VISIR_OLD_SPC_OBS_ECH(7)

📦
version 4.4.2 · 2 versions
, in debian bookworm, ubuntu noble

💖 visir_old_spc_obs_ech(7) — visir recipes 💖

okay bestie, this is the manual page for visir_old_spc_obs_ech, and it lives in section 7 of the visir recipes manual. it's a lot, so grab a snack, we're doing this together 🫶

✨ NAME ✨

visir_old_spc_obs_ech — Old DRS detector: Spectroscopic Observation recipe in Echelle mode 🦋

🌈 SYNOPSIS 🌈

esorex visir_old_spc_obs_ech [OPTIONS] FILE.sof

👑 DESCRIPTION 👑

so like, what does this recipe do, you ask? two things, and it's giving multitasker 💅

  • it estimates the dispersion relation using the atmospheric spectrum in a grism spectroscopy half-cycle frame.
  • it also extracts the spectrum of an observed object using a combined frame.

the files you drop into the Set Of Frames (that's your sof-file, bestie) have to be tagged like this:

VISIR-Echelle-Spectroscopy-file.fits SPEC_OBS_HRG
VISIR-Quantum-Efficiency-Calibration-file.fits SPEC_CAL_QEFF
VISIR-Atmospheric-Emission-Lines-Calibration-file.fits SPEC_CAL_LINES

and as a lil bonus: a bad pixel map with a PRO.CATG of SPEC_BPM may also be added to the Set Of Frames, with the tag BPM. 🎀

