Provided by: cpl-plugin-visir-doc_4.3.7+dfsg-1build2_all bug

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

       --planelimit <int>
              Limit number of processed inputplanes. It will repack until at least this number of
              input images have been processed or the full dataset has been repacked. Always full
              chop cycles need to be repacked so the  number  is  adjusted  upward  to  the  next
              multiple of images per chop cycle.  <= 0 for no limit. (int; default: -1). The full
              name    of    this    option    for    the    EsoRex    configuration    file    is
              visir.visir_util_repack.planelimit [default = -1].

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

       --trimhigh <int>
              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.  (int;
              default:  0).  The  full  name  of this option for the EsoRex configuration file is
              visir.visir_util_repack.trimhigh [default = 0].

       --lincorrect <bool>
              Apply linearity correction. Should only be enabled on high flux  observations,  may
              degrade results otherwise. (bool; default: False). The full name of this option for
              the EsoRex configuration  file  is  visir.visir_util_repack.lincorrect  [default  =
              False].

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

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

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

       --yh <int>
              Coordinate  in  wavelength  direction. See xh (int; 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 <int>
              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  (int; 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 <int>
              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. (int; 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 <int>
              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.
              (int; 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 <int>
              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 (int; 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 <int>
              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)
              (int;  default:  0). The full name of this option for the EsoRex configuration file
              is visir.visir_old_spc_obs.reject_left [default = 0].

       --rr <int>
              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)  (int;  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
       https://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
       https://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 4.3.7

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