librelion-dev-common 1.4+dfsg-3ubuntu1 / usr / include / relion-1.4 / src / metadata_label.h

/***************************************************************************
 *
 * Author: "Sjors H.W. Scheres"
 * MRC Laboratory of Molecular Biology
 *
 * 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.
 *
 * This complete copyright notice must be included in any revised version of the
 * source code. Additional authorship citations may be added, but existing
 * author citations must be preserved.
 ***************************************************************************/
/***************************************************************************
 *
 * Authors:     J.M. De la Rosa Trevin (jmdelarosa@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 METADATA_LABEL_H
#define METADATA_LABEL_H

#include <map>
#include <iostream>
#include <iomanip>
#include <sstream>
#include <fstream>
#include "src/funcs.h"

class EMDLabelData;
class StaticInitialization;

enum EMDLabel
{
    EMDL_UNDEFINED = -1, // Keep the order the same as in StaticInitialization below!!
    EMDL_FIRST_LABEL,
    EMDL_OBJID = EMDL_FIRST_LABEL, ///< object id (int), NOTE: This label is special and shouldn't be used

    EMDL_AREA_ID, ///< ID for the area (or field of view). If one does not use (tilt) series, area would be the same as micrograph...
    EMDL_AREA_NAME, ///< Name for the area (or field of view). If one does not use (tilt) series, area would be the same as micrograph...
    EMDL_COMMENT, // The EMDL_COMMENT is handled specially as well

    EMDL_CTF_BFACTOR, ///< B-factor
    EMDL_CTF_SCALEFACTOR, ///< linear scale-factor
    EMDL_CTF_SAMPLING_RATE, ///< Sampling rate
    EMDL_CTF_VOLTAGE, ///< Microscope voltage (kV)
    EMDL_CTF_DEFOCUSU, ///< Defocus U (Angstroms)
    EMDL_CTF_DEFOCUSV, ///< Defocus V (Angstroms)
    EMDL_CTF_DEFOCUS_ANGLE, ///< Defocus angle (degrees)
    EMDL_CTF_CS, ///< Spherical aberration
    EMDL_CTF_CA, ///< Chromatic aberration
    EMDL_CTF_DETECTOR_PIXEL_SIZE, ///< Pixel size for detector as used in CTF-determination
    EMDL_CTF_ENERGY_LOSS, ///< Energy loss
    EMDL_CTF_FOM, ///< ctffind FOM (CC) for quality of CTF-fit
    EMDL_CTF_IMAGE, ///< name of an image describing the CTF model
    EMDL_CTF_LENS_STABILITY, ///< Lens stability
    EMDL_CTF_MAGNIFICATION, ///< Magnification used for CTF-determination
    EMDL_CTF_CONVERGENCE_CONE, ///< Convergence cone
    EMDL_CTF_LONGITUDINAL_DISPLACEMENT, ///< Longitudinal displacement
    EMDL_CTF_TRANSVERSAL_DISPLACEMENT, ///< Transversal displacemente
    EMDL_CTF_Q0, ///< Amplitude contrast
    EMDL_CTF_K, ///< CTF gain
    EMDL_CTF_VALUE, ///< CTF value

    EMDL_IMAGE_NAME,
    EMDL_IMAGE_ORI_NAME,
    EMDL_IMAGE_RECONSTRUCT_NAME,
    EMDL_IMAGE_ID,
    EMDL_IMAGE_ENABLED,
    EMDL_IMAGE_DATATYPE,
    EMDL_IMAGE_DIMENSIONALITY,
    EMDL_IMAGE_BEAMTILT_X,
    EMDL_IMAGE_BEAMTILT_Y,
    EMDL_IMAGE_BEAMTILT_GROUP,
    EMDL_IMAGE_COORD_X,
    EMDL_IMAGE_COORD_Y,
    EMDL_IMAGE_COORD_Z,
    EMDL_IMAGE_FRAME_NR,
    EMDL_IMAGE_MAGNIFICATION_CORRECTION,
    EMDL_IMAGE_NORM_CORRECTION,
    EMDL_IMAGE_SAMPLINGRATE,
    EMDL_IMAGE_SAMPLINGRATE_X,
    EMDL_IMAGE_SAMPLINGRATE_Y,
    EMDL_IMAGE_SAMPLINGRATE_Z,
    EMDL_IMAGE_SIZE,
    EMDL_IMAGE_SIZEX,
    EMDL_IMAGE_SIZEY,
    EMDL_IMAGE_SIZEZ,
    EMDL_IMAGE_STATS_MIN,
    EMDL_IMAGE_STATS_MAX,
    EMDL_IMAGE_STATS_AVG,
    EMDL_IMAGE_STATS_STDDEV,
    EMDL_IMAGE_STATS_SKEW,
    EMDL_IMAGE_STATS_KURT,
    EMDL_IMAGE_WEIGHT,

    EMDL_MATRIX_1_1,
    EMDL_MATRIX_1_2,
    EMDL_MATRIX_1_3,
    EMDL_MATRIX_2_1,
    EMDL_MATRIX_2_2,
    EMDL_MATRIX_2_3,
    EMDL_MATRIX_3_1,
    EMDL_MATRIX_3_2,
    EMDL_MATRIX_3_3,

    EMDL_MICROGRAPH_ID,
    EMDL_MICROGRAPH_NAME,
    EMDL_MICROGRAPH_TILT_ANGLE,
    EMDL_MICROGRAPH_TILT_AXIS_DIRECTION,
    EMDL_MICROGRAPH_TILT_AXIS_OUTOFPLANE,

    EMDL_MLMODEL_ACCURACY_ROT,
    EMDL_MLMODEL_ACCURACY_TRANS,
    EMDL_MLMODEL_AVE_PMAX,
    EMDL_MLMODEL_CURRENT_RESOLUTION,
    EMDL_MLMODEL_CURRENT_SIZE,
    EMDL_MLMODEL_DATA_VS_PRIOR_REF,
    EMDL_MLMODEL_DIMENSIONALITY,
    EMDL_MLMODEL_DIMENSIONALITY_DATA,
    EMDL_MLMODEL_DIFF2_HALVES_REF,
    EMDL_MLMODEL_FSC_HALVES_REF,
    EMDL_MLMODEL_GROUP_NAME,
    EMDL_MLMODEL_GROUP_NO,
    EMDL_MLMODEL_GROUP_NR_PARTICLES,
    EMDL_MLMODEL_GROUP_SCALE_CORRECTION,
    EMDL_MLMODEL_INTERPOLATOR,
    EMDL_MLMODEL_LL,
    EMDL_MLMODEL_MINIMUM_RADIUS_NN_INTERPOLATION,
    EMDL_MLMODEL_NORM_CORRECTION_AVG,
    EMDL_MLMODEL_NR_CLASSES,
    EMDL_MLMODEL_NR_GROUPS,
    EMDL_MLMODEL_ORIGINAL_SIZE,
    EMDL_MLMODEL_ORIENTABILITY_CONTRIBUTION,
    EMDL_MLMODEL_PADDING_FACTOR,
    EMDL_MLMODEL_PDF_CLASS,
    EMDL_MLMODEL_PRIOR_OFFX_CLASS,
    EMDL_MLMODEL_PRIOR_OFFY_CLASS,
    EMDL_MLMODEL_PDF_ORIENT,
    EMDL_MLMODEL_PIXEL_SIZE,
    EMDL_MLMODEL_POWER_REF,
    EMDL_MLMODEL_PRIOR_MODE,
    EMDL_MLMODEL_SIGMA_OFFSET,
    EMDL_MLMODEL_SIGMA_ROT,
    EMDL_MLMODEL_SIGMA_TILT,
    EMDL_MLMODEL_SIGMA_PSI,
    EMDL_MLMODEL_REF_IMAGE,
    EMDL_MLMODEL_SIGMA2_NOISE,
    EMDL_MLMODEL_SIGMA2_REF,
    EMDL_MLMODEL_SSNR_REF,
    EMDL_MLMODEL_TAU2_FUDGE_FACTOR,
    EMDL_MLMODEL_TAU2_REF,

