XSH_GEOM_IFU(7)

📦 version 3.5.3, in ubuntu jammy, ubuntu noble

💖 NAME 💖

okay so bestie, this is XSH_GEOM_IFU(7) — a manual page from the xshoo recipes era, and the actual tool it's about is xsh_geom_ifu. What does it do? It produces the spatial geometry of the IFU pattern on the sky. That's the whole vibe. ✨

✨ SYNOPSIS ✨

esorex xsh_geom_ifu [OPTIONS] FILE.sof

🌸 DESCRIPTION 🌸

This recipe produces the spatial geometry of the IFU pattern on the sky. No cap, that's literally the job.

🫶 Input Frames 🫶

  • A set of n science frames ( n == 1 or >=3, Tag = TRACE_arm) — yeah bestie, either exactly one or three-plus, the middle ones are not it 💀
  • [UVB,VIS] A master bias frame (Tag = MASTER_BIAS_arm)
  • [OPTIONAL] A master dark frame (Tag = MASTER_DARK_arm)
  • A master flat frame (Tag = MASTER_FLAT_IFU_arm)
  • An AFC corrected model order edges table for IFU frame (Tag = ORDER_TAB_AFC_IFU_arm)
  • [PHYSMOD] An AFC corrected model cfg frame (Tag = XSH_MOD_CFG_OPT_AFC_arm)
  • [POLY] An AFC corrected model wavesol frame (Tag = WAVE_TAB_AFC_arm)
  • An AFC corrected dispersion solution frame (Tag = DISP_TAB_AFC_arm)
  • [OPTIONAL] A badpixel map (Tag = BADPIXEL_MAP_arm)

🎀 Products 🎀

  • A set of shift offset tables (Tag = OFFSET_TAB_slitlet_IFU_arm)

