GPha.cpp

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/***************************************************************************
 *                GPha.cpp - XSPEC Pulse Height Analyzer class             *
 * ----------------------------------------------------------------------- *
 *  copyright (C) 2013-2018 by Juergen Knoedlseder                         *
 * ----------------------------------------------------------------------- *
 *                                                                         *
 *  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 3 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, see <http://www.gnu.org/licenses/>.  *
 *                                                                         *
 ***************************************************************************/
/**
 * @file GPha.cpp
 * @brief XSPEC Pulse Height Analyzer class implementation
 * @author Juergen Knoedlseder
 */

/* __ Includes ___________________________________________________________ */
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
#include "GPha.hpp"
#include "GException.hpp"
#include "GTools.hpp"
#include "GEnergy.hpp"
#include "GFits.hpp"
#include "GFitsTable.hpp"
#include "GFitsBinTable.hpp"
#include "GFitsTableShortCol.hpp"
#include "GFitsTableFloatCol.hpp"
#include "GNdarray.hpp"

/* __ Method name definitions ____________________________________________ */
#define G_OPERATOR_PLUS                             "GPha::operator+=(GPha&)"
#define G_OPERATOR_MINUS                            "GPha::operator-=(GPha&)"
#define G_OPERATOR                           "GPha::operator[](std::string&)"
#define G_AT1                                                "GPha::at(int&)"
#define G_AT2                                          "GPha::at(int&, int&)"
#define G_APPEND           "GPha::append(std::string&, std::vector<double>&)"
#define G_AREASCAL_SET                        "GPha::areascal(int&, double&)"
#define G_AREASCAL_GET                                 "GPha::areascal(int&)"
#define G_BACKSCAL_SET                        "GPha::backscal(int&, double&)"
#define G_BACKSCAL_GET                                 "GPha::backscal(int&)"
#define G_READ                                      "GPha::read(GFitsTable*)"

/* __ Macros _____________________________________________________________ */

/* __ Coding definitions _________________________________________________ */

/* __ Debug definitions __________________________________________________ */


/*==========================================================================
 =                                                                         =
 =                         Constructors/destructors                        =
 =                                                                         =
 ==========================================================================*/

/***********************************************************************//**
 * @brief Void constructor
 ***************************************************************************/
GPha::GPha(void)
{
    // Initialise members
    init_members();

    // Return
    return;
}


/***********************************************************************//**
 * @brief File constructor
 *
 * @param[in] filename File name.
 ***************************************************************************/
GPha::GPha(const GFilename& filename)
{
    // Initialise members
    init_members();

    // Load PHA file
    load(filename);

    // Return
    return;
}


/***********************************************************************//**
 * @brief Energy boundary constructor
 *
 * @param[in] ebds Energy boundaries.
 ***************************************************************************/
GPha::GPha(const GEbounds& ebds)
{
    // Initialise members
    init_members();

    // Set energy boundaries
    m_ebounds = ebds;

    // Initialize spectrum
    alloc(ebds.size());

    // Return
    return;
}


/***********************************************************************//**
 * @brief Energy bins constructor
 *
 * @param[in] bins Number of energy bins.
 ***************************************************************************/
GPha::GPha(const int& bins)
{
    // Initialise members
    init_members();

    // Initialize spectrum
    alloc(bins);

    // Return
    return;
}


/***********************************************************************//**
 * @brief Copy constructor
 *
 * @param[in] pha Pulse Height Analyzer spectrum.
 ***************************************************************************/
GPha::GPha(const GPha& pha)
{
    // Initialise members
    init_members();

    // Copy members
    copy_members(pha);

    // Return
    return;
}


/***********************************************************************//**
 * @brief Destructor
 ***************************************************************************/
GPha::~GPha(void)
{
    // Free members
    free_members();

    // Return
    return;
}


/*==========================================================================
 =                                                                         =
 =                                Operators                                =
 =                                                                         =
 ==========================================================================*/

/***********************************************************************//**
 * @brief Assignment operator
 *
 * @param[in] pha Pulse Height Analyzer spectrum.
 * @return Pulse Height Analyzer spectrum.
 ***************************************************************************/
GPha& GPha::operator=(const GPha& pha)
{
    // Execute only if object is not identical
    if (this != &pha) {

        // Free members
        free_members();

        // Initialise members
        init_members();

        // Copy members
        copy_members(pha);

