VISIR_OLD_SPC_PHOT_ECH(7)

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

🦋 VISIR_OLD_SPC_PHOT_ECH(7) 🦋

okay bestie, welcome to the visir recipes corner of the manpage universe 💖 this is VISIR_OLD_SPC_PHOT_ECH(7) and she is LONG so buckle up, we're doing this in parts. Part 1 starts now, no skips, no shortcuts, every single flag is coming with us 🫶

🌟 NAME 🌟

visir_old_spc_phot_ech — Old DRS detector: Sensitivity computation in echelle spectroscopy ✨

🌈 SYNOPSIS 🌈

esorex visir_old_spc_phot_ech [OPTIONS] FILE.sof

periodt. that's the whole vibe 💅

🎀 DESCRIPTION 🎀

so like, here's what this recipe actually does, and she does three whole things:

  • She estimates the dispersion relation using the atmospheric spectrum in a echelle spectroscopy half-cycle frame. iconic behaviour honestly 🔥
  • She also extracts the spectrum of an observed object using a combined frame.
  • And lastly, she computes the spectral photometry of an observed standard star. queen shit 👑

now the important part — the files in your Set Of Frames (sof-file) must be tagged like this, no exceptions bestie:

  • VISIR-Echelle-Spectroscopy-file.fits → SPEC_CAL_PHOT_HRG
  • VISIR-Quantum-Efficiency-Calibration-file.fits → SPEC_CAL_QEFF
  • VISIR-Atmospheric-Emission-Lines-Calibration-file.fits → SPEC_CAL_LINES
  • VISIR-Spectroscopic-Standard-Star-Catalog.fits → SPEC_STD_CATALOG

and ALSO 💜 — a bad pixel map with a PRO.CATG of SPEC_BPM may be added to the Set Of Frames with tag: BPM. optional but cute, y'know?

✨ OPTIONS ✨

okay this is the main event, the whole menu, every single one, let's GO 🍓

  • --nod <str> — an optional ASCII specification of the nodding positions, for when they're just missing from the FITS-file (rude of them honestly). The file must consist of one line per input FITS-file, and each line must consist of an integer (which is ignored, she's just there for decoration 💀) followed by a 0 or 1 to indicate object or sky. (str; default: ´NONE´). The full name of this option for the EsoRex configuration file is visir.visir_old_spc_phot_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_phot_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_phot_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. yeah, triple-threat misbehaviour gets the boot 🙈 (bool; default: False). The full name of this option for the EsoRex configuration file is visir.visir_old_spc_phot_ech.purge_bad [default = False].
  • --union <bool> — combine images using their union, as opposed to their intersection. deprecated and ignored, see --combine_method — so like, she's still here, she still has a default, but she's not doing anything, she's just vibing 💀 (bool; default: True). The full name of this option for the EsoRex configuration file is visir.visir_old_spc_phot_ech.union [default = True].
  • --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 specifies 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 specifies that for each pixel the largest n2 pixel values shall be ignored in the averaging. so you're literally just yeeting the extremes 🗑️ (str; default: ´0-0´). The full name of this option for the EsoRex configuration file is visir.visir_old_spc_phot_ech.rej [default = 0-0].
  • --plot <int> — the recipe can produce a number of predefined plots. Zero means that none of the plots are produced, while increasing values (e.g. 1 or 2) increases the number of plots produced. If the plotting fails a warning is produced, and the recipe continues. The default behaviour of the plotting is to use gnuplot (with option -persist). The recipe currently produces 1D-plots using gnuplot commands. 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_phot_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_phot_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_phot_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_phot_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_phot_ech.delta [default = 0.0].
  • --orderoffset <int> — Echelle order offset. The offset is relative to the main order. The allowed range of offsets depend 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. so it's giving "pick your lane, wavelength-wise" 🌀 (int; default: 0). The full name of this option for the EsoRex configuration file is visir.visir_old_spc_phot_ech.orderoffset [default = 0].
  • --off <str> — an optional ASCII specification of the offsets in case those in 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_phot_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_phot_ech.refine [default = False].
  • --objs <str> — the shift and add of images needs anchor points that typically are 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 with 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_phot_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 is 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_phot_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. so like… faster, but worse. your call bestie 💅 (bool; default: False). The full name of this option for the EsoRex configuration file is visir.visir_old_spc_phot_ech.fixcombi [default = False].
  • --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_phot_ech.emis_tol [default = 1.0].
  • --destripe_iterations <int> — Max number of destriping iterations (0 to disable destriping). Horizontal destriping is done first and if no horizontal striping is detected, vertical destriping is performed. stripes? not on her watch 🧚 (int; default: 15). The full name of this option for the EsoRex configuration file is visir.visir_old_spc_phot_ech.nstripe [default = 15].