    EMDL_OPTIMISER_ACCURACY_ROT,
    EMDL_OPTIMISER_ACCURACY_TRANS,
    EMDL_OPTIMISER_ADAPTIVE_FRACTION,
    EMDL_OPTIMISER_ADAPTIVE_OVERSAMPLING,
    EMDL_OPTIMISER_AUTO_LOCAL_HP_ORDER,
    EMDL_OPTIMISER_AVAILABLE_MEMORY,
    EMDL_OPTIMISER_BEST_RESOL_THUS_FAR,
	EMDL_OPTIMISER_CHANGES_OPTIMAL_OFFSETS,
	EMDL_OPTIMISER_CHANGES_OPTIMAL_ORIENTS,
	EMDL_OPTIMISER_CHANGES_OPTIMAL_CLASSES,
    EMDL_OPTIMISER_COARSE_SIZE,
    EMDL_OPTIMISER_DATA_ARE_CTF_PHASE_FLIPPED,
    EMDL_OPTIMISER_DATA_STARFILE,
    EMDL_OPTIMISER_DO_AUTO_REFINE,
    EMDL_OPTIMISER_DO_ONLY_FLIP_CTF_PHASES,
    EMDL_OPTIMISER_DO_CORRECT_CTF,
    EMDL_OPTIMISER_DO_CORRECT_MAGNIFICATION,
    EMDL_OPTIMISER_DO_CORRECT_NORM,
    EMDL_OPTIMISER_DO_CORRECT_SCALE,
    EMDL_OPTIMISER_DO_REALIGN_MOVIES,
    EMDL_OPTIMISER_DO_MAP,
    EMDL_OPTIMISER_DO_SOLVENT_FLATTEN,
    EMDL_OPTIMISER_DO_SKIP_ALIGN,
    EMDL_OPTIMISER_DO_SKIP_ROTATE,
    EMDL_OPTIMISER_DO_SPLIT_RANDOM_HALVES,
    EMDL_OPTIMISER_DO_ZERO_MASK,
    EMDL_OPTIMISER_FIX_SIGMA_NOISE,
    EMDL_OPTIMISER_FIX_SIGMA_OFFSET,
    EMDL_OPTIMISER_FIX_TAU,
    EMDL_OPTIMISER_HAS_CONVERGED,
    EMDL_OPTIMISER_HAS_HIGH_FSC_AT_LIMIT,
    EMDL_OPTIMISER_HAS_LARGE_INCR_SIZE_ITER_AGO,
    EMDL_OPTIMISER_HIGHRES_LIMIT_EXP,
    EMDL_OPTIMISER_IGNORE_CTF_UNTIL_FIRST_PEAK,
    EMDL_OPTIMISER_INCR_SIZE,
    EMDL_OPTIMISER_ITERATION_NO,
    EMDL_OPTIMISER_LOWRES_JOIN_RANDOM_HALVES,
    EMDL_OPTIMISER_MAGNIFICATION_RANGE,
    EMDL_OPTIMISER_MAGNIFICATION_STEP,
    EMDL_OPTIMISER_MAX_COARSE_SIZE,
    EMDL_OPTIMISER_MAX_NR_POOL,
    EMDL_OPTIMISER_MODEL_STARFILE,
    EMDL_OPTIMISER_MODEL_STARFILE2,
    EMDL_OPTIMISER_NR_ITERATIONS,
    EMDL_OPTIMISER_NR_ITER_WO_RESOL_GAIN,
    EMDL_OPTIMISER_NR_ITER_WO_HIDDEN_VAR_CHANGES,
    EMDL_OPTIMISER_OUTPUT_ROOTNAME,
    EMDL_OPTIMISER_PARTICLE_DIAMETER,
    EMDL_OPTIMISER_RADIUS_MASK_3D_MAP,
    EMDL_OPTIMISER_RADIUS_MASK_EXP_PARTICLES,
    EMDL_OPTIMISER_RANDOM_SEED,
    EMDL_OPTIMISER_REFS_ARE_CTF_CORRECTED,
    EMDL_OPTIMISER_SAMPLING_STARFILE,
    EMDL_OPTIMISER_SMALLEST_CHANGES_OPT_CLASSES,
    EMDL_OPTIMISER_SMALLEST_CHANGES_OPT_OFFSETS,
    EMDL_OPTIMISER_SMALLEST_CHANGES_OPT_ORIENTS,
    EMDL_OPTIMISER_SOLVENT_MASK_NAME,
    EMDL_OPTIMISER_SOLVENT_MASK2_NAME,
    EMDL_OPTIMISER_TAU_SPECTRUM_NAME,
    EMDL_OPTIMISER_USE_TOO_COARSE_SAMPLING,
    EMDL_OPTIMISER_WIDTH_MASK_EDGE,

    EMDL_ORIENT_FLIP,
    EMDL_ORIENT_ID,
    EMDL_ORIENT_ORIGIN_X,
    EMDL_ORIENT_ORIGIN_X_PRIOR,
    EMDL_ORIENT_ORIGIN_Y,
    EMDL_ORIENT_ORIGIN_Y_PRIOR,
    EMDL_ORIENT_ORIGIN_Z,
    EMDL_ORIENT_ORIGIN_Z_PRIOR,
    EMDL_ORIENT_ROT,
    EMDL_ORIENT_ROT_PRIOR,
    EMDL_ORIENT_TILT,
    EMDL_ORIENT_TILT_PRIOR,
    EMDL_ORIENT_PSI,
    EMDL_ORIENT_PSI_PRIOR,

    EMDL_PARTICLE_AUTOPICK_FOM,
    EMDL_PARTICLE_CLASS,
    EMDL_PARTICLE_DLL,
    EMDL_PARTICLE_ID,
    EMDL_PARTICLE_FOM,
    EMDL_PARTICLE_KL_DIVERGENCE,
    EMDL_PARTICLE_RANDOM_SUBSET,
    EMDL_PARTICLE_NAME,
    EMDL_PARTICLE_ORI_NAME,
    EMDL_PARTICLE_NR_SIGNIFICANT_SAMPLES,
    EMDL_PARTICLE_NR_FRAMES,
    EMDL_PARTICLE_PMAX,

    EMDL_POSTPROCESS_BFACTOR,
    EMDL_POSTPROCESS_FINAL_RESOLUTION,
    EMDL_POSTPROCESS_FSC_GENERAL,
    EMDL_POSTPROCESS_FSC_TRUE,
    EMDL_POSTPROCESS_FSC_MASKED,
    EMDL_POSTPROCESS_FSC_UNMASKED,
    EMDL_POSTPROCESS_FSC_RANDOM_MASKED,
    EMDL_POSTPROCESS_GUINIER_FIT_CORRELATION,
    EMDL_POSTPROCESS_GUINIER_FIT_INTERCEPT,
    EMDL_POSTPROCESS_GUINIER_FIT_SLOPE,
    EMDL_POSTPROCESS_GUINIER_VALUE_IN,
    EMDL_POSTPROCESS_GUINIER_VALUE_INVMTF,
    EMDL_POSTPROCESS_GUINIER_VALUE_WEIGHTED,
    EMDL_POSTPROCESS_GUINIER_VALUE_SHARPENED,
    EMDL_POSTPROCESS_GUINIER_VALUE_INTERCEPT,
    EMDL_POSTPROCESS_GUINIER_RESOL_SQUARED,
    EMDL_POSTPROCESS_MTF_VALUE, ///< Detector MTF value

    EMDL_SAMPLING_IS_3D,
    EMDL_SAMPLING_IS_3D_TRANS,
    EMDL_SAMPLING_HEALPIX_ORDER,
    EMDL_SAMPLING_LIMIT_TILT,
    EMDL_SAMPLING_OFFSET_RANGE,
    EMDL_SAMPLING_OFFSET_STEP,
    EMDL_SAMPLING_PERTURB,
    EMDL_SAMPLING_PERTURBATION_FACTOR,
    EMDL_SAMPLING_PRIOR_MODE,
    EMDL_SAMPLING_PSI_STEP,
    EMDL_SAMPLING_SIGMA_ROT,
    EMDL_SAMPLING_SIGMA_TILT,
    EMDL_SAMPLING_SIGMA_PSI,
    EMDL_SAMPLING_SYMMETRY,

    EMDL_SELECTED,
    EMDL_SELECT_PARTICLES_ZSCORE,
    EMDL_SORTED_IDX,
    EMDL_PERFRAME_CUMULATIVE_WEIGHT,
    EMDL_PERFRAME_RELATIVE_WEIGHT,

