XSH_SCIRED_SLIT_STARE(7)

📦 version 3.5.3, in ubuntu jammy, ubuntu noble

🦋 XSH_SCIRED_SLIT_STARE 🦋

the manual page for xsh_scired_slit_stare(7) — part of the xshoo recipes fam. bestie, we are reducing science exposures in SLIT configuration and stare mode, and honestly? it's giving main character energy. 💅

✨ NAME ✨

xsh_scired_slit_stare — Reduce science exposure in SLIT configuration and stare mode. no cap, that's literally the whole job description. 🎀

💖 SYNOPSIS 💖

esorex xsh_scired_slit_stare [OPTIONS] FILE.sof

🦋 DESCRIPTION 🦋

okay so listen. this recipe reduces science exposure in SLIT configuration and stare mode. that's the vibe. now let's talk about what it eats and what it gives back, because the way that this thing handles frames is genuinely iconic. ✨

🌸 Input Frames 🌸

a set of n Science frames ( n == 1 or >=3, Tag = OBJECT_SLIT_STARE_UVB) — not me pointing out that it's either literally ONE or THREE-PLUS, there is no in-between, the middle is not invited 🫶
a spectral format table (Tag = SPECTRAL_FORMAT_TAB_arm)
[UVB,VIS] a master bias frame (Tag = MASTER_BIAS_arm)
[OPTIONAL] a master dark frame (Tag = MASTER_DARK_arm)
a master flat frame (Tag = MASTER_FLAT_SLIT_arm)
an order table frame (Tag = ORDER_TAB_EDGES_SLIT_arm)
[OPTIONAL] a table with dispersion coefficients (Tag = DISP_TAB_arm, required in poly mode
[poly mode] a wave solution frame (Tag = WAVE_TAB_2D_arm)
[physical model mode] a model cfg table (Format = TABLE, Tag = XSH_MOD_CFG_TAB_arm)
[OPTIONAL] a table specifying multiplying factor for break points (Tag = SKY_SUB_BKPTS_arm) to generate
[OPTIONAL] a non-linear badpixel map (Tag = BP_MAP_NL_arm)
[OPTIONAL] a reference badpixel map (Tag = BP_MAP_RP_arm)
[OPTIONAL,physmod mode] a table listing sky line positions (Tag = SKY_LINE_LIST_arm) — this is used to be able to control quality of sky subtraction, for example projecting guess positions on the product SCI_SLIT_STARE_SUB_SKY_arm, and it is required if sky-method=BSPLINE
[OPTIONAL] the instrument response table (Tag = RESPONSE_MERGE1D_SLIT_arm)
[OPTIONAL] an atmospheric extinction table (Tag = ATMOS_EXT_arm)
[OPTIONAL] a telluric mask (Tag = TELL_MASK_arm)
[OPTIONAL] the instrument master response table (Tag = MRESPONSE_MERGE1D_SLIT_arm).

if both master and individual response are provided, the individual response is preferred. the individual one is the main character here, the master one is just standing behind it holding its purse. 💅

🌈 Products 🌈

PREFIX_ORDER2D_arm — extracted spectrum, order-by-order, 2D
PREFIX_ORDER1D_arm — extracted spectrum, order-by-order, 1D
PREFIX_MERGE2D_arm — merged spectrum, 2D
PREFIX_MERGE1D_arm — merged spectrum, 1D
SKY_SLIT_MERGE2D_arm — merged spectrum sky, 2D
PREFIX_SUB_BACK_SLIT_arm — sci frame bias, (dark), inter-order bkg subtracted
PREFIX_WAVE_MAP_arm, wave map image
PREFIX_SLIT_MAP_arm, slit map image
PREFIX_DIVFF_arm — as PREFIX_SUB_BACK_SLIT_arm, flat fielded
PREFIX_SUB_SKY_arm — as PREFIX_DIVFF_arm, sky subtracted
PREFIX_SKY_arm, 2D sky frame
PREFIX_SKY_ORD1D_arm, 1D sky image (order-by-order)
PREFIX_BACK_SLIT_arm, inter order background image
where PREFIX is SCI, FLUX, TELL if input raw DPR.TYPE contains OBJECT or FLUX or TELLURIC
[OPTIONAL, if response and atm ext are provided] PREFIX_FLUX_ORDER2D_arm (2 dimension)
[OPTIONAL, if response and atm ext are provided] PREFIX_FLUX_ORDER1D_arm (1 dimension)
[OPTIONAL, if response and atm ext are provided] PREFIX_FLUX_MERGE2D_arm (2 dimension)
[OPTIONAL, if response and atm ext are provided] PREFIX_FLUX_MERGE1D_arm (1 dimension)
PREFIX_ON_arm — bias (dark) subtracted sci frame

