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NAME

       xsh_flexcomp - Compute the flexure of the instrument

SYNOPSIS

       esorex xsh_flexcomp [OPTIONS] FILE.sof

DESCRIPTION

       This recipe computes the flexure of the instrument and correct CAL files.

         Input Frames :
           - [UVB, VIS] One RAW frame (Format = RAW, Tag = AFF_ATT_arm)
           - [NIR] Two RAW frames ((Format = RAW,  Tag = AFC_ATT_arm_ON,AFC_ATT_arm_OFF)
           - An arc line list (Format = TABLE, Tag = ARC_LINE_LIST_AFC_arm)
           - A spectral format table frame (Format = TABLE, Tag = SPECTRAL_FORMAT_TAB_arm)
           - [UVB,VIS] A master bias (Format = PRE, Tag = MASTER_BIAS_arm)
           - [UVB,VIS] A master dark (Format = PRE, Tag = MASTER_DARK_arm)
           - An order table frame (Format = TABLE, Tag = ORDER_TAB_EDGES_IFU_arm)
         - [OPTIONAL] A non-linear badpixel map (Tag = BP_MAP_NL_arm)
         - [OPTIONAL] A reference badpixel map (Tag = BP_MAP_RP_arm)
           - [poly mode]  A wave solution frame (Format = TABLE, Tag = WAVE_TAB_2D_arm)
           -   [physical   model   mode]   A   model   cfg   table   (Format   =   TABLE,  Tag  =
       XSH_MOD_CFG_OPT_2D_arm)
         Products :
           - [poly mode]  An updated wave solution frame (Format = TABLE, Tag = WAVE_TAB_AFC_arm)
           - [physical  model  mode]  An  updated   model  cfg  table  (Format  =  TABLE,  Tag  =
       XSH_MOD_CFG_OPT_AFC_arm)
           - An updated order table frame (Format = TABLE, Tag = ORDER_TAB_AFC_IFU_arm)
           - [poly mode] A dispersion table frame (Format = TABLE, Tag =  DISP_TAB_AFC_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_flexcomp.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_flexcomp.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_flexcomp.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_flexcomp.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_flexcomp.pre-overscan-corr [default = 1].

       --detectarclines-fit-win-hsize <int>
              Half  window size (HWS) in pixels for the line 2D fitting window (total window size
              = 2*HWS+1) (int; default:  6).  The  full  name  of  this  option  for  the  EsoRex
              configuration file is xsh.xsh_flexcomp.detectarclines-fit-win-hsize [default = 6].

       --detectarclines-search-win-hsize <int>
              Half  window  size  (HWS)  in  pixels  for  the line search box around the expected
              position (total window size = 2*HWS+1) [bin units] (int; default: 3). The full name
              of     this     option     for     the     EsoRex     configuration     file     is
              xsh.xsh_flexcomp.detectarclines-search-win-hsize [default = 3].

       --detectarclines-running-median-hsize <int>
              Half window size in pixels (HWS) for the running median box (int; default: 0).  The
              full    name    of   this   option   for   the   EsoRex   configuration   file   is
              xsh.xsh_flexcomp.detectarclines-running-median-hsize [default = 0].

       --detectarclines-wavesol-deg-lambda <int>
              Degree  in  lambda  in   the   polynomial   solution   X=f(lambda,order,slit)   and
              Y=f(lambda,order,slit)  (POLY mode) (int; default: 5). The full name of this option
              for          the          EsoRex          configuration           file           is
              xsh.xsh_flexcomp.detectarclines-wavesol-deg-lambda [default = 5].

       --detectarclines-wavesol-deg-order <int>
              Degree   in   order   in   the   polynomial   solution  X=f(lambda,order,slit)  and
              Y=f(lambda,order,slit) (POLY mode) (int; default: 5). The full name of this  option
              for           the           EsoRex          configuration          file          is
              xsh.xsh_flexcomp.detectarclines-wavesol-deg-order [default = 5].

