NAME
        gtsrcid - Creates a counterpart candidate catalog by
        correlating the objects from a list of detected sources
        with the objects of an existing source catalog, such as
        the 3EG catalog.

USAGE

        gtsrcid srcCatName srcCatPrefix cptCatName cptCatPrefix
        outCatName probMethod probThres maxNumCpt


DESCRIPTION

    The gtsrcid tool is an application that finds counterparts for a
    list of detected sources using a catalog of potential counterparts.

    The source catalog as well as the counterpart catalog should be
    either in FITS or TSV (tab-separated values) format. The output
    counterpart candidate catalog will be in FITS format. The gtsrcid
    tool also generates a log file that contains detailed information
    about the counterpart identification. The name for that log file is
    gtsrcid.log. It will be placed at the location from where the
    gtsrcid tool was executed.

    The method used to define the counterpart probability (or function
    of merit) may be either POSITION (e.g. the probability of positional
    coincidence), or any output catalog quantity that can be parameterized
    as a probability between 0 and 1 (see details in probMethod parameter
    description).

    The counterpart probability assigned by gtsrcid is defined as:

    P = P_pos * P_add * (1 - P_chance)

    where P_pos is the positional coincidence probability, P_add any
    additional probability (see below) and P_chance is the chance
    coincidence probability.

    The positional coincidence probability is based on the assumption
    that the source location uncertainties can be modeled by a 2-dimensional
    normal distribution. In the most general form, the location uncertainty
    is described by an error ellipse, parameterized by the major and
    minor axes and the position angle (measured counterclockwise
    from celestial north).

    The user is allowed to enter a maximum number of counterpart candidates
    per source to be included in the output catalog (see the description
    of maxNumCpt parameter). Selection criterion on output catalog
    quantities are possible to enter as well.

    Although gtsrcid is designed to digest a large variety of different
    catalog type and formats, a certain number of rules have to be satisfied
    for gtsrcid to work properly:

    1) Source Position: knowledge of source position is mandatory for
    gtsrcid to work. So far, only celestial coordinates are supported
    (Right Ascension and Declination). The gtsrcid tool tries to find this
    information by first searching for columns with the Unified Content
    Descriptors) POS_EQ_RA_MAIN and POS_EQ_DEC_MAIN. If those are not
    found the following column name pairs are searched for
    (in the specific order): Radeg/DECdeg, RAJ200/DEJ200,_RAJ2000/_DEJ2000,
    or RA/DE.
    2) Position uncertainties: No generic UCDs exist for this information, and
    specific column names ar searched for. First, elliptical errors regions are
    searched for by looking for the column names
    Conf_95_SemiMayor/Conf_95_SemiMinor/Conf_95_PosAng (for 95% error ellipses),
    Conf_68_SemiMayor/Conf_68_SemiMinor/Conf_95_PosAng (for 68% error ellipses),
    and Declination are searched for by looking for the column names e_RAdeg/e_DEdeg
    (for 1 sigma errors), and e_RAJ200/e_DEJ200 (for 1 sigma errors). Finally,
    circular errors are searched for by looking for the column names theta95
    (for 95 % errors), and PosErr (for 1 sigma errors). If no one of these
    column combinations has been found, the positional uncertainty will be taken
    from the parameters srcPosError for the source catalog and from cptPosError
    for the counterpart catalog.
    3) Sourcename: To keep track of the source information each source
    should have a source name. The gtsrcid tool finds the source name by
    first searching for the UCD ID_MAIN. If no such UCD is found it then
    searches for columns named NAME or ID.

    On output, gtsrcid produces a catalog of counterpart candidates.
    Each row (entry) of this catalog present the association of an object
    of the source catalog with an object of the counterpart catalog. For a
    given object of the source catalog, several entries may exit, corresponding
    to the different possible counterparts that have been identified from
    the counterpart catalog. Each of the association will have an assigned
    counterpart probability, allowing to judge on the reality of the proposed
    association. Each counterpart candidate in the output catalog is specified by:

    1) A unique name of the format CC_XXXXX_YYYYY where XXXXX is the source
    number in the source catalog (starting from 1) and YYYYY is the running
    number of the counterpart candidate (starting from 1). For example, the
    2nd counterpart candidate of the 5th source of the source catalog will
    have the identifier CC_00005_00002. The unique name has the FITS column
    name ID and the UCD ID_MAIN.

