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NAME

       xsh_lingain - Computes detector's gain/linearity-map

SYNOPSIS

       esorex xsh_lingain [OPTIONS] FILE.sof

DESCRIPTION

       This recipe computes detector linearity coefficients and gain Input Frames :
         arm = UVB-VIS:
         - A set of n RAW linearity frames (Format=RAW, n >=8, Tag = LINEARITY_arm_ON)
         - A set of n RAW bias frames (Format=RAW, n >=1, Tag = LINEARITY_arm_OFF)
         arm = NIR:
         - A set of n RAW linearity on frames (Format=RAW, n >=8, Tag = LINEARITY_arm_ON)
         - A set of n RAW linearity off frames (Format=RAW, n >=8, Tag = LINEARITY_arm_OFF)
         - [OPTIONAL] a static bad pixel map (PRO.CATG=BP_MAP_RP_arm)
         Note: on and off frames are taken in pairs sequence: OFF-ON-ON-OFF,
         at least 16 frames.

       Products :
         - A linearity map table, PRO.CATG = BP_MAP_LIN_NIR
         - A gain table, PRO.CATG = GAIN_INFO
         - A cube cointaining the linearity coefficients, PRO.CATG = COEFFS_CUBE_arm
         - A linearity map image (RAW format), PRO.CATG = RAW_BP_MAP_NL_arm
         - A linearity map image (PRE format), PRO.CATG = BP_MAP_NL_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_lingain.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_lingain.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_lingain.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_lingain.decode-bp [default = 2144337919].

       --method <str>
              Method to be used when computing GAIN. Methods appliable: <PTC | MED>.  By default PTC method will
              be applied. (str; default: ´PTC´). The full name of this option for the EsoRex configuration  file
              is xshoo.xsh_lingain.method [default = PTC].

       --order <int>
              Polynomial  order  for the fit (Linearity) (int; default: 3). The full name of this option for the
              EsoRex configuration file is xshoo.xsh_lingain.order [default = 3].

       --kappa <float>
              Kappa value for the kappa-sigma clipping (Gain) (float; default:  3.0).  The  full  name  of  this
              option for the EsoRex configuration file is xshoo.xsh_lingain.kappa [default = 3.0].

       --niter <int>
              Number of iterations to compute rms (Gain) (int; default: 5). The full name of this option for the
              EsoRex configuration file is xshoo.xsh_lingain.niter [default = 5].

       --llx <int>
              x coordinate of the lower-left point of the region of interest. If  not  modified,  default  value
              will  be  1. (int; default: -1). The full name of this option for the EsoRex configuration file is
              xshoo.xsh_lingain.llx [default = -1].

       --lly <int>
              y coordinate of the lower-left point of the region of interest. If  not  modified,  default  value
              will  be  1. (int; default: -1). The full name of this option for the EsoRex configuration file is
              xshoo.xsh_lingain.lly [default = -1].

       --urx <int>
              x coordinate of the upper-right point of the region of interest. If not  modified,  default  value
              will  be X dimension of the input image.  (int; default: -1). The full name of this option for the
              EsoRex configuration file is xshoo.xsh_lingain.urx [default = -1].

       --ury <int>
              y coordinate of the upper-right point of the region of interest. If not  modified,  default  value
              will  be Y dimension of the input image.  (int; default: -1). The full name of this option for the
              EsoRex configuration file is xshoo.xsh_lingain.ury [default = -1].

       --ref_level <int>
              User reference level (int;  default:  10000).  The  full  name  of  this  option  for  the  EsoRex
              configuration file is xshoo.xsh_lingain.ref_level [default = 10000].

       --intermediate <bool>
              De-/Activate  intermediate  products  (bool; default: False). The full name of this option for the
              EsoRex configuration file is xshoo.xsh_lingain.intermediate [default = False].

       --autocorr <bool>
              De-/Activate the autocorr option (bool; default: False). The full name  of  this  option  for  the
              EsoRex configuration file is xshoo.xsh_lingain.autocorr [default = False].

       --collapse <bool>
              De-/Activate  the  collapse  option  (bool;  default:  True). The full name of this option for the
              EsoRex configuration file is xshoo.xsh_lingain.collapse [default = True].

       --rescale <bool>
              De-/Activate the image rescale option (bool; default: True). The full name of this option for  the
              EsoRex configuration file is xshoo.xsh_lingain.rescale [default = True].

       --pix2pix <bool>
              De-/Activate  the computation with pixel to pixel accuracy (bool; default: True). The full name of
              this option for the EsoRex configuration file is xshoo.xsh_lingain.pix2pix [default = True].

