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NAME

       xsh_2dmap - Creates a wavelength and spatial resampling solution, a clean arc line list

SYNOPSIS

       esorex xsh_2dmap [OPTIONS] FILE.sof

DESCRIPTION

       This recipe creates a wavelength and spatial resampling solution, a clean arc line list.

        a residual map and a wave map.

       Input Frames:
         Raw Frame (Tag = WAVE_arm)
         Arc Line List (Tag = ARC_LINE_LIST_arm)
         Order Table (Tag = ORDER_TAB_EDGES_arm)
         Master Bias (Tag = MASTER_BIAS_arm)
         [poly mode] Wave Solution (Tag = WAVE_TAB_GUESS_arm)
         [poly mode] Theoretical Map (Tag = THEO_TAB_MULT_arm)
         [physical model mode] model cfg table (Tag = XSH_MOD_CFG_OPT_FMT_arm)
         [OPTIONAL] Master Dark (Tag = MASTER_DARK_arm)
         [OPTIONAL] Non-linear Bad Pixel Map (Tag = BP_MAP_NL_arm)
         [OPTIONAL] Reference Bad Pixel Map (Tag = BP_MAP_RP_arm)
         [OPTIONAL] Reference list to monitor line intensity (Tag = ARC_LINE_LIST_INTMON_arm)
        Prepare the frames.

       For UVB,VIS:
          Subtract Master Bias.

          Subtract Master Dark.

       For NIR:
         Subtract ON OFF
         Compute Wavelength Solution, clean arc line list, residual table, wave map
         Products:
          Wavelength table solution, PRO.CATG = WAVE_TAB_2D_arm [poly mode]
          A Residual tab, PRO.CATG=WAVE_RESID_TAB_SLIT_arm
          A Wavelelength image map, PRO.CATG=WAVE_MAP_arm. [if model-wavemap-compute=TRUE]
          A Slit image map, PRO.CATG=SLIT_MAP_NIR [if model-wavemap-compute=TRUE]
          A Dispersion solution table, PRO.CATG=DISP_TAB_NIR
          An Arc frame in pre format bias subtracted,
          PRO.CATG=WAVE_ON_arm
          The  optimized  model  cfg  frame,  PRO.CATG=XSH_MOD_CFG_OPT_2D_arm  [if physical model
       mode].

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_2dmap.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_2dmap.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_2dmap.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_2dmap.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_2dmap.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_2dmap.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_2dmap.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_2dmap.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_2dmap.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: 4). The full name of this  option
              for the EsoRex configuration file is xsh.xsh_2dmap.detectarclines-wavesol-deg-order
              [default = 4].

       --detectarclines-wavesol-deg-slit <int>
              Degree  in   slit   in   the   polynomial   solution   X=f(lambda,order,slit)   and
              Y=f(lambda,order,slit)  (POLY mode) (int; default: 1). The full name of this option
              for the EsoRex configuration file is  xsh.xsh_2dmap.detectarclines-wavesol-deg-slit
              [default = 1].

       --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_2dmap.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_2dmap.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_2dmap.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: 0). The full name of this option for the EsoRex configuration
              file is xsh.xsh_2dmap.detectarclines-clip-niter [default = 0].

       --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_2dmap.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_2dmap.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_2dmap.dispersol-deg-y [default = 5].

       --model-maxit <int>
              Number/10  of  annealing iterations (physical model mode). (int; default: 500). The
              full   name   of   this   option   for   the   EsoRex   configuration    file    is
              xsh.xsh_2dmap.model-maxit [default = 500].

       --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_2dmap.model-anneal-factor [default = 1.0].

       --model-scenario <int>
              selects preset flag and range combinations appropriate to common scenarios:    0  -
              No  scenario,  input  cfg  flags  and limitsused.  1 - scenario appropriate for the
              startuprecipe (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 single pinhole exposures.  All
              parameters  affecting  1ph  exposures except dist coeffs are included and parameter
              ranges are small. (For use by predict in 1ph  case).   4  -  Like  3  but  includes
              parameters  affecting all ph positions (Standard for use by predict in 9ph case and
              2dmap).   (int;  default:  4).  The  full  name  of  this  option  for  the  EsoRex
              configuration file is xsh.xsh_2dmap.model-scenario [default = 4].

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

VERSION

       xsh_2dmap 3.2.0

AUTHOR

       R. Haigron, P. Bristow, 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