    EMDL_RESOLUTION,
    EMDL_RESOLUTION_ANGSTROM,
    EMDL_RESOLUTION_INVPIXEL,
    EMDL_SPECTRAL_IDX,

    EMDL_LAST_LABEL                       // **** NOTE ****: Do keep this label always at the end
    // it is here for looping purposes
};//close enum Label

enum EMDLabelType
{
    EMDL_INT, EMDL_LONG, EMDL_BOOL, EMDL_DOUBLE, EMDL_FLOAT, EMDL_STRING
};

class EMDL
{
public:
    // This enum defines what MetaDataLabels this class can manage, if
    // you need a new one add it here and modify affected methods:
    //
    //  - static EMDLabel codifyLabel( std::string strLabel );        EMDL::addLabel(EMDL_OPTIMISER_RANDOM_SEED, EMDL_INT, "randomSeed");

    // - static std::string EMDL::label2Str( EMDLabel inputLabel );
    // - void writeValuesToFile( std::ofstream &outfile, EMDLabel inputLabel );
    // - void addValue( std::string name, std::string value );
    //
    // Keep this special structure (using EMDL_FIRSTLABEL and EMDL_LAST_LABEL) so the
    // programmer can iterate through it like this:
    //
    //  for( EMDLabel mdl = EMDL_FIRST_LABEL ; mdl < EMDL_LAST_LABEL ; EMDLabel( mdl+1 ) )
    //

static EMDLabel str2Label(const std::string &labelName);
static std::string label2Str(const EMDLabel &label);

static bool isInt(const EMDLabel &label);
static bool isLong(const EMDLabel &label);
static bool isBool(const EMDLabel &label);
static bool isString(const EMDLabel &label);
static bool isDouble(const EMDLabel &label);
static bool isNumber(const EMDLabel &label);
static bool isValidLabel(const EMDLabel &label);
static bool isValidLabel(const std::string &labelName);

static void printDefinitions(std::ostream& out);

private:
    static std::map<EMDLabel, EMDLabelData> data;
    static std::map<std::string, EMDLabel> names;
    static std::map<std::string, std::string> definitions;
    static StaticInitialization initialization; //Just for initialization

    static void addLabel(EMDLabel label, EMDLabelType type, std::string name, std::string definition = "undocumented");

    friend class StaticInitialization;
}
;//close class MLD definition

//Just an struct to store type and string alias
class EMDLabelData
{
public:
    EMDLabelType type;
    std::string str;
    //Default constructor
    EMDLabelData()
    {
    }
    EMDLabelData(EMDLabelType t, std::string s)
    {
        type = t;
        str = s;
    }
};//close class EMDLabelData c

//Just a class for static initialization
class StaticInitialization
{
private:
    StaticInitialization()
    {
        ///==== Add labels entries from here in the SAME ORDER as declared in ENUM ==========
    	EMDL::addLabel(EMDL_COMMENT, EMDL_STRING, "rlnComment", "A metadata comment (This is treated in a special way)");

        EMDL::addLabel(EMDL_AREA_ID, EMDL_LONG, "rlnAreaId", "ID (i.e. a unique number) of an area (i.e. field-of-view)");
        EMDL::addLabel(EMDL_AREA_NAME, EMDL_STRING, "rlnAreaName", "Name of an area (i.e. field-of-view)");

    	EMDL::addLabel(EMDL_CTF_BFACTOR, EMDL_DOUBLE, "rlnBfactor", "B-factor (in A^2) that describes power spectrum fall-off");
    	EMDL::addLabel(EMDL_CTF_SCALEFACTOR, EMDL_DOUBLE, "rlnCtfScalefactor", "Linear scale-factor on the CTF (values between 0 and 1)");
        EMDL::addLabel(EMDL_CTF_VOLTAGE, EMDL_DOUBLE, "rlnVoltage", "Voltage of the microscope (in kV)");
        EMDL::addLabel(EMDL_CTF_DEFOCUSU, EMDL_DOUBLE, "rlnDefocusU", "Defocus in U-direction (in Angstroms, positive values for underfocus)");
        EMDL::addLabel(EMDL_CTF_DEFOCUSV, EMDL_DOUBLE, "rlnDefocusV", "Defocus in V-direction (in Angstroms, positive values for underfocus)");
        EMDL::addLabel(EMDL_CTF_DEFOCUS_ANGLE, EMDL_DOUBLE, "rlnDefocusAngle", "Angle between X and defocus U direction (in degrees)");
        EMDL::addLabel(EMDL_CTF_CS, EMDL_DOUBLE, "rlnSphericalAberration", "Spherical aberration (in millimeters)");
        EMDL::addLabel(EMDL_CTF_CA, EMDL_DOUBLE, "rlnChromaticAberration", "Chromatic aberration (in millimeters)");
        EMDL::addLabel(EMDL_CTF_DETECTOR_PIXEL_SIZE, EMDL_DOUBLE, "rlnDetectorPixelSize", "Pixel size of the detector (in micrometers)");
        EMDL::addLabel(EMDL_CTF_ENERGY_LOSS, EMDL_DOUBLE, "rlnEnergyLoss", "Energy loss (in eV)");
        EMDL::addLabel(EMDL_CTF_FOM, EMDL_DOUBLE, "rlnCtfFigureOfMerit", "Figure of merit for the fit of the CTF (not used inside relion_refine)");
        EMDL::addLabel(EMDL_CTF_IMAGE, EMDL_STRING, "rlnCtfImage", "Name of an image with all CTF values");
        EMDL::addLabel(EMDL_CTF_LENS_STABILITY, EMDL_DOUBLE, "rlnLensStability", "Lens stability (in ppm)");
        EMDL::addLabel(EMDL_CTF_MAGNIFICATION, EMDL_DOUBLE, "rlnMagnification", "Magnification at the detector (in times)");
        EMDL::addLabel(EMDL_CTF_CONVERGENCE_CONE, EMDL_DOUBLE, "rlnConvergenceCone", "Convergence cone (in mrad)");
        EMDL::addLabel(EMDL_CTF_LONGITUDINAL_DISPLACEMENT, EMDL_DOUBLE, "rlnLongitudinalDisplacement", "Longitudinal displacement (in Angstroms)");
        EMDL::addLabel(EMDL_CTF_TRANSVERSAL_DISPLACEMENT, EMDL_DOUBLE, "rlnTransversalDisplacement", "Transversal displacement (in Angstroms)");
        EMDL::addLabel(EMDL_CTF_Q0, EMDL_DOUBLE, "rlnAmplitudeContrast", "Amplitude contrast (as a fraction, i.e. 10% = 0.1)");
        EMDL::addLabel(EMDL_CTF_VALUE, EMDL_DOUBLE, "rlnCtfValue", "Value of the Contrast Transfer Function");

