UVES_OBS_SCIRED(7)

📦
version 6.1.8 · 2 versions
, in debian bookworm, ubuntu noble

UVES_OBS_SCIRED 💅✨

okay bestie, welcome to the uves_obs_scired glow-up — this is section 7 of the manual (a recipe page, iykyk), and it is literally the whole entire vibe of reducing a science frame. grab a strawberry 🍓 and let's go.

🌸 NAME 🌸

uves_obs_scired — Reduces a science frame 💖

✨ SYNOPSIS ✨

esorex uves_obs_scired [OPTIONS] FILE.sof

that's it. that's the whole entrance. esorex runs it, you feed it a .sof file, and she works. 👑

🦋 DESCRIPTION 🦋

so this recipe reduces a science frame — and when I say "a science frame" I mean any one of these girlies: SCIENCE_BLUE or SCIENCE_RED, or SCI_POINT_BLUE or SCI_POINT_RED, or SCI_EXTND_BLUE or SCI_EXTND_RED or SCI_SLICER_BLUE or SCI_SLICER_RED. 💅

she does this using a combination of steps — which ones actually happen depends on the recipe parameters and which input frames you gave her, no cap:

  • bias subtraction,
  • dark subtraction,
  • background subtraction,
  • extraction/cosmic ray removal,
  • flat field correction,
  • wavelength rebinning,
  • sky subtraction,
  • order merging,
  • response correction (if response curve is provided).

additional input for this recipe is: order table(s) for each chip, ORDER_TABLE_xxxx (where xxxx = BLUE, REDL, REDU), line table(s) for each chip, LINE_TABLE_xxxx, a master bias frame, MASTER_BIAS_xxxx, a master flat, MASTER_FLAT_xxxx, optionally an instrument response table, INSTR_RESPONSE_FINE_xxx, optionally an master response table, MASTER_RESPONSE_xxx, and optionally a table describing the atmospheric extinction, EXTCOEFF_TABLE.

for each chip (xxxx = BLUE, REDL, REDU) the recipe produces a combination of these products, and yes she is serving all of them:

  • RED_SCIENCE_xxxx — Reduced science spectrum
  • MERGED_SCIENCE_xxxx — Merged spectrum, no sky subtraction
  • WCALIB_SCIENCE_xxxx — Extracted, wavelength calibrated frame in (wavelength, order) space
  • WCALIB_FF_SCIENCE_xxxx — Extracted, flat-fielded, wave.cal. frame in (wavelength, order) space (Only if flatfielding done)
  • WCALIB_FLAT_OBJ_xxxx — Extracted, wavelength calibrated flat field in (wavelength, order) space (Only if flatfielding done)
  • ERRORBAR_SCIENCE_xxxx — Error bars of RED_SCIENCE_xxxx
  • VARIANCE_SCIENCE_xxxx — Variance of extracted, flatfielded object in (pixel, order) space
  • ORDER_TRACE_xxxx — Table describing the spatial profile
  • FLUXCAL_SCIENCE_xxxx — Flux-calibrated science spectrum
  • FLUXCAL_ERROR_xxxx — Error bars of FLUXCAL_SCIENCE_xxxx
  • BKG_SCI_xxxx — The subtracted background image
  • CRMASK_xxxx — List of cosmic ray hits
  • MERGED_SKY_xxxx — The merged sky spectrum
  • EXT_2D_SCIENCE_xxxx — The 2d extracted spectrum
  • FF2D_SCIENCE_xxxx — The 2d extracted, flat-fielded spectrum
  • WCAL2D_SCIENCE_xxxx — The 2d extracted, flat-fielded, wave.cal. spectrum
  • MER2D_SCIENCE_xxxx — The 2d reduced, flux-calibrated (if possible) science spectrum
okay so like, that's a LOT of output files and honestly? she ate. 🍽️

