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NAME

       visir_spc_reduce - Spectroscopic Observation recipe

SYNOPSIS

       esorex visir_spc_reduce [OPTIONS] FILE.sof

DESCRIPTION

       This  recipe  performs  a  wavelength  calibration  followed by spectrum extraction from a
       combined image. It can also compute sensitivities for standard star observations.

       It works for low and high resolution including echelle mode.

       The   files   listed   in   the   Set   Of   Frames    (sof-file)    must    be    tagged:
       VISIR-Long-Slit-Spectroscopy-file.fits                                        SPEC_OBS_LMR
       VISIR-Quantum-Efficiency-Calibration-file.fits                               SPEC_CAL_QEFF
       VISIR-Atmospheric-Emission-Lines-Calibration-file.fits                      SPEC_CAL_LINES
       VISIR-Standard-Star-Flux-Catalog.fits (optional)SPEC_STD_CATALOG VISIR-linearty-table.fits
       LINEARITY_TABLE (optional) Additionally, a bad pixel map with a PRO.CATG of IMG_BPM may be
       added to the Set Of Frames with tag: BPM.

OPTIONS

       --planestart <long>
              Plane number to start repacking from, earlier planes are skipped.  (long;  default:
              0).   The   full  name  of  this  option  for  the  EsoRex  configuration  file  is
              visir.visir_util_repack.planestart [default = 0].

       --ncycles <long>
              Number of full on-off cycles to repack. <= 0 for all. (long; default: -1). The full
              name    of    this    option    for    the    EsoRex    configuration    file    is
              visir.visir_util_repack.ncycles [default = -1].

       --trimlow <long>
              Burst data only. Number of additional planes to cut from  before  each  plane  with
              chopper  movement.  (long; default: 0). The full name of this option for the EsoRex
              configuration file is visir.visir_util_repack.trimlow [default = 0].

       --trimhigh <long>
              Burst data only. Number of additional planes to cut  from  after  each  plane  with
              chopper  movement.   A  value of -1 does not skip the plane of the movement. (long;
              default: 0). The full name of this option for  the  EsoRex  configuration  file  is
              visir.visir_util_repack.trimhigh [default = 0].

       --xl <long>
              Coordinate  in  spatial direction. Together with yl it defines the lower point of a
              rectangle containing only  skylines  for  the  wavelength  shift  detection  (long;
              default:  117).  The  full name of this option for the EsoRex configuration file is
              visir.visir_util_undistort.xl [default = 117].

       --yl <long>
              Coordinate in wavelength direction. See xl (long; default: 110). The full  name  of
              this  option  for  the  EsoRex  configuration file is visir.visir_util_undistort.yl
              [default = 110].

       --xh <long>
              Coordinate in spatial direction. Together with yl it defines the higher point of  a
              rectangle  containing  only  skylines  for  the  wavelength  shift detection (long;
              default: 125). The full name of this option for the EsoRex  configuration  file  is
              visir.visir_util_undistort.xh [default = 125].

       --yh <long>
              Coordinate  in  wavelength direction. See xh (long; default: 150). The full name of
              this option for the  EsoRex  configuration  file  is  visir.visir_util_undistort.yh
              [default = 150].

       --slit_skew <float>
              Distortion  correction:  Skew of slit (degrees) (clockwise) (float; default: 0.52).
              The  full  name  of  this   option   for   the   EsoRex   configuration   file   is
              visir.visir_util_undistort.phi [default = 0.52].

       --spectrum_skew <float>
              Distortion  correction:  LMR  Skew  of spectrum (degrees) (counter- clockwise). Not
              used in High Resolution (float; default: 1.73). The full name of  this  option  for
              the EsoRex configuration file is visir.visir_util_undistort.ksi [default = 1.73].

       --vert_arc <float>
              Distortion  correction: LR Detector vertical curvature (pixel). Reduced by a factor
              4 in MR. Not used in HR A-side. Increased by a factor 115/52 in HR  B-side  (float;
              default:  -0.8).  The full name of this option for the EsoRex configuration file is
              visir.visir_util_undistort.eps [default = -0.8].

       --hori_arc <float>
              Distortion correction: LMR Detector horizontal curvature (pixel).  Increased  by  a
              factor  1.5 in HR A-side. Reduced by a factor 2 in HR B-side (float; default: 0.0).
              The  full  name  of  this   option   for   the   EsoRex   configuration   file   is
              visir.visir_util_undistort.delta [default = 0.0].

       --destripe_iterations <long>
              Max  number  of  destriping  iterations  (0  to  disable  destriping).   Horizontal
              destriping is done first and  if  no  horizontal  striping  is  detected,  vertical
              destriping  is  performed (long; default: 15). The full name of this option for the
              EsoRex configuration file is visir.visir_old_util_destripe.nstripe [default = 15].