    } // endif: object was not identical

    // Return
    return *this;
}


/***********************************************************************//**
 * @brief Add spectrum
 *
 * @param[in] pha Pulse Height Analyzer spectrum.
 * @return Sum of Pulse Height Analyzer spectra.
 *
 * @exception GException::invalid_value
 *            Incompatible spectrum.
 *
 * Adds the counts of a spectrum to the counts of the current spectrum. The
 * operator also adds the exposure times of the spectrum to the current
 * exposure time. The area scaling factor \f$\alpha\f$ is recomputed for
 * each spectral bin using
 *
 * \f[
 *    \alpha = \frac{N_1 + N_2}{\frac{N_1}{\alpha_1} + \frac{N_2}{\alpha_2}}
 * \f]
 *
 * where
 * \f$N_1\f$ and \f$N_2\f$ are the number of events in the bin for spectrum
 * 1 and 2, respectively, and
 * \f$\alpha_1\f$ and \f$\alpha_2\f$ are the corresponding area scaling
 * factors.
 *
 * The background scaling factor is not altered.
 *
 * The operator only works if the provide specturm has the same energy
 * binning than the current spectrum.
 ***************************************************************************/
GPha& GPha::operator+=(const GPha& pha)
{
    // Throw an exception if the spectra are not compatible
    if (this->ebounds() != pha.ebounds()) {
        std::string msg = "Incompatible energy binning of Pulse Height "
                          "Analyzer spectrum.";
        throw GException::invalid_value(G_OPERATOR_PLUS, msg);
    }
    
    // Add spectra
    for (int i = 0; i < this->size(); ++i) {

        // Update the area scaling
        double n1     = m_counts[i];
        double n2     = pha.m_counts[i];
        double a1     = m_areascal[i];
        double a2     = pha.m_areascal[i];
        double f1     = (a1 > 0.0) ? n1/a1 : 0.0;
        double f2     = (a2 > 0.0) ? n2/a2 : 0.0;
        double f      = f1 + f2;
        m_areascal[i] = (f > 0.0) ? (n1+n2)/f : 1.0;

        // Add counts
        m_counts[i] += pha.m_counts[i];
    }

    // Add attributes
    m_underflow += pha.m_underflow;
    m_overflow  += pha.m_overflow;
    m_outflow   += pha.m_outflow;
    m_exposure  += pha.m_exposure;

    // Return
    return *this;
}


/***********************************************************************//**
 * @brief Subtract spectrum
 *
 * @param[in] pha Pulse Height Analyzer spectrum.
 * @return Difference of Pulse Height Analyzer spectra.
 *
 * @exception GException::invalid_value
 *            Incompatible spectrum.
 *
 * Subtracts the counts of a spectrum from the counts of the current
 * spectrum. The operator also subtracts the exposure times of the spectrum
 * from the current exposure time.  The area scaling factor \f$\alpha\f$ is
 * recomputed for each spectral bin using
 *
 * \f[
 *    \alpha = \frac{N_1 - N_2}{\frac{N_1}{\alpha_1} - \frac{N_2}{\alpha_2}}
 * \f]
 *
 * where
 * \f$N_1\f$ and \f$N_2\f$ are the number of events in the bin for spectrum
 * 1 and 2, respectively, and
 * \f$\alpha_1\f$ and \f$\alpha_2\f$ are the corresponding area scaling
 * factors.
 *
 * The background scaling factor is not altered.
 *
 * The operator only works if the provide specturm has the same energy
 * binning than the current spectrum.
 ***************************************************************************/
GPha& GPha::operator-=(const GPha& pha)
{
    // Throw an exception if the spectra are not compatible
    if (this->ebounds() != pha.ebounds()) {
        std::string msg = "Incompatible energy binning of Pulse Height "
                          "Analyzer spectrum.";
        throw GException::invalid_value(G_OPERATOR_MINUS, msg);
    }
    
    // Subtract spectra
    for (int i = 0; i < this->size(); ++i) {

        // Update the area scaling
        double n1     = m_counts[i];
        double n2     = pha.m_counts[i];
        double a1     = m_areascal[i];
        double a2     = pha.m_areascal[i];
        double f1     = (a1 > 0.0) ? n1/a1 : 0.0;
        double f2     = (a2 > 0.0) ? n2/a2 : 0.0;
        double f      = f1 - f2;
        m_areascal[i] = (f > 0.0) ? (n1-n2)/f : 1.0;

        // Subtract counts
        m_counts[i] -= pha.m_counts[i];
    }

    // Subtract attributes
    m_underflow -= pha.m_underflow;
    m_overflow  -= pha.m_overflow;
    m_outflow   -= pha.m_outflow;
    m_exposure  -= pha.m_exposure;

    // Return
    return *this;
}


/***********************************************************************//**
 * @brief Scale spectrum values
 *
 * @param[in] scale Scale factor.
 * @return Scaled Pulse Height Analyzer spectrum.
 *
 * Multiplies the counts of a spectrum with a scale factor. The exposure
 * time and area and background scale factors are not altered.
 ***************************************************************************/
GPha& GPha::operator*=(const double& scale)
{
    // Scale spectrums
    for (int i = 0; i < this->size(); ++i) {
        m_counts[i] *= scale;
    }

