NAME

       vmifuscience - Extract spectra from an IFU scientific exposure.

SYNOPSIS

       esorex vmifuscience [OPTIONS] FILE.sof

DESCRIPTION

       This  recipe  extracts  IFU  scientific  spectra  using  the  input extraction mask, after
       aligning it to the brightest fiber spectra detected on the input exposure.  The  extracted
       spectra  are  then  resampled  at  a  constant  wavelength  step, after aligning the input
       wavelength calibration to the positions of a set of identified sky  lines.  The  extracted
       spectra  are  eventually corrected for the relative differences in transmission from fiber
       to fiber.

       Input files:

         DO category:             Type:       Explanation:             Required:
         IFU_SCIENCE              Raw         Scientific spectra          Y
         MASTER_BIAS              Calib       Master bias                 Y
         IFU_TRACE                Calib       Extraction mask             Y
         IFU_IDS                  Calib       Wavelength calibration      Y
         IFU_TRANSMISSION         Calib       Transmission correction     Y
         EXTINCT_TABLE            Calib       Atmospheric extinction      .

         IFU_SPECPHOT_TABLE       Calib       Response curve              .

         CCD_TABLE                Calib       Bad pixel table             .

       Output files:

         DO category:             Data type:  Explanation:
         IFU_SCIENCE_REDUCED      FITS image  Reduced scientific spectra
         IFU_SCIENCE_FLUX_REDUCED FITS image  Reduced scientific spectra
         IFU_FOV                  FITS image  Reconstructed IFU field-of-view
         IFU_SKY_TRACE            FITS table  Science aligned extraction mask

         Only if sky alignment is requested:
         IFU_SKY_IDS              FITS table  Sky  aligned  wavelength  solution  The  extraction
       mask, the wavelength calibration, and the relative transmission table, are those generated
       by the recipe vmifucalib. A CCD table must be specified only if a bad  pixel  cleaning  is
       requested.

       For more details, please refer to the VIMOS Pipeline User´s Guide.

OPTIONS

       --BiasMethod <str>
              Bias  removal  method.  (str; default: ´Zmaster´). The full name of this option for
              the EsoRex configuration file is vimos.Parameters.bias.removing.method  [default  =
              Zmaster].

       --CleanBadPixel <bool>
              Bad pixel correction on master flat field. (bool; default: False). The full name of
              this option for the EsoRex configuration  file  is  vimos.Parameters.badpixel.clean
              [default = False].

       --ApplyTransmission <bool>
              Apply  transmission  correction  to  extracted  scientific  spectra (bool; default:
              True). The  full  name  of  this  option  for  the  EsoRex  configuration  file  is
              vimos.Parameters.apply.transmission [default = True].

       --CalibrateFlux <bool>
              Extracted  spectra  are  flux  calibrated. (bool; default: False). The full name of
              this option for the EsoRex configuration file is  vimos.Parameters.flux.calibration
              [default = False].

       --UseSkylines <bool>
              Use  sky lines to refine the wavelength calibration (bool; default: True). The full
              name of this option for the EsoRex configuration file is vimos.Parameters.sky.align
              [default = True].

       --UseSkyIndividual <bool>
              Use  sky  lines to refine the wavelength calibration individually for each spectrum
              (bool; default: False). The full name of this option for the  EsoRex  configuration
              file is vimos.Parameters.sky.individual [default = False].

       --ComputeQC <bool>
              Compute QC1 parameters (bool; default: False). The full name of this option for the
              EsoRex configuration file is vimos.Parameters.quality.enable [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 vimos pipeline can be downloaded as a PDF  file  using  the
       following URL:

              ftp://ftp.eso.org/pub/dfs/pipelines/vimos/vimos-pipeline-manual-6.9.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  vimos  pipeline  are  vimos_ima_bias(7),  vimos_ima_dark(7),
       vimos_ima_det_noise(7), vimos_ima_fringe(7), vimos_ima_science(7),  vimos_ima_standard(7),
       vimos_ima_twilight_flat(7),     vmbias(7),     vmdark(7),     vmdet(7),     vmifucalib(7),
       vmifucombine(7), vmifucombinecube(7),  vmifustandard(7),  vmmoscalib(7),  vmmosscience(7),
       vmspphot(7)

VERSION

       vmifuscience 4.1.7

AUTHOR

       ESO VIMOS Pipeline Team <https://support.eso.org>

BUG REPORTS

       Please  report  any  problems  to  https://support.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  VIMOS  Instrument  Pipeline  Copyright  (C)  2002-2005  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  02110-1301 USA