👑 OPTIONS 👑

okay bestie, here's the full menu. every single one. we do not skip. we do not summarise. we respect the flags. ✨

--keep-temp <str> — if no, temporary files are deleted. (str; default: no). the full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.keep-temp [default = no].
--debug-level <str> — additional 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_scired_slit_stare.debug-level [default = none].
--time-stamp <bool> — add timestamp to product file name. (bool; default: False). the full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.time-stamp [default = False].
--decode-bp <int> — integer representation of the bits to be considered bad when decoding the bad pixel mask pixel values. most frequent codes relevant for the user: 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_scired_slit_stare.decode-bp [default = 2144337919].
--pre-overscan-corr <int> — pre-overscan correction. 0: no correction 1: mean overscan correction 2: mean prescan correction 3: (mean pre+mean overscan)/2 correction (int; default: 1). the full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.pre-overscan-corr [default = 1].
--stack-method <str> — method used to build master frame. (str; default: median). the full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.stack-method [default = median].
--klow <float> — kappa used to clip low level values, when method is set to mean (float; default: 5.0). the full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.klow [default = 5.0].
--khigh <float> — kappa used to clip high level values, when method is set to mean (float; default: 5.0). the full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.khigh [default = 5.0].
--background-edges-margin <int> — X margin to order edge to define background sampling points (int; default: 1). the full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.background-edges-margin [default = 1].
--background-poly-deg-y <int> — poly mode fit deg along Y. (int; default: 9). the full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.background-poly-deg-y [default = 9].
--background-poly-deg-x <int> — poly mode fit deg along X. (int; default: 9). the full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.background-poly-deg-x [default = 9].
--background-poly-kappa <float> — poly mode kappa value of kappa-sigma-clip outliers removal. (float; default: 10.0). the full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.background-poly-kappa [default = 10.0].
--removecrhsingle-sigmalim <float> — Poisson fluctuation threshold to flag CRHs (see van Dokkum, PASP,113,2001,p1420-27) (float; default: 20.0). the full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.removecrhsingle-sigmalim [default = 20.0].
--removecrhsingle-flim <float> — minimum contrast between the Laplacian image and the fine structure image that a point must have to be flagged as CRH. (see van Dokkum, PASP,113,2001,p1420-27) (float; default: 2.0). the full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.removecrhsingle-flim [default = 2.0].
--removecrhsingle-niter <int> — max number of iterations (int; default: 4). the full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.removecrhsingle-niter [default = 4].
--rectify-kernel <str> — name of the Interpolation Kernel Used. possible values are: tanh, sinc, sinc2, lanczos, hamming, hann. (str; default: tanh). the full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.rectify-kernel [default = tanh].
--rectify-radius <float> — rectify Interpolation radius [bin units]. (float; default: 2.0). the full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.rectify-radius [default = 2.0].
--rectify-bin-lambda <float> — wavelength step in the output spectrum [nm] (float; default: -1.0). the full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.rectify-bin-lambda [default = -1.0].
--rectify-bin-slit <float> — spatial step along the slit in the output spectrum [arcsec] (float; default: -1.0). the full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.rectify-bin-slit [default = -1.0].
--localize-method <str> — localization method (MANUAL, MAXIMUM, GAUSSIAN) used to detect the object centroid and height on the slit (str; default: MANUAL). the full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.localize-method [default = MANUAL].