    // Scale attributes
    m_underflow *= scale;
    m_overflow  *= scale;
    m_outflow   *= scale;

    // Return
    return *this;
}


/***********************************************************************//**
 * @brief Divide spectrum values
 *
 * @param[in] scale Division factor.
 * @return Divided Pulse Height Analyzer spectrum.
 *
 * Divides the counts of a spectrum by a scale factor. The exposure time
 * and the area and background scale factors are not altered.
 ***************************************************************************/
GPha& GPha::operator/=(const double& scale)
{
    // Scale spectrums
    for (int i = 0; i < this->size(); ++i) {
        m_counts[i] /= scale;
    }

    // Scale attributes
    m_underflow /= scale;
    m_overflow  /= scale;
    m_outflow   /= scale;

    // Return
    return *this;
}


/***********************************************************************//**
 * @brief Return additional vector column
 *
 * @param[in] colname Vector column name.
 * @return Vector column.
 *
 * Returns reference to additional vector column.
 ***************************************************************************/
std::vector<double>& GPha::operator[](const std::string& colname)
{
    // Determine index of additional column (-1 if not found)
    int index = column_index(colname);

    // Throw exception if index not found
    if (index == -1) {
        std::string msg = "Could not find additional column with name \""+
                          colname+"\".";
        throw GException::invalid_value(G_OPERATOR, msg);
    }

    // Return reference to vector column
    return (m_coldata[index]);
}


/***********************************************************************//**
 * @brief Return additional vector column (const version)
 *
 * @param[in] colname Vector column name.
 * @return Vector column.
 *
 * Returns reference to additional vector column.
 ***************************************************************************/
const std::vector<double>& GPha::operator[](const std::string& colname) const
{
    // Determine index of additional column (-1 if not found)
    int index = column_index(colname);

    // Throw exception if index not found
    if (index == -1) {
        std::string msg = "Could not find additional column with name \""+
                          colname+"\".";
        throw GException::invalid_value(G_OPERATOR, msg);
    }

    // Return reference to vector column
    return (m_coldata[index]);
}


/*==========================================================================
 =                                                                         =
 =                             Public methods                              =
 =                                                                         =
 ==========================================================================*/

/***********************************************************************//**
 * @brief Clear object.
 *
 * Reset object to a clean initial state.
 ***************************************************************************/
void GPha::clear(void)
{
    // Free memory
    free_members();

    // Initialise members
    init_members();

    // Return
    return;
}


/***********************************************************************//**
 * @brief Clone object
 *
 * @return Pulse Height Analyzer spectrum.
 ***************************************************************************/
GPha* GPha::clone(void) const
{
    // Clone client
    return new GPha(*this);
}


/***********************************************************************//**
 * @brief Return content of spectral bin
 *
 * @param[in] index Bin index [0,...,size()-1].
 *
 * @exception GException::out_of_range
 *            Spectral bin index is out of range.
 *
 * Returns reference to content of spectral bin with specified @p index.
 ***************************************************************************/
double& GPha::at(const int& index)
{
    // Raise exception if index is out of range
    if (index < 0 || index >= size()) {
        throw GException::out_of_range(G_AT1, "Spectral bin index", index, size());
    }

    // Return reference
    return (m_counts[index]);
}


/***********************************************************************//**
 * @brief Return content of spectral bin (const version)
 *
 * @param[in] index Bin index [0,...,size()-1].
 *
 * @exception GException::out_of_range
 *            Spectral bin index is out of range.
 *
 * Returns reference to content of spectral bin with specified @p index.
 ***************************************************************************/
const double& GPha::at(const int& index) const
{
    // Raise exception if index is out of range
    if (index < 0 || index >= size()) {
        throw GException::out_of_range(G_AT1, "Spectral bin index", index, size());
    }

    // Return reference
    return (m_counts[index]);
}


/***********************************************************************//**
 * @brief Return content of additional columns
 *
 * @param[in] index Bin index [0,...,size()-1].
 * @param[in] col Columns index [0,...,columns()-1].
 *
 * @exception GException::out_of_range
 *            Spectral bin or column index is out of range.
 *
 * Returns reference to content of additional columns.
 ***************************************************************************/
double& GPha::at(const int& index, const int& col)
{
    // Throw an exception if bin or column index is out of range
    if (index < 0 || index >= size()) {
        throw GException::out_of_range(G_AT2, "Bin index", index, size());
    }
    if (col < 0 || col >= columns()) {
        throw GException::out_of_range(G_AT2, "Column index", col, columns());
    }