    	EMDL::addLabel(EMDL_IMAGE_NAME, EMDL_STRING, "rlnImageName", "Name of an image");
    	EMDL::addLabel(EMDL_IMAGE_ORI_NAME, EMDL_STRING, "rlnImageOriginalName", "Original name of an image");
    	EMDL::addLabel(EMDL_IMAGE_RECONSTRUCT_NAME, EMDL_STRING, "rlnReconstructImageName", "Name of an image to be used for reconstruction only");
    	EMDL::addLabel(EMDL_IMAGE_ID, EMDL_LONG, "rlnImageId", "ID (i.e. a unique number) of an image");
    	EMDL::addLabel(EMDL_IMAGE_ENABLED, EMDL_BOOL, "rlnEnabled", "Not used in RELION, only included for backward compatibility with XMIPP selfiles");
        EMDL::addLabel(EMDL_IMAGE_DATATYPE, EMDL_INT, "rlnDataType", "Type of data stored in an image (e.g. int, DOUBLE etc)");
        EMDL::addLabel(EMDL_IMAGE_DIMENSIONALITY, EMDL_INT, "rlnImageDimensionality", "Dimensionality of data stored in an image (i.e. 2 or 3)");
        EMDL::addLabel(EMDL_IMAGE_BEAMTILT_X, EMDL_DOUBLE, "rlnBeamTiltX", "Beam tilt in the X-direction (in mrad)");
        EMDL::addLabel(EMDL_IMAGE_BEAMTILT_Y, EMDL_DOUBLE, "rlnBeamTiltY", "Beam tilt in the Y-direction (in mrad)");
        EMDL::addLabel(EMDL_IMAGE_BEAMTILT_GROUP, EMDL_STRING, "rlnBeamTiltGroupName", "Name of a group (of images) with assumedly identical beam-tilts");
        EMDL::addLabel(EMDL_IMAGE_COORD_X, EMDL_DOUBLE, "rlnCoordinateX", "X-Position of an image in a micrograph (in pixels)");
        EMDL::addLabel(EMDL_IMAGE_COORD_Y, EMDL_DOUBLE, "rlnCoordinateY", "Y-Position of an image in a micrograph (in pixels)");
        EMDL::addLabel(EMDL_IMAGE_COORD_Z, EMDL_DOUBLE, "rlnCoordinateZ", "Z-Position of an image in a 3D micrograph, i.e. tomogram (in pixels)");
        EMDL::addLabel(EMDL_IMAGE_FRAME_NR, EMDL_INT, "rlnMovieFrameNumber", "Number of a movie frame");
        EMDL::addLabel(EMDL_IMAGE_NORM_CORRECTION, EMDL_DOUBLE, "rlnNormCorrection", "Normalisation correction value for an image");
        EMDL::addLabel(EMDL_IMAGE_MAGNIFICATION_CORRECTION, EMDL_DOUBLE, "rlnMagnificationCorrection", "Magnification correction value for an image");
        EMDL::addLabel(EMDL_IMAGE_SAMPLINGRATE, EMDL_DOUBLE, "rlnSamplingRate", "Sampling rate of an image (in Angstrom/pixel)");
        EMDL::addLabel(EMDL_IMAGE_SAMPLINGRATE_X, EMDL_DOUBLE, "rlnSamplingRateX", "Sampling rate in X-direction of an image (in Angstrom/pixel)");
        EMDL::addLabel(EMDL_IMAGE_SAMPLINGRATE_Y, EMDL_DOUBLE, "rlnSamplingRateY", "Sampling rate in Y-direction of an image (in Angstrom/pixel)");
        EMDL::addLabel(EMDL_IMAGE_SAMPLINGRATE_Z, EMDL_DOUBLE, "rlnSamplingRateZ", "Sampling rate in Z-direction of an image (in Angstrom/pixel)");
        EMDL::addLabel(EMDL_IMAGE_SIZE, EMDL_INT, "rlnImageSize", "Size of an image (in pixels)");
        EMDL::addLabel(EMDL_IMAGE_SIZEX, EMDL_INT, "rlnImageSizeX", "Size of an image in the X-direction (in pixels)");
        EMDL::addLabel(EMDL_IMAGE_SIZEY, EMDL_INT, "rlnImageSizeY", "Size of an image in the Y-direction (in pixels)");
        EMDL::addLabel(EMDL_IMAGE_SIZEZ, EMDL_INT, "rlnImageSizeZ", "Size of an image in the Z-direction (in pixels)");
        EMDL::addLabel(EMDL_IMAGE_STATS_MIN, EMDL_DOUBLE, "rlnMinimumValue", "Minimum value for the pixels in an image");
        EMDL::addLabel(EMDL_IMAGE_STATS_MAX, EMDL_DOUBLE, "rlnMaximumValue", "Maximum value for the pixels in an image");
        EMDL::addLabel(EMDL_IMAGE_STATS_AVG, EMDL_DOUBLE, "rlnAverageValue", "Average value for the pixels in an image");
        EMDL::addLabel(EMDL_IMAGE_STATS_STDDEV, EMDL_DOUBLE, "rlnStandardDeviationValue", "Standard deviation for the pixel values in an image");
        EMDL::addLabel(EMDL_IMAGE_STATS_SKEW, EMDL_DOUBLE, "rlnSkewnessValue", "Skewness (3rd moment) for the pixel values in an image");
        EMDL::addLabel(EMDL_IMAGE_STATS_KURT, EMDL_DOUBLE, "rlnKurtosisExcessValue", "Kurtosis excess (4th moment - 3) for the pixel values in an image");
        EMDL::addLabel(EMDL_IMAGE_WEIGHT, EMDL_DOUBLE, "rlnImageWeight", "Relative weight of an image");

        EMDL::addLabel(EMDL_MATRIX_1_1, EMDL_DOUBLE, "rlnMatrix_1_1", "Matrix element (1,1) of a 3x3 matrix");
        EMDL::addLabel(EMDL_MATRIX_1_2, EMDL_DOUBLE, "rlnMatrix_1_2", "Matrix element (1,2) of a 3x3 matrix");
        EMDL::addLabel(EMDL_MATRIX_1_3, EMDL_DOUBLE, "rlnMatrix_1_3", "Matrix element (1,3) of a 3x3 matrix");
        EMDL::addLabel(EMDL_MATRIX_2_1, EMDL_DOUBLE, "rlnMatrix_2_1", "Matrix element (2,1) of a 3x3 matrix");
        EMDL::addLabel(EMDL_MATRIX_2_2, EMDL_DOUBLE, "rlnMatrix_2_2", "Matrix element (2,1) of a 3x3 matrix");
        EMDL::addLabel(EMDL_MATRIX_2_3, EMDL_DOUBLE, "rlnMatrix_2_3", "Matrix element (2,1) of a 3x3 matrix");
        EMDL::addLabel(EMDL_MATRIX_3_1, EMDL_DOUBLE, "rlnMatrix_3_1", "Matrix element (3,1) of a 3x3 matrix");
        EMDL::addLabel(EMDL_MATRIX_3_2, EMDL_DOUBLE, "rlnMatrix_3_2", "Matrix element (3,1) of a 3x3 matrix");
        EMDL::addLabel(EMDL_MATRIX_3_3, EMDL_DOUBLE, "rlnMatrix_3_3", "Matrix element (3,1) of a 3x3 matrix");

        EMDL::addLabel(EMDL_MICROGRAPH_ID, EMDL_LONG, "rlnMicrographId", "ID (i.e. a unique number) of a micrograph");
        EMDL::addLabel(EMDL_MICROGRAPH_NAME, EMDL_STRING, "rlnMicrographName", "Name of a micrograph");
        EMDL::addLabel(EMDL_MICROGRAPH_TILT_ANGLE, EMDL_DOUBLE, "rlnMicrographTiltAngle", "Tilt angle (in degrees) used to collect a micrograph");
        EMDL::addLabel(EMDL_MICROGRAPH_TILT_AXIS_DIRECTION, EMDL_DOUBLE, "rlnMicrographTiltAxisDirection", "Direction of the tilt-axis (in degrees) used to collect a micrograph");
        EMDL::addLabel(EMDL_MICROGRAPH_TILT_AXIS_OUTOFPLANE, EMDL_DOUBLE, "rlnMicrographTiltAxisOutOfPlane", "Out-of-plane angle (in degrees) of the tilt-axis used to collect a micrograph (90=in-plane)");

