Provided by: cpl-plugin-uves-doc_6.1.8+dfsg-2build3_all 
NAME
uves_obs_scired - Reduces a science frame
SYNOPSIS
esorex uves_obs_scired [OPTIONS] FILE.sof
DESCRIPTION
This recipe reduces a science frame (SCIENCE_BLUE or SCIENCE_RED, or SCI_POINT_BLUE or SCI_POINT_RED, or
SCI_EXTND_BLUE or SCI_EXTND_RED or SCI_SLICER_BLUE or SCI_SLICER_RED) using a combination (depending on
recipe parameters and provided input frames) of the steps:
- bias subtraction,
- dark subtraction,
- background subtraction,
- extraction/cosmic ray removal,
- flat field correction,
- wavelength rebinning,
- sky subtraction,
- order merging,
- response correction (if response curve is provided).
Additional input for this recipe are: order table(s) for each chip, ORDER_TABLE_xxxx (where xxxx=BLUE,
REDL, REDU), line table(s) for each chip, LINE_TABLE_xxxx, a master bias frame, MASTER_BIAS_xxxx, a
master flat, MASTER_FLAT_xxxx, optionally an instrument response table, INSTR_RESPONSE_FINE_xxx,
optionally an master response table, MASTER_RESPONSE_xxx, and optionally a table describing the
atmospheric extinction, EXTCOEFF_TABLE.
For each chip (xxxx = BLUE, REDL, REDU) the recipe produces a combination of the products:
´RED_SCIENCE_xxxx´ Reduced science spectrum
´MERGED_SCIENCE_xxxx´ Merged spectrum, no sky subtraction
´WCALIB_SCIENCE_xxxx´ Extracted, wavelength calibrated frame in
(wavelength, order) space
´WCALIB_FF_SCIENCE_xxxx´ Extracted, flat-fielded, wave.cal. frame in
(wavelength, order) space
(Only if flatfielding done)
´WCALIB_FLAT_OBJ_xxxx´ Extracted, wavelength calibrated flat field
in (wavelength, order) space
(Only if flatfielding done)
´ERRORBAR_SCIENCE_xxxx´ Error bars of ´RED_SCIENCE_xxxx´
´VARIANCE_SCIENCE_xxxx´ Variance of extracted, flatfielded object in
(pixel, order) space
´ORDER_TRACE_xxxx´ Table describing the spatial profile
´FLUXCAL_SCIENCE_xxxx´ Flux-calibrated science spectrum
´FLUXCAL_ERROR_xxxx´ Error bars of ´FLUXCAL_SCIENCE_xxxx´
´BKG_SCI_xxxx´ The subtracted background image
´CRMASK_xxxx´ List of cosmic ray hits
´MERGED_SKY_xxxx´ The merged sky spectrum
´EXT_2D_SCIENCE_xxxx´ The 2d extracted spectrum
´FF2D_SCIENCE_xxxx´ The 2d extracted, flat-fielded spectrum
´WCAL2D_SCIENCE_xxxx´ The 2d extracted, flat-fielded, wave.cal. spectrum
´MER2D_SCIENCE_xxxx´ The 2d reduced, flux-calibrated (if possible)
science spectrum
OPTIONS
--clean_traps <bool>
Clean detector traps. If TRUE detector traps are interpolated.The bad pixels are replaced by the
average of thenearest good pixels in the same column, or simply marked as bad. The positions of
bad pixels are hard-coded (as function of UVES chip). (bool; default: False). The full name of
this option for the EsoRex configuration file is uves_obs_scired.clean_traps [default = False].
--debug <bool>
Whether or not to save intermediate results to local directory (bool; default: False). The full
name of this option for the EsoRex configuration file is uves.debug [default = False].