    2) The coordinates of the counterpart candidate in Right Ascension
    and Declination for the epoch J2000 in units of degrees. The FITS
    column names of the coordinates are RA_J2000 and DEJ2000, the UCDs
    are POS_EQ_RA_MAIN and POS_EQ_DEC_MAIN.

    3) The position uncertainty of the counterpart candidate in form
    of an error ellipse that defines the 95% confidence interval.
    The major and minor axes of the error ellipse are stored in the columns
    POS_ERR_MAJ and POS_ERR_MIN in unit of degrees. The position angle,
    measured eastwards (or counterclockwise) from North in celestial
    coordinates is stored in the column POS_ERR_ANG in units of degrees.
    The UCD for all the three columns is ERROR.

    4) The counterpart candidate association probability in the range
    of 0 to 1. The FITS column name of the probability is PROB.
    Subsequent columns specify the probability based on the positional
    coincidence, which is also called the likelihood (stored in column PROB_POS),
    the product of any additional probabilities (stored in column PROB_ADD),
    and the chance coincidence probability (stored in column PROB_CHANCE).

    5) The position of the counterpart candidate with respect to the
    source is given in form of angular separation (stored in column ANGSEP
    in units of degrees) and the position angle, measured eastwards
    (or counterclockwise) from North in celestial coordinates
    (stored in column POSANG in units of degrees).

    6) The row of the counterpart in the counterpart catalog (stored in column REF).


    The coordinates and positional uncertainty of the counterpart are
    those of the object that has the smaller positional uncertainty
    in either of the two input catalog.

    In addition to the generic quantities, additional quantities may
    be copied from the input catalog to the output catalog. FITS columns
    for these copied quantities are preceded by @.

    New information can be derived in the output catalog by combining
    information from quantities that are found in both input catalog.
    For example, a spectral index may be calculated from the fluxes given
    at two energies or frequencies in the input catalog. These so called
    "derived quantities" will be added as final columns to the output
    catalog. Note that these derived quantities can also be used to
    specify additional probability laws.

    For reading catalogs, gtsrcid makes use of the interface routines provided
    by the library catalogAccess. Consequently the catalog can be read in all
    formats that are supported by catalog Access. The gtsrcid tool writes the
    output catalog directly using cfitsio routines, thus only the FITS format
    is supported on the output.

    The gtsrcid tool creates an ASCII log-file in the directory where the
    executable is executed with the purpose of logging errors that occurred
    during task execution, logging the actions that gtsrcid performed for
    the counterpart search in order to control the proper execution of the
    task, to provide a detailed report about the task execution in case
    that the result looks suspicious to the user.

    For astronomical catalogs you may see: The HEASARC Catalog website:
    http://heasarc.gsfc.nasa.gov/docs/archive.html or the VizieR Service website:
    http://vizier.u-strasbg.fr/viz-bin/VizieR.


PARAMETERS

Source Catalog Parameters:

    srcCatName [string]
    Name of the input source catalog for which counterpart IDs are desired.
    The input catalog may be either a file that resides on disk [in either
    FITS or TSV (tab-separated values) format], or it may be a catalog accessible
    via the web.
    The source Catalog may typically be the Fermi LAT source Catalog.
    Note: Web access is not yet available in the current version.

    srcCatPrefix [string]
    Prefix that will be applied to the source names in the output catalog.
    Prefixing allows unique names to be assigned for all quantities in the
    output catalog. Source catalog quantities in the output catalog will
    begin with @<srcCatPrefix>_.
    For example: For srcCatPrefix = LAT, the FLUX quantity of the source
    catalog will get the name @LAT_FLUX in the output catalog. Quantities
    already having a prefix in the source catalog will not be prefixed again.

    (srcCatQty = *) [string]
    Specifies which quantities of the input source catalog should be included
    in the output catalog.
    Quantity extraction is useful for keeping track of important source
    parameters, and is mandatory for deriving new quantities. Quantities are
    specified by a comma-separated list.  If srcCatQty = *, all quantities of
    the source catalog will be extracted. If srcCatQty is specified as "blank"
    no quantity will be extracted.
    This is a hidden parameter. The default value is *.

