GISCIENCE(7)

📦
version 2.16.10 · 2 versions
, in debian bookworm, ubuntu noble

💖 GISCIENCE(7) 💖

okay so bestie, welcome to giscience(7) — straight out of the giraf recipes section of the manual, and yes, we're doing this. this page is a whole journey, so buckle up. 🦋

🌸 NAME 🌸

giscience — Process a science observation.

like. that's the whole job. process a science observation. iconic behavior. 👑

✨ SYNOPSIS ✨

esorex giscience [OPTIONS] FILE.sof

that's it, that's the summoning ritual. esorex, then giscience, then your options, then your .sof file. periodt. 💅

🎀 DESCRIPTION 🎀

so for the detailed info, bestie, you gotta go read the GIRAFFE pipeline user manual. it's giving "the real lore lives elsewhere" and honestly? valid.

it lives at http://www.eso.org/pipelines. go get it. 🫶

🔥 OPTIONS 🔥

okay this is the big one. every single flag, every default, every EsoRex config-file name. no skipping. let's GO. 🏃‍♀️💨

  • --remove-bias <bool> — turns bias removal on or off. it's a bool, default True. the full name of this option for the EsoRex configuration file is giraffe.biasremoval.remove [default = True].
  • --bsremove-method <str> — the bias removal method. it's a str, default PROFILE. the full name of this option for the EsoRex configuration file is giraffe.biasremoval.method [default = PROFILE].
  • --bsremove-areas <str> — which bias areas to use, formatted like Xl0:Xr0:Yl0:Yr0, ... ,Xln:Xrn:Yln:Yrn. it's a str, default 5:40:0:4095. the full name of this option for the EsoRex configuration file is giraffe.biasremoval.areas [default = 5:40:0:4095].
  • --bsremove-sigma <float> — sigma clipping: the sigma threshold factor. it's a float, default 2.5. the full name of this option for the EsoRex configuration file is giraffe.biasremoval.sigma [default = 2.5].
  • --bsremove-niter <int> — sigma clipping: max number of iterations. it's an int, default 5. the full name of this option for the EsoRex configuration file is giraffe.biasremoval.iterations [default = 5].
  • --bsremove-mfrac <float> — sigma clipping: minimum fraction of points accepted over total, in the range [0.0..1.0]. it's a float, default 0.8. the full name of this option for the EsoRex configuration file is giraffe.biasremoval.fraction [default = 0.8].
  • --bsremove-xorder <int> — order of the X polynomial fit (CURVE method only, bestie, don't forget). it's an int, default 1. the full name of this option for the EsoRex configuration file is giraffe.biasremoval.xorder [default = 1].
  • --bsremove-yorder <int> — order of the Y polynomial fit (again, CURVE method only). it's an int, default 1. the full name of this option for the EsoRex configuration file is giraffe.biasremoval.yorder [default = 1].
  • --bsremove-xstep <int> — sampling step along X (CURVE method only). it's an int, default 1. the full name of this option for the EsoRex configuration file is giraffe.biasremoval.xstep [default = 1].
  • --bsremove-ystep <int> — sampling step along Y (CURVE method only). it's an int, default 1. the full name of this option for the EsoRex configuration file is giraffe.biasremoval.ystep [default = 1].

