XSH_ORDERPOS(7)

📦 version 3.5.3, in ubuntu jammy, ubuntu noble

💖 xsh_orderpos — the "make the orders centre traces table" era 💖

okay bestie, gather round, because this one is a recipe from the xshoo pipeline fam and it's literally called xsh_orderpos. In manpage-speak: "Create the orders centre traces table file." In our language: it finds where each spectral order actually sits, and writes that down. Iconic behaviour, no notes. ✨

🌸 SYNOPSIS 🌸

esorex xsh_orderpos [OPTIONS] FILE.sof

that's it. that's the whole vibe. a .sof file, some options, and the pipeline does its thing. 💅

🦋 DESCRIPTION 🦋

This recipe creates the orders centre traces table. Periodt.

Here's what it eats for input, bestie, sorted by arm so nobody gets confused:

Input Frames for UVB and VIS:

  • Raw file (Tag = ORDERDEF_arm_D2)
  • Master Dark (Tag = MASTER_DARK_arm)
  • Master Bias (Tag = MASTER_BIAS_arm)

Input Frames for NIR:

  • Raw file ON (Tag = ORDERDEF_NIR_ON)
  • Raw file OFF (Tag = ORDERDEF_NIR_OFF)

Input Frames for all arms:

  • Guess order table (Tag = ORDER_TAB_GUESS_arm)
  • Spectral format table (Tag = SPECTRAL_FORMAT_TAB_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)

Then it prepares PRE structures. Then:

  • For NIR, subtract NIR-OFF from NIR-ON.
  • For UVB and NIR, Substract the master Bias and master dark.
  • Detect Orders and calculate the order table.

(not me spelling it "Substract" the exact way the page does, we keep the facts fr fr 🙈)

The final products it hands you are:

  • An updated Order Table, PRO.CATG=ORDER_TABLE_CENTR_arm.
  • A order trace residuals Table, PRO.CATG=ORDERPOS_RESID_TAB_arm.
  • The order pos frame bias subtracted, PRO.CATG=ORDERDEF_ON_arm.

three products, all yours, go off. 🎀

✨ OPTIONS ✨

okay so here's every single knob, bestie. don't skip any, I checked twice. 👑

  • --keep-temp <str> — If ´no´, temporary files are deleted. (str; default: ´no´). The full name of this option for the EsoRex configuration file is xsh.xsh_orderpos.keep-temp [default = no].
  • --debug-level <str> — Additional xshooter debug level. One of ´none´, ´low´, ´medium´, ´high´ (str; default: ´none´). The full name of this option for the EsoRex configuration file is xsh.xsh_orderpos.debug-level [default = none].
  • --time-stamp <bool> — Add timestamp to product file name. (bool; default: False). The full name of this option for the EsoRex configuration file is xsh.xsh_orderpos.time-stamp [default = False].
  • --decode-bp <int> — Integer representation of the bits to be considered bad when decoding the bad pixel mask pixel values. Most frequent codes relevant for the user: 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_orderpos.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_orderpos.pre-overscan-corr [default = 1].
  • --detectcontinuum-search-win-hsize <int> — Half window size in pixels for the 1D box to search for the maximum in the cross-dispersion profile (int; default: 5). The full name of this option for the EsoRex configuration file is xsh.xsh_orderpos.detectcontinuum-search-win-hsize [default = 5].
  • --detectcontinuum-running-win-hsize <int> — Half window size for the running median box during the search for the maximum in the cross-dispersion profile (int; default: 0). The full name of this option for the EsoRex configuration file is xsh.xsh_orderpos.detectcontinuum-running-win-hsize [default = 0].
  • --detectcontinuum-fit-win-hsize <int> — Half window size for the fit of the cross-dispersion profile (int; default: 5). The full name of this option for the EsoRex configuration file is xsh.xsh_orderpos.detectcontinuum-fit-win-hsize [default = 5].
  • --detectcontinuum-center-thresh-fac <float> — Threshold factor applied to check that the flux at the fitted peak is higher than error. (float; default: 0.0). The full name of this option for the EsoRex configuration file is xsh.xsh_orderpos.detectcontinuum-center-thresh-fac [default = 0.0].
  • --detectcontinuum-ordertab-step-y <int> — Step in Y for order centroid detection (int; default: 1). The full name of this option for the EsoRex configuration file is xsh.xsh_orderpos.detectcontinuum-ordertab-step-y [default = 1].
  • --detectcontinuum-ordertab-deg-y <int> — Degree in Y in the polynomial order tracing X=f(Y) (int; default: 5). The full name of this option for the EsoRex configuration file is xsh.xsh_orderpos.detectcontinuum-ordertab-deg-y [default = 5].
  • --detectcontinuum-clip-res-max <float> — Maximum allowed residual (before kappa-sigma clip) (float; default: 0.5). The full name of this option for the EsoRex configuration file is xsh.xsh_orderpos.detectcontinuum-clip-res-max [default = 0.5].
  • --detectcontinuum-clip-sigma <float> — Kappa value in sigma clipping during order trace polynomial fit (float; default: 5.0). The full name of this option for the EsoRex configuration file is xsh.xsh_orderpos.detectcontinuum-clip-sigma [default = 5.0].
  • --detectcontinuum-clip-niter <int> — Number of iterations in sigma clipping during order trace polynomial fit (int; default: 5). The full name of this option for the EsoRex configuration file is xsh.xsh_orderpos.detectcontinuum-clip-niter [default = 5].
  • --detectcontinuum-clip-frac <float> — Minimal fractions of points accepted / total in sigma clippingduring order trace polynomial fit (float; default: 0.4). The full name of this option for the EsoRex configuration file is xsh.xsh_orderpos.detectcontinuum-clip-frac [default = 0.4].
ngl, you can totally make a configuration file holding all these options with suitable default values. The details are in the esorex --help command. go look, it's giving helpful. 🫶

🔥 SEE ALSO 🔥

The full documentation for the xshoo pipeline can be downloaded as a PDF file using the following URL:

ftp://ftp.eso.org/pub/dfs/pipelines/xshoo/xshoo-pipeline-manual-12.1.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 xshoo pipeline are xsh_2dmap(7), xsh_cfg_recover(7), xsh_flexcomp(7), xsh_geom_ifu(7), xsh_lingain(7), xsh_mbias(7), xsh_mdark(7), xsh_mflat(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 fam, all linked up, we love to see it. 💜

⭐ VERSION ⭐

xsh_orderpos 3.5.3

👑 AUTHOR 👑

L.Guglielmi,R.Haigron,P.Goldoni,F.Royer, 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>.

(if something's cursed, tell them, not me, I'm just the messenger 🫶)

🌈 LICENSE 🌈

This file is part of the X-shooter Instrument Pipeline Copyright (C) 2006 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., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA

okay that's the whole page bestie, and as a lil sign-off: this is from the xshoo recipes manual set, xsh_orderpos version 3.5.3, same version on the bottom line as the top. read it, love it, cite it. mwah 💅💖🦋

📦 where this page comes from