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NAME

       xsh_scired_slit_stare - Reduce science exposure in SLIT configuration and stare mode

SYNOPSIS

       esorex xsh_scired_slit_stare [OPTIONS] FILE.sof

DESCRIPTION

       This recipe reduces science exposure in SLIT configuration and stare mode Input Frames :
         - A set of n Science frames ( n == 1 or >=3, Tag = OBJECT_SLIT_STARE_UVB)
         - A spectral format table (Tag = SPECTRAL_FORMAT_TAB_arm)
         - [UVB,VIS] A master bias frame (Tag = MASTER_BIAS_arm)
         - [OPTIONAL]A master dark frame (Tag = MASTER_DARK_arm)
         - A master flat frame (Tag = MASTER_FLAT_SLIT_arm)
         - An order table frame(Tag = ORDER_TAB_EDGES_SLIT_arm)
         - [OPTIONAL] A table with dispersion coefficients (Tag = DISP_TAB_arm,
           required in poly mode
         - [poly mode] A wave solution frame(Tag = WAVE_TAB_2D_arm)
         - [physical model mode] A model cfg table (Format = TABLE, Tag = XSH_MOD_CFG_TAB_arm)
         - [OPTIONAL] A table specifying multiplying factor for break points
           (Tag = SKY_SUB_BKPTS_arm) to generate
         - [OPTIONAL] A non-linear badpixel map (Tag = BP_MAP_NL_arm)
         - [OPTIONAL] A reference badpixel map (Tag = BP_MAP_RP_arm)
         - [OPTIONAL,physmod mode] A table listing sky line positions (Tag = SKY_LINE_LIST_arm)
           this is used to be able to control quality of sky subtraction, for example
           projecting guess positions on the product SCI_SLIT_STARE_SUB_SKY_arm
         - [OPTIONAL] The instrument response table (Tag = RESPONSE_MERGE1D_SLIT_arm)
         - [OPTIONAL] An atmospheric extinction table (Tag = ATMOS_EXT_arm)
         - [OPTIONAL] A telluric mask (Tag = TELL_MASK_arm)
         - [OPTIONAL] The instrument master response table (Tag = MRESPONSE_MERGE1D_SLIT_arm).

           If  both  master  and  individual  response  are  provided  the individual response is
       preferred.

       Products :
         - PREFIX_ORDER2D_arm extracted spectrum, order-by-order, 2D
         - PREFIX_ORDER1D_arm extracted spectrum, order-by-order, 1D
         - PREFIX_MERGE2D_arm merged spectrum, 2D
         - PREFIX_MERGE1D_arm merged spectrum, 1D
         - SKY_SLIT_MERGE2D_arm merged spectrum sky, 2D
         - PREFIX_SUB_BACK_SLIT_arm sci frame bias, (dark), inter-order bkg subtracted
         - PREFIX_WAVE_MAP_arm, wave map image
         - PREFIX_SLIT_MAP_arm, slit map image
         - PREFIX_DIVFF_arm as PREFIX_SUB_BACK_SLIT_arm, flat fielded
         - PREFIX_SUB_SKY_arm, as PREFIX_DIVFF_arm, sky subtracted
         - PREFIX_SKY_arm, 2D sky frame
         - PREFIX_SKY_ORD1D_arm, 1D sky image (order-by-order)
         - PREFIX_BACK_SLIT_arm, inter order background image
         - where PREFIX is SCI, FLUX, TELL if input raw  DPR.TYPE  contains  OBJECT  or  FLUX  or
       TELLURIC
         -  [OPTIONAL,  if  response  and  atm  ext  are  provided]   PREFIX_FLUX_ORDER2D_arm  (2
       dimension)
         -  [OPTIONAL,  if  response  and  atm  ext  are  provided]   PREFIX_FLUX_ORDER1D_arm  (1
       dimension)
         -  [OPTIONAL,  if  response  and  atm  ext  are  provided]   PREFIX_FLUX_MERGE2D_arm  (2
       dimension)
         -  [OPTIONAL,  if  response  and  atm  ext  are  provided]   PREFIX_FLUX_MERGE1D_arm  (1
       dimension)
         - PREFIX_ON_arm bias (dark) subtracted sci frame

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_scired_slit_stare.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_scired_slit_stare.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_scired_slit_stare.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_scired_slit_stare.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_scired_slit_stare.pre-overscan-corr [default = 1].

       --stack-method <str>
              Method  used to build master frame. (str; default: ´median´). The full name of this
              option for the EsoRex configuration file is  xsh.xsh_scired_slit_stare.stack-method
              [default = median].

