Provided by: cpl-plugin-xshoo-doc_3.2.0+dfsg-1build2_all bug

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 3.2.0

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