Provided by: cpl-plugin-uves-doc_5.3.0+dfsg-2_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 UVES_SCI_POINT_BLUE
or UVES_SCI_POINT_RED, or UVES_SCI_EXTND_BLUE or UVES_SCI_EXTND_RED or
UVES_SCI_SLICER_BLUE or UVES_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_xxx optionally a table describing the atmospheric
extintion, 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
--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].
--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].
--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.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.objoffset <float>
Offset (in pixels) of extraction slit with respect to center of order. This
parameter applies to linear/average/optimal extraction. For linear/average
extraction, if the related parameter objslit is negative, 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). This must be less 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. This
parameter does not apply to optimal extraction. (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.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].
--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 (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.rebin.wavestep <float>
The bin size (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.scale <bool>
Whether or not to multiply by the factor dx/dlambda (pixels per wavelength) during
the rebinning. This option is disabled as default in concordance with the method
used in the MIDAS pipeline. This option should be set to true to convert the
observed flux (in pixel-space) to a flux per wavelength (in wavelength-space).
(bool; default: False). The full name of this option for the EsoRex configuration
file is uves_obs_scired.reduce.rebin.scale [default = False].
--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 <long>
This is the number of columns in interorder space used to sample the background.
(long; 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 <long>
The height (in pixels) of the background sampling window is (2*radiusy + 1). This
parameter is not corrected for binning. (long; 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 <long>
Degree of interpolating splines. Currently only degree = 1 is supported (long;
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.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.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.chunk <long>
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). (long; default: 32). The full name of this option for the
EsoRex configuration file is uves_obs_scired.reduce.extract.chunk [default = 32].
--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.extract.oversample <long>
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 (long; default: -1). The full name of this option for the EsoRex configuration
file is uves_obs_scired.reduce.extract.oversample [default = -1].
--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].
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-5.3.0.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 uves pipeline are uves_cal_response(7),
uves_cal_mflat_combine(7), flames_utl_unpack(7), flames_cal_wavecal(7),
uves_cal_mkmaster(7), flames_obs_redchain(7), uves_cal_wavecal(7), uves_cal_tflat(7),
uves_cal_mflat(7), flames_cal_prep_sff_ofpos(7), uves_utl_remove_crh_single(7),
uves_cal_mbias(7), uves_utl_ima_arith(7), flames_obs_scired(7), uves_cal_orderpos(7),
flames_cal_mkmaster(7), flames_cal_predict(7), uves_cal_mdark(7), uves_cal_cd_align(7),
uves_obs_redchain(7), flames_cal_orderpos(7), uves_cal_predict(7)
VERSION
uves_obs_scired 5.3.0
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