💅 OPTIONS 💅

thirty-five of them. we're not skipping a single one, so grab a snack 🍓

  • --keep-temp <str> — if you set it to no, the temporary files get deleted. (str; default: no). The full name of this option for the EsoRex configuration file is xsh.xsh_geom_ifu.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_geom_ifu.debug-level [default = none].
  • --time-stamp <bool> — slaps a timestamp onto the product file name, cute. (bool; default: False). The full name of this option for the EsoRex configuration file is xsh.xsh_geom_ifu.time-stamp [default = False].
  • --decode-bp <int> — integer representation of the bits to be considered bad when decoding the bad pixel mask pixel values. the codes you'll actually care about as a 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_geom_ifu.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_geom_ifu.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_geom_ifu.stack-method [default = median].
  • --klow <float> — kappa used to clip low level values, 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_geom_ifu.klow [default = 5.0].
  • --khigh <float> — kappa used to clip high level values, 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_geom_ifu.khigh [default = 5.0].
  • --crh-clip-kappa <float> — kappa value in sigma clipping during CRH rejection using multiple frames. (float; default: 5.0). The full name of this option for the EsoRex configuration file is xsh.xsh_geom_ifu.crh-clip-kappa [default = 5.0].
  • --crh-clip-niter <int> — number of iterations in sigma clipping during CRH rejection using multiple frames. (int; default: 5). The full name of this option for the EsoRex configuration file is xsh.xsh_geom_ifu.crh-clip-niter [default = 5].
  • --crh-clip-frac <float> — minimal ratio of points accepted / total in sigma clipping during CRH rejection using multiple frames. (float; default: 0.7). The full name of this option for the EsoRex configuration file is xsh.xsh_geom_ifu.crh-clip-frac [default = 0.7].
  • --background-edges-margin <int> — X margin to order edge, used to define background sampling points. (int; default: 1). The full name of this option for the EsoRex configuration file is xsh.xsh_geom_ifu.background-edges-margin [default = 1].
  • --background-poly-deg-y <int> — poly mode fit deg along Y. (int; default: 9). The full name of this option for the EsoRex configuration file is xsh.xsh_geom_ifu.background-poly-deg-y [default = 9].
  • --background-poly-deg-x <int> — poly mode fit deg along X. (int; default: 9). The full name of this option for the EsoRex configuration file is xsh.xsh_geom_ifu.background-poly-deg-x [default = 9].
  • --background-poly-kappa <float> — poly mode kappa value of kappa-sigma-clip outliers removal. (float; default: 10.0). The full name of this option for the EsoRex configuration file is xsh.xsh_geom_ifu.background-poly-kappa [default = 10.0].
  • --removecrhsingle-sigmalim <float> — Poisson fluctuation threshold to flag CRHs (see van Dokkum, PASP,113,2001,p1420-27). (float; default: 5.0). The full name of this option for the EsoRex configuration file is xsh.xsh_geom_ifu.removecrhsingle-sigmalim [default = 5.0].
  • --removecrhsingle-flim <float> — minimum contrast between the Laplacian image and the fine structure image that a point must have to be flagged as CRH (see van Dokkum, PASP,113,2001,p1420-27). (float; default: 2.0). The full name of this option for the EsoRex configuration file is xsh.xsh_geom_ifu.removecrhsingle-flim [default = 2.0].
  • --removecrhsingle-niter <int> — max number of iterations. (int; default: 4). The full name of this option for the EsoRex configuration file is xsh.xsh_geom_ifu.removecrhsingle-niter [default = 4].
  • --rectify-kernel <str> — name of the Interpolation Kernel Used. possible values are: tanh, sinc, sinc2, lanczos, hamming, hann. (str; default: tanh). The full name of this option for the EsoRex configuration file is xsh.xsh_geom_ifu.rectify-kernel [default = tanh].
  • --rectify-radius <float> — rectify Interpolation radius [bin units]. (float; default: 4.0). The full name of this option for the EsoRex configuration file is xsh.xsh_geom_ifu.rectify-radius [default = 4.0].
  • --rectify-bin-lambda <float> — wavelength step in the output spectrum [nm]. (float; default: -1.0). The full name of this option for the EsoRex configuration file is xsh.xsh_geom_ifu.rectify-bin-lambda [default = -1.0].
  • --rectify-bin-slit <float> — spatial step along the slit in the output spectrum [arcsec]. (float; default: -1.0). The full name of this option for the EsoRex configuration file is xsh.xsh_geom_ifu.rectify-bin-slit [default = -1.0].
  • --localizeifu-bckg-deg <int> — degree (<=2) of the polynomial component in the cross-dispersion profile fit. (int; default: 50). The full name of this option for the EsoRex configuration file is xsh.xsh_geom_ifu.localizeifu-bckg-deg [default = 50].
  • --localizeifu-smooth-hsize <int> — half-size of the median filter for smoothing the cross-dispersion profile prior to localization. (int; default: 3). The full name of this option for the EsoRex configuration file is xsh.xsh_geom_ifu.localizeifu-smooth-hsize [default = 3].
