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NAME

       xsh_scired_ifu_offset - Reduce science IFU on-off exposures and build a 3D cube

SYNOPSIS

       esorex xsh_scired_ifu_offset [OPTIONS] FILE.sof

DESCRIPTION

       This recipe Reduce science IFU on-off exposures and build a 3D cube Input Frames :
         - A set of 2xn Science frames,       Tag = OBJECT_IFU_OFFSET_arm, SKY_IFU_arm
         - A spectral format table (Tag = SPECTRAL_FORMAT_TAB_arm)
         - A master flat frame (Tag = MASTER_FLAT_IFU_arm)
         - An order table frame(Tag = ORDER_TABLE_EDGES_IFU_arm)
         - 3 wave solution frames, one per slitlet (Tag = WAVE_TAB_ARC_IFU_slitlet_arm)
             where ´slitlet´ is DOWN, CEN or UP
         - [OPTIONAL] A dispersion table (Tag = DISP_TAB_IFU_arm)
         - [OPTIONAL] A non-linear badpixel map (Tag = BP_MAP_NL_arm)
         - [OPTIONAL] A reference badpixel map (Tag = BP_MAP_RP_arm) Products :
        - Merged 3D data cube (PREFIX_MERGE3D_DATA_OBJ_arm)
        - QC Traces of 3D data cube (PREFIX_MERGE3D_TRACE_OBJ_arm)
        - Order by order 3D data cube (PREFIX_ORDER3D_DATA_OBJ_arm)
        - Order by order 3D qual cube (IFU_CFG_COR_arm)
        - Order by order 3D qual cube (PREFIX_MERGE3D_DATA_SKY_arm)
        -  where  PREFIX  is  SCI,  FLUX,  TELL  if input raw DPR.TYPE contains OBJECT or FLUX or
       TELLURIC
        - 1 Spectrum merge 3D, PRO.CATG=MERGE3D_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_scired_ifu_offset.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_scired_ifu_offset.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_scired_ifu_offset.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_scired_ifu_offset.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_scired_ifu_offset.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_scired_ifu_offset.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_scired_ifu_offset.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_scired_ifu_offset.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_scired_ifu_offset.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_scired_ifu_offset.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_scired_ifu_offset.crh-clip-frac  [default  =
              0.7].

       --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_scired_ifu_offset.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_scired_ifu_offset.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_scired_ifu_offset.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_scired_ifu_offset.rectify-kernel  [default
              = tanh].

       --rectify-radius <float>
              Rectify  Interpolation  radius [bin units]. (float; default: 2.0). The full name of
              this      option      for      the      EsoRex      configuration      file      is
              xsh.xsh_scired_ifu_offset.rectify-radius [default = 2.0].

       --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_scired_ifu_offset.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_scired_ifu_offset.rectify-bin-slit [default = -1.0].

       --localize-method <str>
              Localization  method (MANUAL, MAXIMUM, GAUSSIAN) used to detect the object centroid
              and height on the slit (str; default: ´MANUAL´). The full name of this  option  for
              the EsoRex configuration file is xsh.xsh_scired_ifu_offset.localize-method [default
              = MANUAL].

       --localize-chunk-nb <int>
              Number of chunks in the full spectrum to localize the object  (int;  default:  10).
              The   full   name   of   this   option   for   the  EsoRex  configuration  file  is
              xsh.xsh_scired_ifu_offset.localize-chunk-nb [default = 10].

       --localize-thresh <float>
              Threshold relative to the peak intensity below which the edges of  the  object  are
              detected  for  MAXIMUM  localization  (float;  default: 0.1). The full name of this
              option       for       the        EsoRex        configuration        file        is
              xsh.xsh_scired_ifu_offset.localize-thresh [default = 0.1].

       --localize-deg-lambda <int>
              Degree  in  lambda  in  the localization polynomial expression slit=f(lambda), used
              only for MAXIMUM and GAUSSIAN (int; default: 0). The full name of this  option  for
              the  EsoRex  configuration  file  is  xsh.xsh_scired_ifu_offset.localize-deg-lambda
              [default = 0].

       --localize-slit-position <float>
              Object position on the slit for MANUAL localization [arcsec] (float; default: 0.0).
              The   full   name   of   this   option   for   the  EsoRex  configuration  file  is
              xsh.xsh_scired_ifu_offset.localize-slit-position [default = 0.0].

       --localize-slit-hheight <float>
              Object half height on the slit for MANUAL localization  [arcsec]  (float;  default:
              2.0).  The  full  name  of  this  option  for  the  EsoRex  configuration  file  is
              xsh.xsh_scired_ifu_offset.localize-slit-hheight [default = 2.0].

       --localize-kappa <float>
              Kappa value for sigma clipping in the localization polynomial fit (float;  default:
              3.0).  The  full  name  of  this  option  for  the  EsoRex  configuration  file  is
              xsh.xsh_scired_ifu_offset.localize-kappa [default = 3.0].

       --localize-niter <int>
              Number of iterations for sigma clipping in the localization  polynomial  fit  (int;
              default:  3).  The  full  name  of this option for the EsoRex configuration file is
              xsh.xsh_scired_ifu_offset.localize-niter [default = 3].

       --localize-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_scired_ifu_offset.localize-use-skymask [default = False].

       --compute-map <bool>
              if  TRUE  recompute  (wave  and  slit)  maps  from  the  dispersion  solution.   If
              sky-subtract  is  set to TRUE this must be set to TRUE. (bool; default: False). The
              full   name   of   this   option   for   the   EsoRex   configuration    file    is
              xsh.xsh_scired_ifu_offset.compute-map [default = False].

       --trace-obj <bool>
              if  TRUE  trace  object position on each IFU slice. In this case order TAB edges is
              required (bool; default: False). The full  name  of  this  option  for  the  EsoRex
              configuration file is xsh.xsh_scired_ifu_offset.trace-obj [default = False].

       --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_scired_ifu_offset.check-afc [default =
              True].

       --cut-uvb-spectrum <bool>
              TRUE if recipe cuts the UVB spectrum at 556 nm (dichroich) (bool;  default:  True).
              The   full   name   of   this   option   for   the  EsoRex  configuration  file  is
              xsh.xsh_scired_ifu_offset.cut-uvb-spectrum [default = True].

       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_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_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_scired_ifu_offset 3.2.0

AUTHOR

       A.Modigliani, J.Vernet, P. Bristow <Andrea.Modigliani@eso.org>

BUG REPORTS

       Please report any problems to Andrea.Modigliani@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