XSH_SCIRED_IFU_OFFSET(7)

📦 version 3.5.3, in ubuntu jammy, ubuntu noble

👑 XSH_SCIRED_IFU_OFFSET — the manual page, bestie edition 💅

okay so this is XSH_SCIRED_IFU_OFFSET(7), part of the xshoo recipes crew, and I'm gonna be so real with you: she's a whole mood. Let's get into it. 🎀

✨ NAME ✨

xsh_scIRED_ifu_offset — Reduce science IFU on-off exposures and build a 3D cube

like. she reduces your science IFU on-off exposures. AND builds a 3D cube. both. at once. main character behaviour fr fr. 🔥

🌈 SYNOPSIS 🌈

esorex xsh_scired_ifu_offset [OPTIONS] FILE.sof

that's it. that's the whole vibe. you hand her a .sof file and some [OPTIONS] and she goes to WORK. periodt. 💅

🦋 DESCRIPTION 🦋

So this recipe? Her whole thing is: Reduce science IFU on-off exposures and build a 3D cube. iconic, honestly.

Now here's what she needs fed to her. The input frames, bestie, no cap:

  • A set of 2xn Science frames, with Tag = OBJECT_IFU_OFFSET_arm, SKY_IFU_arm
  • A spectral format table (Tag = SPECTRAL_FORMAT_TAB_arm)
  • A master flat frame (Tag = MASTER_FLAT_IFU_arm)
  • An order table frame (Tag = ORDER_TABLE_EDGES_IFU_arm)
  • 3 wave solution frames, one per slitlet (Tag = WAVE_TAB_ARC_IFU_slitlet_arm)
    • where slitlet is DOWN, CEN or UP — three little slitlets, three little vibes 🧚
  • [OPTIONAL] A dispersion table (Tag = DISP_TAB_IFU_arm)
  • [OPTIONAL] A non-linear badpixel map (Tag = BP_MAP_NL_arm)
  • [OPTIONAL] A reference badpixel map (Tag = BP_MAP_RP_arm)
note the [OPTIONAL] girlies — those last three? she'll live without them. but the rest? mandatory. she's not flexible on those. 🙈

🌸 Products 🌸

okay so this is what she hands back to you when she's done cooking:

  • Merged 3D data cube (PREFIX_MERGE3D_DATA_OBJ_arm)
  • QC Traces of 3D data cube (PREFIX_MERGE3D_TRACE_OBJ_arm)
  • Order by order 3D data cube (PREFIX_ORDER3D_DATA_OBJ_arm)
  • Order by order 3D qual cube (IFU_CFG_COR_arm)
  • Order by order 3D qual cube (PREFIX_MERGE3D_DATA_SKY_arm)
  • where PREFIX is SCI, FLUX, TELL if input raw DPR.TYPE contains OBJECT or FLUX or TELLURIC 👑
  • 1 Spectrum merge 3D, PRO.CATG=MERGE3D_IFU_arm

like hello?? look at all those cubes. she's giving 3D printer energy but make it astrophysics. obsessed. ✨

more of this page is coming, bestie — don't go anywhere 💖

✨ OPTIONS ✨

okay bestie, this is the part where the recipe gets its whole personality 💅 every single one of these has a default, and every single one has a full EsoRex config-file name so you can set it forever instead of typing it every time. iykyk.

  • --keep-temp <str> — if you set this to ´no´, the temp files get yeeted. that's it, that's the whole thing. (str; default: ´no´). the full name for the EsoRex config file is xsh.xsh_scired_ifu_offset.keep-temp [default = no].
  • --debug-level <str> — extra xshooter debug level, for when you need to see everything. one of ´none´, ´low´, ´medium´, ´high´ (str; default: ´none´). full EsoRex config name: xsh.xsh_scired_ifu_offset.debug-level [default = none].
  • --time-stamp <bool> — adds a timestamp to the product file name so you can tell your babies apart 🎀 (bool; default: False). full EsoRex config name: xsh.xsh_scired_ifu_offset.time-stamp [default = False].
  • --decode-bp <int> — this is an integer representation of the bits that count as bad when decoding the bad pixel mask pixel values. the codes you'll actually see as a user are:
    • 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). full EsoRex config name: xsh.xsh_scired_ifu_offset.decode-bp [default = 2144337919].

