MUSE_AMPL(7)

📦
version 2.8.7 · 2 versions
, in debian bookworm, ubuntu noble

💅 MUSE_AMPL(7) — muse recipes, but make it a group chat

okay bestie, sit down, hydrate, because we're about to talk about muse_ampl, one of the recipes from the muse recipes manual (that's the 7 in MUSE_AMPL(7), iykyk). it's giving spectroscopy, it's giving pipeline, it's giving "why is my throughput wrong". let's go 🦋

✨ NAME ✨

muse_ampl — determine the instrumental throughput from exposures taken with the pico-amplifier / photo diode readings. that's the whole vibe. we're measuring how much light actually made it through, no cap 🔥

🎀 SYNOPSIS 🎀

esorex muse_ampl [OPTIONS] FILE.sof

periodt. that's the summoning spell 💫

🌸 DESCRIPTION 🌸

so here's the tea, bestie. this recipe takes several separate amplifier images (they're flat-fields with special FITS headers that contain pico amplifier measurements — yes, fancy) and combines them into one master image file, then computes the instrumental throughput per IFU (and slice). iconic behavior honestly 👑

the processing pipeline does all of this, in order:

  • trims the raw data and records the overscan statistics
  • subtracts the bias — and yes, it takes account of the overscan if overscan is not "none"
  • optionally subtracts the dark from each raw input image
  • converts them from adu to count
  • scales them according to their exposure time
  • combines them using the input parameters

then, to actually compute the throughput: the image gets converted into a pixel table, the flux is then integrated over the given filter band, and the ratio of the expected flux (that's the FITS header INS.AMPL2.CURR) to the measured flux is taken — in the same units, obviously, we're not chaotic. 🙈

if a geometry table was given as input, the relative area of the IFUs is taken into account when computing the flux per unit area. love that for us.

the resulting ratio is the instrument efficiency (throughput), and it gets saved as QC parameters for the whole input image and per slice in the output pixel table. slay 💖

🌈 OPTIONS 🌈

bestie, there are a LOT of these. every single one. no skipping. 🫶

  • --nifu <int> — which IFU to handle. if it's set to 0, all IFUs are processed serially. if it's 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_ampl.nifu [default = 0].
  • --overscan <str> — if this is "none", it stops when it detects 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_ampl.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_ampl.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 the 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_ampl.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_ampl.ovscignore [default = 3].
  • --combine <str> — type of combination to use (str; default: ´sigclip´). the full name of this option for the EsoRex configuration file is muse.muse_ampl.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_ampl.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_ampl.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_ampl.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_ampl.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_ampl.hsigma [default = 3.0].
  • --fbeam <float> — factor to describe the widening of the beam from the focal plane to photo diode 2. (float; default: 1.1). the full name of this option for the EsoRex configuration file is muse.muse_ampl.fbeam [default = 1.1].
  • --temp <float> — lamp temperature [K] used to create the black body function. (float; default: 3200.0). the full name of this option for the EsoRex configuration file is muse.muse_ampl.temp [default = 3200.0].
  • --savemaster <bool> — save the processed and combined master image before any concolution is done. (bool; default: False). the full name of this option for the EsoRex configuration file is muse.muse_ampl.savemaster [default = False].
  • --savetable <bool> — save the table with all the processed pixel values. (bool; default: False). the full name of this option for the EsoRex configuration file is muse.muse_ampl.savetable [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_ampl.merge [default = False].
💡 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.

the other recipes of the muse pipeline are — and yes, we're listing all of them, they're a whole squad 💜:

⭐ VERSION ⭐

muse_ampl 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

and that's the whole page, bestie ✨ this was muse_ampl — version 2.8.7, straight from the muse recipes manual — so go forth, measure that throughput, and remember: you're the main character of your own pipeline 💅🦋🌸

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