XSH_MDARK(7)

📦 version 3.5.3, in ubuntu jammy, ubuntu noble

💖 XSH_MDARK 💖

okay bestie, welcome to xsh_mdark — it's the <rainbow>xshoo recipes</rainbow> manual, section 7, and this one is literally about making you a master dark frame. yes it's long, no we're not skipping anything, we're doing this together. 🫶

✨ NAME ✨

xsh_mdark — create the master dark frame. that's it, that's the whole vibe. 🎀

✨ SYNOPSIS ✨

esorex xsh_mdark [OPTIONS] FILE.sof

✨ DESCRIPTION ✨

bestie. this recipe creates a master dark frame. iconic behaviour, no cap. 💅

Input Frames :

  • A set of n RAW frames (Format=RAW, n >=3, Tag = DARK_arm)
  • [UVB,VIS] A master bias frame (Format=PRE, Tag = MASTER_BIAS_arm)
  • [OPTIONAL] A map of non linear bad pixels (Format=QUP, Tag = BP_MAP_NL_arm)
  • [OPTIONAL] A map of reference bad pixels (Format = QUP,RAW, Tag = BP_MAP_RP_arm)

Products :

  • A master dark frame (Format=PRE, PRO.CATG = MASTER_DARK_arm)
    • A dark frame, (Format=PRE, PRO.CATG = DARK_arm)

✨ OPTIONS ✨

okay so, the entire option list. every single one. buckle up, we're going all the way through, no skimming. 💀