💅 OPTIONS 💅

okay this is the long part. every single one is here, no skipping, we do not gatekeep in this house ✨
  • --nod <str> — an optional ASCII spec of the nodding positions, for when they're straight-up missing from the FITS-file. the file must have one line per input FITS-file, and each line is an integer (which gets ignored, rude) followed by a 0 or 1 to say object or sky. (str; default: NONE). the full name of this option for the EsoRex configuration file is visir.visir_old_spc_obs_ech.nodding [default = NONE].
  • --auto_bpm <bool> — automatic detection and correction of bad pixels. (bool; default: True). the full name of this option for the EsoRex configuration file is visir.visir_old_spc_obs_ech.auto_bpm [default = True].
  • --g <bool> — automatic filtering of glitches. (bool; default: False). the full name of this option for the EsoRex configuration file is visir.visir_old_spc_obs_ech.rem_glitch [default = False].
  • --p <bool> — automatic purging of half-cycle images whose median deviates more than a factor three from the mean of the medians of half-cycle images, or whose standard deviation deviates more than a factor three from the mean of their standard deviations. (bool; default: False). the full name of this option for the EsoRex configuration file is visir.visir_old_spc_obs_ech.purge_bad [default = False].
  • --union <bool> — combine images using their union, as opposed to their intersection. (deprecated and ignored, see --combine_method) (bool; default: True). the full name of this option for the EsoRex configuration file is visir.visir_old_spc_obs_ech.union [default = True].
💀 heads up: --union is deprecated and ignored — go look at --combine_method instead.
  • --rej <str> — each resulting pixel is the average of the corresponding (interpolated) pixel value in each jittered image. a positive value, n1, for the first of the two integers says that for each pixel the smallest n1 pixel values shall be ignored in the averaging. similarly, a positive value, n2, for the second of the two integers says that for each pixel the largest n2 pixel values shall be ignored in the averaging. (str; default: 0-0). the full name of this option for the EsoRex configuration file is visir.visir_old_spc_obs_ech.rej [default = 0-0].
  • --bkgcorrect <bool> — subtract the median from the spectral column before extracting the wavelength. this is required when the skylines don't correctly cancel due to gratting oscillations. (bool; default: True). the full name of this option for the EsoRex configuration file is visir.visir_old_spc_obs_ech.bkgcorrect [default = True].
  • --plot <int> — the recipe can produce a number of predefined plots. zero means none of the plots are produced, while increasing values (e.g. 1 or 2) increase the number of plots produced. if the plotting fails, a warning is produced and the recipe continues (iconic behaviour, honestly). the default behaviour of the plotting is to use gnuplot (with option -persist). the recipe currently produces 1D-plots using gnuplot commands. you, the recipe user, can control the actual plotting-command used by the recipe to create the plot by setting the environment variable CPL_PLOTTER. currently, if CPL_PLOTTER is set it must contain the string gnuplot. setting it to cat > my_gnuplot_$$.txt causes a number of ASCII-files to be created, which each produce a plot when given as standard input to gnuplot (e.g. later or on a different computer). a finer control of the plotting options can be obtained by writing an executable script, e.g. my_gnuplot.pl, that executes gnuplot after setting the desired gnuplot options (e.g. set terminal pslatex color) and then setting CPL_PLOTTER to my_gnuplot.pl. the predefined plots include plotting of images. images can be plotted not only with gnuplot, but also using the pnm format. this is controlled with the environment variable CPL_IMAGER. if CPL_IMAGER is set to a string that does not contain the word gnuplot, the recipe will generate the plot in pnm format. e.g. setting CPL_IMAGER to display - & will produce a gray-scale image using the image viewer display. (int; default: 0). the full name of this option for the EsoRex configuration file is visir.visir_old_spc_obs_ech.plot [default = 0].
  • --slit_skew <float> — distortion correction: skew of slit (degrees) (clockwise). (float; default: 0.0). the full name of this option for the EsoRex configuration file is visir.visir_old_spc_obs_ech.phi [default = 0.0].
  • --spectrum_skew <float> — distortion correction: LMR skew of spectrum (degrees) (counter-clockwise). not used in High Resolution. (float; default: 0.0). the full name of this option for the EsoRex configuration file is visir.visir_old_spc_obs_ech.ksi [default = 0.0].
  • --vert_arc <float> — distortion correction: LR detector vertical curvature (pixel). reduced by a factor 4 in MR. not used in HR A-side. increased by a factor 115/52 in HR B-side. (float; default: 0.0). the full name of this option for the EsoRex configuration file is visir.visir_old_spc_obs_ech.eps [default = 0.0].
  • --hori_arc <float> — distortion correction: LMR detector horizontal curvature (pixel). increased by a factor 1.5 in HR A-side. reduced by a factor 2 in HR B-side. (float; default: 0.0). the full name of this option for the EsoRex configuration file is visir.visir_old_spc_obs_ech.delta [default = 0.0].
  • --orderoffset <int> — Echelle order offset. the offset is relative to the main order. the allowed range of offsets depends on the selected grism. the offset can never exceed +/-4. if the main order is e.g. 8, an order offset of +1 will cause the recipe to base the data reduction on order 9. with a positive order offset the central wavelength becomes smaller, while for a negative order offset the central wavelength becomes larger. (int; default: 0). the full name of this option for the EsoRex configuration file is visir.visir_old_spc_obs_ech.orderoffset [default = 0].
  • --off <str> — an optional ASCII specification of the offsets, for when the ones in the FITS-headers are missing or wrong. the file must consist of one line per input pair of FITS-files, and each line must consist of two numbers which represent the shift in pixels of that image relative to the first image. the first line should thus comprise two zeros. correct FITS-header offsets mean that the i'th X offset can be gotten from Xoffset_0 - Xoffset_i, where Xoffset_i is the value of ESO SEQ CUMOFFSETX and likewise for Y. (str; default: NONE). the full name of this option for the EsoRex configuration file is visir.visir_old_spc_obs_ech.offsets [default = NONE].
  • --ref <bool> — user-defined refining of the image offsets. see options objs and xcorr. (bool; default: False). the full name of this option for the EsoRex configuration file is visir.visir_old_spc_obs_ech.refine [default = False].
  • --objs <str> — the shift and add of images needs anchor points, which are typically bright objects. these are normally detected automatically, but with user-defined refining of offsets enabled they must be provided by the user through an ASCII file containing one line per anchor point, each line consisting of its x and y coordinate (in pixels). this file is ignored with user-defined refining of offsets disabled. (str; default: NONE). the full name of this option for the EsoRex configuration file is visir.visir_old_spc_obs_ech.objects [default = NONE].
  • --xcorr <str> — if user-defined refining of offsets is enabled, a cross-correlation of the images is performed. in order to speed up this process, this cross-correlation is performed only on smaller rectangles around the anchor points. the first two parameters are the half-size of this rectangle in pixels. the second pair is the maximum shift in x and y (pixels) evaluated by the cross-correlation on the rectangle. used only if user-defined refining of offsets is enabled. (str; default: 10-10-25-25). the full name of this option for the EsoRex configuration file is visir.visir_old_spc_obs_ech.xcorr [default = 10-10-25-25].
  • --fixcombi <bool> — perform the distortion correction on the combined image, and not on each of the jittered images. this will reduce excution time and degrade the quality of the combined image. (bool; default: False). the full name of this option for the EsoRex configuration file is visir.visir_old_spc_obs_ech.fixcombi [default = False].
🙈 yeah, --fixcombi trades quality for speed. it literally says it degrades the combined image. choose wisely, bestie.
  • --emis_tol <float> — the computation of the mean and standard deviation of the sensitivity is done for wavelengths with an atmospheric emissivity of at most emis_min + emis_tol * (emis_max - emis_min), where emis_min is the minimum emissivity in the observed wavelength range and emis_max is the ditto maximum. thus emis_tol = 1 means that all wavelengths are included. (float; default: 1.0). the full name of this option for the EsoRex configuration file is visir.visir_old_spc_obs_ech.emis_tol [default = 1.0].

