reconstruct_ADMM.h

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/***************************************************************************
 *
 * Authors:        Masih Nilchian (masih.nilchian@epfl.ch)
 *                 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 _PROG_RECONSTRUCT_ADMM_HH
#define _PROG_RECONSTRUCT_ADMM_HH

#include <core/xmipp_program.h>
#include <core/matrix1d.h>
#include <core/xmipp_fftw.h>
#include <data/ctf.h>
#include <data/mask.h>
#include <core/symmetries.h>


class AdmmKernel
{
public:
    double supp;
    double projectionStep;
    double autocorrStep;
    double alpha;
    Matrix1D<double> projectionProfile; // Look-up table
    MultidimArray< std::complex<double> > FourierProjectionAutocorr;
    FourierTransformer transformer;
    MultidimArray<double> projectionAutocorrWithCTF;

    void initializeKernel(double alpha, double a, double _projectionStep);

    double projectionValueAt(double u, double v);

    void convolveKernelWithItself(double _autocorrStep);

    void applyCTFToKernelAutocorrelation(CTFDescription &ctf, double Ts, MultidimArray<double> &autocorrelationWithCTF);

    void getKernelAutocorrelation(MultidimArray<double> &autocorrelation);

    /* Direction=x,y,z, mode=L (Lx), T (L^T x), 2 (L^TLx) */
    void computeGradient(MultidimArray<double> &gradient, char direction, bool adjoint=false);

    void computeKernel3D(MultidimArray<double> &kernel);
};

class ProgReconsADMM: public XmippProgram
{
public:
    FileName fnIn; // Set of input images
    FileName fnRoot; // Rootname for output files
    FileName fnFirst; // First reconstruction filename
    FileName fnHtb; // Htb filename
    FileName fnHtKH; // HtKH filename
    String kernelShape;
    double a;     // Kaiser-Bessel maximum radius
    double alpha; // Kaiser-Bessel shape
    double mu; // Augmented Lagrange
    double lambda; // Total variation regularization
    double lambda1; // Tikhonov regularization

    double Ti; // Downsampling factor for the volume
    double Tp; // Downsampling factor for the projections
    bool useWeights; // Use weights if available in the input metadata
    bool useCTF; // Use CTF if available in the input metadata
    int Ncgiter; // Number of conjugate gradient iterations
    int Nadmmiter; // Number of ADMM iterations
    bool positivity; // Positivity constraint
    bool applyMask;
    double Ts; // Sampling rate
    Mask mask; // Mask
    String symmetry;
    bool saveIntermediate;
    size_t Nprocs;
    size_t rank;
public:
    ProgReconsADMM();
    void defineParams();
    void readParams();
    void show();
    void run();

    void produceSideInfo();

    void project(double rot, double tilt, double psi, MultidimArray<double> &P, bool adjoint=false, double weight=1.);

    void project(const Matrix1D<double> &r1, const Matrix1D<double> &r2, MultidimArray<double> &P, bool adjoint=false, double weight=1.);

    void constructHtb();

    void computeHtKH(MultidimArray<double> &kernelV);

    void addRegularizationTerms();

    void applyKernel3D(MultidimArray<double> &x, MultidimArray<double> &AtAx);

    void applyLFilter(MultidimArray< std::complex<double> > &fourierL, bool adjoint=false);
    void applyLtFilter(MultidimArray< std::complex<double> > &fourierL, MultidimArray<double> &u, MultidimArray<double> &d);

    void applyConjugateGradient();

    void doPOCSProjection();

    void updateUD();

    void produceVolume();

    // Share a volume among nodes
    virtual void shareVolume(MultidimArray<double> &V) {}

    // Redefine how to synchronize
    virtual void synchronize() {}

public:
    AdmmKernel           kernel;
    Image<double>        CHtb; // First reconstructed volume
    Image<double>        Ck, Vk; // Reconstructed volume
    MetaDataVec          mdIn; // Set of images and angles
    MultidimArray<std::complex<double> > fourierKernelV;
    MultidimArray<double> paddedx;
    FourierTransformer    transformerPaddedx, transformerL;

    MultidimArray<double> ux, uy, uz, dx, dy, dz, ud;
    MultidimArray< std::complex<double> > fourierLx, fourierLy, fourierLz;
    SymList SL;
};

#endif