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NAME

       muse_scibasic  -  Remove  the instrumental signature from the data of each CCD and convert
       them from an image into a pixel table.

SYNOPSIS

       esorex muse_scibasic [OPTIONS] FILE.sof

DESCRIPTION

       Processing handles each raw input image separately: it trims the raw data and records  the
       overscan  statistics, subtracts the bias (taking account of the overscan, if --overscan is
       not "none"), optionally detects cosmic rays (note that by default cosmic ray rejection  is
       handled  in  the post processing recipes while the data is reformatted into a datacube, so
       that the default setting is cr="none" here),  converts  the  images  from  adu  to  count,
       subtracts  the dark, divides by the flat-field, and (optionally) propagates the integrated
       flux  value  from  the  twilight-sky  cube.  The  reduced  image   is   then   saved   (if
       --saveimage=true).  The  input  calibrations  geometry  table, trace table, and wavelength
       calibration table are used to assign 3D  coordinates  to  each  CCD-based  pixel,  thereby
       creating  a  pixel table for each exposure. If --skylines contains one or more wavelengths
       for (bright and isolated) sky  emission  lines,  these  lines  are  used  to  correct  the
       wavelength  calibration using an offset. The data is then cut to a useful wavelength range
       (if --crop=true). If an ILLUM exposure was given as input, it is then used to correct  the
       relative  illumination  between all slices of one IFU. For this, the data of each slice is
       multiplied by the normalized median flux of that slice in  the  ILLUM  exposure.  As  last
       step,  the  data  is  divided  by  the  normalized  twilight cube (if given), using the 3D
       coordinate of each pixel in the pixel table to interpolate the  twilight  correction  onto
       the data. This pre-reduced pixel table for each exposure is then saved to disk.

OPTIONS

       --nifu <int>
              IFU to handle. If set to 0, all IFUs are processed serially. If set to -1, all IFUs
              are processed in parallel. (int; default: 0). The full name of this option for  the
              EsoRex configuration file is muse.muse_scibasic.nifu [default = 0].

       --overscan <str>
              If  this is "none", stop when detecting discrepant overscan levels (see ovscsigma),
              for "offset" it assumes that the mean overscan level represents the real offset  in
              the  bias  levels  of the exposures involved, and adjusts the data accordingly; for
              "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole
              quadrant.  (str;  default:  ´vpoly´).  The  full name of this option for the EsoRex
              configuration file is muse.muse_scibasic.overscan [default = vpoly].

       --ovscreject <str>
              This influences how values are rejected when computing overscan statistics.  Either
              no  rejection  at  all  ("none"),  rejection  using  the  DCR algorithm ("dcr"), or
              rejection using an iterative constant fit ("fit"). (str; default: ´dcr´). The  full
              name    of    this    option    for    the    EsoRex    configuration    file    is
              muse.muse_scibasic.ovscreject [default = dcr].

       --ovscsigma <float>
              If the deviation of mean  overscan  levels  between  a  raw  input  image  and  the
              reference  image  is  higher  than  |ovscsigma  x  stdev|,  stop the processing. If
              overscan="vpoly",  this  is  used  as  sigma  rejection  level  for  the  iterative
              polynomial  fit (the level comparison is then done afterwards with |100 x stdev| to
              guard against incompatible settings).  Has no effect for overscan="offset". (float;
              default:  30.0).  The full name of this option for the EsoRex configuration file is
              muse.muse_scibasic.ovscsigma [default = 30.0].

       --ovscignore <int>
              The number of pixels of the overscan adjacent to the data section of the  CCD  that
              are  ignored when computing statistics or fits. (int; default: 3). The full name of
              this option for the  EsoRex  configuration  file  is  muse.muse_scibasic.ovscignore
              [default = 3].

       --crop <bool>
              Automatically  crop the output pixel tables in wavelength depending on the expected
              useful wavelength range of the  active  instrument  mode  (4750-9350  Angstrom  for
              nominal  mode  and  NFM,  4700-9350  Angstrom  for  nominal  AO mode, and 4600-9350
              Angstrom for the extended modes).  (bool; default: True). The  full  name  of  this
              option  for  the  EsoRex  configuration  file is muse.muse_scibasic.crop [default =
              True].

       --cr <str>
              Type of cosmic ray  cleaning  to  use  (for  quick-look  data  processing).   (str;
              default: ´none´). The full name of this option for the EsoRex configuration file is
              muse.muse_scibasic.cr [default = none].

       --xbox <int>
              Search box size in x. Only used if cr=dcr. (int; default: 15).  The  full  name  of
              this option for the EsoRex configuration file is muse.muse_scibasic.xbox [default =
              15].

       --ybox <int>
              Search box size in y. Only used if cr=dcr. (int; default: 40).  The  full  name  of
              this option for the EsoRex configuration file is muse.muse_scibasic.ybox [default =
              40].

       --passes <int>
              Maximum number of cleaning passes. Only used if cr=dcr. (int; default: 2). The full
              name  of this option for the EsoRex configuration file is muse.muse_scibasic.passes
              [default = 2].

       --thres <float>
              Threshold for detection gap in factors of standard deviation. Only used if  cr=dcr.
              (float;  default:  5.8).  The full name of this option for the EsoRex configuration
              file is muse.muse_scibasic.thres [default = 5.8].

       --combine <str>
              Type of combination to use. Note that  in  most  cases,  science  exposures  cannot
              easily be combined on the CCD level, so this should usually be kept as "none"! This
              does not pay attention about the type of input  data,  and  will  combine  all  raw
              inputs!  (str;  default:  ´none´).  The  full  name  of  this option for the EsoRex
              configuration file is muse.muse_scibasic.combine [default = none].