        EMDL::addLabel(EMDL_MLMODEL_ACCURACY_ROT, EMDL_DOUBLE, "rlnAccuracyRotations", "Estimated accuracy (in degrees) with which rotations can be assigned");
        EMDL::addLabel(EMDL_MLMODEL_ACCURACY_TRANS, EMDL_DOUBLE, "rlnAccuracyTranslations", "Estimated accuracy (in pixels) with which translations can be assigned");
        EMDL::addLabel(EMDL_MLMODEL_AVE_PMAX, EMDL_DOUBLE, "rlnAveragePmax", "Average value (over all images) of the maxima of the probability distributions");
        EMDL::addLabel(EMDL_MLMODEL_CURRENT_RESOLUTION, EMDL_DOUBLE, "rlnCurrentResolution", "Current resolution where SSNR^MAP drops below 1 (in 1/Angstroms)");
        EMDL::addLabel(EMDL_MLMODEL_CURRENT_SIZE, EMDL_INT, "rlnCurrentImageSize", "Current size of the images used in the refinement");
        EMDL::addLabel(EMDL_MLMODEL_DATA_VS_PRIOR_REF, EMDL_DOUBLE, "rlnSsnrMap", "Spectral signal-to-noise ratio as defined for MAP estimation (SSNR^MAP)");
        EMDL::addLabel(EMDL_MLMODEL_DIMENSIONALITY, EMDL_INT, "rlnReferenceDimensionality", "Dimensionality of the references (2D/3D)");
        EMDL::addLabel(EMDL_MLMODEL_DIMENSIONALITY_DATA, EMDL_INT, "rlnDataDimensionality", "Dimensionality of the data (2D/3D)");
        EMDL::addLabel(EMDL_MLMODEL_DIFF2_HALVES_REF, EMDL_DOUBLE, "rlnDiff2RandomHalves", "Power of the differences between two independent reconstructions from random halves of the data");
        EMDL::addLabel(EMDL_MLMODEL_FSC_HALVES_REF, EMDL_DOUBLE, "rlnGoldStandardFsc", "Fourier shell correlation between two independent reconstructions from random halves of the data");
        EMDL::addLabel(EMDL_MLMODEL_GROUP_NAME, EMDL_STRING, "rlnGroupName", "The name of a group of images (e.g. all images from a micrograph)");
        EMDL::addLabel(EMDL_MLMODEL_GROUP_NO, EMDL_LONG, "rlnGroupNumber", "The number of a group of images");
        EMDL::addLabel(EMDL_MLMODEL_GROUP_NR_PARTICLES, EMDL_LONG, "rlnGroupNrParticles", "Number particles in a group of images");
        EMDL::addLabel(EMDL_MLMODEL_GROUP_SCALE_CORRECTION, EMDL_DOUBLE, "rlnGroupScaleCorrection", "Intensity-scale correction for a group of images");
        EMDL::addLabel(EMDL_MLMODEL_INTERPOLATOR, EMDL_INT, "rlnFourierSpaceInterpolator", "The kernel used for Fourier-space interpolation (NN=0, linear=1)");
        EMDL::addLabel(EMDL_MLMODEL_LL, EMDL_DOUBLE, "rlnLogLikelihood", "Value of the log-likelihood target function");
        EMDL::addLabel(EMDL_MLMODEL_MINIMUM_RADIUS_NN_INTERPOLATION,  EMDL_INT, "rlnMinRadiusNnInterpolation","Minimum radius for NN-interpolation (in Fourier pixels), for smaller radii linear int. is used");
        EMDL::addLabel(EMDL_MLMODEL_NORM_CORRECTION_AVG, EMDL_DOUBLE, "rlnNormCorrectionAverage", "Average value (over all images) of the normalisation correction values");
        EMDL::addLabel(EMDL_MLMODEL_NR_CLASSES, EMDL_INT, "rlnNrClasses", "The number of references (i.e. classes) to be used in refinement");
        EMDL::addLabel(EMDL_MLMODEL_NR_GROUPS, EMDL_INT, "rlnNrGroups", "The number of different groups of images (each group has its own noise spectrum, and intensity-scale correction)");
        EMDL::addLabel(EMDL_MLMODEL_ORIENTABILITY_CONTRIBUTION, EMDL_DOUBLE, "rlnSpectralOrientabilityContribution", "Spectral SNR contribution to the orientability of individual particles");
        EMDL::addLabel(EMDL_MLMODEL_ORIGINAL_SIZE, EMDL_INT, "rlnOriginalImageSize", "Original size of the images (in pixels)");
        EMDL::addLabel(EMDL_MLMODEL_PADDING_FACTOR, EMDL_INT, "rlnPaddingFactor", "Oversampling factor for Fourier transforms of the references");
        EMDL::addLabel(EMDL_MLMODEL_PDF_CLASS, EMDL_DOUBLE, "rlnClassDistribution", "Probability Density Function of the different classes (i.e. fraction of images assigned to each class)");
        EMDL::addLabel(EMDL_MLMODEL_PRIOR_OFFX_CLASS, EMDL_DOUBLE, "rlnClassPriorOffsetX", "Prior in the X-offset for a class (in pixels)");
        EMDL::addLabel(EMDL_MLMODEL_PRIOR_OFFY_CLASS, EMDL_DOUBLE, "rlnClassPriorOffsetY", "Prior in the Y-offset for a class (in pixels)");
        EMDL::addLabel(EMDL_MLMODEL_PDF_ORIENT, EMDL_DOUBLE, "rlnOrientationDistribution", "Probability Density Function of the orientations  (i.e. fraction of images assigned to each orient)");
        EMDL::addLabel(EMDL_MLMODEL_PIXEL_SIZE, EMDL_DOUBLE, "rlnPixelSize", "Size of the pixels in the references and images (in Angstroms)");
        EMDL::addLabel(EMDL_MLMODEL_POWER_REF, EMDL_DOUBLE, "rlnReferenceSpectralPower", "Spherical average of the power of the reference");
        EMDL::addLabel(EMDL_MLMODEL_PRIOR_MODE, EMDL_INT, "rlnOrientationalPriorMode", "Mode for prior distributions on the orientations (0=no prior; 1=(rot,tilt,psi); 2=(rot,tilt); 3=rot; 4=tilt; 5=psi) ");
        EMDL::addLabel(EMDL_MLMODEL_REF_IMAGE, EMDL_STRING, "rlnReferenceImage", "Name of a reference image");
        EMDL::addLabel(EMDL_MLMODEL_SIGMA_OFFSET, EMDL_DOUBLE, "rlnSigmaOffsets","Standard deviation in the origin offsets (in Angstroms)");
        EMDL::addLabel(EMDL_MLMODEL_SIGMA2_NOISE, EMDL_DOUBLE, "rlnSigma2Noise", "Spherical average of the standard deviation in the noise (sigma)");
        EMDL::addLabel(EMDL_MLMODEL_SIGMA2_REF, EMDL_DOUBLE, "rlnReferenceSigma2", "Spherical average of the estimated power in the noise of a reference");
        EMDL::addLabel(EMDL_MLMODEL_SIGMA_ROT, EMDL_DOUBLE, "rlnSigmaPriorRotAngle", "Standard deviation of the prior on the rot (i.e. first Euler) angle");
        EMDL::addLabel(EMDL_MLMODEL_SIGMA_TILT, EMDL_DOUBLE, "rlnSigmaPriorTiltAngle", "Standard deviation of the prior on the tilt (i.e. second Euler) angle");
        EMDL::addLabel(EMDL_MLMODEL_SIGMA_PSI, EMDL_DOUBLE, "rlnSigmaPriorPsiAngle", "Standard deviation of the prior on the psi (i.e. third Euler) angle");
        EMDL::addLabel(EMDL_MLMODEL_SSNR_REF, EMDL_DOUBLE, "rlnSignalToNoiseRatio", "Spectral signal-to-noise ratio for a reference");
        EMDL::addLabel(EMDL_MLMODEL_TAU2_FUDGE_FACTOR, EMDL_DOUBLE, "rlnTau2FudgeFactor", "Regularisation parameter with which estimates for the power in the references will be multiplied (T in original paper)");
        EMDL::addLabel(EMDL_MLMODEL_TAU2_REF, EMDL_DOUBLE, "rlnReferenceTau2", "Spherical average of the estimated power in the signal of a reference");

