fourier_filter.h

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/***************************************************************************
 *
 * Authors:     Carlos Oscar S. Sorzano (coss@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'
 ***************************************************************************/

#ifndef _FOURIER_FILTER_HH
#define _FOURIER_FILTER_HH

#include "filters.h"
#include "data/ctf.h"

class FourierFilter: public XmippFilter
{
public:
#define RAISED_COSINE 1

    int FilterShape;

#define LOWPASS       1
#define HIGHPASS      2
#define BANDPASS      3
#define STOPBAND      4
#define CTF           5
#define WEDGE         7
#define GAUSSIAN      8
#define CONE          9
#define CTFPOS       10
#define BFACTOR      11
#define REALGAUSSIAN 12
#define SPARSIFY     13
#define STOPLOWBANDX 14
#define STOPLOWBANDY 15
#define FSCPROFILE   16
#define BINARYFILE   17
#define ASTIGMATISMPROFILE 18
#define CTFINV       19
#define CTFPOSINV    20
#define CTFDEF       21
#define REALGAUSSIANZ 22
#define REALGAUSSIANZ2 23
#define WEDGE_RC 24

    int FilterBand;

    double w1;

    double w2;

    double sampling_rate;

    double t1;
    double t2;
    double rot;
    double tilt;
    double psi;

    double percentage;

    FileName maskFn;

    double raised_w;

    CTFDescription ctf;
    
    double minCTF;

    FileName fnFSC;

    FileName fnFilter;

    bool do_generate_3dmask;

public:
    static void defineParams(XmippProgram * program);

    void readParams(XmippProgram * program);

    void apply(MultidimArray<double> &img);

    FourierFilter();

    void init();

    void show();

    double maskValue(const Matrix1D<double> &w);

    void generateMask(MultidimArray<double> &v);

    void applyMaskSpace(MultidimArray<double> &v);

    void applyMaskFourierSpace(const MultidimArray<double> &v, MultidimArray<std::complex<double> > &V);

    double maskPower();
    
    void correctPhase();
public:
    // Auxiliary vector for representing frequency values
    Matrix1D<double> w;

    // Auxiliary mask for the filter in 3D
    MultidimArray<int> maskFourier;

    // Auxiliary mask for the filter in 3D
    MultidimArray<double> maskFourierd;

    // Transformer
    FourierTransformer transformer;

    // Auxiliary variables for sparsify
    MultidimArray<double> vMag;
    MultidimArray<double> vMagSorted;

    // Auxiliary variables for FSC profile
    std::vector<double> freqContFSC;
    std::vector<double> FSC;
};

class SoftNegativeFilter: public XmippFilter
{
public:
    double K; // K*sigma
    FileName fnFSC;
    Image<int> mask; // for the case of mask bad pixels
    double Ts; // Sampling rate

    static void defineParams(XmippProgram * program);
    void readParams(XmippProgram * program);
    void apply(MultidimArray<double> &img);
};

void bandpassFilter(MultidimArray<double> &img, double w1, double w2, double raised_w);

void gaussianFilter(MultidimArray<double> &img, double w1);

void realGaussianFilter(MultidimArray<double> &img, double sigma);
#endif