VISIR_OLD_SPC_OBS(7)

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

💖 VISIR_OLD_SPC_OBS(7) — visir recipes 💖

🌸 NAME 🌸

visir_old_spc_obs — Old DRS detector: Spectroscopic Observation recipe

✨ SYNOPSIS ✨

esorex visir_old_spc_obs [OPTIONS] FILE.sof

💅 DESCRIPTION 💅

Okay bestie, this recipe is doing two big things. First, it estimates the dispersion relation using the atmospheric spectrum in a long-slit spectroscopy half-cycle frame. Second, it extracts the spectrum of an observed object using a combined frame. Slay.

The files listed in the Set Of Frames (sof-file) must be tagged:

  • VISIR-Long-Slit-Spectroscopy-file.fits SPEC_OBS_LMR
  • VISIR-Quantum-Efficiency-Calibration-file.fits SPEC_CAL_QEFF
  • VISIR-Atmospheric-Emission-Lines-Calibration-file.fits SPEC_CAL_LINES

Additionally, a bad pixel map with a PRO.CATG of SPEC_BPM may be added to the Set Of Frames with tag: BPM.

🎀 OPTIONS 🎀

  • --nod <str> — An optional ASCII specification of the nodding positions (in case they are missing from the FITS-file). The file must consist of one line per input FITS-file and each line must consist of an integer (which is ignored) 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_obs.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.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.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.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.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. (str; default: ´0-0´). The full name of this option for the EsoRex configuration file is visir.visir_old_spc_obs.rej [default = 0-0].
  • --bkgcorrect <bool> — Subtract the median from the spectral column before extracting the wavelength. This is required when the skylines do not 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.bkgcorrect [default = True].
  • --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_obs.plot [default = 0].
  • --slit_skew <float> — Distortion correction: Skew of slit (degrees) (clockwise) (float; default: 0.52). The full name of this option for the EsoRex configuration file is visir.visir_old_spc_obs.phi [default = 0.52].
  • --spectrum_skew <float> — Distortion correction: LMR Skew of spectrum (degrees) (counter-clockwise). Not used in High Resolution (float; default: 1.73). The full name of this option for the EsoRex configuration file is visir.visir_old_spc_obs.ksi [default = 1.73].
  • --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: -0.8). The full name of this option for the EsoRex configuration file is visir.visir_old_spc_obs.eps [default = -0.8].
  • --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.delta [default = 0.0].
  • --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_obs.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.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_obs.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_obs.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.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_obs.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 (int; default: 15). The full name of this option for the EsoRex configuration file is visir.visir_old_spc_obs.nstripe [default = 15].
  • --destripe_morpho <bool> — Destripe with morphological cleaning (bool; default: False). The full name of this option for the EsoRex configuration file is visir.visir_old_spc_obs.mstripe [default = False].
  • --rl <int> — Reject leftmost columns in spectrum extraction, zero means all columns on the left are used. In cross-dispersion mode a (small) negative number may be used (pixel) (int; default: 0). The full name of this option for the EsoRex configuration file is visir.visir_old_spc_obs.reject_left [default = 0].
  • --rr <int> — reject the rightmost columns when it's extracting a spectrum. If it's 0, that means all the columns on the right get used, no cap. And okay this is the fun part: in cross-dispersion mode you can lowkey throw a negative number in here, in pixels. 💅 (int; default: 0). The full name of this option for the EsoRex configuration file is visir.visir_old_spc_obs.reject_right [default = 0].
  • --apfile <str> — an optional ASCII file spec of the aperture definitions to use during spectral extraction. Bestie, the format matters so listen up ✨: every line has to contain either 3 fields (that's for optimal extraction) or an even number of fields greater than 5 (that's for aperture extraction). For optimal extraction the 1st field should be ´O´, and for aperture extraction it should be ´A´. Either way, the next pair of fields tells you the left & right edges of the source aperture in pixel coordinates. Now for aperture extraction specifically, everything after the 3rd field defines the sky aperture coordinates — the 4th field says which method is used to figure out the sky background, and it's one of ´A´ (average), ´F´ (linear fit), or ´M´ (median) — followed by at least one pair of pixel coordinates giving the left & right edge of a sky aperture. Want more sky apertures? Just keep adding pixel coordinate pairs after the first one. Multiple lines targeting the same order are allowed. 🫶 (str; default: ´NONE´). The full name of this option for the EsoRex configuration file is visir.visir_old_spc_obs.apfile [default = NONE].
  • --ro_noise <float> — the readout noise of the detector. That's it, that's the whole vibe. (float; default: 14.5). The full name of this option for the EsoRex configuration file is visir.visir_old_spc_obs.ron [default = 14.5].
  • --ox_sigma <float> — the sigma to use for clipping during optimal extraction. Clipping? Sigma? She's precise. (float; default: 5.0). The full name of this option for the EsoRex configuration file is visir.visir_old_spc_obs.optex_sigma [default = 5.0].
  • --ox_niters <int> — how many optimal extraction iterations to perform. Rinse and repeat, girlie. 🔁 (int; default: 2). The full name of this option for the EsoRex configuration file is visir.visir_old_spc_obs.optex_niters [default = 2].
  • --ox_smooth <int> — the width of the smoothing window to use along the spectral dimension during optimal extraction. Heads up: a median filter is what's doing the smoothing here. (int; default: 31). The full name of this option for the EsoRex configuration file is visir.visir_old_spc_obs.optex_smooth [default = 31].
  • --gain <float> — the detector gain. Simple. Iconic. (float; default: 0.75). The full name of this option for the EsoRex configuration file is visir.visir_old_spc_obs.gain [default = 0.75].
  • --ox_kernel <int> — the size of the square smoothing kernel, in pixels, applied to the science frame before optimal extraction. And nope, this one is ignored during aperture extraction, so don't come for me. A median filter is used, as always. (int; default: 3). The full name of this option for the EsoRex configuration file is visir.visir_old_spc_obs.optex_kernel [default = 3].
  • --respcal <str> — an optional path to a FITS file holding a 1-D fringe model, which gets divided into the 1-D extracted spectra so the fringes get removed. Fringe? Never heard of her. ✨ (str; default: ´NONE´). The full name of this option for the EsoRex configuration file is visir.visir_old_spc_obs.respcal [default = NONE].
Okay so real talk 💖 — you can 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 visir pipeline can be downloaded as a PDF file using the following URL:

ftp://ftp.eso.org/pub/dfs/pipelines/visir/visir-pipeline-manual-1.4.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 visir pipeline 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_ech(7), visir_old_spc_phot(7), visir_old_spc_phot_ech(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_obs 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 page, bestie 🥹✨ — this cutie is visir_old_spc_obs 4.4.2, dated 4.4.2 in the footer, and she's all yours now. Go extract some spectra and slay 💅💖

📦 where this page comes from