
                        params = new_params;
                        if ((int) params["need_snr"]) {
                                need_snr = true;
                        }
                        else {
                                need_snr = false;
                        }
                }
        };

        class CtfCWautoAverager:public Averager
        {
          public:
            CtfCWautoAverager();

                void add_image( EMData * image);
                EMData * finish();

                string get_name() const
                {
                        return "ctf.auto";
                }

                string get_desc() const
                {
                        return "Averaging with autmatic CTF correction. Does not require a structure factor, but only works with EMAN2's CTF model";
                }

                static Averager *NEW()
                {
                        return new CtfCWautoAverager();
                }

                void set_params(const Dict & new_params)
                {
                        params = new_params;
//                      outfile = params["outfile"];
                }
          protected:
                EMData *snrsum;   // contains the summed SNR for the average
                int nimg;
        };

        template <> Factory < Averager >::Factory();

        void dump_averagers();
        map<string, vector<string> > dump_averagers_list();
}


#endif