SYNOPSIS

esorex vmmosscience [OPTIONS] FILE.sof

DESCRIPTION

This recipe is used to reduce scientific spectra using the extraction mask and the products created by the recipe vimos_calib. The spectra are bias subtracted, flat fielded (if a normalised flat field is specified) and remapped eliminating the optical distortions. The wavelength calibration can be optionally upgraded using a number of sky lines: if no sky lines catalog of wavelengths is specified, an internal one is used instead.

If the alignment to the sky lines is performed, the input dispersion coefficients table is upgraded and saved to disk, and a new CCD wavelengths map is created. A configuration table (typically depending on the grism in use) may also be specified: this table contains a default recipe parameter setting to control the way spectra are extracted for a specific instrument mode, as it is used for automatic run of the pipeline on Paranal and in Garching. If this table is specified, it will modify the default recipe parameter setting, with the exception of those parameters which have been explicitly modifyed on the command line. If a configuration table is not specified, the input recipe parameters values will always be read from the command line, or from an esorex configuration file if present, or from their generic default values (which are rarely meaningful).

Either a scientific or a standard star exposure can be specified in input.

Only in case of a standard star exposure input, the atmospheric extinction table and a table with the physical fluxes of the observed standard star must be specified in input, and a spectro-photometric table is created in output. This table can then be input again to this recipe, always with an atmospheric extinction table, and if a photometric calibration is requested then flux calibrated spectra (in units of erg/cm/cm/s/Angstrom) are also written in output.

Input files:

  DO category:                Type:       Explanation:         Required:
  MOS_SCIENCE                 Raw         Scientific exposure     Y
  or MOS_STANDARD             Raw         Standard star exposure  Y
  MASTER_BIAS                 Calib       Master bias             Y
  SKY_LINE_CATALOG            Calib       Sky lines catalog       .
  MOS_MASTER_SCREEN_FLAT      Calib       Normalised flat field   .
  MOS_DISP_COEFF              Calib       Inverse dispersion      Y
  MOS_CURV_COEFF              Calib       Spectral curvature      Y
  MOS_SLIT_LOCATION           Calib       Slits positions table   Y
  CONFIG_TABLE                Calib       Configuration table     .
  In case MOS_STANDARD is specified in input,
  EXTINCT_TABLE               Calib       Atmospheric extinction  Y
  STD_FLUX_TABLE              Calib       Standard star flux      Y
  In case a photometric calibration is requested for scientific
  data, the following inputs are mandatory:
  EXTINCT_TABLE              Calib       Atmospheric extinction  Y
  MOS_SPECPHOT_TABLE         Calib       Response curves         Y
  If requested for standard star data, the SPECPHOT_TABLE can be dropped:
  in this case the correction is applied using the SPECPHOT_TABLE produced
  in the same run.

Output files (acronym _STD_ replaces _SCI_ and _STANDARD_ replaces _SCIENCE_ in case input is MOS_STANDARD rather than MOS_SCIENCE):

  DO category:                Data type:  Explanation:
  MOS_SCIENCE_REDUCED           Image  Extracted scientific spectra
  MOS_SCI_SKY_REDUCED           Image  Extracted sky spectra
  MOS_SCI_ERROR_REDUCED         Image  Errors on extracted spectra
  MOS_UNMAPPED_SCIENCE          Image  Sky subtracted scientific spectra
  MOS_SCIENCE_EXTRACTED         Image  Rectified scientific spectra
  MOS_SCIENCE_SKY_EXTRACTED     Image  Rectified science spectra with sky
  MOS_SCIENCE_SKY               Image  Rectified sky spectra
  MOS_SCI_UNMAPPED_SKY          Image  Sky on CCD
  MOS_SCI_GLOBAL_SKY_SPECTRUM   Table  Global sky spectrum
  OBJECT_SCI_TABLE              Table  Positions of detected objects
  Only if fringing correction is requested (dithered exposures):
  MOS_SCI_FRINGES               Image  Fringe map
  Only if the sky-alignment of the wavelength solution is requested:
  MOS_SCI_SKYLINES_OFFSETS_SLIT Table  Sky lines offsets
  MOS_SCI_DISP_COEFF_SKY        Table  Upgraded dispersion coefficients
  MOS_SCI_WAVELENGTH_MAP_SKY    Image  Upgraded wavelength map
  Only if a MOS_STANDARD is specified in input:
  MOS_SPECPHOT_TABLE            Table  Efficiency and response curves
  Only if MOS_SPECPHOT_TABLE or MOS_MASTER_RESPONSE are specified in input:
  MOS_SCIENCE_FLUX_REDUCED      Image  Flux calibrated scientific spectra
  MOS_SCI_ERROR_FLUX_REDUCED    Image  Errors on flux calibrated spectra
  MOS_SCIENCE_FLUX_EXTRACTED    Image  Flux calibrated slit spectra