       --detectarclines-min-sn <float>
              Minimum  signal-to-noise  ratio  to  filter  lines  [xsh_predict:  UVB,VIS=5,NIR=4;
              xsh_2dmap:  UVB=3,  VIS=6,  NIR=10]  (float;  default:  5.0). The full name of this
              option for the EsoRex configuration file is  xsh.xsh_flexcomp.detectarclines-min-sn
              [default = 5.0].

       --detectarclines-find-lines-center <str>
              Method used to find the center of the lines: gaussian, barycenter.  Gaussian method
              applies a Gaussian fit to the line. Barycenter method computes the  line  centroid.
              (str;   default:  ´gaussian´).  The  full  name  of  this  option  for  the  EsoRex
              configuration file is xsh.xsh_flexcomp.detectarclines-find-lines-center [default  =
              gaussian].

       --detectarclines-clip-sigma <float>
              Kappa  value  in  sigma  clipping  during  the  polynomial solution fit (POLY mode)
              (float; default: 2.0). The full name of this option for  the  EsoRex  configuration
              file is xsh.xsh_flexcomp.detectarclines-clip-sigma [default = 2.0].

       --detectarclines-clip-niter <int>
              Number  of  iterations  in  sigma clipping during the polynomial solution fit (POLY
              mode) (int; default: 10). The full name of this option for the EsoRex configuration
              file is xsh.xsh_flexcomp.detectarclines-clip-niter [default = 10].

       --detectarclines-clip-frac <float>
              Minimal  fractions  of  bad  pixel  allowed  in sigma clipping duringthe polynomial
              solution fit (POLY mode) (float; default: 0.7). The full name of  this  option  for
              the EsoRex configuration file is xsh.xsh_flexcomp.detectarclines-clip-frac [default
              = 0.7].

       --dispersol-deg-x <int>
              Degree in X in the polynomial dispersion  solution  lambda=f(X,Y)  and  slit=f(X,Y)
              (int;  default:  4). The full name of this option for the EsoRex configuration file
              is xsh.xsh_flexcomp.dispersol-deg-x [default = 4].

       --dispersol-deg-y <int>
              Degree in Y in the polynomial dispersion  solution  lambda=f(X,Y)  and  slit=f(X,Y)
              (int;  default:  5). The full name of this option for the EsoRex configuration file
              is xsh.xsh_flexcomp.dispersol-deg-y [default = 5].

       --model-maxit <int>
              Number/10 of annealing iterations if in physical model mode. (int; default:  1000).
              The   full   name   of   this   option   for   the  EsoRex  configuration  file  is
              xsh.xsh_flexcomp.model-maxit [default = 1000].

       --model-anneal-factor <float>
              Multiplier applied to the automatic parameter ranges (i.e. when  scenario!=0).  For
              routine operations should be 1.0. (physical model mode). (float; default: 1.0). The
              full   name   of   this   option   for   the   EsoRex   configuration    file    is
              xsh.xsh_flexcomp.model-anneal-factor [default = 1.0].

       --model-scenario <int>
              selects  preset  flag  and range combinations appropriate to common scenarios: -1 -
              Only the position across the slit and     camera focal length  are  open   0  -  No
              scenario,  input  cfg  flags and limits     used.  1 - scenario appropriate for the
              startup     recipe (large ranges for parameters      affecting single ph exposures,
              dist       coeff  fixed)  2 - Like 1, but includes parameters      affecting all ph
              positions 3 - Scenario for use in fine tuning  cfg      to  match  routine  wavecal
              exposures.  All      parameters  affecting 1ph exposures     except dist coeffs are
              included and     parameter ranges are small. (For use by flexcomp in 1ph case). 4 -
              Like  3 but includes parameters affecting all ph positions (Standard for     use by
              flexcomp in 9ph case and 2dmap). 5 - Like 4 but includes also dist coeffs 6 -  Just
              dist  coeffs (and chipx, chipy) (int; default: 3). The full name of this option for
              the EsoRex configuration file is xsh.xsh_flexcomp.model-scenario [default = 3].

       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_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_flexcomp 3.2.0

AUTHOR

       P.Goldoni, L.Guglielmi, R. Haigron, F. Royer <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