Provided by: cpl-plugin-muse-doc_2.8.5+dfsg-1_all 
NAME
muse_dark - Combine several separate dark images into one master dark file and locate hot
pixels.
SYNOPSIS
esorex muse_dark [OPTIONS] FILE.sof
DESCRIPTION
This recipe combines several separate dark images into one master dark file. The master
dark contains the combined pixel values of the raw dark exposures, with respect to the
image combination method used and normalization time specified. Processing trims the raw
data and records the overscan statistics, subtracts the bias (taking account of the
overscan, if --overscan is not "none") from each raw input image, converts them from adu
to count, scales them according to their exposure time, and combines them using input
parameters. Hot pixels are then identified using image statistics and marked in the data
quality extension. The combined image is normalized to 1 hour exposure time. QC statistics
are computed on the output master dark. If --model=true, a smooth polynomial model of the
combined master dark is computed, created from several individual 2D polynomials to
describe different features visible in MUSE dark frames. It is only advisable to use this,
if the master dark is the result of at least 50 individual long dark exposures.
OPTIONS
--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_dark.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_dark.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_dark.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_dark.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_dark.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_dark.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_dark.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_dark.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_dark.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_dark.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_dark.hsigma [default
= 3.0].
--scale <bool>
Scale the individual images to a common exposure time before combining them. (bool;
default: True). The full name of this option for the EsoRex configuration file is
muse.muse_dark.scale [default = True].
--normalize <float>
Normalize the master dark to this exposure time (in seconds). To disable
normalization, set this to a negative value. (float; default: 3600.0). The full
name of this option for the EsoRex configuration file is muse.muse_dark.normalize
[default = 3600.0].
--hotsigma <float>
Sigma level, in terms of median deviation above the median dark level, above which
a pixel is detected and marked as ´hot´. (float; default: 5.0). The full name of
this option for the EsoRex configuration file is muse.muse_dark.hotsigma [default =
5.0].
--model <bool>
Model the master dark using a set of polynomials. (bool; default: False). The full
name of this option for the EsoRex configuration file is muse.muse_dark.model
[default = False].
--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_dark.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-2.8.5.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_bias(7),
muse_create_sky(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)
VERSION
muse_dark 2.8.5
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, 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, Inc., 51 Franklin St, Fifth Floor, Boston,
MA 02111-1307 USA