validation_tilt_pairs.h

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/***************************************************************************
 *
 * Authors:    Jose Luis 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'
 ***************************************************************************/

#ifndef VALIDATE_TILT_PAIRS_H
#define VALIDATE_TILT_PAIRS_H

#include <core/xmipp_fftw.h>
#include <core/args.h>
#include <core/xmipp_funcs.h>

#include <core/metadata_extension.h>
#include <core/xmipp_image.h>
#include <core/geometry.h>
#include <data/filters.h>
#include <core/xmipp_program.h>
#include <complex>

class ProgValidationTiltPairs: public XmippProgram
{
public:
    FileName fntiltimage_In;
    FileName fnuntiltimage_In;
    FileName fnOut;

public:
    void defineParams();

    void quaternion2Paulibasis(double rot, double tilt, double psi, std::complex<double>(&L)[4]);

    void Pauliproduct(std::complex<double> A[4], std::complex<double> B[4], std::complex<double> (&P)[4]);

    void inverse_matrixSU2(std::complex<double> Original[4], std::complex<double> (&Inver)[4]);

    void Paulibasis2matrix(std::complex<double> P[4], std::complex<double> (&M)[4]);

    //From a Pauli vecto, its inverse is calculated
    void InversefromPaulibasis(std::complex<double> Original[4],    std::complex<double> (&Inver)[4]);

    //in the Pauli Basis M=P[0] Sigma0 + P[1] Sigma1 + P[2] Sigma2 + P[3] Sigma3
    void matrix2Paulibasis(std::complex<double> M[4], std::complex<double> (&P)[4]);

    void extrarotationangles(std::complex<double> R[4], double &alpha_x, double &alpha_y);

    // and returns the tranformation angles, alpha_x an alpha_y for the transformation Et=R(alpha_y)R(alpha_x)Eu.
    //Where Et an Eu, are the tilted and untilted images.
    void angles2tranformation(double untilt_angles[3], double tilt_angles[3], double alpha_x, double alpha_y);

    void readParams();

    void run();


};
#endif