       --klow <float>
              Kappa  used to clip low level values, when method is set to ´mean´ (float; default:
              5.0).  The  full  name  of  this  option  for  the  EsoRex  configuration  file  is
              xsh.xsh_scired_slit_stare.klow [default = 5.0].

       --khigh <float>
              Kappa used to clip high level values, when method is set to ´mean´ (float; default:
              5.0).  The  full  name  of  this  option  for  the  EsoRex  configuration  file  is
              xsh.xsh_scired_slit_stare.khigh [default = 5.0].

       --background-edges-margin <int>
              X  margin to order edge to define background sampling points (int; default: 1). The
              full   name   of   this   option   for   the   EsoRex   configuration    file    is
              xsh.xsh_scired_slit_stare.background-edges-margin [default = 1].

       --background-poly-deg-y <int>
              Poly  mode fit deg along Y. (int; default: 9). The full name of this option for the
              EsoRex  configuration   file   is   xsh.xsh_scired_slit_stare.background-poly-deg-y
              [default = 9].

       --background-poly-deg-x <int>
              Poly  mode fit deg along X. (int; default: 9). The full name of this option for the
              EsoRex  configuration   file   is   xsh.xsh_scired_slit_stare.background-poly-deg-x
              [default = 9].

       --background-poly-kappa <float>
              Poly mode kappa value of kappa-sigma-clip outliers removal. (float; default: 10.0).
              The  full  name  of  this   option   for   the   EsoRex   configuration   file   is
              xsh.xsh_scired_slit_stare.background-poly-kappa [default = 10.0].

       --removecrhsingle-sigmalim <float>
              Poisson fluctuation threshold to flag CRHs (see van Dokkum, PASP,113,2001,p1420-27)
              (float; default: 20.0). The full name of this option for the  EsoRex  configuration
              file is xsh.xsh_scired_slit_stare.removecrhsingle-sigmalim [default = 20.0].

       --removecrhsingle-flim <float>
              Minimum  contrast  between  the Laplacian image and the fine structure image that a
              point must have to be flagged as  CRH.  (see  van  Dokkum,  PASP,113,2001,p1420-27)
              (float;  default:  2.0).  The full name of this option for the EsoRex configuration
              file is xsh.xsh_scired_slit_stare.removecrhsingle-flim [default = 2.0].

       --removecrhsingle-niter <int>
              Max number of iterations (int; default: 4). The full name of this  option  for  the
              EsoRex   configuration   file   is  xsh.xsh_scired_slit_stare.removecrhsingle-niter
              [default = 4].

       --rectify-kernel <str>
              Name of the Interpolation Kernel Used. Possible values  are:   tanh,  sinc,  sinc2,
              lanczos,  hamming,  hann.  (str; default: ´tanh´). The full name of this option for
              the EsoRex configuration file is xsh.xsh_scired_slit_stare.rectify-kernel  [default
              = tanh].

       --rectify-radius <float>
              Rectify  Interpolation  radius [bin units]. (float; default: 2.0). The full name of
              this      option      for      the      EsoRex      configuration      file      is
              xsh.xsh_scired_slit_stare.rectify-radius [default = 2.0].

       --rectify-bin-lambda <float>
              Wavelength  step  in the output spectrum [nm] (float; default: -1.0). The full name
              of     this     option     for     the     EsoRex     configuration     file     is
              xsh.xsh_scired_slit_stare.rectify-bin-lambda [default = -1.0].

       --rectify-bin-slit <float>
              Spatial step along the slit in the output spectrum [arcsec] (float; default: -1.0).
              The  full  name  of  this   option   for   the   EsoRex   configuration   file   is
              xsh.xsh_scired_slit_stare.rectify-bin-slit [default = -1.0].

       --localize-method <str>
              Localization  method (MANUAL, MAXIMUM, GAUSSIAN) used to detect the object centroid
              and height on the slit (str; default: ´MANUAL´). The full name of this  option  for
              the EsoRex configuration file is xsh.xsh_scired_slit_stare.localize-method [default
              = MANUAL].

       --localize-chunk-nb <int>
              Number of chunks in the full spectrum to localize the object  (int;  default:  10).
              The   full   name   of   this   option   for   the  EsoRex  configuration  file  is
              xsh.xsh_scired_slit_stare.localize-chunk-nb [default = 10].

       --localize-thresh <float>
              Threshold relative to the peak intensity below which the edges of  the  object  are
              detected  for  MAXIMUM  localization  (float;  default: 0.1). The full name of this
              option       for       the        EsoRex        configuration        file        is
              xsh.xsh_scired_slit_stare.localize-thresh [default = 0.1].