       --destripe_morpho <bool>
              Destripe with morphological cleaning (bool; default: False). The full name of  this
              option  for  the EsoRex configuration file is visir.visir_old_util_destripe.mstripe
              [default = False].

       --rej <str>
              Each resulting pixel is the average of the corresponding (interpolated) pixel value
              in  each  jittered  image.  A positive value, n1, for the first of the two integers
              specifies that for each pixel the smallest n1 pixel values shall be ignored in  the
              averaging.   Similarly,  a  positive  value, n2, for the second of the two integers
              specifies that for each pixel the largest n2 pixel values shall be ignored  in  the
              averaging.  (str;  default:  ´0-0´).  The  full  name of this option for the EsoRex
              configuration file is visir.visir_old_spc_obs.rej [default = 0-0].

       --bkgcorrect <bool>
              Subtract the median from the spectral column before extracting the wavelength. This
              is  required when the skylines do not correctly cancel due to gratting oscillations
              (bool; default: False). The full name of this option for the  EsoRex  configuration
              file is visir.visir_old_spc_obs.bkgcorrect [default = False].

       --plot <long>
              The  recipe  can  produce a number of predefined plots. Zero means that none of the
              plots are produced, while increasing values (e.g. 1 or 2) increases the  number  of
              plots  produced.  If  the  plotting  fails  a  warning  is produced, and the recipe
              continues. The default behaviour of the plotting is to  use  gnuplot  (with  option
              -persist).  The  recipe  currently  produces  1D-plots  using gnuplot commands. The
              recipe user can control the actual plotting-command used by the  recipe  to  create
              the plot by setting the environment variable CPL_PLOTTER. Currently, if CPL_PLOTTER
              is  set  it  must  contain  the  string   ´gnuplot´.   Setting   it   to   ´cat   >
              my_gnuplot_$$.txt´ causes a number of ASCII-files to be created, which each produce
              a plot when given as standard input to  gnuplot  (e.g.  later  or  on  a  different
              computer).  A  finer  control of the plotting options can be obtained by writing an
              executable script, e.g. my_gnuplot.pl, that  executes  gnuplot  after  setting  the
              desired  gnuplot  options  (e.g.  set  terminal  pslatex  color)  and  then setting
              CPL_PLOTTER to my_gnuplot.pl. The predefined  plots  include  plotting  of  images.
              Images can be plotted not only with gnuplot, but also using the pnm format. This is
              controlled with the environment variable CPL_IMAGER. If  CPL_IMAGER  is  set  to  a
              string that does not contain the word gnuplot, the recipe will generate the plot in
              pnm format. E.g.  setting CPL_IMAGER to ´display - &´  will  produce  a  gray-scale
              image  using  the  image  viewer display. (long; default: 0). The full name of this
              option for the EsoRex configuration file is visir.visir_old_spc_obs.plot [default =
              0].

       --slit_skew <float>
              Distortion  correction:  Skew of slit (degrees) (clockwise) (float; default: 0.52).
              The  full  name  of  this   option   for   the   EsoRex   configuration   file   is
              visir.visir_old_spc_obs.phi [default = 0.52].

       --spectrum_skew <float>
              Distortion  correction:  LMR  Skew  of spectrum (degrees) (counter- clockwise). Not
              used in High Resolution (float; default: 1.73). The full name of  this  option  for
              the EsoRex configuration file is visir.visir_old_spc_obs.ksi [default = 1.73].

       --vert_arc <float>
              Distortion  correction: LR Detector vertical curvature (pixel). Reduced by a factor
              4 in MR. Not used in HR A-side. Increased by a factor 115/52 in HR  B-side  (float;
              default:  -0.8).  The full name of this option for the EsoRex configuration file is
              visir.visir_old_spc_obs.eps [default = -0.8].

       --hori_arc <float>
              Distortion correction: LMR Detector horizontal curvature (pixel).  Increased  by  a
              factor  1.5 in HR A-side. Reduced by a factor 2 in HR B-side (float; default: 0.0).
              The  full  name  of  this   option   for   the   EsoRex   configuration   file   is
              visir.visir_old_spc_obs.delta [default = 0.0].

       --orderoffset <long>
              Echelle  order  offset. The offset is relative to the main order. The allowed range
              of offsets depend on the selected grism. The offset can never exceed +/-4.  If  the
              main  order  is e.g. 8 an order offset of +1 will cause the recipe to base the data
              reduction on order 9. With a positive order offset the central  wavelength  becomes
              smaller  while  for  a negative order offset the central wavelength becomes larger.
              (long; default: 0). The full name of this option for the EsoRex configuration  file
              is visir.visir_old_spc_obs.orderoffset [default = 0].