    // Return reference
    return (m_coldata[col][index]);
}


/***********************************************************************//**
 * @brief Return content of additional columns (const version)
 *
 * @param[in] index Bin index [0,...,size()-1].
 * @param[in] col Columns index [0,...,columns()-1].
 *
 * @exception GException::out_of_range
 *            Spectral bin or column index is out of range.
 *
 * Returns reference to content of additional columns.
 ***************************************************************************/
const double& GPha::at(const int& index, const int& col) const
{
    // Throw an exception if bin or column index is out of range
    if (index < 0 || index >= size()) {
        throw GException::out_of_range(G_AT2, "Bin index", index, size());
    }
    if (col < 0 || col >= columns()) {
        throw GException::out_of_range(G_AT2, "Column index", col, columns());
    }

    // Return reference
    return (m_coldata[col][index]);
}


/***********************************************************************//**
 * @brief Append additional column to spectrum
 *
 * @param[in] name Additional column name.
 * @param[in] column Additional column data.
 ***************************************************************************/
void GPha::append(const std::string& name, const std::vector<double>& column)
{
    // Throw an exception if the number of elements in the column does not
    // correspond to the size of the spectrum
    if (column.size() != size()) {
        std::string msg = "Size of column "+gammalib::str(column.size())+
                          " is incompatible with size of spectrum "+
                          gammalib::str(size())+".";
        throw GException::invalid_argument(G_APPEND, msg);
    }

    // Append column name
    m_colnames.push_back(name);
    
    // Append column data
    m_coldata.push_back(column);

    // Return
    return;
}


/***********************************************************************//**
 * @brief Set area scaling factor
 *
 * @param[in] index Bin index [0,...,size()-1].
 * @param[in] areascal Area scaling factor.
 *
 * @exception GException::out_of_range
 *            Spectral bin index is out of range.
 *
 * Set area scaling for spectral bin with specified @p index.
 ***************************************************************************/
void GPha::areascal(const int& index, const double& areascal)
{
    // Raise exception if index is out of range
    if (index < 0 || index >= size()) {
        throw GException::out_of_range(G_AREASCAL_SET, "Spectral bin index",
                                       index, size());
    }

    // Set area scaling factor
    m_areascal[index] = areascal;

    // Return
    return;
}


/***********************************************************************//**
 * @brief Return area scaling factor
 *
 * @param[in] index Bin index [0,...,size()-1].
 *
 * @exception GException::out_of_range
 *            Spectral bin index is out of range.
 *
 * Returns reference to area scaling for spectral bin with specified
 * @p index.
 ***************************************************************************/
const double& GPha::areascal(const int& index) const
{
    // Raise exception if index is out of range
    if (index < 0 || index >= size()) {
        throw GException::out_of_range(G_AREASCAL_GET, "Spectral bin index",
                                       index, size());
    }

    // Return reference
    return (m_areascal[index]);
}


/***********************************************************************//**
 * @brief Set background scaling factor
 *
 * @param[in] index Bin index [0,...,size()-1].
 * @param[in] backscal Background scaling factor.
 *
 * @exception GException::out_of_range
 *            Spectral bin index is out of range.
 *
 * Set background scaling for spectral bin with specified @p index.
 ***************************************************************************/
void GPha::backscal(const int& index, const double& backscal)
{
    // Raise exception if index is out of range
    if (index < 0 || index >= size()) {
        throw GException::out_of_range(G_BACKSCAL_SET, "Spectral bin index",
                                       index, size());
    }

    // Set background scaling factor
    m_backscal[index] = backscal;

    // Return
    return;
}


/***********************************************************************//**
 * @brief Return background scaling factor
 *
 * @param[in] index Bin index [0,...,size()-1].
 *
 * @exception GException::out_of_range
 *            Spectral bin index is out of range.
 *
 * Returns reference to background scaling for spectral bin with specified
 * @p index.
 ***************************************************************************/
const double& GPha::backscal(const int& index) const
{
    // Raise exception if index is out of range
    if (index < 0 || index >= size()) {
        throw GException::out_of_range(G_BACKSCAL_GET, "Spectral bin index",
                                       index, size());
    }

    // Return reference
    return (m_backscal[index]);
}


/***********************************************************************//**
 * @brief Number of counts in spectrum
 *
 * Returns the number of counts in the spectrum.
 ***************************************************************************/
double GPha::counts(void) const
{
    // Initialise counts
    double counts = 0.0;
    
    // Compute content
    for (int i = 0; i < m_counts.size(); ++i) {
        counts += m_counts[i];
    }

    // Return counts
    return counts;
}

/***********************************************************************//**
 * @brief Get number of counts in spectrum as GNdarray
 *
 * @return GNdarray of number of counts in spectrum.
 *
 * Returns the number of counts in the spectrum as GNdarray.
 ***************************************************************************/
GNdarray GPha::counts_spectrum(void) const
{
    // Initialise array
    int      size   = m_counts.size();
    GNdarray counts = GNdarray(size);

    // Compute content
    for (int i = 0; i < size; ++i) {
        counts(i) = m_counts[i];
    }

