muse_dark - Combine several separate dark images into one master
dark file and locate hot pixels.
esorex muse_dark [OPTIONS] FILE.sof
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.
- --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.
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)
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
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