muse_bias - Combine several separate bias images into one master
bias file.
esorex muse_bias [OPTIONS] FILE.sof
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.
- --nifu
<int>
- IFU to handle. If set to 0, all IFUs are processed serially. If set to -1,
all IFUs are processed in parallel. (int; 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
<int>
- The number of pixels of the overscan adjacent to the data section of the
CCD that are ignored when computing statistics or fits. (int; 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
<int>
- Number of minimum pixels to reject with minmax. (int; default: 1). The
full name of this option for the EsoRex configuration file is
muse.muse_bias.nlow [default = 1].
- --nhigh
<int>
- Number of maximum pixels to reject with minmax. (int; default: 1). The
full name of this option for the EsoRex configuration file is
muse.muse_bias.nhigh [default = 1].
- --nkeep
<int>
- Number of pixels to keep with minmax. (int; 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.
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-2.8.7.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 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_illum(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_raman(7),
muse_scipost_subtract_sky(7),
muse_scipost_subtract_sky_simple(7), muse_standard(7),
muse_twilight(7), muse_wavecal(7)
Peter Weilbacher <https://support.eso.org>
Please report any problems to https://support.eso.org.
Alternatively, you may send a report to the ESO User Support Department
<usd-help@eso.org>.
This file is part of the MUSE Instrument Pipeline Copyright (C)
2005, 2019 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,
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