🌈 extraction era 🌈

  • --extr-method <str> — the extraction method: SUM, HORNE or OPTIMAL. it's a str, default SUM. the full name of this option for the EsoRex configuration file is giraffe.extraction.method [default = SUM].
  • --extr-ron <float> — new bias sigma (RON) value for the bias- and dark-corrected image. it's a float, default -1.0. the full name of this option for the EsoRex configuration file is giraffe.extraction.ron [default = -1.0].
  • --extr-psfmodel <str> — the PSF profile model: psfexp, psfexp2. it's a str, default psfexp2. the full name of this option for the EsoRex configuration file is giraffe.extraction.psf.model [default = psfexp2].
  • --extr-psfsigma <float> — sigma clipping threshold used for rejecting data points during PSF fitting (Horne's sigma). it's the one that rejects bad pixels and cosmics, bestie — lowkey a bouncer. it's a float, default 7.0. the full name of this option for the EsoRex configuration file is giraffe.extraction.psf.sigma [default = 7.0].
  • --extr-psfniter <int> — max number of iterations used for fitting the PSF profile. it's an int, default 2. the full name of this option for the EsoRex configuration file is giraffe.extraction.psf.iterations [default = 2].
  • --extr-hewidth <int> — Horne extraction method: number of extra pixels added to the fiber half-width. it's an int, default 2. the full name of this option for the EsoRex configuration file is giraffe.extraction.horne.extrawidth [default = 2].
  • --extr-hmingood <int> — Horne extraction method: minimum number of points used for the profile fit. it sets the lower limit of data points for the pixel rejection. it's an int, default 3. the full name of this option for the EsoRex configuration file is giraffe.extraction.horne.mingood [default = 3].
  • --extr-omfrac <float> — optimal extraction method: minimum fraction of the data points used for fitting the fiber profiles. it sets the lower limit for the pixel rejection. it's a float, default 0.9. the full name of this option for the EsoRex configuration file is giraffe.extraction.optimal.fraction [default = 0.9].
  • --extr-owfactor <float> — optimal extraction method: the factor you multiply the fiber PSF half width by. adjacent spectra inside this area are assumed to affect the spectrum being extracted. it's a float, default 3.0. the full name of this option for the EsoRex configuration file is giraffe.extraction.optimal.wfactor [default = 3.0].
  • --extr-obkgorder <int> — optimal extraction method: order of the polynomial background model, which gets fitted for each wavelength bin along the spatial direction. it's an int, default 2. the full name of this option for the EsoRex configuration file is giraffe.extraction.optimal.bkgorder [default = 2].

🧚 flat field & transmission 🧚

  • --flat-apply <bool> — controls the flat field correction. it's a bool, default True. the full name of this option for the EsoRex configuration file is giraffe.flat.apply [default = True].
  • --transmission-apply <bool> — controls the fiber-to-fiber transmission correction. it's a bool, default False. the full name of this option for the EsoRex configuration file is giraffe.flat.transmission [default = False].

⭐ rebinning vibes ⭐

  • --rbin-method <str> — the method to use: linear or spline. it's a str, default linear. the full name of this option for the EsoRex configuration file is giraffe.rebinning.method [default = linear].
  • --rbin-xresid <bool> — use x residuals during rebinning? true/false. it's a bool, default True. the full name of this option for the EsoRex configuration file is giraffe.rebinning.xresiduals [default = True].
  • --rbin-lstep <float> — lambda step size, and heads up bestie: it's only used if the scaling method is linear. it's a float, default 0.005. the full name of this option for the EsoRex configuration file is giraffe.rebinning.lstep [default = 0.005].
  • --rbin-scmethod <str> — the scaling method: log or linear. it's a str, default linear. the full name of this option for the EsoRex configuration file is giraffe.rebinning.scalemethod [default = linear].
  • --rbin-size <int> — size of the output rebinned spectra. 0 means "calculate the size based on wavelength range and lambda stepsize", so it's the ✨do it yourself✨ option. it's an int, default 0. the full name of this option for the EsoRex configuration file is giraffe.rebinning.size [default = 0].
  • --rbin-range <str> — the rebinning range: setup or common. it's a str, default setup. the full name of this option for the EsoRex configuration file is giraffe.rebinning.range [default = setup].

🫶 simultaneous wavelength calibration 🫶

  • --siwc-apply <bool> — enable simultaneous wavelength calibration correction. it's a bool, default True. the full name of this option for the EsoRex configuration file is giraffe.siwc.apply [default = True].