        EMDL::addLabel(EMDL_OPTIMISER_ACCURACY_ROT, EMDL_DOUBLE, "rlnOverallAccuracyRotations", "Overall accuracy of the rotational assignments (in degrees)");
        EMDL::addLabel(EMDL_OPTIMISER_ACCURACY_TRANS, EMDL_DOUBLE, "rlnOverallAccuracyTranslations", "Overall accuracy of the translational assignments (in pixels)");
        EMDL::addLabel(EMDL_OPTIMISER_ADAPTIVE_FRACTION, EMDL_DOUBLE, "rlnAdaptiveOversampleFraction", "Fraction of the weights that will be oversampled in a second pass of the adaptive oversampling strategy");
		EMDL::addLabel(EMDL_OPTIMISER_ADAPTIVE_OVERSAMPLING, EMDL_INT, "rlnAdaptiveOversampleOrder", "Order of the adaptive oversampling (0=no oversampling, 1= 2x oversampling; 2= 4x oversampling, etc)");
		EMDL::addLabel(EMDL_OPTIMISER_AUTO_LOCAL_HP_ORDER, EMDL_INT, "rlnAutoLocalSearchesHealpixOrder", "Healpix order (before oversampling) from which autosampling procedure will use local angular searches");
		EMDL::addLabel(EMDL_OPTIMISER_AVAILABLE_MEMORY, EMDL_DOUBLE, "rlnAvailableMemory", "Available memory per computing node (i.e. per MPI-process)");
        EMDL::addLabel(EMDL_OPTIMISER_BEST_RESOL_THUS_FAR, EMDL_DOUBLE, "rlnBestResolutionThusFar", "The highest resolution that has been obtained in this optimization thus far");
        EMDL::addLabel(EMDL_OPTIMISER_COARSE_SIZE, EMDL_INT, "rlnCoarseImageSize", "Current size of the images to be used in the first pass of the adaptive oversampling strategy (may be smaller than the original image size)");
        EMDL::addLabel(EMDL_OPTIMISER_CHANGES_OPTIMAL_OFFSETS, EMDL_DOUBLE, "rlnChangesOptimalOffsets", "The average change in optimal translation in the last iteration (in pixels) ");
        EMDL::addLabel(EMDL_OPTIMISER_CHANGES_OPTIMAL_ORIENTS, EMDL_DOUBLE, "rlnChangesOptimalOrientations", "The average change in optimal orientation in the last iteration (in degrees) ");
        EMDL::addLabel(EMDL_OPTIMISER_CHANGES_OPTIMAL_CLASSES, EMDL_DOUBLE, "rlnChangesOptimalClasses", "The number of particles that changed their optimal clsas assignment in the last iteration");
        EMDL::addLabel(EMDL_OPTIMISER_DATA_ARE_CTF_PHASE_FLIPPED, EMDL_BOOL, "rlnCtfDataArePhaseFlipped", "Flag to indicate that the input images have been phase-flipped");
        EMDL::addLabel(EMDL_OPTIMISER_DATA_STARFILE, EMDL_STRING, "rlnExperimentalDataStarFile", "STAR file with metadata for the experimental images");
        EMDL::addLabel(EMDL_OPTIMISER_DO_CORRECT_CTF, EMDL_BOOL, "rlnDoCorrectCtf", "Flag to indicate that CTF-correction should be performed");
        EMDL::addLabel(EMDL_OPTIMISER_DO_CORRECT_MAGNIFICATION, EMDL_BOOL, "rlnDoCorrectMagnification", "Flag to indicate that (per-group) magnification correction should be performed");
        EMDL::addLabel(EMDL_OPTIMISER_DO_CORRECT_NORM, EMDL_BOOL, "rlnDoCorrectNorm", "Flag to indicate that (per-image) normalisation-error correction should be performed");
        EMDL::addLabel(EMDL_OPTIMISER_DO_CORRECT_SCALE, EMDL_BOOL, "rlnDoCorrectScale", "Flag to indicate that internal (per-group) intensity-scale correction should be performed");
        EMDL::addLabel(EMDL_OPTIMISER_DO_REALIGN_MOVIES, EMDL_BOOL, "rlnDoRealignMovies", "Flag to indicate that individual frames of movies are being re-aligned");
        EMDL::addLabel(EMDL_OPTIMISER_DO_MAP, EMDL_BOOL, "rlnDoMapEstimation", "Flag to indicate that MAP estimation should be performed (otherwise ML estimation)");
        EMDL::addLabel(EMDL_OPTIMISER_DO_AUTO_REFINE, EMDL_BOOL, "rlnDoAutoRefine", "Flag to indicate that 3D auto-refine procedure is being used");
        EMDL::addLabel(EMDL_OPTIMISER_DO_ONLY_FLIP_CTF_PHASES, EMDL_BOOL, "rlnDoOnlyFlipCtfPhases", "Flag to indicate that CTF-correction should only comprise phase-flipping");
        EMDL::addLabel(EMDL_OPTIMISER_DO_SOLVENT_FLATTEN, EMDL_BOOL, "rlnDoSolventFlattening", "Flag to indicate that the references should be masked to set their solvent areas to a constant density");
        EMDL::addLabel(EMDL_OPTIMISER_DO_SKIP_ALIGN, EMDL_BOOL, "rlnDoSkipAlign", "Flag to indicate that orientational (i.e. rotational and translational) searches will be omitted from the refinement, only marginalisation over classes will take place");
        EMDL::addLabel(EMDL_OPTIMISER_DO_SKIP_ROTATE, EMDL_BOOL, "rlnDoSkipRotate", "Flag to indicate that rotational searches will be omitted from the refinement, only marginalisation over classes and translations will take place");
        EMDL::addLabel(EMDL_OPTIMISER_DO_SPLIT_RANDOM_HALVES, EMDL_BOOL, "rlnDoSplitRandomHalves", "Flag to indicate that the data should be split into two completely separate, random halves");
        EMDL::addLabel(EMDL_OPTIMISER_DO_ZERO_MASK, EMDL_BOOL, "rlnDoZeroMask", "Flag to indicate that the surrounding solvent area in the experimental particles will be masked to zeros (by default random noise will be used");
        EMDL::addLabel(EMDL_OPTIMISER_FIX_SIGMA_NOISE, EMDL_BOOL, "rlnFixSigmaNoiseEstimates", "Flag to indicate that the estimates for the power spectra of the noise should be kept constant");
        EMDL::addLabel(EMDL_OPTIMISER_FIX_SIGMA_OFFSET ,EMDL_BOOL, "rlnFixSigmaOffsetEstimates", "Flag to indicate that the estimates for the stddev in the origin offsets should be kept constant");
        EMDL::addLabel(EMDL_OPTIMISER_FIX_TAU, EMDL_BOOL, "rlnFixTauEstimates", "Flag to indicate that the estimates for the power spectra of the signal (i.e. the references) should be kept constant");
        EMDL::addLabel(EMDL_OPTIMISER_HAS_CONVERGED, EMDL_BOOL, "rlnHasConverged", "Flag to indicate that the optimization has converged");
        EMDL::addLabel(EMDL_OPTIMISER_HAS_HIGH_FSC_AT_LIMIT, EMDL_BOOL, "rlnHasHighFscAtResolLimit", "Flag to indicate that the FSC at the resolution limit is significant");
        EMDL::addLabel(EMDL_OPTIMISER_HAS_LARGE_INCR_SIZE_ITER_AGO, EMDL_INT, "rlnHasLargeSizeIncreaseIterationsAgo", "How many iterations have passed since the last large increase in image size");
        EMDL::addLabel(EMDL_OPTIMISER_HIGHRES_LIMIT_EXP, EMDL_DOUBLE, "rlnHighresLimitExpectation", "High-resolution-limit (in Angstrom) for the expectation step");
        EMDL::addLabel(EMDL_OPTIMISER_IGNORE_CTF_UNTIL_FIRST_PEAK, EMDL_BOOL, "rlnDoIgnoreCtfUntilFirstPeak", "Flag to indicate that the CTFs should be ignored until their first peak");
        EMDL::addLabel(EMDL_OPTIMISER_INCR_SIZE, EMDL_INT, "rlnIncrementImageSize", "Number of Fourier shells to be included beyond the resolution where SSNR^MAP drops below 1");
        EMDL::addLabel(EMDL_OPTIMISER_ITERATION_NO, EMDL_INT, "rlnCurrentIteration", "The number of the current iteration");
        EMDL::addLabel(EMDL_OPTIMISER_LOWRES_JOIN_RANDOM_HALVES, EMDL_DOUBLE, "rlnJoinHalvesUntilThisResolution", "Resolution (in Angstrom) to join the two random half-reconstructions to prevent their diverging orientations (for C-symmetries)");
        EMDL::addLabel(EMDL_OPTIMISER_MAGNIFICATION_RANGE, EMDL_DOUBLE, "rlnMagnificationSearchRange", "Search range for magnification correction");
        EMDL::addLabel(EMDL_OPTIMISER_MAGNIFICATION_STEP, EMDL_DOUBLE, "rlnMagnificationSearchStep", "Step size  for magnification correction");
        EMDL::addLabel(EMDL_OPTIMISER_MAX_COARSE_SIZE, EMDL_INT, "rlnMaximumCoarseImageSize", "Maximum size of the images to be used in the first pass of the adaptive oversampling strategy (may be smaller than the original image size)");
        EMDL::addLabel(EMDL_OPTIMISER_MAX_NR_POOL, EMDL_INT, "rlnMaxNumberOfPooledParticles", "Maximum number particles that are processed together to speed up calculations");
        EMDL::addLabel(EMDL_OPTIMISER_MODEL_STARFILE, EMDL_STRING, "rlnModelStarFile", "STAR file with metadata for the model that is being refined");
        EMDL::addLabel(EMDL_OPTIMISER_MODEL_STARFILE2, EMDL_STRING, "rlnModelStarFile2", "STAR file with metadata for the second model that is being refined (from random halves of the data)");
        EMDL::addLabel(EMDL_OPTIMISER_NR_ITERATIONS, EMDL_INT, "rlnNumberOfIterations", "Maximum number of iterations to be performed");
        EMDL::addLabel(EMDL_OPTIMISER_NR_ITER_WO_RESOL_GAIN, EMDL_INT, "rlnNumberOfIterWithoutResolutionGain", "Number of iterations that have passed without a gain in resolution");
        EMDL::addLabel(EMDL_OPTIMISER_NR_ITER_WO_HIDDEN_VAR_CHANGES, EMDL_INT, "rlnNumberOfIterWithoutChangingAssignments", "Number of iterations that have passed without large changes in orientation and class assignments");
        EMDL::addLabel(EMDL_OPTIMISER_OUTPUT_ROOTNAME, EMDL_STRING, "rlnOutputRootName", "Rootname for all output files (this may include a directory structure, which should then exist)");
        EMDL::addLabel(EMDL_OPTIMISER_PARTICLE_DIAMETER, EMDL_DOUBLE, "rlnParticleDiameter", "Diameter of the circular mask to be applied to all experimental images (in Angstroms)");
        EMDL::addLabel(EMDL_OPTIMISER_RADIUS_MASK_3D_MAP, EMDL_INT, "rlnRadiusMaskMap", "Radius of the spherical mask to be applied to all references (in Angstroms)");
        EMDL::addLabel(EMDL_OPTIMISER_RADIUS_MASK_EXP_PARTICLES, EMDL_INT, "rlnRadiusMaskExpImages", "Radius of the circular mask to be applied to all experimental images (in Angstroms)");
        EMDL::addLabel(EMDL_OPTIMISER_RANDOM_SEED, EMDL_INT, "rlnRandomSeed", "Seed (i.e. a number) for the random number generator");
        EMDL::addLabel(EMDL_OPTIMISER_REFS_ARE_CTF_CORRECTED, EMDL_BOOL, "rlnRefsAreCtfCorrected", "Flag to indicate that the input references have been CTF-amplitude corrected");
        EMDL::addLabel(EMDL_OPTIMISER_SMALLEST_CHANGES_OPT_CLASSES, EMDL_INT, "rlnSmallestChangesClasses", "Smallest changes thus far in the optimal class assignments (in numer of particles).");
        EMDL::addLabel(EMDL_OPTIMISER_SMALLEST_CHANGES_OPT_OFFSETS, EMDL_DOUBLE, "rlnSmallestChangesOffsets", "Smallest changes thus far in the optimal offset assignments (in pixels).");
        EMDL::addLabel(EMDL_OPTIMISER_SMALLEST_CHANGES_OPT_ORIENTS, EMDL_DOUBLE, "rlnSmallestChangesOrientations", "Smallest changes thus far in the optimal orientation assignments (in degrees).");
        EMDL::addLabel(EMDL_OPTIMISER_SAMPLING_STARFILE, EMDL_STRING, "rlnOrientSamplingStarFile", "STAR file with metadata for the orientational sampling");
        EMDL::addLabel(EMDL_OPTIMISER_SOLVENT_MASK_NAME, EMDL_STRING, "rlnSolventMaskName", "Name of an image that contains a (possibly soft) mask for the solvent area (values=0 for solvent, values =1 for protein)");
        EMDL::addLabel(EMDL_OPTIMISER_SOLVENT_MASK2_NAME, EMDL_STRING, "rlnSolventMask2Name", "Name of a secondary solvent mask (e.g. to flatten density inside an icosahedral virus)");
        EMDL::addLabel(EMDL_OPTIMISER_TAU_SPECTRUM_NAME, EMDL_STRING, "rlnTauSpectrumName", "Name of a STAR file that holds a tau2-spectrum");
        EMDL::addLabel(EMDL_OPTIMISER_USE_TOO_COARSE_SAMPLING, EMDL_BOOL, "rlnUseTooCoarseSampling", "Flag to indicate that the angular sampling on the sphere will be one step coarser than needed to speed up calculations");
        EMDL::addLabel(EMDL_OPTIMISER_WIDTH_MASK_EDGE, EMDL_INT, "rlnWidthMaskEdge", "Width (in pixels) of the soft edge for spherical/circular masks to be used for solvent flattening");

