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NAME

       xsh_geom_ifu - Produces the spatial geometry of the IFU pattern on the sky

SYNOPSIS

       esorex xsh_geom_ifu [OPTIONS] FILE.sof

DESCRIPTION

       This recipe Produces the spatial geometry of the IFU pattern on the sky Input Frames :
         - A set of n science frames ( n == 1 or >=3, Tag = TRACE_arm)
         - [UVB,VIS] A master bias frame (Tag = MASTER_BIAS_arm)
         - [OPTIONAL] A master dark frame (Tag = MASTER_DARK_arm)
         - A master flat frame (Tag = MASTER_FLAT_IFU_arm)
         - An AFC corrected model order edges table for IFU frame (Tag = ORDER_TAB_AFC_IFU_arm)
         - [PHYSMOD] An AFC corrected model cfg frame (Tag = XSH_MOD_CFG_OPT_AFC_arm)
         - [POLY] An AFC corrected model wavesol frame (Tag = WAVE_TAB_AFC_arm)
         -  An AFC corrected dispersion solution frame (Tag = DISP_TAB_AFC_arm)
         - [OPTIONAL] A badpixel map (Tag = BADPIXEL_MAP_arm) Products :
         - A set of shift offset tables (Tag = OFFSET_TAB_slitlet_IFU_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_geom_ifu.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_geom_ifu.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_geom_ifu.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_geom_ifu.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_geom_ifu.pre-overscan-corr [default = 1].

       --stack-method <str>
              Method  used to build master frame. (str; default: ´median´). The full name of this
              option for the EsoRex configuration file is xsh.xsh_geom_ifu.stack-method  [default
              = median].

       --klow <float>
              Kappa  used to clip low level values, when method is set to ´mean´ (float; default:
              5.0).  The  full  name  of  this  option  for  the  EsoRex  configuration  file  is
              xsh.xsh_geom_ifu.klow [default = 5.0].

       --khigh <float>
              Kappa used to clip high level values, when method is set to ´mean´ (float; default:
              5.0).  The  full  name  of  this  option  for  the  EsoRex  configuration  file  is
              xsh.xsh_geom_ifu.khigh [default = 5.0].

       --crh-clip-kappa <float>
              Kappa  value  in  sigma clipping during CRH rejection using multiple frames (float;
              default: 5.0). The full name of this option for the EsoRex  configuration  file  is
              xsh.xsh_geom_ifu.crh-clip-kappa [default = 5.0].

       --crh-clip-niter <int>
              Number  of  iterations in sigma clipping during CRH rejection using multiple frames
              (int; default: 5). The full name of this option for the EsoRex  configuration  file
              is xsh.xsh_geom_ifu.crh-clip-niter [default = 5].

       --crh-clip-frac <float>
              Minimal  ratio  of  points  accepted / total in sigma clipping during CRH rejection
              using multiple frames (float; default: 0.7). The full name of this option  for  the
              EsoRex configuration file is xsh.xsh_geom_ifu.crh-clip-frac [default = 0.7].

       --background-edges-margin <int>
              X  margin to order edge to define background sampling points (int; default: 1). The
              full   name   of   this   option   for   the   EsoRex   configuration    file    is
              xsh.xsh_geom_ifu.background-edges-margin [default = 1].

       --background-poly-deg-y <int>
              Poly  mode fit deg along Y. (int; default: 9). The full name of this option for the
              EsoRex configuration file is xsh.xsh_geom_ifu.background-poly-deg-y [default = 9].

       --background-poly-deg-x <int>
              Poly mode fit deg along X. (int; default: 9). The full name of this option for  the
              EsoRex configuration file is xsh.xsh_geom_ifu.background-poly-deg-x [default = 9].

       --background-poly-kappa <float>
              Poly mode kappa value of kappa-sigma-clip outliers removal. (float; default: 10.0).
              The  full  name  of  this   option   for   the   EsoRex   configuration   file   is
              xsh.xsh_geom_ifu.background-poly-kappa [default = 10.0].

