Provided by: cpl-plugin-vimos-doc_2.9.9+dfsg-2_all 
NAME
vmmosobsjitter - Reduce and combine a set of jittered MOS observations.
SYNOPSIS
esorex vmmosobsjitter [OPTIONS] FILE.sof
DESCRIPTION
This recipe is used to apply basic reduction steps to a sequence of exposures made in MOS
mode, to combine them in a single image, to locate objects, and to optimally extract their
spectra. Each input image is processed in the same way as by recipe vmmosobsstare,
therefore what mainly characterises the vmmosobsjitter recipe is the task of combining the
input frames.
Input files:
DO category: Type: Explanation: Required:
MOS_SCIENCE Raw Science exposure Y
MASTER_BIAS Calib Master bias Y
MASTER_DARK Calib Master dark .
MOS_MASTER_SCREEN_FLAT Calib Normalised flat field .
EXTRACT_TABLE Calib Extraction table .
GRISM_TABLE Calib Grism table Y
MOS_FRINGES_SKY Calib Sky+fringes map (´Raw´) .
MOS_FRINGES Calib Fringe map (´Resampled´) .
EXTINCT_TABLE Calib Atmospheric extinction .
MOS_SPECPHOT_TABLE Calib Response curve .
CCD_TABLE Calib Bad pixel table .
Output files:
DO category: Data type: Explanation:
MOS_SCIENCE_REDUCED FITS image Extracted objects spectra
MOS_SCIENCE_FLUX_REDUCED FITS image Flux calibrated objects spectra
MOS_SCIENCE_EXTRACTED FITS image Sky subtracted slit spectra
MOS_SCIENCE_SKY FITS image Sky slit spectra
MOS_SKY_REDUCED FITS image Extracted sky spectra
MOS_FRINGES_SKY FITS image Sky+fringes map (method ´Raw´)
MOS_FRINGES FITS image Fringe map (method ´Resampled´)
OBJECT_TABLE FITS table Objects spectra identification
WINDOW_TABLE FITS table Objects positions in slit
A flat field correction is applied only if a normalised master flat field (produced by the
recipe vmspflat) is specified.
The extraction table is the product of the local spectral distortions modelling performed
by the recipe vmspcaldisp. If an extraction table is not specified, then the global
distortion models read from the science frame header are used.
The grism table contains necessary information to control the way spectra are extracted,
starting from the reference wavelength (header entry PRO WLEN CEN), on a specific range of
pixels above and below its position on the CCD (header entries PRO SPECT LLEN LO and PRO
SPECT LLEN HI). Other parameters, used in the extraction of the science slit spectra, are
the start and the end wavelength of the image of the extracted slit spectra (header
entries PRO WLEN START and PRO WLEN END), and the step of the sampling along the
dispersion direction (header entry PRO WLEN INC). Finally, the wavelengths of the sky
lines used in the alignment of the spectral distortion models, necessary to keep into
account the possible coordinates shifts introduced by a variation of the instrument
flexures between the science and the calibration exposures, are listed in the header
keywords PRO SKY WLENi, with i ranging from 1 to the number specified in the keyword PRO
SKY NO.
A CCD table must be specified in input only if a bad pixel cleaning is requested.
The slit spectra are remapped with the instrument distortions removed and at a fixed
wavelength step. A sky value is estimated for each wavelength and then subtracted from the
data. The result is stored in the MOS_SCIENCE_EXTRACTED image, while the image
MOS_SCIENCE_SKY contains the subtracted sky model. The 1D extracted spectra are stored in
the MOS_SCIENCE_REDUCED image, while the corresponding sky spectra extracted with the same
method are stored in the MOS_SKY_REDUCED image.
The positions of the extracted slit spectra and of the detected objects that they may
contain are listed in the window table.
If a spectro-photometric table (produced by the recipe vmmosstandard) is specified
together with an atmospheric extinction table, and a flux calibration is requested, then a
MOS_SCIENCE_FLUX_REDUCED image is also created. This image is identical to the
MOS_SCIENCE_REDUCED, but the spectra it contains are flux calibrated, and expressed in
units of erg/cm/cm/s/Angstrom.
Sky fringes may be subtracted from the data using two different methods. The ´Raw´ method
will subtract the median sky+fringes pattern from each input image, and then fit away the
residuals possibly introduced by sky variations between exposures. The ´Resampled´ method
will fit the sky first, and then subtract the median image of the residuals (stored in the
product MOS_FRINGES).
For more details, please refer to the VIMOS Pipeline User´s Guide.
OPTIONS
--BiasMethod <str>
Bias removal method. (str; default: ´Zmaster´). The full name of this option for
the EsoRex configuration file is vimos.Parameters.bias.removing.method [default =
Zmaster].
--StackMethod <str>
Frames combination method (str; default: ´Average´). The full name of this option
for the EsoRex configuration file is vimos.Parameters.stacking.method [default =
Average].
--KSigmaLow <float>
Low threshold for K-sigma clipping method. (float; default: 5.0). The full name of
this option for the EsoRex configuration file is
vimos.Parameters.stacking.ksigma.low [default = 5.0].
--KSigmaHigh <float>
High threshold for K-sigma clipping method. (float; default: 5.0). The full name of
this option for the EsoRex configuration file is
vimos.Parameters.stacking.ksigma.high [default = 5.0].
--MinRejection <long>
Number of lowest rejected values for rejection method. (long; default: 1). The full
name of this option for the EsoRex configuration file is
vimos.Parameters.stacking.minmax.minimum [default = 1].