        EMDL::addLabel(EMDL_ORIENT_FLIP, EMDL_BOOL, "rlnIsFlip", "Flag to indicate that an image should be mirrored");
        EMDL::addLabel(EMDL_ORIENT_ID, EMDL_LONG, "rlnOrientationsID", "ID (i.e. a unique number) for an orientation");
        EMDL::addLabel(EMDL_ORIENT_ORIGIN_X, EMDL_DOUBLE, "rlnOriginX", "X-coordinate (in pixels) for the origin of rotation");
        EMDL::addLabel(EMDL_ORIENT_ORIGIN_X_PRIOR, EMDL_DOUBLE, "rlnOriginXPrior", "Center of the prior on the X-coordinate (in pixels) for the origin of rotation");
        EMDL::addLabel(EMDL_ORIENT_ORIGIN_Y, EMDL_DOUBLE, "rlnOriginY", "Y-coordinate (in pixels) for the origin of rotation");
        EMDL::addLabel(EMDL_ORIENT_ORIGIN_Y_PRIOR, EMDL_DOUBLE, "rlnOriginYPrior", "Center of the prior on the X-coordinate (in pixels) for the origin of rotation");
        EMDL::addLabel(EMDL_ORIENT_ORIGIN_Z, EMDL_DOUBLE, "rlnOriginZ", "Z-coordinate (in pixels) for the origin of rotation");
        EMDL::addLabel(EMDL_ORIENT_ORIGIN_Z_PRIOR, EMDL_DOUBLE, "rlnOriginZPrior", "Center of the prior on the X-coordinate (in pixels) for the origin of rotation");
        EMDL::addLabel(EMDL_ORIENT_ROT, EMDL_DOUBLE, "rlnAngleRot", "First Euler angle (rot, in degrees)");
        EMDL::addLabel(EMDL_ORIENT_ROT_PRIOR, EMDL_DOUBLE, "rlnAngleRotPrior", "Center of the prior (in degrees) on the first Euler angle (rot)");
        EMDL::addLabel(EMDL_ORIENT_TILT, EMDL_DOUBLE, "rlnAngleTilt", "Second Euler angle (tilt, in degrees)");
        EMDL::addLabel(EMDL_ORIENT_TILT_PRIOR, EMDL_DOUBLE, "rlnAngleTiltPrior", "Center of the prior (in degrees) on the second Euler angle (tilt)");
        EMDL::addLabel(EMDL_ORIENT_PSI, EMDL_DOUBLE, "rlnAnglePsi", "Third Euler, or in-plane angle (psi, in degrees)");
        EMDL::addLabel(EMDL_ORIENT_PSI_PRIOR, EMDL_DOUBLE, "rlnAnglePsiPrior", "Center of the prior (in degrees) on the third Euler angle (psi)");

        EMDL::addLabel(EMDL_PARTICLE_AUTOPICK_FOM, EMDL_DOUBLE, "rlnAutopickFigureOfMerit", "Autopicking FOM for a particle");
        EMDL::addLabel(EMDL_PARTICLE_CLASS, EMDL_INT, "rlnClassNumber", "Class number for which a particle has its highest probability");
        EMDL::addLabel(EMDL_PARTICLE_DLL, EMDL_DOUBLE, "rlnLogLikeliContribution", "Contribution of a particle to the log-likelihood target function");
        EMDL::addLabel(EMDL_PARTICLE_ID, EMDL_LONG, "rlnParticleId", "ID (i.e. a unique number) for a particle");
        EMDL::addLabel(EMDL_PARTICLE_FOM, EMDL_DOUBLE, "rlnParticleFigureOfMerit", "Developmental FOM for a particle");
        EMDL::addLabel(EMDL_PARTICLE_KL_DIVERGENCE, EMDL_DOUBLE, "rlnKullbackLeibnerDivergence", "Kullback-Leibner divergence for a particle");
        EMDL::addLabel(EMDL_PARTICLE_RANDOM_SUBSET, EMDL_INT, "rlnRandomSubset", "Random subset to which this particle belongs");
        EMDL::addLabel(EMDL_PARTICLE_NAME, EMDL_STRING, "rlnParticleName", "Name for a particles");
        EMDL::addLabel(EMDL_PARTICLE_ORI_NAME, EMDL_STRING, "rlnOriginalParticleName", "Original name for a particles");
        EMDL::addLabel(EMDL_PARTICLE_NR_SIGNIFICANT_SAMPLES, EMDL_INT, "rlnNrOfSignificantSamples", "Number of orientational/class assignments (for a particle) with sign.probabilities in the 1st pass of adaptive oversampling"); /**< particle, Number of orientations contributing to weights*/
        EMDL::addLabel(EMDL_PARTICLE_NR_FRAMES, EMDL_INT, "rlnNrOfFrames", "Number of movie frames that were collected for this particle");
        EMDL::addLabel(EMDL_PARTICLE_PMAX, EMDL_DOUBLE, "rlnMaxValueProbDistribution", "Maximum value of the (normalised) probability function for a particle"); /**< particle, Maximum value of probability distribution */