       --removecrhsingle-sigmalim <float>
              Poisson fluctuation threshold to flag CRHs (see van Dokkum, PASP,113,2001,p1420-27)
              (float; default: 5.0). The full name of this option for  the  EsoRex  configuration
              file is xsh.xsh_geom_ifu.removecrhsingle-sigmalim [default = 5.0].

       --removecrhsingle-flim <float>
              Minimum  contrast  between  the Laplacian image and the fine structure image that a
              point must have to be flagged as  CRH.  (see  van  Dokkum,  PASP,113,2001,p1420-27)
              (float;  default:  2.0).  The full name of this option for the EsoRex configuration
              file is xsh.xsh_geom_ifu.removecrhsingle-flim [default = 2.0].

       --removecrhsingle-niter <int>
              Max number of iterations (int; default: 4). The full name of this  option  for  the
              EsoRex configuration file is xsh.xsh_geom_ifu.removecrhsingle-niter [default = 4].

       --rectify-kernel <str>
              Name  of  the  Interpolation  Kernel Used. Possible values are:  tanh, sinc, sinc2,
              lanczos, hamming, hann. (str; default: ´tanh´). The full name of  this  option  for
              the EsoRex configuration file is xsh.xsh_geom_ifu.rectify-kernel [default = tanh].

       --rectify-radius <float>
              Rectify  Interpolation  radius [bin units]. (float; default: 4.0). The full name of
              this option for the EsoRex configuration  file  is  xsh.xsh_geom_ifu.rectify-radius
              [default = 4.0].

       --rectify-bin-lambda <float>
              Wavelength  step  in the output spectrum [nm] (float; default: -1.0). The full name
              of     this     option     for     the     EsoRex     configuration     file     is
              xsh.xsh_geom_ifu.rectify-bin-lambda [default = -1.0].

       --rectify-bin-slit <float>
              Spatial step along the slit in the output spectrum [arcsec] (float; default: -1.0).
              The  full  name  of  this   option   for   the   EsoRex   configuration   file   is
              xsh.xsh_geom_ifu.rectify-bin-slit [default = -1.0].

       --localizeifu-bckg-deg <int>
              Degree  (<=2) of the polynomial component in the cross-dispersion profile fit (int;
              default: 50). The full name of this option for the  EsoRex  configuration  file  is
              xsh.xsh_geom_ifu.localizeifu-bckg-deg [default = 50].

       --localizeifu-smooth-hsize <int>
              Half-size  of the median filter for smoothing the cross-dispersion profile prior to
              localization (int; default: 3). The  full  name  of  this  option  for  the  EsoRex
              configuration file is xsh.xsh_geom_ifu.localizeifu-smooth-hsize [default = 3].

       --localizeifu-wavelet-nscales <int>
              Number  of  scales  used  for wavelet a trous algorithm (int; default: 5). The full
              name    of    this    option    for    the    EsoRex    configuration    file    is
              xsh.xsh_geom_ifu.localizeifu-wavelet-nscales [default = 5].

       --localizeifu-wavelet-hf-skip <int>
              Number  of  high  frequency  scales  skipped  from  the wavelet decomposition (int;
              default: 2). The full name of this option for  the  EsoRex  configuration  file  is
              xsh.xsh_geom_ifu.localizeifu-wavelet-hf-skip [default = 2].

       --localizeifu-sigma-low <float>
              Gaussian  fits  of the cross-dispersion profile whose FWHM is lower than this value
              are rejected (float; default: 0.05). The full name of this option  for  the  EsoRex
              configuration file is xsh.xsh_geom_ifu.localizeifu-sigma-low [default = 0.05].

       --localizeifu-sigma-up <float>
              Gaussian  fits of the cross-dispersion profile whose FWHM is larger than this value
              are rejected (float; default: 0.95). The full name of this option  for  the  EsoRex
              configuration file is xsh.xsh_geom_ifu.localizeifu-sigma-up [default = 0.95].