OPTIONS

--dispersion <float>

Resampling step (Angstrom/pixel) (float; default: 0.0). The full name of this option for the EsoRex configuration file is vimos.vmmosscience.dispersion [default = 0.0].

--skyalign <long>

Polynomial order for sky lines alignment, or -1 to avoid alignment (long; default: 0). The full name of this option for the EsoRex configuration file is vimos.vmmosscience.skyalign [default = 0].

--wcolumn <str>

Name of sky line catalog table column with wavelengths (str; default: \'WLEN\'). The full name of this option for the EsoRex configuration file is vimos.vmmosscience.wcolumn [default = WLEN].

--startwavelength <float>

Start wavelength in spectral extraction (float; default: 0.0). The full name of this option for the EsoRex configuration file is vimos.vmmosscience.startwavelength [default = 0.0].

--endwavelength <float>

End wavelength in spectral extraction (float; default: 0.0). The full name of this option for the EsoRex configuration file is vimos.vmmosscience.endwavelength [default = 0.0].

--reference <float>

Reference wavelength for calibration (float; default: 0.0). The full name of this option for the EsoRex configuration file is vimos.vmmosscience.reference [default = 0.0].

--flux <bool>

Apply flux conservation (bool; default: True). The full name of this option for the EsoRex configuration file is vimos.vmmosscience.flux [default = True].

--flatfield <bool>

Apply flat field (bool; default: True). The full name of this option for the EsoRex configuration file is vimos.vmmosscience.flatfield [default = True].

--skyglobal <bool>

Subtract global sky spectrum from CCD (bool; default: False). The full name of this option for the EsoRex configuration file is vimos.vmmosscience.skyglobal [default = False].

--skymedian <bool>

Sky subtraction from extracted slit spectra (bool; default: False). The full name of this option for the EsoRex configuration file is vimos.vmmosscience.skymedian [default = False].

--skylocal <bool>

Sky subtraction from CCD slit spectra (bool; default: True). The full name of this option for the EsoRex configuration file is vimos.vmmosscience.skylocal [default = True].

--cosmics <bool>

Eliminate cosmic rays hits (only if global or local sky subtraction is also requested) (bool; default: True). The full name of this option for the EsoRex configuration file is vimos.vmmosscience.cosmics [default = True].

--slit_margin <long>

Number of pixels to exclude at each slit in object detection and extraction (long; default: 3). The full name of this option for the EsoRex configuration file is vimos.vmmosscience.slit_margin [default = 3].

--ext_radius <long>

Maximum extraction radius for detected objects (pixel) (long; default: 6). The full name of this option for the EsoRex configuration file is vimos.vmmosscience.ext_radius [default = 6].

--cont_radius <long>

Minimum distance at which two objects of equal luminosity do not contaminate each other (pixel) (long; default: 0). The full name of this option for the EsoRex configuration file is vimos.vmmosscience.cont_radius [default = 0].

--ext_mode <long>

Object extraction method: 0 = aperture, 1 = Horne optimal extraction (long; default: 1). The full name of this option for the EsoRex configuration file is vimos.vmmosscience.ext_mode [default = 1].