    // Return counts
    return counts;
}


/***********************************************************************//**
 * @brief Get background scaling factors as GNdarray
 *
 * @return GNdarray of background scaling factors.
 *
 * Returns the background scaling factors as GNdarray.
 ***************************************************************************/
GNdarray GPha::backscal_spectrum(void) const
{
    // Initialise array
    int      size  = m_backscal.size();
    GNdarray alpha = GNdarray(size);

    // Compute content
    for (int i = 0; i < size; ++i) {
        alpha(i) = m_backscal[i];
    }

    // Return background scaling factors
    return alpha;
}


/***********************************************************************//**
 * @brief Fill spectrum with a value.
 *
 * @param[in] energy Energy.
 * @param[in] value Fill value (defaults to 1.0).
 *
 * Fills the specified @p value at a given @p energy in the spectrum.
 ***************************************************************************/
void GPha::fill(const GEnergy& energy, const double& value)
{
    // Get index
    int index = m_ebounds.index(energy);

    // If index is not valid, then check for underflow, overflow or outflow
    if (index == -1) {
        if (energy < m_ebounds.emin()) {
            m_underflow += value;
        }
        else if (energy >= m_ebounds.emax()) {
            m_overflow += value;
        }
        else {
            m_outflow += value;
        }
    }

    // ... otherwise fill the histogram
    else {
        m_counts[index] += value;
    }

    // Return
    return;
}


/***********************************************************************//**
 * @brief Load Pulse Height Analyzer spectrum
 *
 * @param[in] filename File name.
 *
 * Loads the Pulse Height Analyzer spectrum from a FITS file.
 ***************************************************************************/
void GPha::load(const GFilename& filename)
{
    // Clear spectrum
    clear();

    // Open FITS file (without extension name as the user is not allowed
    // to modify the extension names)
    GFits fits(filename.url());

    // Read PHA data
    read(fits);

    // Close FITS file
    fits.close();

    // Store filename
    m_filename = filename.url();

    // Return
    return;
}


/***********************************************************************//**
 * @brief Save Pulse Height Analyzer spectrum
 *
 * @param[in] filename File name.
 * @param[in] clobber Overwrite existing file?
 *
 * Saves the Pulse Height Analyzer spectrum and energy boundaries into a
 * FITS file. If a file with the given @p filename does not yet exist it
 * will be created. If the file exists it can be overwritten if the
 * @p clobber flag is set to `true`. Otherwise an exception is thrown.
 *
 * The method will save two binary FITS tables into the FITS file: a
 * `SPECTRUM` extension that contains the channel values of the Pulse
 * Height Analyzer spectrum and an `EBOUNDS` extension that contains the
 * energy boundaries for all channels.
 ***************************************************************************/
void GPha::save(const GFilename& filename, const bool& clobber) const
{
    // Create FITS file
    GFits fits;

    // Write PHA into file
    write(fits);

    // Save to file (without extension name since the requested extension
    // may not yet exist in the file)
    fits.saveto(filename.url(), clobber);

    // Store filename
    m_filename = filename.url();

    // Return
    return;
}


/***********************************************************************//**
 * @brief Read Pulse Height Analyzer spectrum
 *
 * @param[in] fits File file.
 *
 * Reads the Pulse Height Analyzer spectrum from the `SPECTRUM` extension
 * of the FITS file. If the file contains also an `EBOUNDS` extension the
 * energy boundaries of all Pulse Height Analyzer channels are also loaded.
 ***************************************************************************/
void GPha::read(const GFits& fits)
{
    // Clear spectrum
    clear();

    // Get PHA table
    const GFitsTable& pha = *fits.table(gammalib::extname_pha);

    // Read PHA data
    read(pha);

    // Optionally read energy boundaries
    if (fits.contains(gammalib::extname_ebounds)) {

        // Get energy boundary table
        const GFitsTable& ebounds = *fits.table(gammalib::extname_ebounds);

        // Read energy boundaries
        m_ebounds.read(ebounds);

    } // endif: had energy boundary table

    // Return
    return;
}


/***********************************************************************//**
 * @brief Read Pulse Height Analyzer spectrum
 *
 * @param[in] table FITS table.
 *
 * @exception GException::invalid_value
 *            Mismatch between PHA file and energy boundaries.
 *
 * Reads the Pulse Height Analyzer spectrum from a FITS table. The channel
 * values are expected in the `COUNTS` column of the table. All other
 * columns are ignored.
 *
 * See
 * https://heasarc.gsfc.nasa.gov/docs/heasarc/ofwg/docs/spectra/ogip_92_007/node5.html
 * for details about the Pulse Height Analyzer spectrum format.
 ***************************************************************************/
void GPha::read(const GFitsTable& table)
{
    // Clear spectrum
    clear();