--localize-chunk-nb <int> — number of chunks in the full spectrum to localize the object (int; default: 10). the full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.localize-chunk-nb [default = 10].
--localize-thresh <float> — threshold relative to the peak intensity below which the edges of the object are detected for MAXIMUM localization (float; default: 0.1). the full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.localize-thresh [default = 0.1].
--localize-deg-lambda <int> — degree in lambda in the localization polynomial expression slit=f(lambda), used only for MAXIMUM and GAUSSIAN (int; default: 0). the full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.localize-deg-lambda [default = 0].
--localize-slit-position <float> — object position on the slit for MANUAL localization [arcsec] (float; default: 0.0). the full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.localize-slit-position [default = 0.0].
--localize-slit-hheight <float> — object half height on the slit for MANUAL localization [arcsec] (float; default: 2.0). the full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.localize-slit-hheight [default = 2.0].
--localize-kappa <float> — kappa value for sigma clipping in the localization polynomial fit (float; default: 3.0). the full name of this option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.localize-kappa [default = 3.0].
--localize-niter <int> — how many rounds of sigma clipping we do in the localization polynomial fit. (int; default: 3). EsoRex config name: xsh.xsh_scired_slit_stare.localize-niter [default = 3].
--localize-use-skymask <bool> — TRUE if we're masking sky lines using the SKY_LINE_LIST file, bestie. (bool; default: False). EsoRex config name: xsh.xsh_scired_slit_stare.localize-use-skymask [default = False].
--sky-subtract <bool> — TRUE means we subtract sky, single. That's it, that's the whole vibe. (bool; default: True). EsoRex config name: xsh.xsh_scired_slit_stare.sky-subtract [default = True].
--sky-bspline-nbkpts-first <int> — how many break points the Bezier curve fitting gets when there's no localization. (int; default: 3000). EsoRex config name: xsh.xsh_scired_slit_stare.sky-bspline-nbkpts-first [default = 3000].
--sky-bspline-nbkpts-second <int> — same break-point count energy, but for Bezier curve fitting with localization. (int; default: 3000). EsoRex config name: xsh.xsh_scired_slit_stare.sky-bspline-nbkpts-second [default = 3000].
--sky-bspline-order <int> — the Bezier spline order, periodt. (int; default: 7). EsoRex config name: xsh.xsh_scired_slit_stare.sky-bspline-order [default = 7].
--sky-bspline-niter <int> — number of iterations. That's the whole job description. (int; default: 20). EsoRex config name: xsh.xsh_scired_slit_stare.sky-bspline-niter [default = 20].
--sky-bspline-kappa <float> — the kappa value used to kappa-sigma-clip the object. (float; default: 5.0). EsoRex config name: xsh.xsh_scired_slit_stare.sky-bspline-kappa [default = 5.0].
--sky-method <str> — the sky subtract method: BSPLINE, BSPLINE1, BSPLINE2 MEDIAN. And heads up: BSPLINE is equivalent to BSPLINE1. (str; default: ´MEDIAN´). EsoRex config name: xsh.xsh_scired_slit_stare.sky-method [default = MEDIAN].
--bspline-sampling <str> — BSPLINE sampling, and listen: UNIFORM uses the user-defined nbkpts value, corrected for binning, for all orders. FINE multiplies the user-defined nbkpts value, corrected for binning, by a hard coded coefficient optimized on each arm-order. (str; default: ´FINE´). EsoRex config name: xsh.xsh_scired_slit_stare.bspline-sampling [default = FINE].
--sky-median-hsize <int> — half size of the running median. Only kicks in if sky-method=MEDIAN. (int; default: 20). EsoRex config name: xsh.xsh_scired_slit_stare.sky-median-hsize [default = 20].
--sky-slit-edges-mask <float> — size of the edges mask, in arcsec. (float; default: 0.5). EsoRex config name: xsh.xsh_scired_slit_stare.sky-slit-edges-mask [default = 0.5].
--sky-position1 <float> — central position of the sky window #1, in [arcsec]. (float; default: 0.0). EsoRex config name: xsh.xsh_scired_slit_stare.sky-position1 [default = 0.0].
