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NAME

       xsh_orderpos - Create the orders centre traces table file

SYNOPSIS

       esorex xsh_orderpos [OPTIONS] FILE.sof

DESCRIPTION

       This recipe creates the orders centre traces table.

       Input Frames for UVB and VIS:
         Raw file (Tag = ORDERDEF_arm_D2)
         Master Dark (Tag = MASTER_DARK_arm)
         Master Bias (Tag = MASTER_BIAS_arm) Input Frames for NIR:
         Raw file ON(Tag = ORDERDEF_NIR_ON)
         Raw file OFF(Tag = ORDERDEF_NIR_OFF) Input Frames for all arms
         Guess order table (Tag = ORDER_TAB_GUESS_arm)
         Spectral format table (Tag = SPECTRAL_FORMAT_TAB_arm)
         - [OPTIONAL] A map of non linear bad pixels (Format=QUP, Tag = BP_MAP_NL_arm)
         -  [OPTIONAL]  A  map  of  reference  bad pixels (Format = QUP,RAW, Tag = BP_MAP_RP_arm)
       Prepare PRE structures.

       For NIR, subtract NIR-OFF from NIR-ON.

       For UVB and NIR, Substract the master Bias and master dark.

       Detect Orders and calculate the order table.

       The final products are:
          An updated Order Table, PRO.CATG=ORDER_TABLE_CENTR_arm.

          A order trace residuals Table, PRO.CATG=ORDERPOS_RESID_TAB_arm.

          The order pos frame bias subtracted, PRO.CATG=ORDERDEF_ON_arm.

OPTIONS

       --keep-temp <str>
              If ´no´, temporary files are deleted. (str; default: ´no´). The full name  of  this
              option  for  the EsoRex configuration file is xsh.xsh_orderpos.keep-temp [default =
              no].

       --debug-level <str>
              Additional xshooter debug level. One  of  ´none´,  ´low´,  ´medium´,  ´high´  (str;
              default: ´none´). The full name of this option for the EsoRex configuration file is
              xsh.xsh_orderpos.debug-level [default = none].

       --time-stamp <bool>
              Add timestamp to product file name. (bool; default: False). The full name  of  this
              option  for the EsoRex configuration file is xsh.xsh_orderpos.time-stamp [default =
              False].

       --decode-bp <int>
              Integer representation of the bits to be considered bad when decoding the bad pixel
              mask  pixel  values.    Most frequent codes relevant for the user:   0: good pixel,
              8: pick-up noise,   16: cosmic-ray  removed,    32:  cosmic-ray  unremoved,    128:
              calibration  file  defect, 256: hot pixel,   512: dark pixel,   4096: A/D converted
              saturation, 32768: non linear pixel,   1048576: extrapolated flux in NIR,  4194304:
              Interpolated  flux  during extraction. (int; default: 2144337919). The full name of
              this  option  for  the  EsoRex  configuration  file  is  xsh.xsh_orderpos.decode-bp
              [default = 2144337919].

       --pre-overscan-corr <int>
              pre-overscan  correction.0: no correction1: mean overscan correction2: mean prescan
              correction3: (mean pre+mean overscan)/2 correction (int; default: 1). The full name
              of     this     option     for     the     EsoRex     configuration     file     is
              xsh.xsh_orderpos.pre-overscan-corr [default = 1].

       --detectcontinuum-search-win-hsize <int>
              Half window size in pixels for the  1D  box  to  search  for  the  maximum  in  the
              cross-dispersion  profile  (int;  default: 5). The full name of this option for the
              EsoRex  configuration  file  is   xsh.xsh_orderpos.detectcontinuum-search-win-hsize
              [default = 5].

       --detectcontinuum-running-win-hsize <int>
              Half  window  size  for the running median box during the search for the maximum in
              the cross-dispersion profile (int; default: 0). The full name of  this  option  for
              the EsoRex configuration file is xsh.xsh_orderpos.detectcontinuum-running-win-hsize
              [default = 0].