  • --keep-temp <str> — if it's set to 'no', temporary files get deleted. (str; default: 'no'). the full name of this option for the EsoRex configuration file is xsh.xsh_mdark.keep-temp [default = no].
  • --debug-level <str> — extra xshooter debug level, pick one of 'none', 'low', 'medium', 'high'. (str; default: 'none'). the full name of this option for the EsoRex configuration file is xsh.xsh_mdark.debug-level [default = none].
  • --time-stamp <bool> — slaps a timestamp onto the product file name. (bool; default: False). the full name of this option for the EsoRex configuration file is xsh.xsh_mdark.time-stamp [default = False].
  • --decode-bp <int> — the integer representation of the bits we treat as bad when decoding the bad pixel mask pixel values. here are the most frequent codes that actually matter to you: 0: good pixel, 8: pick-up noise, 16: cosmic-ray removed, 32: cosmic-ray unremoved, 128: calibration file defect, 256: hot pixel, 512: dark pixel, 4096: A/D converted saturation, 32768: non linear pixel, 1048576: extrapolated flux in NIR, 4194304: Interpolated flux during extraction. (int; default: 2144337919). the full name of this option for the EsoRex configuration file is xsh.xsh_mdark.decode-bp [default = 2144337919].
  • --pre-overscan-corr <int> — pre-overscan correction. 0: no correction, 1: mean overscan correction, 2: mean prescan correction, 3: (mean pre+mean overscan)/2 correction. (int; default: 1). the full name of this option for the EsoRex configuration file is xsh.xsh_mdark.pre-overscan-corr [default = 1].
  • --stack-method <str> — the method used to build the master frame. (str; default: 'median'). the full name of this option for the EsoRex configuration file is xsh.xsh_mdark.stack-method [default = median].
  • --klow <float> — the kappa used to clip low level values, and this one kicks in when the method is set to 'mean'. (float; default: 5.0). the full name of this option for the EsoRex configuration file is xsh.xsh_mdark.klow [default = 5.0].
  • --khigh <float> — the kappa used to clip high level values, again only when the method is set to 'mean'. (float; default: 5.0). the full name of this option for the EsoRex configuration file is xsh.xsh_mdark.khigh [default = 5.0].
  • --bp-output <bool> — a flag saying whether the noise bad pixel map should be computed. (bool; default: False). the full name of this option for the EsoRex configuration file is xsh.xsh_mdark.bp-output [default = False].
  • --crh-clip-kappa <float> — the kappa value used in sigma clipping during CRH rejection across multiple frames. (float; default: -1.0). the full name of this option for the EsoRex configuration file is xsh.xsh_mdark.crh-clip-kappa [default = -1.0].
  • --crh-clip-niter <int> — how many iterations of sigma clipping happen during CRH rejection across multiple frames. (int; default: 3). the full name of this option for the EsoRex configuration file is xsh.xsh_mdark.crh-clip-niter [default = 3].
  • --crh-clip-frac <float> — the minimal ratio of points accepted over total during sigma clipping in CRH rejection across multiple frames. (float; default: 0.7). the full name of this option for the EsoRex configuration file is xsh.xsh_mdark.crh-clip-frac [default = 0.7].
  • --noise-clip-kappa <float> — a multiple of sigma, used in sigma clipping. (float; default: 9.0). the full name of this option for the EsoRex configuration file is xsh.xsh_mdark.noise-clip-kappa [default = 9.0].
  • --noise-clip-niter <int> — number of iterations in sigma clipping. (int; default: 5). the full name of this option for the EsoRex configuration file is xsh.xsh_mdark.noise-clip-niter [default = 5].
  • --noise-clip-frac <float> — minimal fractions of bad pixel allowed. (float; default: 0.7). the full name of this option for the EsoRex configuration file is xsh.xsh_mdark.noise-clip-frac [default = 0.7].
  • --noise-clip-diff <float> — minimum relative change in sigma for sigma clipping. (float; default: 0.0). the full name of this option for the EsoRex configuration file is xsh.xsh_mdark.noise-clip-diff [default = 0.0].
  • --noise-lower-rejection <float> — the lower rejection percentile for flagging bad pixels via noise. (float; default: 10.0). the full name of this option for the EsoRex configuration file is xsh.xsh_mdark.noise-lower-rejection [default = 10.0].
  • --noise-higher-rejection <float> — the upper rejection percentile for flagging bad pixels via noise. (float; default: 10.0). the full name of this option for the EsoRex configuration file is xsh.xsh_mdark.noise-higher-rejection [default = 10.0].
  • --ref1_llx <int> — lower left X of the reference region. (int; default: -1). the full name of this option for the EsoRex configuration file is xsh.xsh_mdark.ref1_llx [default = -1].
  • --ref1_lly <int> — lower left Y of the reference region. (int; default: -1). the full name of this option for the EsoRex configuration file is xsh.xsh_mdark.ref1_lly [default = -1].
  • --ref1_urx <int> — upper right X of the reference region. (int; default: -1). the full name of this option for the EsoRex configuration file is xsh.xsh_mdark.ref1_urx [default = -1].
  • --ref1_ury <int> — upper right Y of the reference region. (int; default: -1). the full name of this option for the EsoRex configuration file is xsh.xsh_mdark.ref1_ury [default = -1].
  • --ron_llx <int> — lower left X of the reference region used to measure RON. (int; default: -1). the full name of this option for the EsoRex configuration file is xsh.xsh_mdark.ron_llx [default = -1].
  • --ron_lly <int> — lower left Y of the reference region used to measure RON. (int; default: -1). the full name of this option for the EsoRex configuration file is xsh.xsh_mdark.ron_lly [default = -1].
  • --ron_urx <int> — upper right X of the reference region used to measure RON. (int; default: -1). the full name of this option for the EsoRex configuration file is xsh.xsh_mdark.ron_urx [default = -1].
  • --ron_ury <int> — upper right Y of the reference region used to measure RON. (int; default: -1). the full name of this option for the EsoRex configuration file is xsh.xsh_mdark.ron_ury [default = -1].
  • --ron_hsize <int> — sampling area size. (int; default: 4). the full name of this option for the EsoRex configuration file is xsh.xsh_mdark.ron_hsize [default = 4].
  • --ron_nsamples <int> — number of random samples. (int; default: 100). the full name of this option for the EsoRex configuration file is xsh.xsh_mdark.ron_nsamples [default = 100].
  • --fpn_llx <int> — lower left reference area X coordinate for Fixed Pattern Noise computation. (int; default: -1). the full name of this option for the EsoRex configuration file is xsh.xsh_mdark.fpn_llx [default = -1].
  • --fpn_lly <int> — lower left reference area Y coordinate for Fixed Pattern Noise computation. (int; default: -1). the full name of this option for the EsoRex configuration file is xsh.xsh_mdark.fpn_lly [default = -1].
  • --fpn_urx <int> — upper right reference area X coordinate for Fixed Pattern Noise computation. (int; default: -1). the full name of this option for the EsoRex configuration file is xsh.xsh_mdark.fpn_urx [default = -1].
  • --fpn_ury <int> — upper right reference area Y coordinate for Fixed Pattern Noise computation. (int; default: -1). the full name of this option for the EsoRex configuration file is xsh.xsh_mdark.fpn_ury [default = -1].
  • --fpn_hsize <int> — sample size for Fixed Pattern Noise computation. (int; default: 4). the full name of this option for the EsoRex configuration file is xsh.xsh_mdark.fpn_hsize [default = 4].
  • --fpn_nsamples <int> — number of sampling points for Fixed Pattern Noise computation. (int; default: 100). the full name of this option for the EsoRex configuration file is xsh.xsh_mdark.fpn_nsamples [default = 100].
ok so fun fact bestie: you can make a configuration file holding all these options with suitable default values. wanna know the deets? go check what 'esorex --help' tells you. ✨

