Provided by: cpl-plugin-fors-doc_5.5.7+dfsg-2build1_all 
NAME
fors_extract - Extraction of scientific spectra
SYNOPSIS
esorex fors_extract [OPTIONS] FILE.sof
DESCRIPTION
This recipe is used to reduce scientific spectra using the global distortion table 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 applied dispersion coefficient 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. Either a scientific or a standard star exposure can be specified in input (not
both).
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 .
MASTER_DISTORTION_TABLE Calib Global distortion model .
or, in case of LSS-like MOS/MXU data,
MASTER_NORM_FLAT_LONG_MXU Calib Normalised flat field .
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
GLOBAL_SKY_SPECTRUM_MXU FITS table Global sky spectrum
OBJECT_TABLE_SCI_MXU FITS table Positions of detected objects
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
OPTIONS
--dispersion <float>
Resampling step (Angstrom/pixel) (float; default: 0.0). The full name of this option for the
EsoRex configuration file is fors.fors_extract.dispersion [default = 0.0].
--skyalign <int>
Polynomial order for sky lines alignment, or -1 to avoid alignment (int; default: 0). The full
name of this option for the EsoRex configuration file is fors.fors_extract.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 fors.fors_extract.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 fors.fors_extract.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 fors.fors_extract.endwavelength [default = 0.0].
--flux <bool>
Apply flux conservation (bool; default: True). The full name of this option for the EsoRex
configuration file is fors.fors_extract.flux [default = True].
--flatfield <bool>
Apply flat field (bool; default: False). The full name of this option for the EsoRex configuration
file is fors.fors_extract.flatfield [default = False].
--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_extract.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_extract.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_extract.skylocal [default = True].
--cosmics <bool>
Eliminate cosmic rays hits (only if global sky subtraction is also requested) (bool; default:
False). The full name of this option for the EsoRex configuration file is
fors.fors_extract.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_extract.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 fors.fors_extract.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
fors.fors_extract.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_extract.ext_mode [default = 1].
--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 fors.fors_extract.time_normalise [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_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_science(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_extract 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) 2002-2010 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