--plotter <str>
Any plots produced by the recipe are redirected to the command specified by this parameter. The
plotting command must contain the substring ´gnuplot´ and must be able to parse gnuplot syntax on
its standard input. Valid examples of such a command may include ´gnuplot -persist´ and ´cat >
mygnuplot$$.gp´. A finer control of the plotting options can be obtained by writing an executable
script, e.g. my_gnuplot.pl, that executes gnuplot after setting the desired gnuplot options (e.g.
set terminal pslatex color). To turn off plotting, set this parameter to ´no´ (str; default:
´no´). The full name of this option for the EsoRex configuration file is uves.plotter [default =
no].
--process_chip <str>
For RED arm data process the redl, redu, or both chip(s) (str; default: ´both´). The full name of
this option for the EsoRex configuration file is uves.process_chip [default = both].
--reduce.backsub.mmethod <str>
Background measuring method. If equal to ´median´ the background is sampled using the median of a
subwindow. If ´minimum´, the subwindow minimum value is used. If ´no´, no background subtraction
is done. (str; default: ´median´). The full name of this option for the EsoRex configuration file
is uves_obs_scired.reduce.backsub.mmethod [default = median].
--reduce.backsub.npoints <int>
This is the number of columns in interorder space used to sample the background. (int; default:
82). The full name of this option for the EsoRex configuration file is
uves_obs_scired.reduce.backsub.npoints [default = 82].
--reduce.backsub.radiusy <int>
The height (in pixels) of the background sampling window is (2*radiusy + 1). This parameter is not
corrected for binning. (int; default: 2). The full name of this option for the EsoRex
configuration file is uves_obs_scired.reduce.backsub.radiusy [default = 2].
--reduce.backsub.sdegree <int>
Degree of interpolating splines. Currently only degree = 1 is supported (int; default: 1). The
full name of this option for the EsoRex configuration file is
uves_obs_scired.reduce.backsub.sdegree [default = 1].
--reduce.backsub.smoothx <float>
If spline interpolation is used to measure the background, the x-radius of the post-smoothing
window is (smoothx * image_width). Here, ´image_width´ is the image width after binning. If
negative, the default values are used: (25.0/4096) for blue flat-field frames, (50.0/4096) for red
flat-field frames, (300.0/4096) for blue science frames and (300.0/4096) for red science frames.
(float; default: -1.0). The full name of this option for the EsoRex configuration file is
uves_obs_scired.reduce.backsub.smoothx [default = -1.0].
--reduce.backsub.smoothy <float>
If spline interpolation is used to measure the background, the y-radius of the post-smoothing
window is (smoothy * image_height). Here, ´image_height´ is the image height after binning. If
negative, the default values are used: (100.0/2048) for blue flat-field frames, (300.0/2048) for
red flat-field frames, (200.0/2048) for blue science frames and (500.0/2048) for red science
frames. (float; default: -1.0). The full name of this option for the EsoRex configuration file is
uves_obs_scired.reduce.backsub.smoothy [default = -1.0].
--reduce.extract.best <bool>
(optimal extraction only) If false (fastest), the spectrum is extracted only once. If true (best),
the spectrum is extracted twice, the second time using improved variance estimates based on the
first iteration. Better variance estimates slightly improve the obtained signal to noise but at
the cost of increased execution time (bool; default: True). The full name of this option for the
EsoRex configuration file is uves_obs_scired.reduce.extract.best [default = True].
--reduce.extract.chunk <int>
In optimal extraction mode, the chunk size (in pixels) used for fitting the analytical profile (a
fit of the analytical profile to single bins would suffer from low statistics). (int; default:
32). The full name of this option for the EsoRex configuration file is
uves_obs_scired.reduce.extract.chunk [default = 32].
--reduce.extract.kappa <float>
In optimal extraction mode, this is the threshold for bad (i.e. hot/cold) pixel rejection. If a
pixel deviates more than kappa*sigma (where sigma is the uncertainty of the pixel flux) from the
inferred spatial profile, its weight is set to zero. Range: [-1,100]. If this parameter is
negative, no rejection is performed. (float; default: 10.0). The full name of this option for the
EsoRex configuration file is uves_obs_scired.reduce.extract.kappa [default = 10.0].