       --bpmbin <bool>
              De-/Activate the binary bpm option (bool; default: False). The full name of this  option  for  the
              EsoRex configuration file is xshoo.xsh_lingain.bpmbin [default = False].

       --m <int>
              Maximum  x-shift  for the autocorr (int; default: 26). The full name of this option for the EsoRex
              configuration file is xshoo.xsh_lingain.m [default = 26].

       --filter <int>
              Upper limit of Median flux to be filtered (int; default: -1). The full name of this option for the
              EsoRex configuration file is xshoo.xsh_lingain.filter [default = -1].

       --n <int>
              Maximum  y-shift  for the autocorr (int; default: 26). The full name of this option for the EsoRex
              configuration file is xshoo.xsh_lingain.n [default = 26].

       --tolerance <float>
              Tolerance for pair discrimination (float; default: 0.1). The full name  of  this  option  for  the
              EsoRex configuration file is xshoo.xsh_lingain.tolerance [default = 0.1].

       --pafgen <bool>
              Generate  PAF  file  (bool;  default:  False).  The  full  name  of  this  option  for  the EsoRex
              configuration file is xshoo.xsh_lingain.pafgen [default = False].

       --pafname <str>
              Specific name for PAF file (str; default: ´xsh_lingain´). The full name of  this  option  for  the
              EsoRex configuration file is xshoo.xsh_lingain.pafname [default = xsh_lingain].

       --exts <int>
              Activate  the  multi-exts option. Choose -1 to process all extensions.  Choose an extension number
              to process the appropriate extension. (int; default: 0). The full name  of  this  option  for  the
              EsoRex configuration file is xshoo.xsh_lingain.exts [default = 0].

       --fpn_method <str>
              Method  for  computing  Fixed Pattern Noise (SMOOTH or HISTOGRAM) (str; default: ´HISTOGRAM´). The
              full name of this  option  for  the  EsoRex  configuration  file  is  xshoo.xsh_lingain.fpn_method
              [default = HISTOGRAM].

       --fpn_smooth <int>
              template  size  in  pixels  for  smoothing  during  FPN computation (only for SMOOTH method) (int;
              default:  13).  The  full  name  of  this  option   for   the   EsoRex   configuration   file   is
              xshoo.xsh_lingain.fpn_smooth [default = 13].

       --saturation_limit <float>
              all frames with mean saturation above the limit would not be used in linearity calculation (float;
              default:  65535.0).  The  full  name  of  this  option  for  the  EsoRex  configuration  file   is
              xshoo.xsh_lingain.saturation_limit [default = 65535.0].

       --gain_threshold <float>
              all  frames  with  mean  flux  above  the  threshold would not be used in gain calculation (float;
              default:  65535.0).  The  full  name  of  this  option  for  the  EsoRex  configuration  file   is
              xshoo.xsh_lingain.gain_threshold [default = 65535.0].

       --coeffs_cube_split <bool>
              if TRUE, the recipe writes as many COEFFS_CUBE_Pi (i=0..order) as the value of the order parameter
              in a separate file  (bool;  default:  False).  The  full  name  of  this  option  for  the  EsoRex
              configuration file is xshoo.xsh_lingain.coeffs_cube_split [default = False].

       --llx1 <int>
              x  coord  of  the  lower-left  point of the first field used for contamination measurement. If not
              modified, default value will be 1.  (int; default: -1). The full  name  of  this  option  for  the
              EsoRex configuration file is xshoo.xsh_lingain.llx1 [default = -1].

       --lly1 <int>
              y  coord  of  the  lower-left  point of the first field used for contamination measurement. If not
              modified, default value will be 1.  (int; default: -1). The full  name  of  this  option  for  the
              EsoRex configuration file is xshoo.xsh_lingain.lly1 [default = -1].

       --urx1 <int>
              x  coord  of  the  upper-right point of the first field used for contamination measurement. If not
              modified, default value will be X dimension of the input image. (int; default: -1). The full  name
              of this option for the EsoRex configuration file is xshoo.xsh_lingain.urx1 [default = -1].

       --ury1 <int>
              y  coord  of  the  upper-right point of the first field used for contamination measurement. If not
              modified, default value will be Y dimension of the input image. (int; default: -1). The full  name
              of this option for the EsoRex configuration file is xshoo.xsh_lingain.ury1 [default = -1].