✨ SEE ALSO ✨

the full documentation for the xshoo pipeline can be downloaded as a PDF file from this URL:

ftp://ftp.eso.org/pub/dfs/pipelines/xshoo/xshoo-pipeline-manual-12.1.pdf

there's also an overview of all the existing ESO pipelines chilling on the web page https://www.eso.org/sci/software/pipelines/.

basic documentation about the EsoRex program lives at the esorex (1) man page. 💖

and yes, you can call the pipelines from python using the python-cpl package. see https://packages.python.org/python-cpl/index.html for more info. 🐍

the other recipes of the xshoo pipeline are xsh_2dmap(7), xsh_cfg_recover(7), xsh_flexcomp(7), xsh_geom_ifu(7), xsh_lingain(7), xsh_mbias(7), xsh_mflat(7), xsh_orderpos(7), xsh_predict(7), xsh_respon_slit_nod(7), xsh_respon_slit_offset(7), xsh_respon_slit_stare(7), xsh_scired_ifu_offset(7), xsh_scired_ifu_offset_drl(7), xsh_scired_ifu_stare(7), xsh_scired_ifu_stare_drl(7), xsh_scired_slit_nod(7), xsh_scired_slit_offset(7), xsh_scired_slit_stare(7), xsh_util_physmod(7), xsh_wavecal(7). the whole squad. 👑

✨ VERSION ✨

xsh_mdark 3.5.3

✨ AUTHOR ✨

P.Goldoni, L.Guglielmi, R. Haigron, F. Royer, D. Bramich, A. Modigliani <amodigli@eso.org>

✨ BUG REPORTS ✨

please report any problems to amodigli@eso.org. alternatively, you may send a report to the ESO User Support Department <usd-help@eso.org>. 🫶

📜 LICENSE 📜

okay bestie, legal time, but make it cute 💖

This file is part of the X-shooter Instrument Pipeline — Copyright (C) 2006 European Southern Observatory. yes, 2006, we've been iconic for a minute.

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. slay, your choice, no pressure 🫶

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. fr fr, no warranty, don't come for us 😭

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., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA — like, actual paper mail, vintage behavior honestly ✨

💀 reminder: none of this is a vibe check on your code, it's just the legal text. read it, love it, respect it.

and that's the whole page, bestie, we made it to the end 🎀 this one came from xsh_mdark version 3.5.3 and it lives at section XSH_MDARK(7) — go forth and dark-subtract responsibly, ily 💜🦋🌸

📦 where this page comes from