basis.h

Go to the documentation of this file.

/***************************************************************************
 *
 * 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 _CORE_BASIS_HH
#define _CORE_BASIS_HH

#include "blobs.h"
#include "splines.h"
#include "xmipp_image_over.h"
#include <core/xmipp_program.h>

const int BLOB_SUBSAMPLING = 10;
const int PIXEL_SUBSAMPLING = 1;
const int SPLINE_SUBSAMPLING = 1;

class Basis
{
public:
    typedef enum {blobs, voxels, splines} tBasisFunction;

    tBasisFunction type;

    MultidimArray<double> *VolPSF; // If NULL then standard blob is used

    double Tm;

    struct blobtype blob;

    double grid_relative_size;

    Matrix2D<double> *D;

    ImageOver       blobprint;

    ImageOver       blobprint2;

    double          sum_on_grid;

    Matrix1D<double> aux;

public:
    Basis();

    void setDefault();

    String basisName() const;

    void read(int argc, char **argv);

    void read(const FileName &fn);

    static void defineParams(XmippProgram * program, const char* prefix=NULL, const char* comment=NULL);

    void readParams(XmippProgram * program);

    void produceSideInfo(const Grid &grid);

    friend std::ostream & operator << (std::ostream &out, const Basis &basis);

    void setSamplingRate(double _Tm);

    void setD(Matrix2D<double> *_D)
    {
        D = _D;
    }

    double maxLength() const;

    void changeToVoxels(GridVolume &vol_basis, MultidimArray<double> *vol_voxels,
                        int Zdim, int Ydim, int Xdim, int threads = 1 ) const;

    void changeFromVoxels(const MultidimArray<double> &vol_voxels,
                          GridVolume &vol_basis, int grid_type, double grid_relative_size,
                          const MultidimArray<double> *vol_mask,
                          const Matrix2D<double> *D, double R,int threads=1) const;

    double valueAt(const Matrix1D<double> &r) const;

    double projectionAt(const Matrix1D<double> &u, const Matrix1D<double> &r)
    const;
};

void createZernike3DBasis(const MultidimArray<double> &Vin, MultidimArray<double> &Vbasis, int l1, int n, int l2, int m, int Rmax=-1);
#endif