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NAME

       xsh_cfg_recover - Optimizes a model configuration to match data taken after a major format
       change

SYNOPSIS

       esorex xsh_cfg_recover [OPTIONS] FILE.sof

DESCRIPTION

       This recipe creates a wavelength solution and an order table.

         Input Frames :
           - [UVB, VIS] A RAW frame (Format = RAW, Tag = FMTCHK_arm)
           - [NIR] Two RAW frames (Format = RAW, Tag = FMTCHK_arm_ON,FMTCHK_arm_OFF)
           - The old model cfg table (Format = TABLE, Tag = XSH_MOD_CFG_TAB_arm)
           - A ref. line list. The model computes corresponding positions
             (Format = TABLE, Tag = ARC_LINE_LIST_arm)
           - [UVB,VIS,OPTIONAL] A master bias (Format = PRE, Tag = MASTER_BIAS_arm)
           - [UVB,VIS,OPTIONAL] A master dark (Format = PRE, Tag = MASTER_DARK_arm)
           - [OPTIONAL-Required if method=pm,peaks]
            An order table (Format = TABLE, Tag = ORDER_TAB_CENTR_arm)
           - [OPTIONAL-Required if first-anneal=TRUE]
             A table with measured line positions (Format = TABLE, Tag = XSH_MEASCOORD_arm)
         Products :
           - if first-anneal=FALSE & last-step=FALSE
             nothing
           - if first-anneal=TRUE & last-step=FALSE
             an optimized model configuration, PRO.CATG=XSH_MOD_CFG_arm
           - if last-step=TRUE
             an optimized model configuration, PRO.CATG=XSH_MOD_FAN_arm
             an optimized model configuration, PRO.CATG=XSH_MOD_CFG_OPT_arm
             an quality control table, PRO.CATG=MODEL_GUESS_XY_arm
             the model theoretical map corresponding to the optimized model config,
             PRO.CATG=THEO_TAB_MULT_arm, THEO_TAB_IFU_arm, and THEO_TAB_SING_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_cfg_recover.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_cfg_recover.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_cfg_recover.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_cfg_recover.decode-bp
              [default = 2144337919].

       --first-anneal <bool>
              Run  first annealing (TRUE) or not (FALSE)See recipe man-page % Input frames (bool;
              default: False). The full name of this option for the EsoRex configuration file  is
              xsh.xsh_cfg_recover.first-anneal [default = False].

       --arm <str>
              Arm  setting:   (str;  default: ´vis´). The full name of this option for the EsoRex
              configuration file is xsh.xsh_model_compute.arm [default = vis].

       --name_i <str>
              Filename with wavelength,x,y,order:  (str; default:  ´line_xy_ord.txt´).  The  full
              name    of    this    option    for    the    EsoRex    configuration    file    is
              xsh.xsh_model_compute.name_i [default = line_xy_ord.txt].

       --niter <int>
              No of iterations for first anneal (int; default: 100000). The  full  name  of  this
              option  for the EsoRex configuration file is xsh.xsh_model_compute.niter [default =
              100000].

       --coord_frame <int>
              Co-ordinate frame for centroids (0=raw,1=pre) (int; default: 1). The full  name  of
              this  option for the EsoRex configuration file is xsh.xsh_model_compute.coord_frame
              [default = 1].

       --last-step <bool>
              Run last step (TRUE) or not  (FALSE)See  recipe  man-page  %  Input  frames  (bool;
              default:  False). The full name of this option for the EsoRex configuration file is
              xsh.xsh_cfg_recover.last-step [default = False].

       --plot <bool>
              Display plot (TRUE) or not (FALSE) (bool; default: False). The full  name  of  this
              option  for  the  EsoRex  configuration file is xsh.xsh_cfg_recover.plot [default =
              False].

       --ima_tresh_min <float>
              Min thresh raw image. (float; default: 40.0). The full name of this option for  the
              EsoRex configuration file is xsh.xsh_cfg_recover.ima_thresh_min [default = 40.0].

