bionic (7) vmmosobsjitter.7.gz
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 vmbias(7), vmdark(7), vmdet(7), vmifucalib(7),
vmifucombine(7), vmifucombinecube(7), vmifuscience(7), vmifustandard(7), vmimcalphot(7),
vmimflatscreen(7), vmimflatsky(7), vmimobsjitter(7), vmimobsstare(7), vmimpreimaging(7), vmimstandard(7),
vmmoscalib(7), vmmoscombine(7), vmmosobsstare(7), vmmosscience(7), vmmosstandard(7), vmspcaldisp(7),
vmspflat(7), vmspphot(7)
VERSION
vmmosobsjitter 3.1.9
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