    (srcPosError = 0.0) [double]
    If no positional uncertainties are given in the source catalog, srcPosError
    specifies the positional uncertainty for all objects (in units of degrees).


Counterpart Catalog Parameters:

    cptCatName [string]
    Name of the counterpart catalog used for source identification.
    The counterpart catalog may be either a file residing on disk [in either
    FITS or TSV (tab-separated values) format], or it may be a catalog that
    is accessible via the web. This catalog is typically taken from a database,
    such as CDS or HEASARC.
    Note: Web access is not yet available in the current version.

    cptCatPrefix [string]
    Prefix used to build the counterpart catalog quantity names in the output
    catalog. Prefixing allows unique names to be assigned for all quantities
    in the output catalog. Counterpart catalog quantities in the output catalog
    will begin with @<cptCatPrefix>_.
    For example: For cptCatPrefix = 1RXS, the COUNTS quantity of the counterpart
    catalog will get the name @1RXS_COUNTS in the output catalog. Quantities in
    the counterpart catalog that already have a prefix will not be prefixed again.

    (cptCatQty = *) [string]
    Specifies which quantities of the counterpart catalog should be extracted
    into the output catalog.
    Quantity extraction is useful for keeping track of important counterpart
     parameters, and is mandatory for deriving new quantities. Quantities
    are specified by a comma-separated list, i.e. 3EG,RAJ2000,DEJ2000. If
    cptCatQty = *, all quantities of the counterpart catalog will be extracted.
    If cptCatQty is "blank" no quantity will be extracted. This is a hidden
    parameter. The default value is *.

    (cptPosError = 0.0) [double]
    If no positional uncertainties are given in the counterpart catalog,
    cptPosError specifies the positional uncertainty for all objects
    (in units of degrees). This is a hidden parameter. The default value is 0.0.

    (cptDensFile) [string]
    Counterpart catalog density file.

Output Catalog Parameters

    outCatName [string]
    Name of the output catalog FITS file.

    (outCatQty01)[string]
    Allows a new quantity to be derived from quantities that exist in the
    output catalog.
    Quantities in the output catalog may be either generic quantities (such
    as the counterpart candidate name, position, and position uncertainty),
    or quantities that have been extracted from the source or the counterpart
    catalogs.
    A quantity is derived using the syntax <Q_NEW> = <FCT_Q>, where <Q_NEW>
    is the name of the new quantity, and <FCT_Q> is an arithmetic function
    that describes how the quantity is derived (the allowed arithmetic is
    the FTOOLS column evaluation interface).
    For example: outCatQty01 = "RATIO = $@LAT_FLUX$ / $@1RXS_COUNTS$" derives
    a new quantity RATIO that describes the ratio between the LAT source
    flux and the 1RXS counterpart count rate.
    Note the enclosure of the source and counterpart quantities within $...$.
    This  syntax is mandatory in order to correctly interpret the presence of
    a non-alphanumeric letter (i.e. the @ prefix) in the specified quantity
    names. If the parameter is left blank, no new quantity will be derived.

    outCatQty02, ..., outCatQyt09 = [string]
    These parameters allow additional new quantities to be derived, similar to
    outCatQty01.
    In addition, quantities derived using these parameters may be included in
    the arithmetic function.
    For example: outCatQty02 = "PROB_RATIO = exp(-0.5 * ((RATIO - 2.7)/0.5)^2)"
    is a valid parameter that uses the result of outCatQty01 to assign a Gaussian
    shaped probability density function for the quantity RATIO. If the parameters
    are left blank, no new quantities will be derived.