--detection <float>

Object detection threshold (ADU) (float; default: 2.0). The full name of this option for the EsoRex configuration file is vimos.vmmosscience.detection [default = 2.0].

--time_normalise <bool>

Normalise output spectra by the exposure time (bool; default: True). The full name of this option for the EsoRex configuration file is vimos.vmmosscience.time_normalise [default = True].

--anyframe <bool>

Look for a standard star in any frame classified as MOS_STANDARD (bool; default: False). The full name of this option for the EsoRex configuration file is vimos.vmmosscience.anyframe [default = False].

--response <long>

Order of polynomial modeling the instrument response (long; default: 5). The full name of this option for the EsoRex configuration file is vimos.vmmosscience.response [default = 5].

--alignment <str>

Type of alignment of dithered frames, either to the nearest neighbour pixel or to fractions of pixel (str; default: \'integer\'). The full name of this option for the EsoRex configuration file is vimos.vmmosscience.alignment [default = integer].

--stack_method <str>

Frames combination method (str; default: \'average\'). The full name of this option for the EsoRex configuration file is vimos.vmmosscience.stack_method [default = average].

--minrejection <long>

Number of lowest values to be rejected (long; default: 1). The full name of this option for the EsoRex configuration file is vimos.vmmosscience.minrejection [default = 1].

--maxrejection <long>

Number of highest values to be rejected (long; default: 1). The full name of this option for the EsoRex configuration file is vimos.vmmosscience.maxrejection [default = 1].

--klow <float>

Low threshold in ksigma method (float; default: 3.0). The full name of this option for the EsoRex configuration file is vimos.vmmosscience.klow [default = 3.0].

--khigh <float>

High threshold in ksigma method (float; default: 3.0). The full name of this option for the EsoRex configuration file is vimos.vmmosscience.khigh [default = 3.0].

--kiter <long>

Max number of iterations in ksigma method (long; default: 999). The full name of this option for the EsoRex configuration file is vimos.vmmosscience.kiter [default = 999].

--dither <bool>

Align dithered frames before stacking(for multiple input frames) (bool; default: True). The full name of this option for the EsoRex configuration file is vimos.vmmosscience.dither [default = True].

--compute <bool>

Compute offsets of dithered images from detected objects (true), or read offsets from header (false) (bool; default: False). The full name of this option for the EsoRex configuration file is vimos.vmmosscience.dither.compute [default = False].

--fringing <bool>

Apply fringing correction (only for dithered observations) (bool; default: True). The full name of this option for the EsoRex configuration file is vimos.vmmosscience.fringing [default = True].

--offset <float>

Minimum required offset between exposures for applying the sky fringing correction. (float; default: 3.0). The full name of this option for the EsoRex configuration file is vimos.vmmosscience.fringing.offset [default = 3.0].

--qc <bool>

Compute QC1 parameters (bool; default: True). The full name of this option for the EsoRex configuration file is vimos.vmmosscience.qc [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.

RELATED TO vmmosscience…

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 http://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 http://packages.python.org/python-cpl/index.html for further information.

The other recipes of the vimos pipeline are vmifucombinecube(7), vmifucalib(7), vmimflatsky(7), vmspflat(7), vmmosobsstare(7), vmimflatscreen(7), vmimpreimaging(7), vmimcalphot(7), vmmoscombine(7), vmimstandard(7), vmmosobsjitter(7), vmifucombine(7), vmimobsjitter(7), vmspphot(7), vmdet(7), vmmosstandard(7), vmspcaldisp(7), vmifustandard(7), vmbias(7), vmmoscalib(7), vmimobsstare(7), vmdark(7), vmifuscience(7)

VERSION

vmmosscience 2.9.15

AUTHOR

Carlo Izzo <[email protected]>

BUG REPORTS

Please report any problems to [email protected] Alternatively, you may send a report to the ESO User Support Department <[email protected]>.

LICENSE

This file is currently part of the VIMOS Instrument Pipeline Copyright (C) 2002-2011 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