1 Language WEEDS\ Package to analyze spectral surveys

    Weeds is a CLASS extension to analyze spectral surveys or spectral lines
    observations with large bandwidths.  It  provides  several  commands  to
    identify lines on a spectrum and to model it.

    Available commands:
        LID       Identify lines on the current spectra
        LFIND     Find lines from a species within a frequency range
        LLIST     List lines from the line index
        LGET      Get a line from the line index
        LPLOT     Plot a line from the current line index
        MODSOURCE Model the emission of a source at the LTE
        MODSHOW   Show the results of MODSOURCE

    For more information of each command, type 'help <command>'
1 LFIND
        [WEEDS\]LFIND [SPECIES [FMIN FMAX]] [/SORTBY ORDER] [/ENERGY ENERGY]
    [/AIJ AMIN]

    Find the lines within a frequency range and create  a  line  index.  The
    command  looks  for  the lines between FMIN and FMAX in the database se-
    lected with the USE IN command. If not specified, the values of FMIN and
    FMAX are taken from the current spectra.

    Arguments:
        SPECIES   the name of the species. Default is "All".

        FMIN      the minimum frequency in MHz.

        FMAX      the maximum frequency in MHz

    Options:
        /SORTBY   sort the lines according to ORDER, which can be any combi-
                  nation of "frequency", "energy" and "aeinstein",  and  all
                  the subsequent permutations.

        /ENERGY   refine  the  search to lines with upper level energy lower
                  than ENERGY, expressed in Kelvins.

        /AIJ      refine the search to lines  with  einstein  A  coefficient
                  greater than AMIN, expressed s-1.

1 LGET
        [WEEDS\]LGET [LINEINDEX] [/INDEX]

    Get a line from the line index. The commands checks if the line frequen-
    cy is covered by the current scan. If yes, the scan frequency  is  modi-
    fied  so  that the rest frequency corresponds to the line frequency. The
    command works in a similar fashion than GET: for example LGET F will get
    the  first  line in the line list, LGET N will get the next one, etc. It
    is especially useful when one want  to  search  for  lines  of  a  given
    species.  For example, one can list all methanol lines in the 3 mm band,
    ordered by increasing upper level energy, with:

    LAS> LLIST "CH3OH, vt=0,1" 80000 110000 /SORTBY e

    and then examine each of the line candidates with:

    LAS> LGET F
    LAS> LPLOT
    LAS> LGET N
    LAS> LPLOT
    LAS> ...

    Options:

      /INDEX      search for the line in all scans of the  scan  index.   If
                  this option is set, LGET begins by searching for the first
                  scan in scan index (from the last FIND command) that  cov-
                  ers  the  line  frequency.  It is useful when working with
                  line surveys that consists in several scans, each covering
                  a different frequency band.

    Arguments:
        LINEINDEX the line index. It can be either:

                  1) One of the following letters:
                     "f"   get the first line of the index
                     "l"   get the last line of the index
                     "p"   get the previous line in the index
                     "n"   get the next line of the index

                  2) An integer

1 LID
        [WEEDS\]LID  [/SPECIES Name1 Name2 ...] [/ENERGY ENERGY] [/AIJ AMIN]
    [[/DELTA DFREQ] | [/FULL]] [/IMAGE] [/LOOP]

    Search for lines in the database around a  central  frequency  and  mark
    them  on  the  current spectra. By default, the central frequency is se-
    lected with the mouse left button. The search is done in an interval  of
    width  DFREQ around the selected frequency; alternatively, the /FULL op-
    tion may be used to search for lines over  the  entire  frequency  range
    covered by the current spectra. The line database in which the search is
    performed may be selected with the USE IN command.

    Options:
        /SPECIES  refine the search to lines of one  or  more  species.  The
                  species  name  should  match exactly that in the database.
                  Wildcards '*' are accepted. Default is "All".

        /ENERGY   refine the search to lines with upper level  energy  lower
                  than ENERGY, expressed in Kelvins.