--MaxRejection <long>
Number of highest rejected values for rejection method. (long; default: 1). The
full name of this option for the EsoRex configuration file is
vimos.Parameters.stacking.minmax.maximum [default = 1].
--SkyMethod <str>
Sky level determination method. (str; default: ´Median´). The full name of this
option for the EsoRex configuration file is vimos.Parameters.sky.method [default =
Median].
--PolyOrder <long>
Degree of polynomial used when the SkyMethod is set to Fit. (long; default: 2). The
full name of this option for the EsoRex configuration file is
vimos.Parameters.sky.order [default = 2].
--SkyKSigmaLow <float>
Low threshold for K-sigma rejection in sky fitting. (float; default: 1.0). The full
name of this option for the EsoRex configuration file is
vimos.Parameters.sky.ksigma.low [default = 1.0].
--SkyKSigmaHigh <float>
High threshold for K-sigma rejection in sky fitting. (float; default: 1.0). The
full name of this option for the EsoRex configuration file is
vimos.Parameters.sky.ksigma.high [default = 1.0].
--Fuzz <long>
Extra pixels from expected position of spectrum edge in extraction. (long;
default: 5). The full name of this option for the EsoRex configuration file is
vimos.Parameters.extraction.fuzz [default = 5].
--SlitMargin <long>
Number of excluded pixels at slit ends in object search or in sky level
determination. (long; default: 2). The full name of this option for the EsoRex
configuration file is vimos.Parameters.detection.exclude [default = 2].
--LineWidth <long>
Size of spectrum to extract around any skyline. (long; default: 16). The full name
of this option for the EsoRex configuration file is vimos.Parameters.sky.linewidth
[default = 16].
--DetectionLevel <float>
Object detection level in units of sigma. (float; default: 2.0). The full name of
this option for the EsoRex configuration file is vimos.Parameters.detection.sigma
[default = 2.0].
--WatershedLevels <long>
Number of levels in the watershed method in object detection. (long; default: 32).
The full name of this option for the EsoRex configuration file is
vimos.Parameters.detection.levels [default = 32].
--WatershedFraction <float>
Flux fraction to use in watershed. (float; default: 0.01). The full name of this
option for the EsoRex configuration file is vimos.Parameters.detection.fraction
[default = 0.01].
--MinObjectSize <long>
Minimal size for an object candidate to be considered an object. (long; default:
2). The full name of this option for the EsoRex configuration file is
vimos.Parameters.detection.minsize [default = 2].
--MaxObjectSize <long>
Maximal size for an object candidate for not trying deblend into sub- objects.
(long; default: 7). The full name of this option for the EsoRex configuration file
is vimos.Parameters.detection.maxsize [default = 7].
--CleanBadPixel <bool>
Bad pixel correction on MOS science exposure. (bool; default: False). The full name
of this option for the EsoRex configuration file is vimos.Parameters.badpixel.clean
[default = False].
--CalibrateFlux <bool>
Extracted spectra are flux calibrated. (bool; default: False). The full name of
this option for the EsoRex configuration file is vimos.Parameters.flux.calibration
[default = False].
--FringingCorr <bool>
Apply fringing corrections. (bool; default: False). The full name of this option
for the EsoRex configuration file is vimos.Parameters.fringing [default = False].
--FringingMethod <str>
Sky fringes removal method. (str; default: ´Raw´). The full name of this option for
the EsoRex configuration file is vimos.Parameters.fringing.removing.method [default
= Raw].
--FringingOffset <float>
Minimum required offset between exposures for applying the sky fringing correction.
(float; default: 3.0). The full name of this option for the EsoRex configuration
file is vimos.Parameters.fringing.offset [default = 3.0].
--HorneExtraction <bool>
Use 1D Horne extraction (bool; default: False). The full name of this option for
the EsoRex configuration file is vimos.Parameters.extraction.optimal [default =
False].
--ModelSlit <bool>
Model wavelength solution within each slit. (bool; default: True). The full name of
this option for the EsoRex configuration file is vimos.Parameters.slit.model
[default = True].
--ModelSlitOrder <long>
Order of polynomial for wavelength solution modeling within each slit. (long;
default: 0). The full name of this option for the EsoRex configuration file is
vimos.Parameters.slit.order [default = 0].
--UseSkylines <bool>
Use sky lines to refine the wavelength calibration (bool; default: True). The full
name of this option for the EsoRex configuration file is vimos.Parameters.sky.align
[default = True].
--SaveIntermediate <bool>
Save intermediate reduction steps (bool; default: False). The full name of this
option for the EsoRex configuration file is vimos.Parameters.save.intermediate
[default = False].
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 vimos pipeline can be downloaded as a PDF file using the
following URL:
ftp://ftp.eso.org/pub/dfs/pipelines/vimos/vimos-pipeline-manual-6.9.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 vimos pipeline are vmifucombinecube(7), vmifucalib(7),
vmimflatsky(7), vmspflat(7), vmmosobsstare(7), vmimflatscreen(7), vmimpreimaging(7),
vmimcalphot(7), vmmoscombine(7), vmimstandard(7), vmimobsstare(7), vmimobsjitter(7),
vmspphot(7), vmdet(7), vmmosscience(7), vmmosstandard(7), vmspcaldisp(7),
vmifustandard(7), vmbias(7), vmmoscalib(7), vmifucombine(7), vmdark(7), vmifuscience(7)
VERSION
vmmosobsjitter 2.9.9
AUTHOR
ESO VIMOS Pipeline Team and VIMOS Consortium <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 VIMOS 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