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NAME

       giscience - Process a science observation.

SYNOPSIS

       esorex giscience [OPTIONS] FILE.sof

DESCRIPTION

       For detailed information please refer to the GIRAFFE pipeline user manual.

       It is available at http://www.eso.org/pipelines.

OPTIONS

       --remove-bias <bool>
              Enable  bias  removal  (bool;  default: True). The full name of this option for the
              EsoRex configuration file is giraffe.biasremoval.remove [default = True].

       --bsremove-method <str>
              Bias removal method (str; default: ´PROFILE´). The full name of this option for the
              EsoRex configuration file is giraffe.biasremoval.method [default = PROFILE].

       --bsremove-areas <str>
              Bias   areas   to   use  (Xl0:Xr0:Yl0:Yr0,  ...  ,Xln:Xrn:Yln:Yrn)  (str;  default:
              ´5:40:0:4095´). The full name of this option for the EsoRex configuration  file  is
              giraffe.biasremoval.areas [default = 5:40:0:4095].

       --bsremove-sigma <float>
              Sigma Clipping: sigma threshold factor (float; default: 2.5). The full name of this
              option for the EsoRex configuration file is  giraffe.biasremoval.sigma  [default  =
              2.5].

       --bsremove-niter <int>
              Sigma  Clipping:  maximum  number of iterations (int; default: 5). The full name of
              this option for the EsoRex  configuration  file  is  giraffe.biasremoval.iterations
              [default = 5].

       --bsremove-mfrac <float>
              Sigma  Clipping:  minimum  fraction  of  points  accepted/total  [0.0..1.0] (float;
              default: 0.8). The full name of this option for the EsoRex  configuration  file  is
              giraffe.biasremoval.fraction [default = 0.8].

       --bsremove-xorder <int>
              Order  of  X polynomial fit (CURVE method only) (int; default: 1). The full name of
              this  option  for  the  EsoRex  configuration  file  is  giraffe.biasremoval.xorder
              [default = 1].

       --bsremove-yorder <int>
              Order  of  Y polynomial fit (CURVE method only) (int; default: 1). The full name of
              this  option  for  the  EsoRex  configuration  file  is  giraffe.biasremoval.yorder
              [default = 1].

       --bsremove-xstep <int>
              Sampling  step along X (CURVE method only) (int; default: 1). The full name of this
              option for the EsoRex configuration file is  giraffe.biasremoval.xstep  [default  =
              1].

       --bsremove-ystep <int>
              Sampling  step along Y (CURVE method only) (int; default: 1). The full name of this
              option for the EsoRex configuration file is  giraffe.biasremoval.ystep  [default  =
              1].

       --extr-method <str>
              Extraction method: ´SUM´, ´HORNE´ or ´OPTIMAL´ (str; default: ´SUM´). The full name
              of this option for  the  EsoRex  configuration  file  is  giraffe.extraction.method
              [default = SUM].

       --extr-ron <float>
              New  bias  sigma  (RON)  value  for  bias and dark corrected image (float; default:
              -1.0). The  full  name  of  this  option  for  the  EsoRex  configuration  file  is
              giraffe.extraction.ron [default = -1.0].

       --extr-psfmodel <str>
              PSF  profile model: `psfexp´, `psfexp2´ (str; default: ´psfexp2´). The full name of
              this option for  the  EsoRex  configuration  file  is  giraffe.extraction.psf.model
              [default = psfexp2].

       --extr-psfsigma <float>
              Sigma  clippging  threshold  used  for  rejecting  data  points  during PSF fitting
              (Horne´s sigma). It is used to reject bad pixels  and  cosmics.   (float;  default:
              7.0).  The  full  name  of  this  option  for  the  EsoRex  configuration  file  is
              giraffe.extraction.psf.sigma [default = 7.0].

       --extr-psfniter <int>
              Maximum number of iterations used for fitting the PSF profile. (int;  default:  2).
              The   full   name   of   this   option   for   the  EsoRex  configuration  file  is
              giraffe.extraction.psf.iterations [default = 2].