        /AIJ      refine  the  search  to  lines with Einstein A coefficient
                  greater than AMIN, expressed in s-1.

        /DELTA    search for lines within DFREQ, expressed in MHz, from  the
                  cursor position. Default is 10 times the channel width.

        /FULL     search  for  lines  in the full frequency range covered by
                  the current spectra.

        /IMAGE    search for lines in the image sideband. Note that this  is
                  the default if the spectra lower axis unit is I (image).

        /LOOP      by  default, the cursor is invoked only once, but you can
                  iterate indefinitely with the option /LOOP.  Type  'E'  to
                  exit the loop.
1 LLIST
        [WEEDS\]LLIST

    List  the  lines  from  the line index. The line index is built with the
    LFIND command.
1 LPLOT
        [WEEDS\]LPLOT [NCHAN]

    Plot the line from the current line index (built from the last  FINDLINE
    command). A vertical line is drawn at the rest frequency of the line. An
    optional NCHAN parameter may be given to define the  frequency  interval
    to  be plotted around the line, expressed in number of channels (default
    100)

    Arguments:
        NCHAN     the frequency interval to be plotted, in channels (default
    100)
1 MODSHOW
        [WEEDS\]MODSHOW

    Plot  the  results  of MODSHOW over the current spectra. The command en-
    sures that the x-axis range and y-axis range are fixed so one  can  com-
    pare the predictions of the model with the observed spectra.
1 MODSOURCE
        [WEEDS\]MODSOURCE  MODFILE  ANTSIZE  [/BACKGROUND  TBG] [/OPACITY I]
    [/VERBOSE]

    Model the emission of a source at the  local  thermodynamic  equilibrium
    (LTE). The model paramaters (column density, kinetic temperature, source
    size, line width and velocity offset for each  species)  are  read  from
    MODFILE. The modeled antenna temperature is stored in the TB_MODEL memo-
    ry. For convenience the current spectra is also stored in a memory, OBS,
    so one can easily overplot the result of the model on the observed spec-
    tra.

    Arguments:
      MODFILE     the name of the file containing the parameters.  The  file
                  must  have  one line per species with at least six columns
                  containing respectively:

                  1) The species name
                  2) The column density for this species in cm-2
                  3) The exitation temperature in K
                  4) The source size in arcsecs
                  5) The offset velocity from the source VLSR, in km/s
                  6) The line FWHM in km/s

                  One additional column may be used to  select  a  different
                  origin for each species:

                  7)  The origin of this species (e.g. JPL or CDMS). If emp-
                  ty, species with any origin are selected.

                  The following options may be used at the end of the line:

                  /ABSORPTION  If this option is set, the component  is  as-
                  sumed  to  be  a foreground layer. See Belloche et al. A&A
                  559, A47 (2013) for details.

                  /PARTFUNC Q  Set the log10 of the  partition  function  at
                  the excitation temperature to Q. If not set, the partition
                  function values (log-log interpolated/extrapolated at  the
                  excitation  temperature)  from  the  selected database are
                  used.

                  Lines that start with a "!" are treated as comments.

      ANTSIZE     the antenna size in meters

    Options:
      /BACKGROUND set the background temperature to TBG, in  K.  Default  is
                  2.73.

      /OPACITY  I store  the  opacity  of the Ith component in the TAU_MODEL
                  memory. Components are numbered in the same  order  as  in
                  MODFILE, starting from 1.

      /VERBOSE    prints  partition function, lines frequencies, upper level
                  energies and degeneracies, Einstein coefficients and opac-
                  ity at the line center.
1 SCANFIND
        [WEEDS\]SCANFIND RESTFREQ

    This  function  loops over the scan index until it finds one that covers
    the given rest frequency. When the scan is found,  it  is  loaded.  Note
    that  if  several scans covers the same frequency, the command will find
    only the first one; other will be ignored.

    Arguments:
        RESTFREQ  the rest frequency to search, in MHz.
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