🌸 and that's part 1, bestie — more is coming, don't go anywhere 🦋

  • --destripe_iterations <int> — max number of destriping iterations. 0 disables destriping completely. Horizontal destriping happens first; if no horizontal striping is detected, vertical destriping is performed. (int; default: 15). EsoRex config name: visir.visir_old_spc_obs_ech.nstripe [default = 15].
  • --destripe_morpho <bool> — destripe with morphological cleaning (bool; default: False). EsoRex config name: visir.visir_old_spc_obs_ech.mstripe [default = False].
  • --rl <int> — reject leftmost columns in spectrum extraction. 0 means all columns on the left are used. In cross-dispersion mode, a (small) negative number may be used (pixel). (int; default: 0). EsoRex config name: visir.visir_old_spc_obs_ech.reject_left [default = 0].
  • --rr <int> — reject rightmost columns in spectrum extraction. 0 means all columns on the right are used. In cross-dispersion mode, a (small) negative number may be used (pixel). (int; default: 0). EsoRex config name: visir.visir_old_spc_obs_ech.reject_right [default = 0].
  • --ro_noise <float> — readout noise of the detector (float; default: 14.5). EsoRex config name: visir.visir_old_spc_obs_ech.ron [default = 14.5].
  • --ox_sigma <float> — sigma to use for clipping in optimal extraction (float; default: 5.0). EsoRex config name: visir.visir_old_spc_obs_ech.optex_sigma [default = 5.0].
  • --ox_niters <int> — number of optimal extraction iterations to perform (int; default: 2). EsoRex config name: visir.visir_old_spc_obs_ech.optex_niters [default = 2].
  • --ox_smooth <int> — width of smoothing window to use along the spectral dimension during optimal extraction. A median filter is used. (int; default: 31). EsoRex config name: visir.visir_old_spc_obs_ech.optex_smooth [default = 31].
  • --gain <float> — detector gain (float; default: 0.75). EsoRex config name: visir.visir_old_spc_obs_ech.gain [default = 0.75].
  • --ox_kernel <int> — size of square smoothing kernel, in pixels, to apply to the science frame before optimal extraction (ignored during aperture extraction). A median filter is used. (int; default: 3). EsoRex config name: visir.visir_old_spc_obs_ech.optex_kernel [default = 3].

Also bestie, yes: you can create a configuration file with these options and suitable default values. The details are in the esorex --help command. periodt. 💖

✨ SEE ALSO ✨

The full documentation for the visir pipeline can be downloaded as a PDF using this URL:

ftp://ftp.eso.org/pub/dfs/pipelines/visir/visir-pipeline-manual-1.4.pdf

An overview of the existing ESO pipelines is on the web page:

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

Basic documentation about the EsoRex program is in the esorex(1) man page.

You can also call the pipelines from python using the python-cpl package. See https://packages.python.org/python-cpl/index.html for more info.

The other recipes of the visir pipeline are:

🌸 VERSION 🌸

visir_old_spc_obs_ech 4.4.2

🎀 AUTHOR 🎀

Lars Lundin <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>.

👑 LICENSE 👑

This file is part of the VISIR Instrument Pipeline Copyright (C) 2004, 2005 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 02111-1307 USA

And that’s the whole vibe, bestie — visir_old_spc_obs_ech 4.4.2, aka VISIR_OLD_SPC_OBS_ECH(7). Slay. 💅✨

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