and that's the options section DONE, you ate that 💖 but bestie we are not done, there's more coming in part 2, so don't go anywhere 🌸

  • --destripe_morpho <bool> — destripe but make it morphological cleaning ✨ (bool; default: False). EsoRex config file name: visir.visir_old_spc_phot_ech.mstripe [default = False].
  • --rl <int> — reject the leftmost columns during spectrum extraction. Zero means all the columns on the left stay in the party (pixel) (int; default: 0). Also, in cross-dispersion mode you're allowed to use a (small) negative number, no cap. EsoRex config file name: visir.visir_old_spc_phot_ech.reject_left [default = 0].
  • --rr <int> — reject the rightmost columns during spectrum extraction. Zero means all the columns on the right are kept (pixel) (int; default: 0). And same deal in cross-dispersion mode — a (small) negative number is fair game. EsoRex config file name: visir.visir_old_spc_phot_ech.reject_right [default = 0].
  • --ro_noise <float> — readout noise of the detector (float; default: 14.5). EsoRex config file name: visir.visir_old_spc_phot_ech.ron [default = 14.5].
  • --ox_sigma <float> — the sigma used for clipping in optimal extraction (float; default: 5.0). EsoRex config file name: visir.visir_old_spc_phot_ech.optex_sigma [default = 5.0].
  • --ox_niters <int> — how many optimal extraction iterations we're doing, bestie (int; default: 2). EsoRex config file name: visir.visir_old_spc_phot_ech.optex_niters [default = 2].
  • --ox_smooth <int> — width of the smoothing window used along the spectral dimension during optimal extraction. It's a median filter, periodt (int; default: 31). EsoRex config file name: visir.visir_old_spc_phot_ech.optex_smooth [default = 31].
  • --gain <float> — detector gain (float; default: 0.75). EsoRex config file name: visir.visir_old_spc_phot_ech.gain [default = 0.75].
  • --ox_kernel <int> — size of the square smoothing kernel, in pixels, applied to the science frame before optimal extraction. Median filter again. And heads up: this one gets ignored during aperture extraction 🙈 (int; default: 3). EsoRex config file name: visir.visir_old_spc_phot_ech.optex_kernel [default = 3].
Okay so like — yes, you can build a whole configuration file out of these options with cute default values baked in. But pls go read what esorex --help has to say first, it's got the details. 💖

🌈 SEE ALSO 🌈

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

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

There's also a whole overview of the existing ESO pipelines on this web page:

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

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

And get this — you can call the pipelines from python using the python-cpl package 🐍✨. Go look at https://packages.python.org/python-cpl/index.html for more info.

The other recipes of the visir pipeline, in all their iconic glory, are:

  • visir_img_dark(7)
  • visir_img_ff(7)
  • visir_img_reduce(7)
  • visir_img_trans(7)
  • visir_old_img_combine(7)
  • visir_old_img_phot(7)
  • visir_old_spc_obs(7)
  • visir_old_spc_obs_ech(7)
  • visir_old_spc_phot(7)
  • visir_old_spc_wcal(7)
  • visir_old_spc_wcal_ech(7)
  • visir_old_util_destripe(7)
  • visir_spc_reduce(7)
  • visir_util_apply_calib(7)
  • visir_util_clip(7)
  • visir_util_convert_weight(7)
  • visir_util_detect_shift(7)
  • visir_util_img_std_cat(7)
  • visir_util_join(7)
  • visir_util_qc(7)
  • visir_util_repack(7)
  • visir_util_run_swarp(7)
  • visir_util_spc_std_cat(7)
  • visir_util_spc_txt2fits(7)
  • visir_util_undistort(7)

🎀 VERSION 🎀

visir_old_spc_phot_ech 4.4.2

👑 AUTHOR 👑

Lars Lundin <https://support.eso.org> — actual legend, we stan 🫶

💌 BUG REPORTS 💌

If something's acting up, pls report it to https://support.eso.org. Or if you'd rather, you can send a report to the ESO User Support Department <usd-help@eso.org>. They're nice, fr fr, don't be shy.

📜 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, bestie — that's the whole point of it.

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 page, babe 💅 — visir_old_spc_phot_ech version 4.4.2, dated with all the 4.4.2 energy, from the VISIR_OLD_SPC_PHOT_ECH(7) manual family. Go extract some spectra, you absolute main character 🌟🦋

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