    // Get data column
    const GFitsTableCol* col_data = table["COUNTS"];
    const GFitsTableCol* col_area = table["AREASCAL"];
    const GFitsTableCol* col_back = table["BACKSCAL"];

    // Extract number of channels in FITS file
    int length = col_data->nrows();

    // Check whether column length is consistent with energy boundaries
    if (m_ebounds.size() > 0) {
        if (m_ebounds.size() != length) {
            std::string msg = "Mismatch between the "+gammalib::str(length)+
                              " channels in the PHA file and the "+
                              gammalib::str(m_ebounds.size())+" energy "
                              "boundaries. Please correct either the energy "
                              "boundaris or the PHA file.";
            throw GException::invalid_value(G_READ, msg);
        }
    }

    // Initialize spectrum
    alloc(length);

    // Copy data
    for (int i = 0; i < length; ++i) {
        m_counts[i]   = col_data->real(i);
        m_areascal[i] = col_area->real(i);
        m_backscal[i] = col_back->real(i);
    }

    // Read any additional columns
    for (int icol = 0; icol < table.ncols(); ++icol) {

        // Fall through if the column is a standard column
        std::string colname(table[icol]->name());
        if ((colname == "CHANNEL")  ||
            (colname == "COUNTS")   ||
            (colname == "STAT_ERR") ||
            (colname == "SYS_ERR")  ||
            (colname == "QUALITY")  ||
            (colname == "GROUPING") ||
            (colname == "AREASCAL") ||
            (colname == "BACKSCAL")) {
            continue;
        }

        // Get pointer to column
        const GFitsTableCol* column = table[icol];

        // Set column vector
        std::vector<double> coldata;
        for (int i = 0; i < length; ++i) {
            coldata.push_back(column->real(i));
        }

        // Append column
        append(colname, coldata);

    } // endfor: looped over all additional columns

    // Read file names
    std::string backfile = (table.has_card("BACKFILE")) ? table.string("BACKFILE") : "";
    std::string corrfile = (table.has_card("CORRFILE")) ? table.string("CORRFILE") : "";
    std::string respfile = (table.has_card("RESPFILE")) ? table.string("RESPFILE") : "";
    std::string ancrfile = (table.has_card("ANCRFILE")) ? table.string("ANCRFILE") : "";

    // Set file names
    m_backfile = (gammalib::tolower(backfile) != "none") ? backfile : "";
    m_corrfile = (gammalib::tolower(corrfile) != "none") ? corrfile : "";
    m_respfile = (gammalib::tolower(respfile) != "none") ? respfile : "";
    m_ancrfile = (gammalib::tolower(ancrfile) != "none") ? ancrfile : "";

    // Read energy band for observations
    if (table.has_card("EMIN_OBS")) {
        m_emin_obs.MeV(table.real("EMIN_OBS"));
    }
    if (table.has_card("EMAX_OBS")) {
        m_emax_obs.MeV(table.real("EMAX_OBS"));
    }

    // Read keywords
    m_underflow = (table.has_card("UNDEFLOW")) ? table.real("UNDEFLOW") : 0.0;
    m_overflow  = (table.has_card("OVERFLOW")) ? table.real("OVERFLOW") : 0.0;
    m_outflow   = (table.has_card("OUTFLOW"))  ? table.real("OUTFLOW")  : 0.0;
    m_exposure  = (table.has_card("EXPOSURE")) ? table.real("EXPOSURE") : 0.0;

    // Store FITS header
    m_header = table.header();

    // Return
    return;
}


/***********************************************************************//**
 * @brief Write Pulse Height Analyzer spectrum
 *
 * @param[in] fits FITS file.
 *
 * Writes the Pulse Height Analyzer spectrum into `SPECTRUM` and `EBOUNDS`
 * extensions of the FITS file. Extensions with these names will be removed
 * from the FITS file before writing.
 *
 * The columns `CHANNEL`, `COUNTS`, `STAT_ERR`, `SYS_ERR`, `QUALITY`,
 * `GROUPING`, `AREASCAL`, and `BACKSCAL` will be written into the `SPECTRUM`
 * extension, but only the `CHANNEL` and `COUNTS` columns will be filled with
 * values. Note that the channels start from 1 in the Pulse Height Analyzer
 * spectrum.
 *
 * See
 * https://heasarc.gsfc.nasa.gov/docs/heasarc/ofwg/docs/spectra/ogip_92_007/node5.html
 * for details about the PHA file format.
 ***************************************************************************/
void GPha::write(GFits& fits) const
{
    // Remove extensions if they exist already
    if (fits.contains(gammalib::extname_ebounds)) {
        fits.remove(gammalib::extname_ebounds);
    }
    if (fits.contains(gammalib::extname_pha)) {
        fits.remove(gammalib::extname_pha);
    }

    // Set column length
    int length = size();

