tomo_tiltseries_dose_filter.h

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/***************************************************************************
 *
 * Authors:    J.L. Vilas jlvilas@cnb.csic.es           
 *
 * 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'
 ***************************************************************************/
/* This program is strongly based on the unblur code
 * (http://grigoriefflab.janelia.org/unblur)
which has been realeased under the following copyright:

The Janelia Farm Research Campus Software Copyright 1.1

Copyright (c) 2014, Howard Hughes Medical Institute, All rights reserved.

Redistribution and use in source and binary forms, with or without
modification, are permitted provided that the following conditions are met:


Redistributions of source code must retain the above copyright notice,
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#ifndef _PROG_TOMO_TILTSERIOES_DOSE_FILTER
#define _PROG_TOMO_TILTSERIOES_DOSE_FILTER

#include <complex>
#include "core/xmipp_program.h"
#include "core/xmipp_filename.h"
#include "core/metadata_vec.h"

template<typename T>
class MultidimArray;


class ProgTomoTSFilterDose: public XmippProgram
{
public:

    double critical_dose_a;
    double critical_dose_b;
    double critical_dose_c;

    double critical_dose_at_dc;

    double voltage_scaling_factor;
    double accVoltage;
    double dose_per_image;
    double pre_exposure_amount;

    FileName fnTs;

    FileName fnOut;

    int user_supplied_first_frame;
    int user_supplied_last_frame;

    double sampling;

    double maxFreq;


    bool restore_power;

    // Fourier transforms of the input images
    std::vector< MultidimArray<std::complex<double> > * > frameFourierVec;

public:
    void readParams();

    void show();

    void defineParams();

    void run();

    void initParameters();

    void readInputData(MetaDataVec &md);

    // factor due to radiation damage (as used by summovie)
    double doseFilter(double dose_at_end_of_frame, double critical_dose);

    double criticalDose(double spatial_frequency);


   double optimalDoseGivenCriticalDose(double critical_dose);

   void applyDoseFilterToImage(int Ydim, int Xdim, const MultidimArray< std::complex<double> > &FFT1, const double dose_finish);

};
#endif