align_tilt_pairs.h

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/***************************************************************************
 *
 * Authors:    Sjors Scheres           scheres@cnb.csic.es (2002)
 *             Carlos Oscar 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 ALIGN_TILT_PAIRS_H
#define ALIGN_TILT_PAIRS_H

#include "core/xmipp_program.h"
#include "core/xmipp_filename.h"

template<typename T>
class MultidimArray;
class CorrelationAux;

class ProgAlignTiltPairs: public XmippProgram
{
public:
    FileName fnIn;
    FileName fnRef;
    FileName fnOut;
    double max_shift;
    bool do_stretch;
    bool do_not_align_tilted;
public:
    void defineParams();

    void readParams();

    void show();

    void processImage();

    void run();

    bool centerTiltedImage(const MultidimArray<double> &imgU, bool flip,
            double inPlaneU, double shiftXu, double shiftYu,
            double alphaT, double alphaU, double tilt,
            const MultidimArray<double> &imgT,
            double &shiftX, double &shiftY, CorrelationAux &auxCorr);
};
#endif //ALIGN_TILT_PAIRS_H