    // Continue only if there are bins
    if (length > 0) {

        // Create new binary table
        GFitsBinTable hdu;

        // Allocate floating point vector columns
        GFitsTableShortCol col_chan("CHANNEL",  length);
        GFitsTableFloatCol col_data("COUNTS",   length);
        GFitsTableFloatCol col_stat("STAT_ERR", length);
        GFitsTableFloatCol col_syst("SYS_ERR",  length);
        GFitsTableShortCol col_qual("QUALITY",  length);
        GFitsTableShortCol col_grpg("GROUPING", length);
        GFitsTableFloatCol col_area("AREASCAL", length);
        GFitsTableFloatCol col_back("BACKSCAL", length);

        // Fill columns
        for (int i = 0; i < length; ++i) {
            col_chan(i) = i+1; // Channels start at 1
            col_data(i) = float(m_counts[i]);
            col_stat(i) = float(std::sqrt(std::abs(m_counts[i])));
            col_grpg(i) = 1;
            col_area(i) = float(m_areascal[i]);
            col_back(i) = float(m_backscal[i]);
        }

        // Set table attributes
        hdu.extname(gammalib::extname_pha);

        // Append columns to table
        hdu.append(col_chan);
        hdu.append(col_data);
        hdu.append(col_stat);
        hdu.append(col_syst);
        hdu.append(col_qual);
        hdu.append(col_grpg);
        hdu.append(col_area);
        hdu.append(col_back);

        // Append any additional columns
        for (int icol = 0; icol < columns(); ++icol) {

            // Allocate floating point vector columns
            GFitsTableFloatCol column(m_colnames[icol], length);

            // Fill columns
            for (int i = 0; i < length; ++i) {
                column(i) = (float)m_coldata[icol][i];
            }

            // Append columns to table
            hdu.append(column);

        } // endfor: looped over all additional columns

        // Set file names
        std::string backfile = (m_backfile.empty()) ? "none" : m_backfile;
        std::string corrfile = (m_corrfile.empty()) ? "none" : m_corrfile;
        std::string respfile = (m_respfile.empty()) ? "none" : m_respfile;
        std::string ancrfile = (m_ancrfile.empty()) ? "none" : m_ancrfile;

        // Write header keywords
        hdu.card("TELESCOP", "unknown",        "Telescope");
        hdu.card("INSTRUME", "unknown",        "Instrument");
        hdu.card("FILTER",   "none",           "Filter");
        hdu.card("EXPOSURE", m_exposure,       "[s] Deadtime corrected exposure time");
        hdu.card("BACKFILE", backfile,         "Associated background filename");
        hdu.card("CORRFILE", corrfile,         "Associated correction filename");
        hdu.card("CORRSCAL", 1.0,              "Correction scaling factor");
        hdu.card("RESPFILE", respfile,         "Associated RMF filename");
        hdu.card("ANCRFILE", ancrfile,         "Associated ARF filename");
        hdu.card("HDUCLASS", "OGIP",           "Format conforms to OGIP standard");
        hdu.card("HDUCLAS1", "SPECTRUM",       "PHA dataset");
        hdu.card("HDUVERS",  "1.2.1",          "Version of the file format");
        hdu.card("POISSERR", true,             "Poisson errors to be assumed");
        hdu.card("CHANTYPE", "PI",             "Channel type");
        hdu.card("DETCHANS", size(),           "Total number of possible channels");
        hdu.card("EMIN_OBS", m_emin_obs.MeV(), "[MeV] Minimum energy of observation");
        hdu.card("EMAX_OBS", m_emax_obs.MeV(), "[MeV] Maximum energy of observation");
        hdu.card("UNDEFLOW", m_underflow,      "Number of underflowing events");
        hdu.card("OVERFLOW", m_overflow,       "Number of overflowing events");
        hdu.card("OUTFLOW",  m_outflow,        "Number of outflowing events");

        // Write additional header keywords (do not overwrite any existing
        // keywords, except of "TELESCOP", "INSTRUME" and "FILTER")
        for (int i = 0; i < m_header.size(); ++i) {
            if ((!hdu.has_card(m_header[i].keyname())) ||
                (m_header[i].keyname() == "TELESCOP")  ||
                (m_header[i].keyname() == "INSTRUME")  ||
                (m_header[i].keyname() == "FILTER")) {
                hdu.card(m_header[i]);
            }
        }

        // Append HDU to FITS file
        fits.append(hdu);

        // Optionally append energy boundaries
        if (m_ebounds.size() > 0) {
            m_ebounds.write(fits);
        }

    } // endif: there were data to write

    // Return
    return;
}


/***********************************************************************//**
 * @brief Print Pulse Height Analyzer spectrum
 *
 * @param[in] chatter Chattiness.
 * @return String containing Pulse Height Analyzer spectrum information.
 ***************************************************************************/
std::string GPha::print(const GChatter& chatter) const
{
    // Initialise result string
    std::string result;