💖 OPTIONS 💖

one bullet per option, bestie, we are not skipping a single one 🫶

  • --clean_traps <bool> — Clean detector traps. If TRUE detector traps are interpolated. The bad pixels are replaced by the average of thenearest good pixels in the same column, or simply marked as bad. The positions of bad pixels are hard-coded (as function of UVES chip). (bool; default: False). The full name of this option for the EsoRex configuration file is uves_obs_scired.clean_traps [default = False].
  • --debug <bool> — Whether or not to save intermediate results to local directory (bool; default: False). The full name of this option for the EsoRex configuration file is uves.debug [default = False].
  • --plotter <str> — Any plots produced by the recipe are redirected to the command specified by this parameter. The plotting command must contain the substring ´gnuplot´ and must be able to parse gnuplot syntax on its standard input. Valid examples of such a command may include ´gnuplot -persist´ and ´cat > mygnuplot$$.gp´. 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). To turn off plotting, set this parameter to ´no´ (str; default: ´no´). The full name of this option for the EsoRex configuration file is uves.plotter [default = no].
  • --process_chip <str> — For RED arm data process the redl, redu, or both chip(s) (str; default: ´both´). The full name of this option for the EsoRex configuration file is uves.process_chip [default = both].
  • --reduce.backsub.mmethod <str> — Background measuring method. If equal to ´median´ the background is sampled using the median of a subwindow. If ´minimum´, the subwindow minimum value is used. If ´no´, no background subtraction is done. (str; default: ´median´). The full name of this option for the EsoRex configuration file is uves_obs_scired.reduce.backsub.mmethod [default = median].
  • --reduce.backsub.npoints <int> — This is the number of columns in interorder space used to sample the background. (int; default: 82). The full name of this option for the EsoRex configuration file is uves_obs_scired.reduce.backsub.npoints [default = 82].
  • --reduce.backsub.radiusy <int> — The height (in pixels) of the background sampling window is (2*radiusy + 1). This parameter is not corrected for binning. (int; default: 2). The full name of this option for the EsoRex configuration file is uves_obs_scired.reduce.backsub.radiusy [default = 2].
  • --reduce.backsub.sdegree <int> — Degree of interpolating splines. Currently only degree = 1 is supported (int; default: 1). The full name of this option for the EsoRex configuration file is uves_obs_scired.reduce.backsub.sdegree [default = 1].
  • --reduce.backsub.smoothx <float> — If spline interpolation is used to measure the background, the x-radius of the post-smoothing window is (smoothx * image_width). Here, ´image_width´ is the image width after binning. If negative, the default values are used: (25.0/4096) for blue flat-field frames, (50.0/4096) for red flat-field frames, (300.0/4096) for blue science frames and (300.0/4096) for red science frames. (float; default: -1.0). The full name of this option for the EsoRex configuration file is uves_obs_scired.reduce.backsub.smoothx [default = -1.0].
  • --reduce.backsub.smoothy <float> — If spline interpolation is used to measure the background, the y-radius of the post-smoothing window is (smoothy * image_height). Here, ´image_height´ is the image height after binning. If negative, the default values are used: (100.0/2048) for blue flat-field frames, (300.0/2048) for red flat-field frames, (200.0/2048) for blue science frames and (500.0/2048) for red science frames. (float; default: -1.0). The full name of this option for the EsoRex configuration file is uves_obs_scired.reduce.backsub.smoothy [default = -1.0].
  • --reduce.extract.best <bool> — (optimal extraction only) If false (fastest), the spectrum is extracted only once. If true (best), the spectrum is extracted twice, the second time using improved variance estimates based on the first iteration. Better variance estimates slightly improve the obtained signal to noise but at the cost of increased execution time (bool; default: True). The full name of this option for the EsoRex configuration file is uves_obs_scired.reduce.extract.best [default = True].
  • --reduce.extract.chunk <int> — In optimal extraction mode, the chunk size (in pixels) used for fitting the analytical profile (a fit of the analytical profile to single bins would suffer from low statistics). (int; default: 32). The full name of this option for the EsoRex configuration file is uves_obs_scired.reduce.extract.chunk [default = 32].
  • --reduce.extract.kappa <float> — In optimal extraction mode, this is the threshold for bad (i.e. hot/cold) pixel rejection. If a pixel deviates more than kappa*sigma (where sigma is the uncertainty of the pixel flux) from the inferred spatial profile, its weight is set to zero. Range: [-1,100]. If this parameter is negative, no rejection is performed. (float; default: 10.0). The full name of this option for the EsoRex configuration file is uves_obs_scired.reduce.extract.kappa [default = 10.0].
  • --reduce.extract.method <str> — Extraction method. (2d/optimal not supported by uves_cal_wavecal, weighted supported only by uves_cal_wavecal, 2d not supported by uves_cal_response) (str; default: ´optimal´). The full name of this option for the EsoRex configuration file is uves_obs_scired.reduce.extract.method [default = optimal].
  • --reduce.extract.oversample <int> — The oversampling factor used for the virtual resampling algorithm. If negative, the value 5 is used for S/N <=200, and the value 10 is used if the estimated S/N is > 200 (int; default: -1). The full name of this option for the EsoRex configuration file is uves_obs_scired.reduce.extract.oversample [default = -1].
  • --reduce.extract.profile <str> — In optimal extraction mode, the kind of profile to use. ´gauss´ gives a Gaussian profile, ´moffat´ gives a Moffat profile with beta=4 and a possible linear sky contribution. ´virtual´ uses a virtual resampling algorithm (i.e. measures and uses the actual object profile). ´constant´ assumes a constant spatial profile and allows optimal extraction of wavelength calibration frames. ´auto´ will automatically select the best method based on the estimated S/N of the object. For low S/N, ´moffat´ or ´gauss´ are recommended (for robustness). For high S/N, ´virtual´ is recommended (for accuracy). In the case of virtual resampling, a precise determination of the order positions is required; therefore the order-definition is repeated using the (assumed non-low S/N) science frame (str; default: ´auto´). The full name of this option for the EsoRex configuration file is uves_obs_scired.reduce.extract.profile [default = auto].