--sky-hheight1 <float> — half size of sky window #1, in [arcsec]. (float; default: 0.0). EsoRex config name: xsh.xsh_scired_slit_stare.sky-hheight1 [default = 0.0].
--sky-position2 <float> — central position of the sky window #2, in [arcsec]. (float; default: 0.0). EsoRex config name: xsh.xsh_scired_slit_stare.sky-position2 [default = 0.0].
--sky-hheight2 <float> — half size of sky window #2, in [arcsec]. (float; default: 0.0). EsoRex config name: xsh.xsh_scired_slit_stare.sky-hheight2 [default = 0.0].
--stdextract-interp-hsize <int> — half size of the mask used to define the object cross order profile. (int; default: 30). EsoRex config name: xsh.xsh_scired_slit_stare.stdextract-interp-hsize [default = 30].
--do-optextract <bool> — TRUE if we're doing the optimal extraction, queen. (bool; default: False). EsoRex config name: xsh.xsh_scired_slit_stare.do-optextract [default = False].
--optextract-oversample <int> — oversample factor for the science image. (int; default: 5). EsoRex config name: xsh.xsh_scired_slit_stare.optextract-oversample [default = 5].
--optextract-box-half-size <int> — extraction box, in [pixel]. (int; default: 10). EsoRex config name: xsh.xsh_scired_slit_stare.optextract-box-half-size [default = 10].
--optextract-chunk-size <int> — chunk size, in [bin]. (int; default: 50). EsoRex config name: xsh.xsh_scired_slit_stare.optextract-chunk-size [default = 50].
--optextract-step-lambda <float> — lambda step, in [nm]. (float; default: 0.02). EsoRex config name: xsh.xsh_scired_slit_stare.optextract-step-lambda [default = 0.02].
--optextract-clip-kappa <float> — kappa for cosmics ray hits rejection. Bye cosmic rays 💀. (float; default: 3.0). EsoRex config name: xsh.xsh_scired_slit_stare.optextract-clip-kappa [default = 3.0].
--optextract-clip-frac <float> — maximum bad pixels fraction for cosmics ray hits rejection. (float; default: 0.4). EsoRex config name: xsh.xsh_scired_slit_stare.optextract-clip-frac [default = 0.4].
--optextract-clip-niter <int> — maximum number of iterations for cosmics ray hits rejection. (int; default: 2). EsoRex config name: xsh.xsh_scired_slit_stare.optextract-clip-niter [default = 2].
--optextract-niter <int> — number of iterations. (int; default: 1). EsoRex config name: xsh.xsh_scired_slit_stare.optextract-niter [default = 1].
--optextract-method <str> — extraction method: GAUSSIAN | GENERAL. Pick your fighter. (str; default: ´GAUSSIAN´). EsoRex config name: xsh.xsh_scired_slit_stare.optextract-method [default = GAUSSIAN].
--cut-uvb-spectrum <bool> — TRUE if the recipe cuts the UVB spectrum at 556 nm (dichroich). (bool; default: True). EsoRex config name: xsh.xsh_scired_slit_stare.cut-uvb-spectrum [default = True].
--generate-SDP-format <bool> — TRUE if additional files should be generated in Science Data Product (SDP) format. Extra files, extra slay. (bool; default: False). EsoRex config name: xsh.xsh_scired_slit_stare.generate-SDP-format [default = False].
--dummy-association-keys <int> — sets the number of dummy (empty) ASSONi, ASSOCi and ASSOMi keywords to create. (int; default: 0). EsoRex config name: xsh.xsh_scired_slit_stare.dummy-association-keys [default = 0].

Oh also, bestie, quick PSA: you can totally create a configuration file containing these options, along with suitable default values. Just go look at the details provided by the 'esorex --help' command. ✨

🌈 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_lingain(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_util_physmod(7), xsh_wavecal(7)

💅 VERSION 💅

xsh_scired_slit_stare 3.5.3

👑 AUTHOR 👑

P.Goldoni, L.Guglielmi, R. Haigron, F. Royer, D. Bramich, 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>.

Not me begging you to actually report the bugs 🙈 — if something's broken, tell them, don't just suffer in silence.

🎀 LICENSE 🎀

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

And that's the whole page, bestie!! 🦋 This was xsh_scired_slit_stare 3.5.3, the XSH_SCIRED_SLIT_STARE(7) man page — you read the entire thing, no skimming, I'm so proud of you fr fr 💖✨ Now go stare at a slit (respectfully). 🌸

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ubuntu jammy: cpl-plugin-xshoo-doc 3.5.3+dfsg-1build1 · GPL-v2+
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