       --localizeifu-snr-low <float>
              Gaussian  fits  of  the cross-dispersion profile whose SNR is lower than this value
              are rejected (float; default: 0.05). The full name of this option  for  the  EsoRex
              configuration file is xsh.xsh_geom_ifu.localizeifu-snr-low [default = 0.05].

       --localizeifu-snr-up <float>
              Gaussian  fits  of the cross-dispersion profile whose SNR is larger than this value
              are rejected (float; default: 0.95). The full name of this option  for  the  EsoRex
              configuration file is xsh.xsh_geom_ifu.localizeifu-snr-up [default = 0.95].

       --localizeifu-slitlow-edges-mask <float>
              in  arsec  (float;  default:  0.0).  The  full  name  of this option for the EsoRex
              configuration file is  xsh.xsh_geom_ifu.localizeifu-slitlow-edges-mask  [default  =
              0.0].

       --localizeifu-slitup-edges-mask <float>
              in  arsec  (float;  default:  0.0).  The  full  name  of this option for the EsoRex
              configuration file  is  xsh.xsh_geom_ifu.localizeifu-slitup-edges-mask  [default  =
              0.0].

       --localizeifu-use-skymask <bool>
              TRUE if we want to mask sky lines using SKY_LINE_LIST file. (bool; default: False).
              The  full  name  of  this   option   for   the   EsoRex   configuration   file   is
              xsh.xsh_geom_ifu.localizeifu-use-skymask [default = False].

       --localizeifu-chunk-hsize <int>
              Half  size  of  chunk [bin] (int; default: 0). The full name of this option for the
              EsoRex configuration file is  xsh.xsh_geom_ifu.localizeifu-chunk-hsize  [default  =
              0].

       --correctifu-niter <int>
              Number of iterations in computing the localization shifts of the IFU slitlets (int;
              default: 3). The full name of this option for  the  EsoRex  configuration  file  is
              xsh.xsh_geom_ifu.correctifu-niter [default = 3].

       --correctifu-lambdaref <float>
              Reference wavelength where the reference localization on the slit is chosen (float;
              default: -1.0). The full name of this option for the EsoRex configuration  file  is
              xsh.xsh_geom_ifu.correctifu-lambdaref [default = -1.0].

       --correctifu-lambdaref-hsize <float>
              HAlf  size  in  nm to estimate reference wavelength (float; default: 2.5). The full
              name    of    this    option    for    the    EsoRex    configuration    file    is
              xsh.xsh_geom_ifu.correctifu-lambdaref-hsize [default = 2.5].

       --do-cube <bool>
              if  TRUE  creates  a data cube (bool; default: False). The full name of this option
              for the EsoRex configuration file is xsh.xsh_geom_ifu.do-cube [default = False].

       --compute-map <bool>
              if TRUE recompute (wave and  slit)  maps  from  the  dispersion  solution.   (bool;
              default:  True).  The full name of this option for the EsoRex configuration file is
              xsh.xsh_geom_ifu.compute-map [default = True].

       --check-afc <bool>
              Input AFC corrected model/wave solution and science frame check.If TRUE the  recipe
              verify  that  the  input mode/wave solution is AFC corrected, its INS.OPTIi.NAME is
              ´Pin_0.5 ´, and its OBS.ID and OBS.TARG.NAME values matches with the  corresponding
              values  of  the  science frame. (bool; default: True). The full name of this option
              for the EsoRex configuration file is xsh.xsh_geom_ifu.check-afc [default = True].

       --flat-method <str>
              method adopted for flat: (str; default: ´blaze´). The full name of this option  for
              the EsoRex configuration file is xsh.xsh_geom_ifu.flat-method [default = blaze].

       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_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_geom_ifu 3.2.0

AUTHOR

       P.Goldoni, L.Guglielmi, R. Haigron, F. Royer <regis.haigron@obspm.fr>

BUG REPORTS

       Please report any problems to regis.haigron@obspm.fr. 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