okay bestie that's part 1 and I am NOT done yet — more of this page is coming, so stay perched 💜

  • --reduce.extract.skymethod <str> — bestie, in optimal extraction mode this is the sky subtraction method you're rolling with. Set it to median and the sky gets estimated as the median of the pixels along the slit (and it just like, ignores the pixels hanging out near the object, rude but fair). Set it to optimal and it does a chi square minimization along the slit to get the best combined object + sky levels 💅. The optimal one gives you the most accurate sky determination ever, but it's also a lil slower than median (str; default: optimal). The full name of this option for the EsoRex configuration file is uves_obs_scired.reduce.extract.skymethod [default = optimal].
  • --reduce.ffmethod <str> — flat-fielding method, the moment we've all been waiting for ✨. If you set it to pixel, flat-fielding happens in pixel-pixel space (so, before extraction). If you set it to extract, flat-fielding gets performed in pixel-order space (i.e. after extraction, iykyk). And if you set it to no, there's no flat-field correction at all — in which case reduce.rebin.scale should be set to true to keep the flux conserved (both for response and science data) (str; default: extract). The full name of this option for the EsoRex configuration file is uves_obs_scired.reduce.ffmethod [default = extract].
  • --reduce.merge <str> — the order merging method 🫶. If it's optimal, the flux in the overlapping region gets set to the (optimally computed, using the uncertainties) average of single order spectra. If it's sum, the flux in the overlapping region is computed as the sum of the single order spectra. If it's noappend the spectrum is simply rebinned but not merged. If flat-fielding is done, method optimal is recommended, otherwise sum. (str; default: optimal). The full name of this option for the EsoRex configuration file is uves_obs_scired.reduce.merge [default = optimal].
  • --reduce.merge_delt1 <float> — order merging left hand (short wavelength) cut ✂️. So the whole point here: to reduce the amount of order overlapping regions, we're allowed to cut short and long wavelength ranges. This may reduce the ripple that might get introduced by the order merging (not the ripple, no). Suggested values are: 10 (W<=390), 12 (390<W<=437, 520<W<=564), 14 (437<W<=520, 564<W) (float; default: 0.0). The full name of this option for the EsoRex configuration file is uves_obs_scired.reduce.merge_delt1 [default = 0.0].
  • --reduce.merge_delt2 <float> — order merging right hand (long wavelength) cut ✂️ same energy, other side. Again, to reduce the amount of order overlapping regions we allow cutting short and long wavelength ranges, and this may reduce the ripple possibly introduced by the order merging. Suggested values is 4 (float; default: 0.0). The full name of this option for the EsoRex configuration file is uves_obs_scired.reduce.merge_delt2 [default = 0.0].
  • --reduce.objoffset <float> — offset (in pixels) of the extraction slit with respect to the center of order 👀. For optimal extraction the full slit is offset. For linear/average extraction, reduce.objoffset is ignored if reduce.objslit [default -1.0] is negative — and in that case the offset is automatically determined by measuring the actual object position (she measures, she provides). (float; default: 0.0). The full name of this option for the EsoRex configuration file is uves_obs_scired.reduce.objoffset [default = 0.0].
  • --reduce.objslit <float> — object window size (in pixels), and it's ignored for optimal extraction, so don't even worry about it there. The value must be smaller than the total slit length. If it's negative, the default value (half of full slit length) is used. The upper and lower sky windows are defined as the part of the full slit (if any) outside the object window, and the center of the object window is determined by the offset parameter. (float; default: -1.0). The full name of this option for the EsoRex configuration file is uves_obs_scired.reduce.objslit [default = -1.0].
  • --reduce.rebin.scale <bool> — whether or not to multiply by the factor dx/dlambda (pixels per wavelength) during the rebinning to conserve the flux 🌈. This option is disabled as default because applying the flat field correction already ensures flux conservation. So therefore this parameter should be TRUE (for response and science data) only if reduce.ffmethd = no. (bool; default: False). The full name of this option for the EsoRex configuration file is uves_obs_scired.reduce.rebin.scale [default = False].
  • --reduce.rebin.wavestep <float> — the bin size used for BLUE/REDL data (in w.l.u.) in wavelength space 🌸. If it's negative, a step size of 2/3 * ( average pixel size ) is used. (float; default: -1.0). The full name of this option for the EsoRex configuration file is uves_obs_scired.reduce.rebin.wavestep [default = -1.0].
  • --reduce.rebin.wavestep_redu <float> — the bin size used for REDU data (in w.l.u.) in wavelength space 💜. If it's negative, a step size of 2/3 * ( average pixel size ) is used. (float; default: -1.0). The full name of this option for the EsoRex configuration file is uves_obs_scired.reduce.rebin.wavestep_redu [default = -1.0].
  • --reduce.skysub <bool> — do sky-subtraction? (only applicable to linear and average extractions, bestie) (bool; default: True). The full name of this option for the EsoRex configuration file is uves_obs_scired.reduce.skysub [default = True].
  • --reduce.slitlength <float> — extraction slit length (in pixels) 📏. If negative, the value inferred from the raw frame header is used (float; default: -1.0). The full name of this option for the EsoRex configuration file is uves_obs_scired.reduce.slitlength [default = -1.0].
  • --reduce.tiltcorr <bool> — if enabled (recommended, and yes bestie it is the vibe), the provided dispersion solutions obtained at different slit positions are interpolated linearly at the actually measured position of the object/sky 🎯. Line tilt correction is currently not supported for 2d extraction, in which case the dispersion solution obtained at the middle of the slit is always used. (bool; default: True). The full name of this option for the EsoRex configuration file is uves_obs_scired.reduce.tiltcorr [default = True].