--reduce.extract.method <str>
Extraction method. (2d/optimal not supported by uves_cal_wavecal, weighted supported only by
uves_cal_wavecal, 2d not supported by uves_cal_response) (str; default: ´optimal´). The full name
of this option for the EsoRex configuration file is uves_obs_scired.reduce.extract.method [default
= optimal].
--reduce.extract.oversample <int>
The oversampling factor used for the virtual resampling algorithm. If negative, the value 5 is
used for S/N <=200, and the value 10 is used if the estimated S/N is > 200 (int; default: -1). The
full name of this option for the EsoRex configuration file is
uves_obs_scired.reduce.extract.oversample [default = -1].
--reduce.extract.profile <str>
In optimal extraction mode, the kind of profile to use. ´gauss´ gives a Gaussian profile, ´moffat´
gives a Moffat profile with beta=4 and a possible linear sky contribution. ´virtual´ uses a
virtual resampling algorithm (i.e. measures and uses the actual object profile). ´constant´
assumes a constant spatial profile and allows optimal extraction of wavelength calibration frames.
´auto´ will automatically select the best method based on the estimated S/N of the object. For low
S/N, ´moffat´ or ´gauss´ are recommended (for robustness). For high S/N, ´virtual´ is recommended
(for accuracy). In the case of virtual resampling, a precise determination of the order positions
is required; therefore the order-definition is repeated using the (assumed non-low S/N) science
frame (str; default: ´auto´). The full name of this option for the EsoRex configuration file is
uves_obs_scired.reduce.extract.profile [default = auto].
--reduce.extract.skymethod <str>
In optimal extraction mode, the sky subtraction method to use. ´median´ estimates the sky as the
median of pixels along the slit (ignoring pixels close to the object), whereas ´optimal´ does a
chi square minimization along the slit to obtain the best combined object and sky levels. The
optimal method gives the most accurate sky determination but is also a bit slower than the median
method (str; default: ´optimal´). The full name of this option for the EsoRex configuration file
is uves_obs_scired.reduce.extract.skymethod [default = optimal].
--reduce.ffmethod <str>
Flat-fielding method. If set to ´pixel´, flat-fielding is done in pixel-pixel space (before
extraction); if set to ´extract´, flat- fielding is performed in pixel-order space (i.e. after
extraction). If set to ´no´, no flat-field correction is done, in which case reduce.rebin.scale
should be set to true to ensure flux conservation (both for response and science data) (str;
default: ´extract´). The full name of this option for the EsoRex configuration file is
uves_obs_scired.reduce.ffmethod [default = extract].
--reduce.merge <str>
Order merging method. If ´optimal´, the flux in the overlapping region is set to the (optimally
computed, using the uncertainties) average of single order spectra. If ´sum´, the flux in the
overlapping region is computed as the sum of the single order spectra. If ´noappend´ the spectrum
is simply rebinned but not merged.If flat-fielding is done, method ´optimal´ is recommended,
otherwise ´sum´. (str; default: ´optimal´). The full name of this option for the EsoRex
configuration file is uves_obs_scired.reduce.merge [default = optimal].
--reduce.merge_delt1 <float>
Order merging left hand (short wavelength) cut. To reduce the amount of order overlapping regions
we allow to cut short and long wavelength ranges. This may reduce the ripple possibly introduced
by the order merging. Suggested values are: 10 (W<=390), 12 (390<W<=437, 520<W<=564), 14
(437<W<=520, 564<W) (float; default: 0.0). The full name of this option for the EsoRex
configuration file is uves_obs_scired.reduce.merge_delt1 [default = 0.0].
--reduce.merge_delt2 <float>
Order merging right hand (long wavelength) cut. To reduce the amount of order overlapping regions
we allow to cut short and long wavelength ranges. This may reduce the ripple possibly introduced
by the order merging. Suggested values is 4 (float; default: 0.0). The full name of this option
for the EsoRex configuration file is uves_obs_scired.reduce.merge_delt2 [default = 0.0].