  • --localizeifu-wavelet-nscales <int> — number of scales used for wavelet a trous algorithm. (int; default: 5). The full name of this option for the EsoRex configuration file is xsh.xsh_geom_ifu.localizeifu-wavelet-nscales [default = 5].
  • --localizeifu-wavelet-hf-skip <int> — number of high frequency scales skipped from the wavelet decomposition. (int; default: 2). The full name of this option for the EsoRex configuration file is xsh.xsh_geom_ifu.localizeifu-wavelet-hf-skip [default = 2].
  • --localizeifu-sigma-low <float> — Gaussian fits of the cross-dispersion profile whose FWHM is lower than this value are rejected. (float; default: 0.05). The full name of this option for the EsoRex configuration file is xsh.xsh_geom_ifu.localizeifu-sigma-low [default = 0.05].
  • --localizeifu-sigma-up <float> — Gaussian fits of the cross-dispersion profile whose FWHM is larger than this value are rejected. (float; default: 0.95). The full name of this option for the EsoRex configuration file is xsh.xsh_geom_ifu.localizeifu-sigma-up [default = 0.95].
  • --localizeifu-snr-low <float> — Gaussian fits of the cross-dispersion profile whose SNR is lower than this value are rejected. (float; default: 0.05). The full name of this option for the EsoRex configuration file is xsh.xsh_geom_ifu.localizeifu-snr-low [default = 0.05].
  • --localizeifu-snr-up <float> — Gaussian fits of the cross-dispersion profile whose SNR is larger than this value are rejected. (float; default: 0.95). The full name of this option for the EsoRex configuration file is xsh.xsh_geom_ifu.localizeifu-snr-up [default = 0.95].
  • --localizeifu-slitlow-edges-mask <float> — in arsec. (float; default: 0.0). The full name of this option for the EsoRex configuration file is xsh.xsh_geom_ifu.localizeifu-slitlow-edges-mask [default = 0.0].
  • --localizeifu-slitup-edges-mask <float> — in arsec. (float; default: 0.0). The full name of this option for the EsoRex configuration file is xsh.xsh_geom_ifu.localizeifu-slitup-edges-mask [default = 0.0].
  • --localizeifu-use-skymask <bool> — TRUE if we want to mask sky lines using SKY_LINE_LIST file. (bool; default: False). The full name of this option for the EsoRex configuration file is xsh.xsh_geom_ifu.localizeifu-use-skymask [default = False].
  • --localizeifu-chunk-hsize <int> — half size of chunk [bin]. (int; default: 0). The full name of this option for the EsoRex configuration file is xsh.xsh_geom_ifu.localizeifu-chunk-hsize [default = 0].
  • --correctifu-niter <int> — number of iterations in computing the localization shifts of the IFU slitlets. (int; default: 3). The full name of this option for the EsoRex configuration file is xsh.xsh_geom_ifu.correctifu-niter [default = 3].
  • --correctifu-lambdaref <float> — bestie, this is the reference wavelength where we pick the reference localization on the slit 💅 (float; default: -1.0). In the EsoRex config file its full glow-up name is xsh.xsh_geom_ifu.correctifu-lambdaref [default = -1.0].
  • --correctifu-lambdaref-hsize <float> — the HAlf size in nm used to estimate that reference wavelength ✨ (float; default: 2.5). EsoRex config file full name: xsh.xsh_geom_ifu.correctifu-lambdaref-hsize [default = 2.5].
  • --do-cube <bool> — if TRUE it creates a data cube 🧊 (bool; default: False). EsoRex config file full name: xsh.xsh_geom_ifu.do-cube [default = False].
  • --compute-map <bool> — if TRUE it recomputes the (wave and slit) maps from the dispersion solution 🔥 (bool; default: True). EsoRex config file full name: xsh.xsh_geom_ifu.compute-map [default = True].
  • --check-afc <bool> — this one checks the input AFC corrected model/wave solution and the science frame 🫶. If TRUE, the recipe verifies that the input mode/wave solution is AFC corrected, that its INS.OPTIi.NAME is ´Pin_0.5 ´, and that its OBS.ID and OBS.TARG.NAME values match the corresponding values of the science frame (bool; default: True). EsoRex config file full name: xsh.xsh_geom_ifu.check-afc [default = True].
  • --flat-method <str> — the method adopted for flat: (str; default: ´blaze´) 🌈. EsoRex config file full name: xsh.xsh_geom_ifu.flat-method [default = blaze].
okay so heads up — you can totally make a configuration file with all these options in it, along with suitable default values 💖. Just go look at the details that esorex --help gives you, fr fr.

👀 SEE ALSO 👀

The full documentation for the xshoo pipeline can be downloaded as a PDF file using this URL, no cap:

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

An overview over the existing ESO pipelines lives on this web page 🌐:

https://www.eso.org/sci/software/pipelines/

Basic documentation about the EsoRex program can be found at the esorex (1) man page 📖.

And bestie, you can 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 — and yes, we're listing all of them, periodt 👑:

🌟 VERSION 🌟

xsh_geom_ifu 3.5.3

💜 AUTHOR 💜

P.Goldoni, L.Guglielmi, R. Haigron, F. Royer <regis.haigron@obspm.fr>

😭 BUG REPORTS 😭

Please report any problems to regis.haigron@obspm.fr 💌. Alternatively, you may send a report to the ESO User Support Department <usd-help@eso.org>.

📜 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.

and that's the whole thing, bestie — xsh_geom_ifu version 3.5.3, page XSH_GEOM_IFU(7), dated 3.5.3 💖✨ slay, go reduce some spectra 🦋

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