       --localize-deg-lambda <int>
              Degree  in  lambda  in  the localization polynomial expression slit=f(lambda), used
              only for MAXIMUM and GAUSSIAN (int; default: 0). The full name of this  option  for
              the  EsoRex  configuration  file  is  xsh.xsh_scired_slit_stare.localize-deg-lambda
              [default = 0].

       --localize-slit-position <float>
              Object position on the slit for MANUAL localization [arcsec] (float; default: 0.0).
              The   full   name   of   this   option   for   the  EsoRex  configuration  file  is
              xsh.xsh_scired_slit_stare.localize-slit-position [default = 0.0].

       --localize-slit-hheight <float>
              Object half height on the slit for MANUAL localization  [arcsec]  (float;  default:
              2.0).  The  full  name  of  this  option  for  the  EsoRex  configuration  file  is
              xsh.xsh_scired_slit_stare.localize-slit-hheight [default = 2.0].

       --localize-kappa <float>
              Kappa value for sigma clipping in the localization polynomial fit (float;  default:
              3.0).  The  full  name  of  this  option  for  the  EsoRex  configuration  file  is
              xsh.xsh_scired_slit_stare.localize-kappa [default = 3.0].

       --localize-niter <int>
              Number of iterations for sigma clipping in the localization  polynomial  fit  (int;
              default:  3).  The  full  name  of this option for the EsoRex configuration file is
              xsh.xsh_scired_slit_stare.localize-niter [default = 3].

       --localize-use-skymask <bool>
              TRUE if we want to mask sky lines using SKY_LINE_LIST file. (bool; default: False).
              The   full   name   of   this   option   for   the  EsoRex  configuration  file  is
              xsh.xsh_scired_slit_stare.localize-use-skymask [default = False].

       --sky-subtract <bool>
              TRUE to use subtract sky single. (bool; default:  True).  The  full  name  of  this
              option  for the EsoRex configuration file is xsh.xsh_scired_slit_stare.sky-subtract
              [default = True].

       --sky-bspline-nbkpts-first <int>
              Nb of break points for Bezier curve fitting (without localization)  (int;  default:
              3000).  The  full  name  of  this  option  for  the  EsoRex  configuration  file is
              xsh.xsh_scired_slit_stare.sky-bspline-nbkpts-first [default = 3000].

       --sky-bspline-nbkpts-second <int>
              Nb of break points for Bezier curve  fitting  (with  localization)  (int;  default:
              3000).  The  full  name  of  this  option  for  the  EsoRex  configuration  file is
              xsh.xsh_scired_slit_stare.sky-bspline-nbkpts-second [default = 3000].

       --sky-bspline-order <int>
              Bezier spline order (int; default: 7). The full name of this option for the  EsoRex
              configuration file is xsh.xsh_scired_slit_stare.sky-bspline-order [default = 7].

       --sky-bspline-niter <int>
              Nb  of  iterations  (int; default: 20). The full name of this option for the EsoRex
              configuration file is xsh.xsh_scired_slit_stare.sky-bspline-niter [default = 20].

       --sky-bspline-kappa <float>
              Kappa value used to kappa-sigma-clip object (float; default: 5.0). The full name of
              this      option      for      the      EsoRex      configuration      file      is
              xsh.xsh_scired_slit_stare.sky-bspline-kappa [default = 5.0].

       --sky-method <str>
              Sky subtract Method (BSPLINE, BSPLINE1, BSPLINE2 MEDIAN). BSPLINE is equivalent  to
              BSPLINE1  (str;  default:  ´MEDIAN´).  The  full name of this option for the EsoRex
              configuration file is xsh.xsh_scired_slit_stare.sky-method [default = MEDIAN].

       --bspline-sampling <str>
              BSPLINE sampling.  UNIFORM-uses  the  user  defined  nbkpts  value,  corrected  for
              binning,  for all orders. FINE: multiplies the user defined nbkpts value, corrected
              for binning, by a  hard  coded  coefficient  optimized  on  each  arm-order)  (str;
              default: ´FINE´). The full name of this option for the EsoRex configuration file is
              xsh.xsh_scired_slit_stare.bspline-sampling [default = FINE].

       --sky-median-hsize <int>
              Half size of the running median. If sky-method=MEDIAN .  (int;  default:  20).  The
              full    name    of   this   option   for   the   EsoRex   configuration   file   is
              xsh.xsh_scired_slit_stare.sky-median-hsize [default = 20].

       --sky-slit-edges-mask <float>
              Size of edges mask in arcsec (float; default: 0.5). The full name  of  this  option
              for  the EsoRex configuration file is xsh.xsh_scired_slit_stare.sky-slit-edges-mask
              [default = 0.5].