Task Parameters

    probMethod = POSITION [string]
    Method used to define the counterpart probability (or function of merit).
    The method may be either POSITION (e.g. the probability of positional
    coincidence), or any output catalog quantity that is comprised between 0 and 1.
    Methods can be combined using the multiplication symbol *. In this case, the
    probabilities of the specified methods are multiplied.
    For example: probMethod = "POSITION * PROB_RATIO" specifies a counterpart
    probability that is the product between the spatial coincidence probability and
    the flux ratio probability function PROB_RATIO, as derive by parameter
    outCatQty02.
    The default value is POSITION.

    probPrior = 0.01 [double]
    Prior association probability

    probThres = 0.10 [double]
    Probability threshold for counterpart candidates.
    Only objects with counterpart probabilities larger than this threshold will
    be included in the output catalog.
    The default value is 0.01.

    maxNumCpt = 100 [int]
    Maximum number of counterpart candidates per source that are included in
    the output catalog.
    Since counterpart candidates are stored in decreasing order of probability,
    the less probable counterpart candidates will be suppressed if necessary.
    If maxNumCpt = 0, no limitation will be applied.
    The default value is 100.

    fom
    Figure of merit.

    (select01 = )[string]
    Selection criterion on output catalog quantities.
    Counterpart candidates that do not meet the selection criterion will be
    excluded
    from the output catalog. The syntax of this parameter corresponds to the
    FTOOLS row filtering specification. All quantities present in the output
    catalog (including in particular derived quantities) may be used for
    selection. If the parameter is left blank, no selection criterion will
    be applied. This is a hidden parameter.

    select02, ..., select09 = [string]
    Additional selection criteria, similar to the one specified by the parameter
    select01. If the parameters are left blank, no selection will be applied.
    These are hidden parameters.

Standard Parameters

    (chatter)
    This parameter fixes the output verbosity:
    chatter = 0: no information will be logged
    chatter = 1: only errors will be logged
    chatter = 2: errors and actions will be logged
    chatter = 3: report about the task execution
    chatter = 4: detailed report about the task execution
    This is a hidden parameter. The default value is 1.

    (clobber = yes)
    If true, an existing file of the same name will be overwritten.
    This is a hidden parameter. The default value is "yes".

    (debug = no)
    Activate debugging mode. The default value is "no". When debug is
    "no", all exceptions that are not caught and handled by individual tool-specific
    code are caught by a top-level exception handler that displays information
    about the exception and then exits. When debug is "yes", such exceptions are
    not caught by the top level code. Instead the tool produces a segmentation
    violation, which is more useful for debugging. When debugging mode is enabled,
    the tool produces more verbose output describing any errors or exceptions that
    are encountered.

    (gui = no)
    Graphical user Interface (GUI) mode activated if "yes" is specified. The
    default value is "no".

    (mode = ql)
    Mode of automatic parameters. The default value is "ql".


EXAMPLES

    The way that the parameters are passed follows the FTOOLs model. They could be
    passed by answering from a prompt, as a list in a command line, or by editing
    the parameter file.

    To be prompted for gtsrcid simply type in the command line:

    > gtsrcid

    This will prompt for parameter values. Beware that not all parameters are
    prompted. Some of the parameters are "hidden".  If you want to change one
    of the "hidden" parameter you should specify its value in the command line.
    For example, it is possible to change the counterpart position uncertainty
    in this way:

    >gtsrcid cptPosError=0.01

    Here is an example of how to run the tool:

    A catalog of LAT sources (for a simulated LAT sky) is compared to the
    Third EGRET Catalog (http://heasarc.gsfc.nasa.gov/docs/cgro/egret/3rd_EGRET_Cat.html).
    In this case, you may run the gtsrcid tool in the following way:

    > gtsrcid
    Source catalog name [] : LATSourceCatalog_v1.fits
    Source catalog column prefix [] : DC2_Cat
    Counterpart catalog name [] : 3EG.fits
    Counterpart catalog column prefix [] : 3EG
    Output catalog name [] : DC2_LATSourceCatalog_v1-3EG.fits
    Probability method [POSITION] :
    Probability threshold [0.10] : 0.2
    Maximum number of counterpart candidates [100] : 1

    In this example the LAT Catalog is named LATSourceCatalog_v1.fits while the
    counterpart Catalog is called 3EG.fits. The name of the output catalog is
    data/DC2_LATSourceCatalog_v1-3EG.fits. The position probability method was
    used (see formula 1). The maximum number of counterpart candidates was chosen
    to be 1 and the probability threshold was 0.2.

SEE ALSO