       --llx2 <int>
              x  coord  of  the  lower-left point of the second field used for contamination measurement. If not
              modified, default value will be 1.  (int; default: -1). The full  name  of  this  option  for  the
              EsoRex configuration file is xshoo.xsh_lingain.llx2 [default = -1].

       --lly2 <int>
              y  coord  of  the  lower-left point of the second field used for contamination measurement. If not
              modified, default value will be 1.  (int; default: -1). The full  name  of  this  option  for  the
              EsoRex configuration file is xshoo.xsh_lingain.lly2 [default = -1].

       --urx2 <int>
              x  coord  of  the upper-right point of the second field used for contamination measurement. If not
              modified, default value will be half of the X dimension of the input image.  (int;  default:  -1).
              The  full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.urx2 [default
              = -1].

       --ury2 <int>
              y coord of the upper-right point of the second field used for contamination  measurement.  If  not
              modified,  default  value  will be half of the Y dimension of the input image. (int; default: -1).
              The full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.ury2  [default
              = -1].

       --llx3 <int>
              x  coord  of  the  lower-left  point of the third field used for contamination measurement. If not
              modified, default value will be 1.  (int; default: -1). The full  name  of  this  option  for  the
              EsoRex configuration file is xshoo.xsh_lingain.llx3 [default = -1].

       --lly3 <int>
              y  coord  of  the  lower-left  point of the third field used for contamination measurement. If not
              modified, default value will be half of the Y dimension of the input image.  (int;  default:  -1).
              The  full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.lly3 [default
              = -1].

       --urx3 <int>
              x coord of the upper-right point of the third field used for  contamination  measurement.  If  not
              modified,  default  value  will  be half of X dimension of the image. (int; default: -1). The full
              name of this option for the EsoRex configuration file is xshoo.xsh_lingain.urx3 [default = -1].

       --ury3 <int>
              y coord of the upper-right point of the third field used for  contamination  measurement.  If  not
              modified,  default  value  will  be Y dimension of the image. (int; default: -1). The full name of
              this option for the EsoRex configuration file is xshoo.xsh_lingain.ury3 [default = -1].

       --llx4 <int>
              x coord of the lower-left point of the fourth field used for  contamination  measurement.  If  not
              modified,  default  value  will  be half of X dimension of the image. (int; default: -1). The full
              name of this option for the EsoRex configuration file is xshoo.xsh_lingain.llx4 [default = -1].

       --lly4 <int>
              y coord of the lower-left point of the fourth field used for  contamination  measurement.  If  not
              modified,  default  value  will be half of the Y dimension of the input image. (int; default: -1).
              The full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.lly4  [default
              = -1].

       --urx4 <int>
              x  coord  of  the upper-right point of the fourth field used for contamination measurement. If not
              modified, default value will be X dimension of the image. (int; default: -1).  The  full  name  of
              this option for the EsoRex configuration file is xshoo.xsh_lingain.urx4 [default = -1].

       --ury4 <int>
              y  coord  of  the upper-right point of the fourth field used for contamination measurement. If not
              modified, default value will be Y dimension of the input image. (int; default: -1). The full  name
              of this option for the EsoRex configuration file is xshoo.xsh_lingain.ury4 [default = -1].

       --llx5 <int>
              x  coord  of  the  lower-left  point of the fifth field used for contamination measurement. If not
              modified, default value will be half of the X dimension of the input image.  (int;  default:  -1).
              The  full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.llx5 [default
              = -1].

       --lly5 <int>
              y coord of the lower-left point of the fifth field used  for  contamination  measurement.  If  not
              modified,  default  value  will  be  1.   (int; default: -1). The full name of this option for the
              EsoRex configuration file is xshoo.xsh_lingain.lly5 [default = -1].

       --urx5 <int>
              x coord of the upper-right point of the fifth field used for  contamination  measurement.  If  not
              modified,  default  value  will  be X dimension of the image. (int; default: -1). The full name of
              this option for the EsoRex configuration file is xshoo.xsh_lingain.urx5 [default = -1].

       --ury5 <int>
              y coord of the upper-right point of the fifth field used for  contamination  measurement.  If  not
              modified,  default  value  will be half of Y dimension of the input image. (int; default: -1). The
              full name of this option for the EsoRex configuration file is  xshoo.xsh_lingain.ury5  [default  =
              -1].

       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_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_scired_slit_stare(7),    xsh_util_physmod(7),
       xsh_wavecal(7)

VERSION

       xsh_lingain 3.5.3

AUTHOR

       Lander de Bilbao,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