Provided by: cpl-plugin-vimos-doc_4.1.7+dfsg-2build3_all 
NAME
vmmosscience - Extraction of scientific spectra
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
TELLURIC_CONTAMINATION Calib Telluric regions list .
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
--skyalign <int>
Polynomial order for sky lines alignment, or -1 to avoid alignment (int; default: -1). The full
name of this option for the EsoRex configuration file is vimos.vmmosscience.skyalign [default =
-1].
--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 <int>
Number of pixels to exclude at each slit in object detection and extraction (int; default: 3). The
full name of this option for the EsoRex configuration file is vimos.vmmosscience.slit_margin
[default = 3].
--ext_radius <int>
Maximum extraction radius for detected objects (pixel) (int; default: 6). The full name of this
option for the EsoRex configuration file is vimos.vmmosscience.ext_radius [default = 6].
--cont_radius <int>
Minimum distance at which two objects of equal luminosity do not contaminate each other (pixel)
(int; default: 0). The full name of this option for the EsoRex configuration file is
vimos.vmmosscience.cont_radius [default = 0].
--ext_mode <int>
Object extraction method: 0 = aperture, 1 = Horne optimal extraction (int; 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].
--resp_fit_nknots <int>
Number of knots in spline fitting of the instrument response. (-1: No fitting. -2: Read from grism
table) (int; default: -2). The full name of this option for the EsoRex configuration file is
vimos.vmmosscience.resp_fit_nknots [default = -2].
--resp_fit_degree <int>
Degree of polynomial in fitting of the instrument response. (-1: No fitting. -2: Read from grism
table) (int; default: -2). The full name of this option for the EsoRex configuration file is
vimos.vmmosscience.resp_fit_degree [default = -2].
--resp_ignore_mode <str>
Types of lines/regions to ignore in response. Valid ones are ´stellar_absorption´, ´telluric´ and
´command_line´ (from parameter resp_ignore_lines) (str; default:
´stellar_absorption,telluric,command_line´). The full name of this option for the EsoRex
configuration file is vimos.vmmosscience.resp_ignore_mode [default =
stellar_absorption,telluric,command_line].
--resp_ignore_points <str>
Extra lines/regions to ignore in response. Use a comma separated list of values. A range can be
specified like 4500.0-4600.0 (str; default: ´´). The full name of this option for the EsoRex
configuration file is vimos.vmmosscience.resp_ignore_points [default = ].
--resp_use_flat_sed <str>
Use the flat SED to normalise the observed spectra. Value are true, false, grism_table. (str;
default: ´grism_table´). The full name of this option for the EsoRex configuration file is
vimos.vmmosscience.resp_use_flat_sed [default = grism_table].
--resp_shift <float>
The extracted standard star will be shifted these many angstroms before using it to compute the
response. This is useful for observed std stars not centered in the slits. Positive values will
shift the spectrum to the red. Shift is given in Angstroms but no fraction of pixels will be
shifted. (float; default: 0.0). The full name of this option for the EsoRex configuration file is
vimos.vmmosscience.resp_shift [default = 0.0].
--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].
--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 <int>
Number of lowest values to be rejected (int; default: 1). The full name of this option for the
EsoRex configuration file is vimos.vmmosscience.minrejection [default = 1].
--maxrejection <int>
Number of highest values to be rejected (int; 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 <int>
Max number of iterations in ksigma method (int; 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].
--generate_idp <bool>
Generate IDP products (bool; default: False). The full name of this option for the EsoRex
configuration file is vimos.vmmosscience.generate_idp [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), vmifuscience(7),
vmifustandard(7), vmmoscalib(7), vmspphot(7)
VERSION
vmmosscience 4.1.7
AUTHOR
Carlo Izzo <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) 2019 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