       --detectcontinuum-fit-win-hsize <int>
              Half window size for the fit of the cross-dispersion profile (int; default: 5). The
              full    name    of   this   option   for   the   EsoRex   configuration   file   is
              xsh.xsh_orderpos.detectcontinuum-fit-win-hsize [default = 5].

       --detectcontinuum-center-thresh-fac <float>
              Threshold factor applied to check that the flux at the fitted peak is  higher  than
              error.  (float;  default:  0.0).  The  full  name  of  this  option  for the EsoRex
              configuration file is xsh.xsh_orderpos.detectcontinuum-center-thresh-fac [default =
              0.0].

       --detectcontinuum-ordertab-step-y <int>
              Step  in  Y  for  order centroid detection (int; default: 1). The full name of this
              option       for       the        EsoRex        configuration        file        is
              xsh.xsh_orderpos.detectcontinuum-ordertab-step-y [default = 1].

       --detectcontinuum-ordertab-deg-y <int>
              Degree in Y in the polynomial order tracing X=f(Y) (int; default: 5). The full name
              of     this     option     for     the     EsoRex     configuration     file     is
              xsh.xsh_orderpos.detectcontinuum-ordertab-deg-y [default = 5].

       --detectcontinuum-clip-res-max <float>
              Maximum  allowed residual (before kappa-sigma clip) (float; default: 0.5). The full
              name    of    this    option    for    the    EsoRex    configuration    file    is
              xsh.xsh_orderpos.detectcontinuum-clip-res-max [default = 0.5].

       --detectcontinuum-clip-sigma <float>
              Kappa  value  in  sigma clipping during order trace polynomial fit (float; default:
              5.0).  The  full  name  of  this  option  for  the  EsoRex  configuration  file  is
              xsh.xsh_orderpos.detectcontinuum-clip-sigma [default = 5.0].

       --detectcontinuum-clip-niter <int>
              Number  of  iterations  in  sigma  clipping during order trace polynomial fit (int;
              default: 5). The full name of this option for  the  EsoRex  configuration  file  is
              xsh.xsh_orderpos.detectcontinuum-clip-niter [default = 5].

       --detectcontinuum-clip-frac <float>
              Minimal  fractions  of  points accepted / total in sigma clippingduring order trace
              polynomial fit (float; default: 0.4). The full name of this option for  the  EsoRex
              configuration file is xsh.xsh_orderpos.detectcontinuum-clip-frac [default = 0.4].

       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 xshoo pipeline can be downloaded as a PDF file using the
       following URL:

              ftp://ftp.eso.org/pub/dfs/pipelines/xshoo/xshoo-pipeline-manual-12.1.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  xshoo   pipeline   are   xsh_2dmap(7),   xsh_cfg_recover(7),
       xsh_flexcomp(7),     xsh_geom_ifu(7),    xsh_lingain(7),    xsh_mbias(7),    xsh_mdark(7),
       xsh_mflat(7),    xsh_predict(7),    xsh_respon_slit_nod(7),     xsh_respon_slit_offset(7),
       xsh_respon_slit_stare(7),      xsh_scired_ifu_offset(7),     xsh_scired_ifu_offset_drl(7),
       xsh_scired_ifu_stare(7),       xsh_scired_ifu_stare_drl(7),        xsh_scired_slit_nod(7),
       xsh_scired_slit_offset(7), xsh_scired_slit_stare(7), xsh_util_physmod(7), xsh_wavecal(7)

VERSION

       xsh_orderpos 3.2.0

AUTHOR

       L.Guglielmi,R.Haigron,P.Goldoni,F.Royer, A. Modigliani <amodigli@eso.org>

BUG REPORTS

       Please  report  any  problems to amodigli@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  X-shooter  Instrument  Pipeline  Copyright  (C)  2006  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., 59 Temple Place, Suite  330,  Boston,
       MA  02111-1307  USA