       --extr-hewidth <int>
              Horne extraction method: Number of extra pixels  added  to  the  fiber  half-width.
              (int;  default:  2). The full name of this option for the EsoRex configuration file
              is giraffe.extraction.horne.extrawidth [default = 2].

       --extr-hmingood <int>
              Horne extraction method: Minimum number of points used for the profile fit. It sets
              the  lower  limit  of  data points for the pixel rejection.  (int; default: 3). The
              full   name   of   this   option   for   the   EsoRex   configuration    file    is
              giraffe.extraction.horne.mingood [default = 3].

       --extr-omfrac <float>
              Optimal extraction method: Minimum fraction of the data points used for fitting the
              fiber profiles. It sets the lower limit for the pixel rejection.  (float;  default:
              0.9).  The  full  name  of  this  option  for  the  EsoRex  configuration  file  is
              giraffe.extraction.optimal.fraction [default = 0.9].

       --extr-owfactor <float>
              Optimal extraction method: Factor by which the fiber PSF half width is  multiplied.
              Adjacent  spectra  within  this  area  are  assumed  to  affect  the spectrum being
              extracted. (float; default: 3.0). The full name  of  this  option  for  the  EsoRex
              configuration file is giraffe.extraction.optimal.wfactor [default = 3.0].

       --extr-obkgorder <int>
              Optimal  extraction  method:  Order  of  the  polynomial background model, which is
              fitted for each wavelength bin along the spatial direction.  (int; default: 2). The
              full    name    of   this   option   for   the   EsoRex   configuration   file   is
              giraffe.extraction.optimal.bkgorder [default = 2].

       --flat-apply <bool>
              Controls the flat field correction. (bool; default: True). The full  name  of  this
              option for the EsoRex configuration file is giraffe.flat.apply [default = True].

       --transmission-apply <bool>
              Controls  the  fiber  to fiber transmission correction. (bool; default: False). The
              full   name   of   this   option   for   the   EsoRex   configuration    file    is
              giraffe.flat.transmission [default = False].

       --rbin-method <str>
              Method  to  use  :  `linear´ or `spline´ (str; default: ´linear´). The full name of
              this option for the EsoRex configuration file is giraffe.rebinning.method  [default
              = linear].

       --rbin-xresid <bool>
              Use  x  residuals  during rebinning? `true´/`false´ (bool; default: True). The full
              name    of    this    option    for    the    EsoRex    configuration    file    is
              giraffe.rebinning.xresiduals [default = True].

       --rbin-lstep <float>
              Lambda  step size, only used if scaling method is ´linear´ (float; default: 0.005).
              The  full  name  of  this   option   for   the   EsoRex   configuration   file   is
              giraffe.rebinning.lstep [default = 0.005].

       --rbin-scmethod <str>
              Scaling  method:  `log´ or `linear´ (str; default: ´linear´). The full name of this
              option for the EsoRex configuration file is giraffe.rebinning.scalemethod  [default
              = linear].

       --rbin-size <int>
              Size  of  output rebinned spectra, 0 means calculate size based on wavelength range
              and lambda stepsize (int; default: 0). The full name of this option for the  EsoRex
              configuration file is giraffe.rebinning.size [default = 0].

       --rbin-range <str>
              Rebinning range: `setup´ or `common´ (str; default: ´setup´). The full name of this
              option for the EsoRex configuration  file  is  giraffe.rebinning.range  [default  =
              setup].

       --siwc-apply <bool>
              Enable  simultaneous  wavelength calibration correction. (bool; default: True). The
              full name of this option for the EsoRex configuration  file  is  giraffe.siwc.apply
              [default = True].

       --scal-cniter <int>
              Slit geometry calibration maximum number of iterations. (int; default: 1). The full
              name    of    this    option    for    the    EsoRex    configuration    file    is
              giraffe.sgcalibration.iterations [default = 1].

       --scal-zmax <float>
              Maximum  allowed  pixel  value.  To be effective it must be larger than 0.  (float;
              default: 10000.0). The full name of this option for the EsoRex  configuration  file
              is giraffe.sgcalibration.zmax [default = 10000.0].