       --fixcombi <bool>
              Perform  the  distortion  correction  on the combined image, and not on each of the
              jittered images. This will reduce excution time and  degrade  the  quality  of  the
              combined  image (bool; default: False). The full name of this option for the EsoRex
              configuration file is visir.visir_old_spc_obs.fixcombi [default = False].

       --emis_tol <float>
              The computation of the mean and standard deviation of the sensitivity is  done  for
              wavelengths  with  an  atmospheric  emissivity  of  at  most  emis_min + emis_tol *
              (emis_max - emis_min), where emis_min is the minimum  emissivity  in  the  observed
              wavelength  range  and  emis_max is the ditto maximum. Thus emis_tol = 1 means that
              all wavelengths are included. (float; default: 1.0). The full name of  this  option
              for  the  EsoRex  configuration file is visir.visir_old_spc_obs.emis_tol [default =
              1.0].

       --destripe_iterations <long>
              Max  number  of  destriping  iterations  (0  to  disable  destriping).   Horizontal
              destriping  is  done  first  and  if  no  horizontal striping is detected, vertical
              destriping is performed (long; default: 15). The full name of this option  for  the
              EsoRex configuration file is visir.visir_old_spc_obs.nstripe [default = 15].

       --destripe_morpho <bool>
              Destripe  with morphological cleaning (bool; default: False). The full name of this
              option  for  the  EsoRex  configuration  file  is   visir.visir_old_spc_obs.mstripe
              [default = False].

       --rl <long>
              Reject  leftmost columns in spectrum extraction, zero means all columns on the left
              are used. In cross-dispersion mode a (small) negative number may  be  used  (pixel)
              (long;  default: 0). The full name of this option for the EsoRex configuration file
              is visir.visir_old_spc_obs.reject_left [default = 0].

       --rr <long>
              Reject rightmost columns in spectrum extraction, zero  means  all  columns  on  the
              right  are  used.  In  cross-dispersion  mode a (small) negative number may be used
              (pixel)  (long;  default:  0).  The  full  name  of  this  option  for  the  EsoRex
              configuration file is visir.visir_old_spc_obs.reject_right [default = 0].

       --delete-temp <bool>
              Delete  temporary  files  created during processing (bool; default: True). The full
              name    of    this    option    for    the    EsoRex    configuration    file    is
              visir.visir_spc_reduce.delete-temp [default = True].

       --destripe <bool>
              Attempt  to remove stripes (bool; default: False). The full name of this option for
              the EsoRex configuration file is visir.visir_spc_reduce.destripe [default = False].

       Note that it is possible to create a configuration file containing  these  options,  along
       with  suitable default values. Please refer to the details provided by the 'esorex --help'
       command.

SEE ALSO

       The full documentation for the visir pipeline can be downloaded as a PDF  file  using  the
       following URL:

              ftp://ftp.eso.org/pub/dfs/pipelines/visir/visir-pipeline-manual-1.4.pdf

       An   overview   over   the   existing   ESO  pipelines  can  be  found  on  the  web  page
       http://www.eso.org/sci/software/pipelines/.

       Basic documentation about the EsoRex program can be found at the esorex (1) man page.

       It is possible to call the pipelines  from  python  using  the  python-cpl  package.   See
       http://packages.python.org/python-cpl/index.html for further information.

       The   other   recipes  of  the  visir  pipeline  are  visir_img_dark(7),  visir_img_ff(7),
       visir_img_reduce(7), visir_img_trans(7), visir_old_img_combine(7),  visir_old_img_phot(7),
       visir_old_spc_obs(7),           visir_old_spc_obs_ech(7),           visir_old_spc_phot(7),
       visir_old_spc_phot_ech(7),        visir_old_spc_wcal(7),        visir_old_spc_wcal_ech(7),
       visir_old_util_destripe(7),         visir_util_apply_calib(7),         visir_util_clip(7),
       visir_util_convert_weight(7),    visir_util_detect_shift(7),    visir_util_img_std_cat(7),
       visir_util_join(7),   visir_util_qc(7),   visir_util_repack(7),   visir_util_run_swarp(7),
       visir_util_spc_std_cat(7), visir_util_spc_txt2fits(7), visir_util_undistort(7)

VERSION

       visir_spc_reduce 4.1.0

AUTHOR

       Julian Taylor <jtaylor@partner.eso.org>

BUG REPORTS

       Please report any problems to  jtaylor@partner.eso.org.  Alternatively,  you  may  send  a
       report to the ESO User Support Department <usd-help@eso.org>.

LICENSE

       This  file  is  part of the VISIR Instrument Pipeline Copyright (C) 2015 European Southern
       Observatory

       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., 51 Franklin St, Fifth Floor, Boston,
       MA  02111-1307  USA