👑 slit geometry calibration 👑

  • --scal-cniter <int> — slit geometry calibration maximum number of iterations. it's an int, default 1. the full name of this option for the EsoRex configuration file is giraffe.sgcalibration.iterations [default = 1].
  • --scal-zmax <float> — maximum allowed pixel value. > to actually do anything it has to be larger than 0, so don't come in with a 0 and expect magic, bestie. it's a float, default 10000.0. the full name of this option for the EsoRex configuration file is giraffe.sgcalibration.zmax [default = 10000.0].
  • --scal-cstep <float> — cross-correlation step. it's a float, default -0.005. the full name of this option for the EsoRex configuration file is giraffe.sgcalibration.cc.step [default = -0.005].
  • --scal-cdomain <str> — restricts the cross-correlation to the given domain. it's a str, default 0.,0.. the full name of this option for the EsoRex configuration file is giraffe.sgcalibration.cc.domain [default = 0.,0.].
  • --scal-rvlimits <str> — delta RV limits of the cross-correlation window, in km/s. it's a str, default -200.,200.. the full name of this option for the EsoRex configuration file is giraffe.sgcalibration.rv.limits [default = -200.,200.].
  • --scal-rvniter <int> — maximum number of iterations used for the RV determination. it's an int, default 3. the full name of this option for the EsoRex configuration file is giraffe.sgcalibration.rv.iterations [default = 3].
  • --scal-rvwfactor <float> — data window width factor. the FWHM times this value is what determines the window width. it's a float, default 1.5. the full name of this option for the EsoRex configuration file is giraffe.sgcalibration.rv.wfactor [default = 1.5].
  • --scal-pfniter <int> — peak model fit maximum number of iterations. it's an int, default 50. the full name of this option for the EsoRex configuration file is giraffe.sgcalibration.peak.iterations [default = 50].
  • --scal-pfntest <int> — cross-correlation peak fit maximum number of tests. it's an int, default 7. the full name of this option for the EsoRex configuration file is giraffe.sgcalibration.peak.tests [default = 7].
  • --scal-pfdchisq <float> — cross-correlation peak fit minimum chi-square difference. it's a float, default 0.0001. the full name of this option for the EsoRex configuration file is giraffe.sgcalibration.peak.dchisquare [default = 0.0001].

🍓 image reconstruction 🍓

  • --recon-min <float> — minimum wavelength for image reconstruction. it's a float, default 0.0. the full name of this option for the EsoRex configuration file is giraffe.fov.range.minimum [default = 0.0].
  • --recon-max <float> — maximum wavelength for image reconstruction. it's a float, default 0.0. the full name of this option for the EsoRex configuration file is giraffe.fov.range.maximum [default = 0.0].

okay bestie, we are SO not done — that's just part one and the rest is still loading in the group chat… 💜✨

okay bestie, we're still deep in OPTIONS, last little batch, don't scroll away 💅

  • --recon-cube <bool> — turns data cube creation on and off (bool; default: True). The full name of this option for the EsoRex configuration file is giraffe.fov.cube [default = True]. ✨ iconic toggle energy ✨
  • --recon-format <str> — selects the file format for cubes (str; default: ´single´). The full name of this option for the EsoRex configuration file is giraffe.fov.cube.format [default = single]. cube format, but make it fashion 💜
  • --generate-SDP-format <bool> — TRUE if additional files should be generated in Science Data Product (SDP) format. (bool; default: False). The full name of this option for the EsoRex configuration file is giraffe.sdp.format.generate [default = False]. science data product moment 🧚
  • --dummy-association-keys <int> — sets the number of dummy (empty) ASSONi, ASSOCi and ASSOMi keywords to create. (int; default: 0). The full name of this option for the EsoRex configuration file is giraffe.sdp.nassoc.keys [default = 0]. keyword goblin behavior, honestly 👑
also just so you know: 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 giraf pipeline can be downloaded as a PDF file using the following URL:

ftp://ftp.eso.org/pub/dfs/pipelines/giraffe/giraf-pipeline-manual-2.11.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 giraf pipeline are giframestack(7), gimasterbias(7), gimasterdark(7), gimasterflat(7), gistandard(7), giwavecalibration(7). 💖

👑 VERSION 👑

giscience 2.16.10 — periodt. 💅

💖 AUTHOR 💖

Giraffe Pipeline <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>. they will help you, bestie, no cap 💌

🌈 LICENSE 🌈

This file is part of the GIRAFFE Instrument Pipeline Copyright (C) 2002-2014 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 02110-1301 USA.

and that's the whole manual page, bestie ✨ source/version: giscience 2.16.10, manual section: GISCIENCE(7). mwah 💋

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