       --cor_prescan <bool>
              Correct  for  prescan  (bool; default: False). The full name of this option for the
              EsoRex configuration file is xsh.xsh_cfg_recover.cor_prescan [default = False].

       --method <str>
              Model predictions correction  method.  safefit:  safe  fitgfit:  2D  Gaussian  line
              fitpeaks:  line  peaks  detectionpm:  line  peaks  detection  & pattern match (str;
              default: ´safefit´). The full name of this option for the EsoRex configuration file
              is xsh.xsh_cfg_recover.method [default = safefit].

       --offx <float>
              X  offset  to model predictions (float; default: 0.0). The full name of this option
              for the EsoRex configuration file is xsh.xsh_cfg_recover.offx [default = 0.0].

       --offy <float>
              Y offset to model predictions (float; default: 0.0). The full name of  this  option
              for the EsoRex configuration file is xsh.xsh_cfg_recover.offy [default = 0.0].

       --slit <int>
              Extraction  slit  (int;  default:  5).  The full name of this option for the EsoRex
              configuration file is xsh.xsh_cfg_recover.slit [default = 5].

       --gfit_box_sy <int>
              Gauss fit Y search box size for lines on actual frame (int; default: 20). The  full
              name    of    this    option    for    the    EsoRex    configuration    file    is
              xsh.xsh_cfg_recover.gfit_box_sy [default = 20].

       --peak_line_fwhm <int>
              The FWHM used in line convolution, in pixel units (int; default: 4). The full  name
              of     this     option     for     the     EsoRex     configuration     file     is
              xsh.xsh_cfg_recover.peak_line_fwhm [default = 4].

       --peak_kappa <float>
              The kappa value, used to identify line peaks if max>kappa*stdev+median,  max  is  a
              valid  peak  where max, stdev,median are computed on the extracted spectrum (float;
              default: 5.0). The full name of this option for the EsoRex  configuration  file  is
              xsh.xsh_cfg_recover.peak_kappa [default = 5.0].

       --peak_factor <float>
              Relative  Intensity  threshold  factor  for  line  peaks detection (float; default:
              10.0). The  full  name  of  this  option  for  the  EsoRex  configuration  file  is
              xsh.xsh_cfg_recover.peak_factor [default = 10.0].

       --peak_match_x <int>
              Radii  for  line peaks matches (int; default: 10). The full name of this option for
              the EsoRex configuration file is xsh.xsh_cfg_recover.peak_match_x [default = 10].

       --peak_match_y <int>
              Radii for line peaks matches (int; default: 20). The full name of this  option  for
              the EsoRex configuration file is xsh.xsh_cfg_recover.peak_match_y [default = 20].

       --pm_ord_sel <int>
              From  guess  line  and  peaks  positions  are  extracted  the  ones  in  the  range
              [ord_min,ord_min+pm_ord_sel]  (int; default: 1). The full name of this  option  for
              the EsoRex configuration file is xsh.xsh_cfg_recover.pm_ord_sel [default = 1].

       --pm_radius <float>
              Search  radius  applied  in  final  pattern matching (data units). (float; default:
              20.0). The  full  name  of  this  option  for  the  EsoRex  configuration  file  is
              xsh.xsh_cfg_recover.pm_radius [default = 20.0].

       --pm_tolerance <float>
              Max  relative  difference  of  angles  and scales from their median value for match
              acceptance. (float; default: 0.1). The full name of  this  option  for  the  EsoRex
              configuration file is xsh.xsh_cfg_recover.pm_tolerance [default = 0.1].

       --anneal_niter <int>
              Simulated  annealing  iterations (int; default: 1000). The full name of this option
              for the EsoRex configuration file is  xsh.xsh_cfg_recover.anneal_niter  [default  =
              1000].

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

VERSION

       xsh_cfg_recover 3.2.0

AUTHOR

       A. Modigliani, P. Bristow <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