Provided by: cpl-plugin-muse-doc_2.8.7+dfsg-3build1_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-2.8.7.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_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 2.8.7
AUTHOR
Peter Weilbacher <https://support.eso.org>
BUG REPORTS
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>.
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