        EMDL::addLabel(EMDL_POSTPROCESS_FINAL_RESOLUTION, EMDL_DOUBLE, "rlnFinalResolution", "Final estimated resolution after postprocessing (in Angstroms)");
        EMDL::addLabel(EMDL_POSTPROCESS_BFACTOR, EMDL_DOUBLE, "rlnBfactorUsedForSharpening", "Applied B-factor in the sharpening of the map");
        EMDL::addLabel(EMDL_POSTPROCESS_FSC_GENERAL, EMDL_DOUBLE, "rlnFourierShellCorrelation", "FSC value (of unspecified type, e.g. masked or unmasked)");
        EMDL::addLabel(EMDL_POSTPROCESS_FSC_TRUE, EMDL_DOUBLE, "rlnFourierShellCorrelationCorrected", "Final FSC value: i.e. after correction based on masking of randomized-phases maps");
        EMDL::addLabel(EMDL_POSTPROCESS_FSC_MASKED, EMDL_DOUBLE, "rlnFourierShellCorrelationMaskedMaps", "FSC value after masking of the original maps");
        EMDL::addLabel(EMDL_POSTPROCESS_FSC_UNMASKED, EMDL_DOUBLE, "rlnFourierShellCorrelationUnmaskedMaps", "FSC value before masking of the original maps");
        EMDL::addLabel(EMDL_POSTPROCESS_FSC_RANDOM_MASKED, EMDL_DOUBLE, "rlnCorrectedFourierShellCorrelationPhaseRandomizedMaskedMaps", "FSC value after masking of the randomized-phases maps");
        EMDL::addLabel(EMDL_POSTPROCESS_GUINIER_FIT_INTERCEPT, EMDL_DOUBLE, "rlnFittedInterceptGuinierPlot", "The fitted intercept of the Guinier-plot");
        EMDL::addLabel(EMDL_POSTPROCESS_GUINIER_FIT_SLOPE, EMDL_DOUBLE, "rlnFittedSlopeGuinierPlot", "The fitted slope of the Guinier-plot");
        EMDL::addLabel(EMDL_POSTPROCESS_GUINIER_FIT_CORRELATION, EMDL_DOUBLE, "rlnCorrelationFitGuinierPlot", "The correlation coefficient of the fitted line through the Guinier-plot");
        EMDL::addLabel(EMDL_POSTPROCESS_GUINIER_VALUE_IN, EMDL_DOUBLE, "rlnLogAmplitudesOriginal", "Y-value for Guinier plot: the logarithm of the radially averaged amplitudes of the input map");
        EMDL::addLabel(EMDL_POSTPROCESS_GUINIER_VALUE_INVMTF, EMDL_DOUBLE, "rlnLogAmplitudesMTFCorrected", "Y-value for Guinier plot: the logarithm of the radially averaged amplitudes after MTF correction");
        EMDL::addLabel(EMDL_POSTPROCESS_GUINIER_VALUE_WEIGHTED, EMDL_DOUBLE, "rlnLogAmplitudesWeighted", "Y-value for Guinier plot: the logarithm of the radially averaged amplitudes after FSC-weighting");
        EMDL::addLabel(EMDL_POSTPROCESS_GUINIER_VALUE_SHARPENED, EMDL_DOUBLE, "rlnLogAmplitudesSharpened", "Y-value for Guinier plot: the logarithm of the radially averaged amplitudes after sharpening");
        EMDL::addLabel(EMDL_POSTPROCESS_GUINIER_VALUE_INTERCEPT, EMDL_DOUBLE, "rlnLogAmplitudesIntercept", "Y-value for Guinier plot: the fitted plateau of the logarithm of the radially averaged amplitudes");
        EMDL::addLabel(EMDL_POSTPROCESS_GUINIER_RESOL_SQUARED, EMDL_DOUBLE, "rlnResolutionSquared", "X-value for Guinier plot: squared resolution in 1/Angstrom^2");
		EMDL::addLabel(EMDL_POSTPROCESS_MTF_VALUE, EMDL_DOUBLE, "rlnMtfValue", "Value of the detectors modulation transfer function (between 0 and 1)");

        EMDL::addLabel(EMDL_SAMPLING_IS_3D, EMDL_BOOL, "rlnIs3DSampling", "Flag to indicate this concerns a 3D sampling ");
        EMDL::addLabel(EMDL_SAMPLING_IS_3D_TRANS, EMDL_BOOL, "rlnIs3DTranslationalSampling", "Flag to indicate this concerns a x,y,z-translational sampling ");
        EMDL::addLabel(EMDL_SAMPLING_HEALPIX_ORDER, EMDL_INT, "rlnHealpixOrder", "Healpix order for the sampling of the first two Euler angles (rot, tilt) on the 3D sphere");
        EMDL::addLabel(EMDL_SAMPLING_LIMIT_TILT, EMDL_DOUBLE, "rlnTiltAngleLimit", "Values to which to limit the tilt angles (positive for keeping side views, negative for keeping top views)");
        EMDL::addLabel(EMDL_SAMPLING_OFFSET_RANGE, EMDL_DOUBLE, "rlnOffsetRange", "Search range for the origin offsets (in Angstroms)");
        EMDL::addLabel(EMDL_SAMPLING_OFFSET_STEP, EMDL_DOUBLE, "rlnOffsetStep", "Step size for the searches in the origin offsets (in Angstroms)");
        EMDL::addLabel(EMDL_SAMPLING_PERTURB, EMDL_DOUBLE, "rlnSamplingPerturbInstance", "Random instance of the random perturbation on the orientational sampling");
        EMDL::addLabel(EMDL_SAMPLING_PERTURBATION_FACTOR, EMDL_DOUBLE, "rlnSamplingPerturbFactor", "Factor for random perturbation on the orientational sampling (between 0 no perturbation and 1 very strong perturbation)");
        EMDL::addLabel(EMDL_SAMPLING_PSI_STEP, EMDL_DOUBLE, "rlnPsiStep", "Step size (in degrees) for the sampling of the in-plane rotation angle (psi)");
        EMDL::addLabel(EMDL_SAMPLING_SYMMETRY, EMDL_STRING, "rlnSymmetryGroup", "Symmetry group (e.g., C1, D7, I2, I5, etc.)");

        EMDL::addLabel(EMDL_SELECTED, EMDL_BOOL, "rlnSelected", "Flag whether an entry in a metadatatable is selected in the viewer or not");
        EMDL::addLabel(EMDL_SELECT_PARTICLES_ZSCORE, EMDL_DOUBLE, "rlnParticleSelectZScore", "Sum of Z-scores from particle_select. High Z-scores are likely to be outliers.");
        EMDL::addLabel(EMDL_SORTED_IDX, EMDL_LONG, "rlnSortedIndex", "Index of a metadata entry after sorting (first sorted index is 0).");
		EMDL::addLabel(EMDL_PERFRAME_CUMULATIVE_WEIGHT, EMDL_DOUBLE, "rlnPerFrameCumulativeWeight", "Sum of the resolution-dependent relative weights from the first frame until the given frame");
		EMDL::addLabel(EMDL_PERFRAME_RELATIVE_WEIGHT, EMDL_DOUBLE, "rlnPerFrameRelativeWeight", "The resolution-dependent relative weights for a given frame");

        EMDL::addLabel(EMDL_RESOLUTION, EMDL_DOUBLE, "rlnResolution", "Resolution (in 1/Angstroms)");
        EMDL::addLabel(EMDL_RESOLUTION_ANGSTROM, EMDL_DOUBLE, "rlnAngstromResolution", "Resolution (in Angstroms)");
        EMDL::addLabel(EMDL_RESOLUTION_INVPIXEL, EMDL_DOUBLE, "rlnResolutionInversePixel", "Resolution (in 1/pixel, Nyquist = 0.5)");
        EMDL::addLabel(EMDL_SPECTRAL_IDX, EMDL_INT, "rlnSpectralIndex", "Spectral index (i.e. distance in pixels to the origin in Fourier space) ");


     }

    ~StaticInitialization()
    {
    }
    friend class EMDL;
};

/**Just an utility function */
bool vectorContainsLabel(const std::vector<EMDLabel>& labelsVector, const EMDLabel label);



#endif