XSH_LINGAIN(7)

📦 version 3.5.3, in ubuntu jammy, ubuntu noble

💖 XSH_LINGAIN 💖

okay bestie, welcome to the xsh_lingain page from the xshoo recipes manual (that's the XSH_LINGAIN(7) one, section 7, iykyk). it computes the detector's gain and linearity map. yes it's a whole thing. yes we're gonna get through it together. grab a snack 🍓

✨ NAME ✨

xsh_lingain — Computes detector's gain/linearity-map. that's it, that's the job, no cap 💅

🌸 SYNOPSIS 🌸

esorex xsh_lingain [OPTIONS] FILE.sof

🦋 DESCRIPTION 🦋

so this recipe computes the detector linearity coefficients and the gain. that's the whole main character arc right there.

📥 Input Frames 📥

arm = UVB-VIS:

  • a set of n RAW linearity frames (Format=RAW, n >=8, Tag = LINEARITY_arm_ON)
  • a set of n RAW bias frames (Format=RAW, n >=1, Tag = LINEARITY_arm_OFF)

arm = NIR:

  • a set of n RAW linearity on frames (Format=RAW, n >=8, Tag = LINEARITY_arm_ON)
  • a set of n RAW linearity off frames (Format=RAW, n >=8, Tag = LINEARITY_arm_OFF)
  • [OPTIONAL] a static bad pixel map (PRO.CATG=BP_MAP_RP_arm)
note bestie: on and off frames are taken in pairs sequence — OFF-ON-ON-OFF, at least 16 frames. don't freestyle this, the pairs matter fr fr.

📤 Products 📤

  • a linearity map table, PRO.CATG = BP_MAP_LIN_NIR
  • a gain table, PRO.CATG = GAIN_INFO
  • a cube cointaining the linearity coefficients, PRO.CATG = COEFFS_CUBE_arm
  • a linearity map image (RAW format), PRO.CATG = RAW_BP_MAP_NL_arm
  • a linearity map image (PRE format), PRO.CATG = BP_MAP_NL_arm

(yes, "cointaining" — that's how the original spells it, we don't edit the lore ✨)

💅 OPTIONS 💅

this is the long part and honestly? iconic of it. every single one, in order, here we go 🫶

