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NAME

       xsh_mflat - Create the master flat and the orders edges traces table frames

SYNOPSIS

       esorex xsh_mflat [OPTIONS] FILE.sof

DESCRIPTION

       This recipe creates the master flat and the orders edges traces table frames.

         Input Frames :
           -  [UVB]  A  set  of  n  RAW  frames  (Format  =  RAW,  n>=3,  Tag = FLAT_D2_mode_UVB,
       mode=SLIT/IFU)
           - [UVB] A set of n RAW frames (Format = RAW, n>=3, Tag = FLAT_QTH_mode_UVB)
           - [VIS] A set of n RAW frames (Format = RAW, n>=3, Tag = FLAT_mode_VIS)
           - [NIR] A set of n x n RAW frames  ((Format  =  RAW,  n>=3,  Tag  =  FLAT_mode_NIR_ON,
       FLAT_mode_NIR_OFF)
           - A spectral format table (Format = PRE, Tag = SPECTRAL_FORMAT_TAB_arm)
           - An order table (Format = TABLE, Tag = ORDER_TAB_CENTR_arm)
           - [UVB,VIS] A master bias (Format = PRE, Tag = MASTER_BIAS_arm)
           - [OPTIONAL] A map of reference bad pixel (Format = QUP,RAW, Tag = BP_MAP_RP_arm)
           - [OPTIONAL] A map of non linear pixel (Format = QUP,RAW, Tag = BP_MAP_NL_arm)
           - [OPTIONAL,UVB,VIS] A master dark (Format = PRE, Tag = MASTER_DARK_arm)
         Products :
           -  An  updated  order  table  with  edge  UP  and  edge  LOW  (Format  =  TABLE, TAG =
       ORDER_TAB_EDGES_mode_arm)
           - A master flat (Format = PRE, PRO.CATG = MASTER_FLAT_mode_arm)
           - The inter-order background frame (Format = PRE, PRO.CATG = MFLAT_BACK_mode_arm)
           - The inter-order background sampling points grid table
             (Format = PRE, PRO.CATG = MFLAT_GRID_BACK_mode_arm)
         Prepare the flat frames.

         Stack and sigma clip all the flat frames.

         Subtract master bias.

         Subtract master dark.

         Detect order edge.

         Subtract background.

         Create the Master Flat.

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_mflat.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_mflat.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_mflat.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_mflat.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_mflat.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_mflat.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_mflat.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_mflat.khigh [default = 5.0].

       --detectorder-edges-search-win-hsize <int>
              During  extraction  the  local  spatial  profile  (=cross-order) of the spectrum is
              determined by collapsing the 2-dimensional spectrum along the dispersion axis. This
              parameter  defines  the  half  size  of  the  region  across  which the spectrum is
              collapsed. This parameter affects flagged pixels interpolation. In case of spectrum
              gaps  the recommended optimal value is: (size_of_gap [nm]/(2*size_of_pixel [nm])+1)
              (int; default: 50). The full name of this option for the EsoRex configuration  file
              is xsh.xsh_mflat.detectorder-edges-search-win-hsize [default = 50].

       --detectorder-edges-flux-thresh <float>
              Threshold  in  relative  flux  (compared to the central flux) below which the order
              edges are defined (float; default: 0.4). The full  name  of  this  option  for  the
              EsoRex configuration file is xsh.xsh_mflat.detectorder-edges-flux-thresh [default =
              0.4].

       --detectorder-min-sn <float>
              Minimum  signal-to-noise  ratio  at  the   centroid   of   the   orders   (60   for
              SLIT-UVB,VIS,NIR,  20  for  IFU-UVB,VIS,  4 for IFU-NIR (float; default: -1.0). The
              full   name   of   this   option   for   the   EsoRex   configuration    file    is
              xsh.xsh_mflat.detectorder-min-sn [default = -1.0].

       --detectorder-min-order-size-x <int>
              Minimum  order  size in pixels along X direction [60 for UVB,VIS, 40 for NIR] (int;
              default: -1). The full name of this option for the  EsoRex  configuration  file  is
              xsh.xsh_mflat.detectorder-min-order-size-x [default = -1].

       --detectorder-chunk-half-size <int>
              Half  size  in pixels of the chunks in Y direction (int; default: 1). The full name
              of     this     option     for     the     EsoRex     configuration     file     is
              xsh.xsh_mflat.detectorder-chunk-half-size [default = 1].

       --detectorder-slitlet-low-factor <float>
              Factor for slitlet on lower edge slitlet (IFU) (float; default: 1.0). The full name
              of     this     option     for     the     EsoRex     configuration     file     is
              xsh.xsh_mflat.detectorder-slitlet-low-factor [default = 1.0].

       --detectorder-slitlet-up-factor <float>
              Factor for slitlet on upper edge (IFU) (float; default: 1.0). The full name of this
              option       for       the        EsoRex        configuration        file        is
              xsh.xsh_mflat.detectorder-slitlet-up-factor [default = 1.0].

       --detectorder-fixed-slice <bool>
              If  true the size of slitlet is fixed (IFU) (bool; default: True). The full name of
              this      option      for      the      EsoRex      configuration      file      is
              xsh.xsh_mflat.detectorder-fixed-slice [default = True].

       --detectorder-slice-trace-method <str>
              method  adopted for IFU slice tracing (´fixed´ for SLIT and ´sobel´ for IFU): (str;
              default: ´auto´). The full name of this option for the EsoRex configuration file is
              xsh.xsh_mflat.detectorder-slice-trace-method [default = auto].

       --detectorder-qc-mode <bool>
              If  true allows one to skip edge detection on orders below detectorder- min-sn (oly
              for QC mode, not to be set by normal users) (bool; default: False). The  full  name
              of     this     option     for     the     EsoRex     configuration     file     is
              xsh.xsh_mflat.detectorder-qc-mode [default = False].

       --detectorder-d2-min-sn <float>
              minimum signal noise ratio in D2 lamp frame in order (float;  default:  60.0).  The
              full    name    of   this   option   for   the   EsoRex   configuration   file   is
              xsh.xsh_mflat.detectorder-d2-min-sn [default = 60.0].

       --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_mflat.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_mflat.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_mflat.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_mflat.background-poly-kappa [default = 10.0].

       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_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_mflat 3.2.0

AUTHOR

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