       --scal-cstep <float>
              Cross-correlation  step. (float; default: -0.005). The full name of this option for
              the EsoRex configuration file is giraffe.sgcalibration.cc.step [default = -0.005].

       --scal-cdomain <str>
              Restricts the cross-correlation to the given domain. (str; default:  ´0.,0.´).  The
              full    name    of   this   option   for   the   EsoRex   configuration   file   is
              giraffe.sgcalibration.cc.domain [default = 0.,0.].

       --scal-rvlimits <str>
              Delta  RV  limits  of  the  cross-correlation  window  in  km/s.   (str;   default:
              ´-200.,200.´).  The  full  name of this option for the EsoRex configuration file is
              giraffe.sgcalibration.rv.limits [default = -200.,200.].

       --scal-rvniter <int>
              Maximum number of iterations used for the RV determination. (int; default: 3).  The
              full    name    of   this   option   for   the   EsoRex   configuration   file   is
              giraffe.sgcalibration.rv.iterations [default = 3].

       --scal-rvwfactor <float>
              Data window width factor. The FWHM times this value determines  the  window  width.
              (float;  default:  1.5).  The full name of this option for the EsoRex configuration
              file is giraffe.sgcalibration.rv.wfactor [default = 1.5].

       --scal-pfniter <int>
              Peak model fit maximum number of iterations. (int; default: 50). The full  name  of
              this      option      for      the      EsoRex      configuration      file      is
              giraffe.sgcalibration.peak.iterations [default = 50].

       --scal-pfntest <int>
              Cross-correlation peak fit maximum number of tests (int; default: 7). The full name
              of     this     option     for     the     EsoRex     configuration     file     is
              giraffe.sgcalibration.peak.tests [default = 7].

       --scal-pfdchisq <float>
              Cross-correlation peak fit minimum chi-square difference. (float; default: 0.0001).
              The   full   name   of   this   option   for   the  EsoRex  configuration  file  is
              giraffe.sgcalibration.peak.dchisquare [default = 0.0001].

       --recon-min <float>
              Minimum wavelength for image reconstruction (float; default: 0.0). The full name of
              this option for the EsoRex configuration file is giraffe.fov.range.minimum [default
              = 0.0].

       --recon-max <float>
              Maximum wavelength for image reconstruction (float; default: 0.0). The full name of
              this option for the EsoRex configuration file is giraffe.fov.range.maximum [default
              = 0.0].

       --recon-cube <bool>
              Turns data cube creation on and off (bool; default: True). The full  name  of  this
              option for the EsoRex configuration file is giraffe.fov.cube [default = True].

       --recon-format <str>
              Selects  the  file format for cubes (str; default: ´single´). The full name of this
              option for the EsoRex configuration  file  is  giraffe.fov.cube.format  [default  =
              single].

       --generate-SDP-format <bool>
              TRUE  if additional files should be generated in Science Data Product (SDP) format.
              (bool; default: False). The full name of this option for the  EsoRex  configuration
              file is giraffe.sdp.format.generate [default = False].

       --dummy-association-keys <int>
              Sets  the  number  of  dummy  (empty) ASSONi, ASSOCi and ASSOMi keywords to create.
              (int; default: 0). The full name of this option for the EsoRex  configuration  file
              is giraffe.sdp.nassoc.keys [default = 0].

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

              ftp://ftp.eso.org/pub/dfs/pipelines/giraffe/giraf-pipeline-manual-2.11.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  giraf   pipeline   are   giframestack(7),   gimasterbias(7),
       gimasterdark(7), gimasterflat(7), gistandard(7), giwavecalibration(7)

VERSION

       giscience 2.16.8

AUTHOR

       Giraffe Pipeline <usd-help@eso.org>

BUG REPORTS

       Please  report  any  problems to usd-help@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 GIRAFFE Instrument Pipeline
        Copyright (C) 2002-2014 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  02110-1301  USA