--reduce.objoffset <float>
Offset (in pixels) of extraction slit with respect to center of order. For optimal extraction the
full slit is offset. For linear/average extraction, reduce.objoffset is ignored if reduce.objslit
[default -1.0] is negative. In this case the offset is automatically determined by measuring the
actual object position. (float; default: 0.0). The full name of this option for the EsoRex
configuration file is uves_obs_scired.reduce.objoffset [default = 0.0].
--reduce.objslit <float>
Object window size (in pixels), ignored for optimal extraction. The value must be smaller than the
total slit length. If negative, the default value (half of full slit length) is used. The upper
and lower sky windows are defined as the part of the full slit (if any) outside the object window.
The center of the object window is determined by the offset parameter. (float; default: -1.0). The
full name of this option for the EsoRex configuration file is uves_obs_scired.reduce.objslit
[default = -1.0].
--reduce.rebin.scale <bool>
Whether or not to multiply by the factor dx/dlambda (pixels per wavelength) during the rebinning
to conserve the flux. This option is disabled as default because applying the flat field
correction already ensures flux conservation. Therefore this parameter should be TRUE (for
response and science data) only if reduce.ffmethd = no. (bool; default: False). The full name of
this option for the EsoRex configuration file is uves_obs_scired.reduce.rebin.scale [default =
False].
--reduce.rebin.wavestep <float>
The bin size used for BLUE/REDL data (in w.l.u.) in wavelength space. If negative, a step size of
2/3 * ( average pixel size ) is used. (float; default: -1.0). The full name of this option for
the EsoRex configuration file is uves_obs_scired.reduce.rebin.wavestep [default = -1.0].
--reduce.rebin.wavestep_redu <float>
The bin size used for REDU data (in w.l.u.) in wavelength space. If negative, a step size of 2/3 *
( average pixel size ) is used. (float; default: -1.0). The full name of this option for the
EsoRex configuration file is uves_obs_scired.reduce.rebin.wavestep_redu [default = -1.0].
--reduce.skysub <bool>
Do sky-subtraction (only applicable to linear and average extractions)? (bool; default: True). The
full name of this option for the EsoRex configuration file is uves_obs_scired.reduce.skysub
[default = True].
--reduce.slitlength <float>
Extraction slit length (in pixels). If negative, the value inferred from the raw frame header is
used (float; default: -1.0). The full name of this option for the EsoRex configuration file is
uves_obs_scired.reduce.slitlength [default = -1.0].
--reduce.tiltcorr <bool>
If enabled (recommended), the provided dispersion solutions obtained at different slit positions
are interpolated linearly at the actually measured position of the object/sky. Line tilt
correction is currently not supported for 2d extraction, in which case the dispersion solution
obtained at the middle of the slit is always used. (bool; default: True). The full name of this
option for the EsoRex configuration file is uves_obs_scired.reduce.tiltcorr [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 uves pipeline can be downloaded as a PDF file using the following URL:
ftp://ftp.eso.org/pub/dfs/pipelines/uves/uves-pipeline-manual-6.1.8.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 uves pipeline are flames_cal_mkmaster(7), flames_cal_orderpos(7),
flames_cal_predict(7), flames_cal_prep_sff_ofpos(7), flames_cal_wavecal(7), flames_obs_redchain(7),
flames_obs_scired(7), flames_utl_unpack(7), uves_cal_cd_align(7), uves_cal_mbias(7), uves_cal_mdark(7),
uves_cal_mflat(7), uves_cal_mflat_combine(7), uves_cal_mkmaster(7), uves_cal_orderpos(7),
uves_cal_predict(7), uves_cal_response(7), uves_cal_tflat(7), uves_cal_wavecal(7), uves_obs_redchain(7),
uves_utl_ima_arith(7), uves_utl_remove_crh_single(7)
VERSION
uves_obs_scired 6.1.8
AUTHOR
Jonas M. Larsen <cpl@eso.org>
BUG REPORTS
Please report any problems to cpl@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 FLAMES/UVES Pipeline Copyright (C) 2004, 2005, 2006, 2007 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 02111-1307 USA
uves_obs_scired 6.1.8 UVES_OBS_SCIRED(7)