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muse_bias - Combine several separate bias images into one master bias file.

MUSE_BIAS(7) muse recipes MUSE_BIAS(7)

NAME

muse_bias - Combine several separate bias images into one master bias file.
 

SYNOPSIS

esorex muse_bias [OPTIONS] FILE.sof
 

DESCRIPTION

This recipe combines several separate bias images into one master bias file. The master bias contains the combined pixel values, in adu, of the raw bias exposures, with respect to the image combination method used. Processing trims the raw data and records the overscan statistics, corrects the data levels using the overscan (if overscan is not &none&) and combines the exposures using input parameters. The read-out noise is computed for each quadrant of the raw input images and stored as QC parameter. The variance extension is filled with an initial value accordingly, before image combination. Further QC statistics are computed on the output master bias. Additionally, bad columns are searched for and marked in the data quality extension.
 

OPTIONS

--nifu <long>
IFU to handle. If set to 0, all IFUs are processed serially. If set to -1, all IFUs are processed in parallel. (long; default: 0). The full name of this option for the EsoRex configuration file is muse.muse_bias.nifu [default = 0].
--overscan <str>
If this is "none", stop when detecting discrepant overscan levels (see ovscsigma), for "offset" it assumes that the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly; for "vpoly", a polynomial is fit to the vertical overscan and subtracted from the whole quadrant. (str; default: ´vpoly´). The full name of this option for the EsoRex configuration file is muse.muse_bias.overscan [default = vpoly].
--ovscreject <str>
This influences how values are rejected when computing overscan statistics. Either no rejection at all ("none"), rejection using the DCR algorithm ("dcr"), or rejection using an iterative constant fit ("fit"). (str; default: ´dcr´). The full name of this option for the EsoRex configuration file is muse.muse_bias.ovscreject [default = dcr].
--ovscsigma <float>
If the deviation of mean overscan levels between a raw input image and the reference image is higher than |ovscsigma x stdev|, stop the processing. If overscan="vpoly", this is used as sigma rejection level for the iterative polynomial fit (the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings). Has no effect for overscan="offset". (float; default: 30.0). The full name of this option for the EsoRex configuration file is muse.muse_bias.ovscsigma [default = 30.0].
--ovscignore <long>
The number of pixels of the overscan adjacent to the data section of the CCD that are ignored when computing statistics or fits. (long; default: 3). The full name of this option for the EsoRex configuration file is muse.muse_bias.ovscignore [default = 3].
--combine <str>
Type of image combination to use. (str; default: ´sigclip´). The full name of this option for the EsoRex configuration file is muse.muse_bias.combine [default = sigclip].
--nlow <long>
Number of minimum pixels to reject with minmax. (long; default: 1). The full name of this option for the EsoRex configuration file is muse.muse_bias.nlow [default = 1].
--nhigh <long>
Number of maximum pixels to reject with minmax. (long; default: 1). The full name of this option for the EsoRex configuration file is muse.muse_bias.nhigh [default = 1].
--nkeep <long>
Number of pixels to keep with minmax. (long; default: 1). The full name of this option for the EsoRex configuration file is muse.muse_bias.nkeep [default = 1].
--lsigma <float>
Low sigma for pixel rejection with sigclip. (float; default: 3.0). The full name of this option for the EsoRex configuration file is muse.muse_bias.lsigma [default = 3.0].
--hsigma <float>
High sigma for pixel rejection with sigclip. (float; default: 3.0). The full name of this option for the EsoRex configuration file is muse.muse_bias.hsigma [default = 3.0].
--losigmabadpix <float>
Low sigma to find dark columns in the combined bias (float; default: 30.0). The full name of this option for the EsoRex configuration file is muse.muse_bias.losigmabadpix [default = 30.0].
--hisigmabadpix <float>
High sigma to find bright columns in the combined bias (float; default: 3.0). The full name of this option for the EsoRex configuration file is muse.muse_bias.hisigmabadpix [default = 3.0].
--merge <bool>
Merge output products from different IFUs into a common file. (bool; default: False). The full name of this option for the EsoRex configuration file is muse.muse_bias.merge [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 muse pipeline can be downloaded as a PDF file using the following URL:
ftp://ftp.eso.org/pub/dfs/pipelines/muse/muse-pipeline-cookbook-2.0.3.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 muse pipeline are muse_ampl(7), muse_astrometry(7), muse_create_sky(7), muse_dark(7), muse_exp_align(7), muse_exp_combine(7), muse_flat(7), muse_geometry(7), muse_lingain(7), muse_lsf(7), muse_qi_mask(7), muse_scibasic(7), muse_scipost(7), muse_scipost_apply_astrometry(7), muse_scipost_calibrate_flux(7), muse_scipost_combine_pixtables(7), muse_scipost_correct_dar(7), muse_scipost_correct_rv(7), muse_scipost_make_cube(7), muse_scipost_subtract_sky(7), muse_scipost_subtract_sky_simple(7), muse_standard(7), muse_twilight(7), muse_wavecal(7)
 

VERSION

muse_bias 2.0.3
 

AUTHOR

Peter Weilbacher <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 part of the MUSE Instrument Pipeline Copyright (C) 2005, 2017 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
2.0.3 muse_bias