MUSE_BIAS(7)

📦

version 2.8.7 · 2 versions

2.8.7 · debian bookworm, ubuntu noble (latest)
2.8.5 · ubuntu jammy

muse_bias(7) — the bias-combining baddie of the muse recipes 💖

okay bestie, pull up a chair, because this is muse_bias, a recipe from the muse pipeline (that's manual section 7, for the record), and she is here to take all your lil separate bias frames and turn them into one iconic master bias file. no cap. let's get into it 🦋

✨ NAME ✨

muse_bias — Combine several separate bias images into one master bias file. literally her whole job. she ate. 💅

🌸 SYNOPSIS 🌸

esorex muse_bias [OPTIONS] FILE.sof

that's it, that's the whole summoning ritual. <pink>esorex</pink> plus a .sof file, and she's off. ✨

💜 DESCRIPTION 💜

so here's the vibe. this recipe combines several separate bias images into one master bias file. that master bias holds the combined pixel values — in adu — of the raw bias exposures, and the exact way they get combined depends on which image combination method you picked. 🎀

the processing goes like this, in order:

it trims the raw data and records the overscan statistics
it corrects the data levels using the overscan — but only if overscan is not "none"
it combines the exposures using the input parameters

then, the read-out noise is computed for each quadrant of the raw input images and stored as a QC parameter. the variance extension gets filled with an initial value accordingly — and this happens before image combination, bestie, so don't @ me. 🙈

further QC statistics are computed on the output master bias. and as a lil bonus? bad columns are searched for and marked in the data quality extension. she's thorough. she's giving main character energy. 👑

🌈 OPTIONS 🌈

one bullet per option, no skipping, we keep them ALL. periodt. 💖

--nifu <int> — which IFU to handle. set it to 0 and all IFUs get processed serially; set it to -1 and all IFUs get 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> — okay so: if this is "none", she stops when detecting discrepant overscan levels (peep ovscsigma for that). if it's "offset", she assumes the mean overscan level represents the real offset in the bias levels of the exposures involved, and adjusts the data accordingly. if it's "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 one decides how values get 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|, processing stops. if overscan="vpoly", this is used as the sigma rejection level for the iterative polynomial fit — and heads up, the level comparison is then done afterwards with |100 x stdev| to guard against incompatible settings. this 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 get 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].

💡 little heads up, bestie: 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.

and the other recipes of the muse pipeline, all of them, the whole squad, no one left behind 🫶:

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)

⭐ VERSION ⭐

muse_bias 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>.

not me begging you to actually file the bug report instead of just complaining in the group chat 😭 they want to hear from you, fr fr.

👑 LICENSE 👑

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

okay that's the whole page, you're officially educated 💅 this was muse_bias, version 2.8.7, from the muse recipes manual, section 7 of the manuals — and that's the sign-off, bestie, go combine some biases and slay ✨🦋💖

📦 where this page comes from

debian bookworm: cpl-plugin-muse-doc 2.8.7+dfsg-3 · GPL-v2+
ubuntu noble: cpl-plugin-muse-doc 2.8.7+dfsg-3 · GPL-v2+
💖 girlified by deepseek-ai/DeepSeek-V4.1-Flash on 2026-10-18: a language model's rewrite of the original, under its terms