Okay and one more lil note before we move on: 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 uves pipeline can be downloaded as a PDF file using the following URL:

ftp://ftp.eso.org/pub/dfs/pipelines/uves/uves-pipeline-manual-6.1.8.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 uves pipeline are flames_cal_mkmaster(7), flames_cal_orderpos(7), flames_cal_predict(7), flames_cal_prep_sff_ofpos(7), flames_cal_wavecal(7), flames_obs_redchain(7), flames_obs_scired(7), flames_utl_unpack(7), uves_cal_cd_align(7), uves_cal_mbias(7), uves_cal_mdark(7), uves_cal_mflat(7), uves_cal_mflat_combine(7), uves_cal_mkmaster(7), uves_cal_orderpos(7), uves_cal_predict(7), uves_cal_response(7), uves_cal_tflat(7), uves_cal_wavecal(7), uves_obs_redchain(7), uves_utl_ima_arith(7), uves_utl_remove_crh_single(7) — the whole squad, fr fr 👑

💫 VERSION 💫

uves_obs_scired 6.1.8

👑 AUTHOR 👑

Jonas M. Larsen <cpl@eso.org>

😭 BUG REPORTS 😭

Please report any problems to cpl@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 FLAMES/UVES Pipeline Copyright (C) 2004, 2005, 2006, 2007 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 a wrap bestie!! 🎉 this whole page is uves_obs_scired version 6.1.8, dated 6.1.8 (the man page footer keeps it real with the recipe name on the left, the version in the middle and UVES_OBS_SCIRED(7) on the right) — slay, go read your spectra 💖✨

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