XSH_CFG_RECOVER(7)

📦 version 3.5.3, in ubuntu jammy, ubuntu noble

🌟 NAME 🌟

xsh_cfg_recover — ok so bestie, this recipe optimizes a model configuration to match data taken after a major format change. Like, the instrument got a glow-up and now the old model needs to catch up. 💅

🦋 SYNOPSIS 🦋

esorex xsh_cfg_recover [OPTIONS] FILE.sof

✨ DESCRIPTION ✨

This recipe creates a wavelength solution and an order table. Slay. That's the whole vibe. Here's what it eats and what it gives back:

Input Frames :

  • [UVB, VIS] A RAW frame (Format = RAW, Tag = FMTCHK_arm)
  • [NIR] Two RAW frames (Format = RAW, Tag = FMTCHK_arm_ON,FMTCHK_arm_OFF)
  • The old model cfg table (Format = TABLE, Tag = XSH_MOD_CFG_TAB_arm)
  • A ref. line list. The model computes corresponding positions (Format = TABLE, Tag = ARC_LINE_LIST_arm)
  • [UVB,VIS,OPTIONAL] A master bias (Format = PRE, Tag = MASTER_BIAS_arm)
  • [UVB,VIS,OPTIONAL] A master dark (Format = PRE, Tag = MASTER_DARK_arm)
  • [OPTIONAL-Required if method=pm,peaks] An order table (Format = TABLE, Tag = ORDER_TAB_CENTR_arm)
  • [OPTIONAL-Required if first-anneal=TRUE] A table with measured line positions (Format = TABLE, Tag = XSH_MEASCOORD_arm)

Products :

  • if first-anneal=FALSE & last-step=FALSE → nothing 😭 (yeah, literally nothing, it just vibes)
  • if first-anneal=TRUE & last-step=FALSE → an optimized model configuration, PRO.CATG=XSH_MOD_CFG_arm
  • if last-step=TRUE → all of these queens:
    • an optimized model configuration, PRO.CATG=XSH_MOD_FAN_arm
    • an optimized model configuration, PRO.CATG=XSH_MOD_CFG_OPT_arm
    • an quality control table, PRO.CATG=MODEL_GUESS_XY_arm
    • the model theoretical map corresponding to the optimized model config, PRO.CATG=THEO_TAB_MULT_arm, THEO_TAB_IFU_arm, and THEO_TAB_SING_arm