  • --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_lingain.keep-temp [default = no].
  • --debug-level <str> — extra 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_lingain.debug-level [default = none].
  • --time-stamp <bool> — add a timestamp to the product file name. (bool; default: False). the full name of this option for the EsoRex configuration file is xsh.xsh_lingain.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 most frequent codes relevant for the user are: 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_lingain.decode-bp [default = 2144337919].
  • --method <str> — the method to be used when computing GAIN. methods appliable: <PTC | MED>. by default the PTC method will be applied. (str; default: PTC). the full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.method [default = PTC].
  • --order <int> — polynomial order for the fit (Linearity) (int; default: 3). the full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.order [default = 3].
  • --kappa <float> — kappa value for the kappa-sigma clipping (Gain) (float; default: 3.0). the full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.kappa [default = 3.0].
  • --niter <int> — number of iterations to compute rms (Gain) (int; default: 5). the full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.niter [default = 5].
  • --llx <int> — x coordinate of the lower-left point of the region of interest. if not modified, the default value will be 1. (int; default: -1). the full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.llx [default = -1].
  • --lly <int> — y coordinate of the lower-left point of the region of interest. if not modified, the default value will be 1. (int; default: -1). the full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.lly [default = -1].
  • --urx <int> — x coordinate of the upper-right point of the region of interest. if not modified, the default value will be the X dimension of the input image. (int; default: -1). the full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.urx [default = -1].
  • --ury <int> — y coordinate of the upper-right point of the region of interest. if not modified, the default value will be the Y dimension of the input image. (int; default: -1). the full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.ury [default = -1].
  • --ref_level <int> — user reference level (int; default: 10000). the full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.ref_level [default = 10000].
  • --intermediate <bool> — de-/activate intermediate products (bool; default: False). the full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.intermediate [default = False].
  • --autocorr <bool> — de-/activate the autocorr option (bool; default: False). the full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.autocorr [default = False].
  • --collapse <bool> — de-/activate the collapse option (bool; default: True). the full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.collapse [default = True].
  • --rescale <bool> — de-/activate the image rescale option (bool; default: True). the full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.rescale [default = True].
  • --pix2pix <bool> — de-/activate the computation with pixel to pixel accuracy (bool; default: True). the full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.pix2pix [default = True].
  • --bpmbin <bool> — de-/activate the binary bpm option (bool; default: False). the full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.bpmbin [default = False].
  • --m <int> — maximum x-shift for the autocorr (int; default: 26). the full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.m [default = 26].
  • --filter <int> — upper limit of Median flux to be filtered (int; default: -1). the full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.filter [default = -1].
  • --n <int> — maximum y-shift for the autocorr (int; default: 26). the full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.n [default = 26].
  • --tolerance <float> — tolerance for pair discrimination (float; default: 0.1). the full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.tolerance [default = 0.1].
  • --pafgen <bool> — generate PAF file (bool; default: False). the full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.pafgen [default = False].
  • --pafname <str> — specific name for PAF file (str; default: xsh_lingain). the full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.pafname [default = xsh_lingain].
  • --exts <int> — activate the multi-exts option. choose -1 to process all extensions. choose an extension number to process the appropriate extension. (int; default: 0). the full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.exts [default = 0].
  • --fpn_method <str> — method for computing Fixed Pattern Noise (SMOOTH or HISTOGRAM) (str; default: HISTOGRAM). the full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.fpn_method [default = HISTOGRAM].
  • --fpn_smooth <int> — template size in pixels for smoothing during FPN computation (only for the SMOOTH method) (int; default: 13). the full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.fpn_smooth [default = 13].
  • --saturation_limit <float> — all frames with mean saturation above the limit would not be used in linearity calculation (float; default: 65535.0). the full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.saturation_limit [default = 65535.0].
  • --gain_threshold <float> — all frames with mean flux above the threshold would not be used in gain calculation (float; default: 65535.0). the full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.gain_threshold [default = 65535.0].
  • --coeffs_cube_split <bool> — if TRUE, the recipe writes as many COEFFS_CUBE_Pi (i=0..order) as the value of the order parameter in a separate file (bool; default: False). the full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.coeffs_cube_split [default = False].
  • --llx1 <int> — x coord of the lower-left point of the first field used for contamination measurement. if not modified, the default value will be 1. (int; default: -1). the full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.llx1 [default = -1].
  • --lly1 <int> — y coord of the lower-left point of the first field used for contamination measurement. if not modified, the default value will be 1. (int; default: -1). the full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.lly1 [default = -1].
  • --urx1 <int> — x coord of the upper-right point of the first field used for contamination measurement. if not modified, the default value will be the X dimension of the input image. (int; default: -1). the full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.urx1 [default = -1].
  • --ury1 <int> — y coord of the upper-right point of the first field used for contamination measurement. if not modified, the default value will be the Y dimension of the input image. (int; default: -1). the full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.ury1 [default = -1].
  • --llx2 <int> — x coord of the lower-left point of the second field used for contamination measurement. if not modified, the default value will be 1. (int; default: -1). the full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.llx2 [default = -1].
  • --lly2 <int> — the y coord of the lower-left point of the second field used for contamination measurement. If you don't touch it, the default value will be 1. (int; default: -1). The full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.lly2 [default = -1].
  • --urx2 <int> — the x coord of the upper-right point of the second field used for contamination measurement. If you don't touch it, the default value will be half of the X dimension of the input image. (int; default: -1). The full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.urx2 [default = -1].
  • --ury2 <int> — the y coord of the upper-right point of the second field used for contamination measurement. If you don't touch it, the default value will be half of the Y dimension of the input image. (int; default: -1). The full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.ury2 [default = -1].
  • --llx3 <int> — the x coord of the lower-left point of the third field used for contamination measurement. If you don't touch it, the default value will be 1. (int; default: -1). The full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.llx3 [default = -1].
  • --lly3 <int> — the y coord of the lower-left point of the third field used for contamination measurement. If you don't touch it, the default value will be half of the Y dimension of the input image. (int; default: -1). The full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.lly3 [default = -1].
  • --urx3 <int> — the x coord of the upper-right point of the third field used for contamination measurement. If you don't touch it, the default value will be half of X dimension of the image. (int; default: -1). The full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.urx3 [default = -1].
  • --ury3 <int> — the y coord of the upper-right point of the third field used for contamination measurement. If you don't touch it, the default value will be Y dimension of the image. (int; default: -1). The full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.ury3 [default = -1].
  • --llx4 <int> — the x coord of the lower-left point of the fourth field used for contamination measurement. If you don't touch it, the default value will be half of X dimension of the image. (int; default: -1). The full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.llx4 [default = -1].
  • --lly4 <int> — the y coord of the lower-left point of the fourth field used for contamination measurement. If you don't touch it, the default value will be half of the Y dimension of the input image. (int; default: -1). The full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.lly4 [default = -1].
  • --urx4 <int> — the x coord of the upper-right point of the fourth field used for contamination measurement. If you don't touch it, the default value will be X dimension of the image. (int; default: -1). The full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.urx4 [default = -1].
  • --ury4 <int> — the y coord of the upper-right point of the fourth field used for contamination measurement. If you don't touch it, the default value will be Y dimension of the input image. (int; default: -1). The full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.ury4 [default = -1].
  • --llx5 <int> — the x coord of the lower-left point of the fifth field used for contamination measurement. If you don't touch it, the default value will be half of the X dimension of the input image. (int; default: -1). The full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.llx5 [default = -1].
  • --lly5 <int> — the y coord of the lower-left point of the fifth field used for contamination measurement. If you don't touch it, the default value will be 1. (int; default: -1). The full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.lly5 [default = -1].
  • --urx5 <int> — the x coord of the upper-right point of the fifth field used for contamination measurement. If you don't touch it, the default value will be X dimension of the image. (int; default: -1). The full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.urx5 [default = -1].
  • --ury5 <int> — the y coord of the upper-right point of the fifth field used for contamination measurement. If you don't touch it, the default value will be half of Y dimension of the input image. (int; default: -1). The full name of this option for the EsoRex configuration file is xshoo.xsh_lingain.ury5 [default = -1].

okay bestie, lowkey the most important glow-up here: you can totally make a configuration file containing these options, along with suitable default values. 💅 Please refer to the details provided by the 'esorex --help' command. iykyk 🫶

🌈 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_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) ✨ (the whole friend group fr fr 💖)

🎀 VERSION 🎀

xsh_lingain 3.5.3

👑 AUTHOR 👑

Lander de Bilbao,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>. (they want to help you, bestie, don't be shy 🫶)

📜 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

fr fr, that warranty disclaimer is doing the most — no warranty, no promises, periodt. 💀

and that's a wrap on xsh_lingain, bestie — recipe version 3.5.3, and this page is dated 3.5.3, same energy, no cap. go get that linearity gain, you main character 👑✨

📦 where this page comes from