    // Continue only if chatter is not silent
    if (chatter != SILENT) {

        // Append header
        result.append("=== GPha ===");

        // Append energy boundary information
        result.append("\n"+gammalib::parformat("Exposure"));
        result.append(gammalib::str(exposure())+" s");
        result.append("\n"+gammalib::parformat("Number of bins"));
        result.append(gammalib::str(size()));
        result.append("\n"+gammalib::parformat("Energy range"));
        if (m_ebounds.size() > 0) {
            result.append(m_ebounds.emin().print());
            result.append(" - ");
            result.append(m_ebounds.emax().print());
        }
        else {
            result.append("not specified");
        }

        // Append observation energy range
        result.append("\n"+gammalib::parformat("Observation energy range"));
        if (m_emax_obs > m_emin_obs) {
            result.append(m_emin_obs.print());
            result.append(" - ");
            result.append(m_emax_obs.print());
        }
        else {
            result.append("not specified");
        }

        // Append content information
        result.append("\n"+gammalib::parformat("Total number of counts"));
        result.append(gammalib::str(counts()));
        result.append("\n"+gammalib::parformat("Underflow counts"));
        result.append(gammalib::str(m_underflow));
        result.append("\n"+gammalib::parformat("Overflow counts"));
        result.append(gammalib::str(m_overflow));
        result.append("\n"+gammalib::parformat("Outflow counts"));
        result.append(gammalib::str(m_outflow));

    } // endif: chatter was not silent

    // Return result
    return result;
}


/*==========================================================================
 =                                                                         =
 =                             Private methods                             =
 =                                                                         =
 ==========================================================================*/

/***********************************************************************//**
 * @brief Initialise class members
 ***************************************************************************/
void GPha::init_members(void)
{
    // Initialise members
    m_filename.clear();
    m_ebounds.clear();
    m_counts.clear();
    m_areascal.clear();
    m_backscal.clear();
    m_colnames.clear();
    m_coldata.clear();
    m_emin_obs.clear();
    m_emax_obs.clear();
    m_underflow = 0.0;
    m_overflow  = 0.0;
    m_outflow   = 0.0;
    m_exposure  = 0.0;
    m_backfile.clear();
    m_corrfile.clear();
    m_respfile.clear();
    m_ancrfile.clear();
    m_header.clear();

    // Return
    return;
}


/***********************************************************************//**
 * @brief Copy class members
 *
 * @param[in] pha Pulse Height Analyzer spectrum.
 ***************************************************************************/
void GPha::copy_members(const GPha& pha)
{
    // Copy members
    m_filename  = pha.m_filename;
    m_counts    = pha.m_counts;
    m_areascal  = pha.m_areascal;
    m_backscal  = pha.m_backscal;
    m_colnames  = pha.m_colnames;
    m_coldata   = pha.m_coldata;
    m_emin_obs  = pha.m_emin_obs;
    m_emax_obs  = pha.m_emax_obs;
    m_underflow = pha.m_underflow;
    m_overflow  = pha.m_overflow;
    m_outflow   = pha.m_outflow;
    m_ebounds   = pha.m_ebounds;
    m_exposure  = pha.m_exposure;
    m_backfile  = pha.m_backfile;
    m_corrfile  = pha.m_corrfile;
    m_respfile  = pha.m_respfile;
    m_ancrfile  = pha.m_ancrfile;
    m_header    = pha.m_header;

    // Return
    return;
}


/***********************************************************************//**
 * @brief Delete class members
 ***************************************************************************/
void GPha::free_members(void)
{
    // Return
    return;
}


/***********************************************************************//**
 * @brief Allocate spectrum
 *
 * @param[in] size Size of spectrum.
 *
 * Allocates memory for a spectrum of given @p size and sets number of counts
 * to zero and area and background scaling factors to one.
 ***************************************************************************/
void GPha::alloc(const int& size)
{
    // Initialise attributes
    m_underflow = 0.0;
    m_overflow  = 0.0;
    m_outflow   = 0.0;
    m_exposure  = 0.0;

    // Initialize vectors
    m_counts.assign(size, 0.0);
    m_areascal.assign(size, 1.0);
    m_backscal.assign(size, 1.0);

    // Return
    return;
}


/***********************************************************************//**
 * @brief Returns index of additional vector column
 *
 * @param[in] colname Vector column name.
 * @return Vector column index.
 *
 * Returns index of additional vector column. Returns -1 if the vector column
 * has not found.
 ***************************************************************************/
int GPha::column_index(const std::string& colname) const
{
    // Initialise index
    int index(-1);

    // Search vector column name
    for (int i = 0; i < columns(); ++i) {
        if (m_colnames[i] == colname) {
            index = i;
            break;
        }
    }

    // Return index
    return index;
}