Provided by: cpl-plugin-fors-doc_4.11.12+dfsg-3_all 
NAME
fors_pmos_science - Extraction of scientific spectra
SYNOPSIS
esorex fors_pmos_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_mpol_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).
Either a scientific or a standard star exposure can be specified in input.
The acronym SCI on products should be read STD in case of standard stars observations.
Input files:
DO category: Type: Explanation: Required:
SCIENCE_PMOS Raw Scientific exposure Y
or STANDARD_PMOS 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_PMOS Calib Normalised flat field .
DISP_COEFF_PMOS Calib Inverse dispersion Y
CURV_COEFF_PMOS Calib Spectral curvature Y
SLIT_LOCATION_PMOS Calib Slits positions table Y
RETARDER_WAVEPLATE_CHROMATISM Calib Chromatism correction .
STD_PMOS_TABLE Calib Linear pol. of std stars .
Output files:
DO category: Data type: Explanation:
REDUCED_SCI_PMOS FITS image Extracted scientific spectra
REDUCED_SKY_SCI_PMOS FITS image Extracted sky spectra
REDUCED_ERROR_SCI_PMOS FITS image Errors on extracted spectra
REDUCED_X_SCI_PMOS FITS image X Stokes parameter (and L)
REDUCED_ERROR_X_SCI_PMOS FITS image Error on X Stokes parameter
REDUCED_NUL_X_SCI_PMOS FITS image Null parameter for X
REDUCED_ANGLE_SCI_PMOS FITS image Direction of linear polarization
REDUCED_ERROR_ANGLE_SCI_PMOS FITS image Error on polarization direction
UNMAPPED_SCI_PMOS FITS image Sky subtracted scientific spectra
MAPPED_SCI_PMOS FITS image Rectified scientific spectra
MAPPED_ALL_SCI_PMOS FITS image Rectified science spectra with sky
MAPPED_SKY_SCI_PMOS FITS image Rectified sky spectra
UNMAPPED_SKY_SCI_PMOS FITS image Sky on CCD
OBJECT_TABLE_SCI_PMOS FITS table Positions of detected objects
OBJECT_TABLE_POL_SCI_PMOS FITS table Positions of real objects
Only if the sky-alignment of the wavelength solution is requested:
DISP_COEFF_SCI_PMOS FITS table Upgraded dispersion coefficients
WAVELENGTH_MAP_SCI_PMOS FITS image Upgraded wavelength map
OPTIONS
--dispersion <float>
Expected spectral dispersion (Angstrom/pixel) (float; default: 0.0). The full name
of this option for the EsoRex configuration file is
fors.fors_pmos_science.dispersion [default = 0.0].
--rebin <long>
Rebin (pixel) (long; default: 1). The full name of this option for the EsoRex
configuration file is fors.fors_pmos_science.rebin [default = 1].
--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
fors.fors_pmos_science.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_pmos_science.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_pmos_science.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_pmos_science.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_pmos_science.flux [default = True].
--flatfield <bool>
Apply flat field (bool; default: True). The full name of this option for the EsoRex
configuration file is fors.fors_pmos_science.flatfield [default = True].
--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_pmos_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_pmos_science.skylocal
[default = True].
--cosmics <bool>
Eliminate cosmic rays hits (only if local sky subtraction is also requested) (bool;
default: False). The full name of this option for the EsoRex configuration file is
fors.fors_pmos_science.cosmics [default = False].
--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
fors.fors_pmos_science.slit_margin [default = 3].
--ext_radius <long>
Maximum extraction radius for detected objects (pixel) (long; default: 12). The
full name of this option for the EsoRex configuration file is
fors.fors_pmos_science.ext_radius [default = 12].
--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 fors.fors_pmos_science.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
fors.fors_pmos_science.ext_mode [default = 1].
--match_tolerance <float>
Tolerance for matching spectra from the same object at different angles and beams
(pixel) (float; default: 5.0). The full name of this option for the EsoRex
configuration file is fors.fors_pmos_science.match_tolerance [default = 5.0].
--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
fors.fors_pmos_science.time_normalise [default = True].
--chromatism <bool>
Chromatism correction to polarization angles (bool; default: True). The full name
of this option for the EsoRex configuration file is
fors.fors_pmos_science.chromatism [default = True].
--wollaston <bool>
Wollaston mounting (FORS2 only): true = 0 degrees (ord. beam on top, extr. beam on
bottom), false = 180 degrees (beams are reversed), for FORS1 is frozen to true
(bool; default: True). The full name of this option for the EsoRex configuration
file is fors.fors_pmos_science.wollaston [default = True].
--check <bool>
Create intermediate products (bool; default: False). The full name of this option
for the EsoRex configuration file is fors.fors_pmos_science.check [default =
False].
--qc <bool>
Compute QC1 parameters (bool; default: True). The full name of this option for the
EsoRex configuration file is fors.fors_pmos_science.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.
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-4.7.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 fors pipeline are fors_wave_calib_lss(7), fors_img_sky_flat(7),
fors_resample(7), fors_config(7), fors_extract_objects(7), fors_calib(7),
fors_wave_calib(7), fors_detect_objects(7), fors_zeropoint(7), fors_extract_slits(7),
fors_extract(7), fors_remove_bias(7), fors_subtract_sky(7), fors_normalise_flat(7),
fors_photometry(7), fors_img_screen_flat(7), fors_dark(7), fors_subtract_sky_lss(7),
fors_trace_flat(7), fors_flatfield(7), fors_img_science(7), fors_detect_spectra(7),
fors_sumflux(7), fors_pmos_extract(7), fors_align_sky_lss(7), fors_bias(7),
fors_align_sky(7), fors_pmos_calib(7), fors_spec_mflat(7), fors_science(7)
VERSION
fors_pmos_science 4.11.12
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