       --nlow <int>
              Number of minimum pixels to reject with minmax (int; default: 1). The full name  of
              this option for the EsoRex configuration file is muse.muse_scibasic.nlow [default =
              1].

       --nhigh <int>
              Number of maximum pixels to reject with minmax (int; default: 1). The full name  of
              this  option for the EsoRex configuration file is muse.muse_scibasic.nhigh [default
              = 1].

       --nkeep <int>
              Number of pixels to keep with minmax (int; default:  1).  The  full  name  of  this
              option for the EsoRex configuration file is muse.muse_scibasic.nkeep [default = 1].

       --lsigma <float>
              Low  sigma for pixel rejection with sigclip (float; default: 3.0). The full name of
              this option for the EsoRex configuration file is muse.muse_scibasic.lsigma [default
              = 3.0].

       --hsigma <float>
              High sigma for pixel rejection with sigclip (float; default: 3.0). The full name of
              this option for the EsoRex configuration file is muse.muse_scibasic.hsigma [default
              = 3.0].

       --scale <bool>
              Scale the individual images to a common exposure time before combining them. (bool;
              default: True). The full name of this option for the EsoRex configuration  file  is
              muse.muse_scibasic.scale [default = True].

       --saveimage <bool>
              Save  the  pre-processed  CCD-based  image  of  each  input  exposure  before it is
              transformed into a pixel table. (bool; default: True). The full name of this option
              for the EsoRex configuration file is muse.muse_scibasic.saveimage [default = True].

       --skylines <str>
              List  of  wavelengths  of  sky emission lines (in Angstrom) to use as reference for
              wavelength offset  correction  using  a  Gaussian  fit.  It  can  contain  multiple
              (isolated) lines, as comma-separated list, individual shifts are then combined into
              one  weighted  average  offset.   Set  to  "none"  to  deactivate.  (str;  default:
              ´5577.339,6300.304´).  The  full  name  of this option for the EsoRex configuration
              file is muse.muse_scibasic.skylines [default = 5577.339,6300.304].

       --skyhalfwidth <float>
              Half-width of the extraction box (in  Angstrom)  around  each  sky  emission  line.
              (float;  default:  5.0).  The full name of this option for the EsoRex configuration
              file is muse.muse_scibasic.skyhalfwidth [default = 5.0].

       --skybinsize <float>
              Size of the bins (in Angstrom per pixel) for the intermediate spectrum  to  do  the
              Gaussian  fit  to  each  sky emission line. (float; default: 0.1). The full name of
              this option for the  EsoRex  configuration  file  is  muse.muse_scibasic.skybinsize
              [default = 0.1].

       --skyreject <str>
              Sigma  clipping  parameters for the intermediate spectrum to do the Gaussian fit to
              each sky emission line. Up to three comma-separated numbers can be given, which are
              interpreted  as high sigma-clipping limit (float), low limit (float), and number of
              iterations (integer), respectively. (str; default: ´15.,15.,1´). The full  name  of
              this  option  for  the  EsoRex  configuration  file is muse.muse_scibasic.skyreject
              [default = 15.,15.,1].

       --resample <bool>
              Resample the input  science  data  into  2D  spectral  images  using  all  supplied
              calibrations  for  a  visual  check.  Note  that the image produced will show small
              wiggles even when the input calibrations are good and  were  applied  successfully!
              (bool;  default:  False). The full name of this option for the EsoRex configuration
              file is muse.muse_scibasic.resample [default = False].

       --dlambda <float>
              Wavelength step (in Angstrom per pixel) to use  for  resampling.  (float;  default:
              1.25).  The  full  name  of  this  option  for  the  EsoRex  configuration  file is
              muse.muse_scibasic.dlambda [default = 1.25].

       --merge <bool>
              Merge output products from different IFUs  into  a  common  file.  (bool;  default:
              False).  The  full  name  of  this  option  for  the  EsoRex  configuration file is
              muse.muse_scibasic.merge [default = False].

       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 muse pipeline can be downloaded as a  PDF  file  using  the
       following URL:

              ftp://ftp.eso.org/pub/dfs/pipelines/muse/muse-pipeline-cookbook-2.6.2.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 muse pipeline are muse_ampl(7), muse_astrometry(7), muse_bias(7),
       muse_create_sky(7), muse_dark(7),  muse_exp_align(7),  muse_exp_combine(7),  muse_flat(7),
       muse_geometry(7),    muse_illum(7),    muse_lingain(7),    muse_lsf(7),   muse_qi_mask(7),
       muse_scipost(7),     muse_scipost_apply_astrometry(7),     muse_scipost_calibrate_flux(7),
       muse_scipost_combine_pixtables(7),                            muse_scipost_correct_dar(7),
       muse_scipost_correct_rv(7),       muse_scipost_make_cube(7),        muse_scipost_raman(7),
       muse_scipost_subtract_sky(7),    muse_scipost_subtract_sky_simple(7),    muse_standard(7),
       muse_twilight(7), muse_wavecal(7)

VERSION

       muse_scibasic 2.6.2

AUTHOR

       Peter Weilbacher <usd-help@eso.org>

BUG REPORTS

       Please report any problems to usd-help@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  MUSE  Instrument Pipeline Copyright (C) 2005, 2018 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., 51 Franklin St, Fifth Floor, Boston,
       MA  02111-1307  USA