Provided by: cpl-plugin-fors-doc_5.5.7+dfsg-2build1_all 
NAME
fors_science - Extraction of scientific spectra
SYNOPSIS
esorex fors_science [OPTIONS] FILE.sof
DESCRIPTION
This recipe is used to reduce scientific spectra using the extraction mask and the products created by
the recipe fors_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.
This recipe accepts both FORS1 and FORS2 frames. A grism table (typically depending on the instrument
mode, and in particular on the grism used) 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 grism 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 (that are rarely meaningful).
In the table below the MXU acronym can be read alternatively as MOS and LSS, depending on the instrument
mode of the input data. The acronym SCI on products should be read STD in case of standard stars
observations A CURV_COEFF table is not (yet) expected for LSS data.
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:
SCIENCE_MXU Raw Scientific exposure Y
or STANDARD_MXU Raw Standard star exposure Y
MASTER_BIAS Calib Master bias Y
GRISM_TABLE Calib Grism table .
MASTER_SKYLINECAT Calib Sky lines catalog .
MASTER_NORM_FLAT_MXU Calib Normalised flat field .
DISP_COEFF_MXU Calib Inverse dispersion Y
CURV_COEFF_MXU Calib Spectral curvature Y
SLIT_LOCATION_MXU Calib Slits positions table Y
FLAT_SED_MXU Calib Slits dispersion profile .
or, in case of LSS-like MOS/MXU data,
MASTER_NORM_FLAT_LONG_MXU Calib Normalised flat field .
DISP_COEFF_LONG_MXU Calib Inverse dispersion Y
SLIT_LOCATION_LONG_MXU Calib Slits positions table Y
GLOBAL_DISTORTION_TABLE Calib Global distortion .
In case STANDARD_MXU is specified in input,
EXTINCT_TABLE Calib Atmospheric extinction Y
STD_FLUX_TABLE Calib Standard star flux Y
TELLURIC_CONTAMINATION Calib Telluric regions list .
The following input files are mandatory if photometric calibrated spectra are desired:
EXTINCT_TABLE Calib Atmospheric extinction Y
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:
DO category: Data type: Explanation:
REDUCED_SCI_MXU FITS image Extracted scientific spectra
REDUCED_SKY_SCI_MXU FITS image Extracted sky spectra
REDUCED_ERROR_SCI_MXU FITS image Errors on extracted spectra
UNMAPPED_SCI_MXU FITS image Sky subtracted scientific spectra
MAPPED_SCI_MXU FITS image Rectified scientific spectra
MAPPED_ALL_SCI_MXU FITS image Rectified science spectra with sky
MAPPED_SKY_SCI_MXU FITS image Rectified sky spectra
UNMAPPED_SKY_SCI_MXU FITS image Sky on CCD
OBJECT_TABLE_SCI_MXU FITS table Positions of detected objects
Only if the global sky subtraction is requested:
GLOBAL_SKY_SPECTRUM_MXU FITS table Global sky spectrum
Only if the sky-alignment of the wavelength solution is requested:
SKY_SHIFTS_LONG_SCI_MXU FITS table Sky lines offsets (LSS-like data)
or SKY_SHIFTS_SLIT_SCI_MXU FITS table Sky lines offsets (MOS-like data)
DISP_COEFF_SCI_MXU FITS table Upgraded dispersion coefficients
WAVELENGTH_MAP_SCI_MXU FITS image Upgraded wavelength map
Only if a STANDARD_MXU is specified in input:
SPECPHOT_TABLE FITS table Efficiency and response curves
Only if a photometric calibration was requested:
REDUCED_FLUX_SCI_MXU FITS image Flux calibrated scientific spectra
REDUCED_FLUX_ERROR_SCI_MXU FITS image Errors on flux calibrated spectra
MAPPED_FLUX_SCI_MXU FITS 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 fors.fors_science.skyalign [default =
-1].
--flatfield <bool>
Apply flat field (bool; default: True). The full name of this option for the EsoRex configuration
file is fors.fors_science.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 fors.fors_science.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 fors.fors_science.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 fors.fors_science.skylocal [default = True].
--cosmics <bool>
Eliminate cosmic rays hits, only if either global or local (not for LSS) sky subtraction is also
requested. (bool; default: False). The full name of this option for the EsoRex configuration file
is fors.fors_science.cosmics [default = False].
--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 fors.fors_science.slit_margin
[default = 3].
--ext_radius <int>
Maximum extraction radius for detected objects (unbinned pixel) (int; default: 12). The full name
of this option for the EsoRex configuration file is fors.fors_science.ext_radius [default = 12].
--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
fors.fors_science.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 fors.fors_science.ext_mode [default = 1].
--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
fors.fors_science.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
fors.fors_science.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 fors.fors_science.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 fors.fors_science.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
fors.fors_science.resp_use_flat_sed [default = grism_table].
--nonlinear_level <float>
Level above which the detector is not linear (float; default: 60000.0). The full name of this
option for the EsoRex configuration file is fors.fors_science.nonlinear_level [default = 60000.0].
--generate_idp <bool>
Set to TRUE to request IDP generation (bool; default: True). The full name of this option for the
EsoRex configuration file is fors.fors_science.generate_idp [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.
SEE ALSO
The full documentation for the fors pipeline can be downloaded as a PDF file using the following URL:
ftp://ftp.eso.org/pub/dfs/pipelines/fors/fors-pipeline-manual-4.9.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 fors pipeline are fors_align_sky(7), fors_align_sky_lss(7), fors_bias(7),
fors_calib(7), fors_config(7), fors_dark(7), fors_detect_objects(7), fors_detect_spectra(7),
fors_extract(7), fors_extract_objects(7), fors_extract_slits(7), fors_flatfield(7), fors_img_science(7),
fors_img_screen_flat(7), fors_img_sky_flat(7), fors_normalise_flat(7), fors_photometry(7),
fors_pmos_calib(7), fors_pmos_extract(7), fors_pmos_science(7), fors_remove_bias(7), fors_resample(7),
fors_spec_mflat(7), fors_subtract_sky(7), fors_subtract_sky_lss(7), fors_sumflux(7), fors_trace_flat(7),
fors_wave_calib(7), fors_wave_calib_lss(7), fors_zeropoint(7)
VERSION
fors_science 5.5.7
AUTHOR
Carlo Izzo <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 currently part of the FORS 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