💖 OPTIONS 💖

  • --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_cfg_recover.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_cfg_recover.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_cfg_recover.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_cfg_recover.decode-bp [default = 2144337919].
  • --first-anneal <bool> — Run first annealing (TRUE) or not (FALSE)See recipe man-page % Input frames (bool; default: False). The full name of this option for the EsoRex configuration file is xsh.xsh_cfg_recover.first-anneal [default = False].
  • --arm <str> — Arm setting: (str; default: ´vis´). The full name of this option for the EsoRex configuration file is xsh.xsh_model_compute.arm [default = vis].
  • --name_i <str> — Filename with wavelength,x,y,order: (str; default: ´line_xy_ord.txt´). The full name of this option for the EsoRex configuration file is xsh.xsh_model_compute.name_i [default = line_xy_ord.txt].
  • --niter <int> — No of iterations for first anneal (int; default: 100000). The full name of this option for the EsoRex configuration file is xsh.xsh_model_compute.niter [default = 100000].
  • --coord_frame <int> — Co-ordinate frame for centroids (0=raw,1=pre) (int; default: 1). The full name of this option for the EsoRex configuration file is xsh.xsh_model_compute.coord_frame [default = 1].
  • --last-step <bool> — Run last step (TRUE) or not (FALSE)See recipe man-page % Input frames (bool; default: False). The full name of this option for the EsoRex configuration file is xsh.xsh_cfg_recover.last-step [default = False].
  • --plot <bool> — Display plot (TRUE) or not (FALSE) (bool; default: False). The full name of this option for the EsoRex configuration file is xsh.xsh_cfg_recover.plot [default = False].
  • --ima_tresh_min <float> — Min thresh raw image. (float; default: 40.0). The full name of this option for the EsoRex configuration file is xsh.xsh_cfg_recover.ima_thresh_min [default = 40.0].
  • --cor_prescan <bool> — Correct for prescan (bool; default: False). The full name of this option for the EsoRex configuration file is xsh.xsh_cfg_recover.cor_prescan [default = False].
  • --method <str> — Model predictions correction method. safefit: safe fitgfit: 2D Gaussian line fitpeaks: line peaks detectionpm: line peaks detection & pattern match (str; default: ´safefit´). The full name of this option for the EsoRex configuration file is xsh.xsh_cfg_recover.method [default = safefit].
  • --offx <float> — X offset to model predictions (float; default: 0.0). The full name of this option for the EsoRex configuration file is xsh.xsh_cfg_recover.offx [default = 0.0].
  • --offy <float> — Y offset to model predictions (float; default: 0.0). The full name of this option for the EsoRex configuration file is xsh.xsh_cfg_recover.offy [default = 0.0].
  • --slit <int> — Extraction slit (int; default: 5). The full name of this option for the EsoRex configuration file is xsh.xsh_cfg_recover.slit [default = 5].
  • --gfit_box_sy <int> — Gauss fit Y search box size for lines on actual frame (int; default: 20). The full name of this option for the EsoRex configuration file is xsh.xsh_cfg_recover.gfit_box_sy [default = 20].
  • --peak_line_fwhm <int> — The FWHM used in line convolution, in pixel units (int; default: 4). The full name of this option for the EsoRex configuration file is xsh.xsh_cfg_recover.peak_line_fwhm [default = 4].
  • --peak_kappa <float> — The kappa value, used to identify line peaks if max>kappa*stdev+median, max is a valid peak where max, stdev,median are computed on the extracted spectrum (float; default: 5.0). The full name of this option for the EsoRex configuration file is xsh.xsh_cfg_recover.peak_kappa [default = 5.0].
  • --peak_factor <float> — Relative Intensity threshold factor for line peaks detection (float; default: 10.0). The full name of this option for the EsoRex configuration file is xsh.xsh_cfg_recover.peak_factor [default = 10.0].
  • --peak_match_x <int> — Radii for line peaks matches (int; default: 10). The full name of this option for the EsoRex configuration file is xsh.xsh_cfg_recover.peak_match_x [default = 10].
  • --peak_match_y <int> — Radii for line peaks matches (int; default: 20). The full name of this option for the EsoRex configuration file is xsh.xsh_cfg_recover.peak_match_y [default = 20].
  • --pm_ord_sel <int> — From guess line and peaks positions are extracted the ones in the range [ord_min,ord_min+pm_ord_sel] (int; default: 1). The full name of this option for the EsoRex configuration file is xsh.xsh_cfg_recover.pm_ord_sel [default = 1].
  • --pm_radius <float> — Search radius applied in final pattern matching (data units). (float; default: 20.0). The full name of this option for the EsoRex configuration file is xsh.xsh_cfg_recover.pm_radius [default = 20.0].
  • --pm_tolerance <float> — Max relative difference of angles and scales from their median value for match acceptance. (float; default: 0.1). The full name of this option for the EsoRex configuration file is xsh.xsh_cfg_recover.pm_tolerance [default = 0.1].
  • --anneal_niter <int> — Simulated annealing iterations (int; default: 1000). The full name of this option for the EsoRex configuration file is xsh.xsh_cfg_recover.anneal_niter [default = 1000].
💡 Not me reminding you: 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 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_flexcomp(7), xsh_geom_ifu(7), xsh_lingain(7), xsh_mbias(7), xsh_mdark(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)

⭐ VERSION ⭐

xsh_cfg_recover 3.5.3

👑 AUTHOR 👑

A. Modigliani, P. Bristow <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 era incoming — but it's actually important so don't scroll. ✨

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. 😭 (yes she's loud but that's literally the point, no cap)

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 💌

🫶 fr fr: if you're out here shipping or forking this, read the license first. It's giving "respect the terms" and honestly that's iconic of you.

And that's the whole page, bestie!! 🌸 You made it to the very end — main character energy, truly. 👑

This little beauty is xsh_cfg_recover, version 3.5.3, and it lives in section XSH_CFG_RECOVER(7) of the manual. Go forth and recover those configs responsibly. 💅✨🦋

the end!! 🎀💖🌈

📦 where this page comes from