       --sky-position1 <float>
              Central position of the sky window #1 [arcsec] (float; default: 0.0). The full name
              of     this     option     for     the     EsoRex     configuration     file     is
              xsh.xsh_scired_slit_stare.sky-position1 [default = 0.0].

       --sky-hheight1 <float>
              Half size of sky window #1 [arcsec] (float; default: 0.0). The full  name  of  this
              option  for the EsoRex configuration file is xsh.xsh_scired_slit_stare.sky-hheight1
              [default = 0.0].

       --sky-position2 <float>
              Central position of the sky window #2 [arcsec] (float; default: 0.0). The full name
              of     this     option     for     the     EsoRex     configuration     file     is
              xsh.xsh_scired_slit_stare.sky-position2 [default = 0.0].

       --sky-hheight2 <float>
              Half size of the sky window #2 [arcsec] (float; default: 0.0).  The  full  name  of
              this      option      for      the      EsoRex      configuration      file      is
              xsh.xsh_scired_slit_stare.sky-hheight2 [default = 0.0].

       --stdextract-interp-hsize <int>
              Half size of mask used to define object cross order profile (int; default: 30). The
              full    name    of   this   option   for   the   EsoRex   configuration   file   is
              xsh.xsh_scired_slit_stare.stdextract-interp-hsize [default = 30].

       --do-optextract <bool>
              TRUE if we do the optimal extraction (bool; default: False). The full name of  this
              option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.do-optextract
              [default = False].

       --optextract-oversample <int>
              Oversample factor for the science image (int; default: 5). The full  name  of  this
              option        for        the        EsoRex        configuration       file       is
              xsh.xsh_scired_slit_stare.optextract-oversample [default = 5].

       --optextract-box-half-size <int>
              Extraction box [pixel] (int; default: 10). The full name of  this  option  for  the
              EsoRex  configuration  file  is  xsh.xsh_scired_slit_stare.optextract-box-half-size
              [default = 10].

       --optextract-chunk-size <int>
              Chunk size [bin] (int; default: 50). The full name of this option  for  the  EsoRex
              configuration  file  is  xsh.xsh_scired_slit_stare.optextract-chunk-size [default =
              50].

       --optextract-step-lambda <float>
              Lambda step [nm] (float; default: 0.02). The full  name  of  this  option  for  the
              EsoRex   configuration   file  is  xsh.xsh_scired_slit_stare.optextract-step-lambda
              [default = 0.02].

       --optextract-clip-kappa <float>
              Kappa for cosmics ray hits rejection (float; default: 3.0). The full name  of  this
              option        for        the        EsoRex        configuration       file       is
              xsh.xsh_scired_slit_stare.optextract-clip-kappa [default = 3.0].

       --optextract-clip-frac <float>
              Maximum bad pixels fraction for cosmics ray hits rejection (float;  default:  0.4).
              The   full   name   of   this   option   for   the  EsoRex  configuration  file  is
              xsh.xsh_scired_slit_stare.optextract-clip-frac [default = 0.4].

       --optextract-clip-niter <int>
              Maximum number of iterations for cosmics ray hits rejection (int; default: 2).  The
              full    name    of   this   option   for   the   EsoRex   configuration   file   is
              xsh.xsh_scired_slit_stare.optextract-clip-niter [default = 2].

       --optextract-niter <int>
              Number of iterations (int; default: 1). The full name of this option for the EsoRex
              configuration file is xsh.xsh_scired_slit_stare.optextract-niter [default = 1].

       --optextract-method <str>
              Extraction  method  GAUSSIAN | GENERAL (str; default: ´GAUSSIAN´). The full name of
              this      option      for      the      EsoRex      configuration      file      is
              xsh.xsh_scired_slit_stare.optextract-method [default = GAUSSIAN].

       --cut-uvb-spectrum <bool>
              TRUE  if  recipe cuts the UVB spectrum at 556 nm (dichroich) (bool; default: True).
              The  full  name  of  this   option   for   the   EsoRex   configuration   file   is
              xsh.xsh_scired_slit_stare.cut-uvb-spectrum [default = True].

       --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 xsh.xsh_scired_slit_stare.generate-SDP-format [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 xsh.xsh_scired_slit_stare.dummy-association-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 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_orderpos(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_util_physmod(7), xsh_wavecal(7)

VERSION

       xsh_scired_slit_stare 3.2.0

AUTHOR

       P.Goldoni, L.Guglielmi, R. Haigron, F. Royer, D. Bramich, 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