  • --pre-overscan-corr <int> — pre-overscan correction, pick your fighter: 0 = no correction, 1 = mean overscan correction, 2 = mean prescan correction, 3 = (mean pre+mean overscan)/2 correction (int; default: 1). full EsoRex config name: xsh.xsh_scired_ifu_offset.pre-overscan-corr [default = 1].
  • --stack-method <str> — the method used to build the master frame, aka how the girlies get combined. (str; default: ´median´). full EsoRex config name: xsh.xsh_scired_ifu_offset.stack-method [default = median].
  • --klow <float> — kappa used to clip low level values, but only when the method is set to ´mean´ (float; default: 5.0). full EsoRex config name: xsh.xsh_scired_ifu_offset.klow [default = 5.0].
  • --khigh <float> — same energy but for the high level values, again only when the method is ´mean´ (float; default: 5.0). full EsoRex config name: xsh.xsh_scired_ifu_offset.khigh [default = 5.0].
  • --crh-clip-kappa <float> — the kappa value used in sigma clipping during CRH rejection across multiple frames (float; default: 5.0). full EsoRex config name: xsh.xsh_scired_ifu_offset.crh-clip-kappa [default = 5.0].
  • --crh-clip-niter <int> — how many iterations of sigma clipping happen during CRH rejection across multiple frames (int; default: 5). full EsoRex config name: xsh.xsh_scired_ifu_offset.crh-clip-niter [default = 5].
  • --crh-clip-frac <float> — the minimal ratio of accepted points to total points in sigma clipping during CRH rejection across multiple frames (float; default: 0.7). full EsoRex config name: xsh.xsh_scired_ifu_offset.crh-clip-frac [default = 0.7].
  • --removecrhsingle-sigmalim <float> — the Poisson fluctuation threshold used to flag CRHs (peep van Dokkum, PASP,113,2001,p1420-27 for the lore) (float; default: 5.0). full EsoRex config name: xsh.xsh_scired_ifu_offset.removecrhsingle-sigmalim [default = 5.0].
  • --removecrhsingle-flim <float> — the minimum contrast between the Laplacian image and the fine structure image that a point needs before it gets flagged as a CRH. (again, van Dokkum, PASP,113,2001,p1420-27) (float; default: 2.0). full EsoRex config name: xsh.xsh_scired_ifu_offset.removecrhsingle-flim [default = 2.0].
  • --removecrhsingle-niter <int> — max number of iterations, no more, we're done (int; default: 4). full EsoRex config name: xsh.xsh_scired_ifu_offset.removecrhsingle-niter [default = 4].
  • --rectify-kernel <str> — the name of the interpolation kernel used. possible values are: tanh, sinc, sinc2, lanczos, hamming, hann. (str; default: ´tanh´). full EsoRex config name: xsh.xsh_scired_ifu_offset.rectify-kernel [default = tanh].
  • --rectify-radius <float> — the rectify interpolation radius, in bin units (float; default: 2.0). full EsoRex config name: xsh.xsh_scired_ifu_offset.rectify-radius [default = 2.0].
  • --rectify-bin-lambda <float> — the wavelength step in the output spectrum, in nm (float; default: -1.0). full EsoRex config name: xsh.xsh_scired_ifu_offset.rectify-bin-lambda [default = -1.0].
  • --rectify-bin-slit <float> — the spatial step along the slit in the output spectrum, in arcsec (float; default: -1.0). full EsoRex config name: xsh.xsh_scired_ifu_offset.rectify-bin-slit [default = -1.0].
  • --localize-method <str> — the localization method used to detect the object centroid and its height on the slit. your options are MANUAL, MAXIMUM, GAUSSIAN (str; default: ´MANUAL´). full EsoRex config name: xsh.xsh_scired_ifu_offset.localize-method [default = MANUAL].
  • --localize-chunk-nb <int> — how many chunks in the full spectrum get used to localize the object (int; default: 10). full EsoRex config name: xsh.xsh_scired_ifu_offset.localize-chunk-nb [default = 10].
  • --localize-thresh <float> — a threshold relative to the peak intensity; below it, the edges of the object get detected for MAXIMUM localization (float; default: 0.1). full EsoRex config name: xsh.xsh_scired_ifu_offset.localize-thresh [default = 0.1].
  • --localize-deg-lambda <int> — the degree in lambda in the localization polynomial expression slit=f(lambda), used only for MAXIMUM and GAUSSIAN (int; default: 0). full EsoRex config name: xsh.xsh_scired_ifu_offset.localize-deg-lambda [default = 0].
  • --localize-slit-position <float> — the object position on the slit for MANUAL localization, in arcsec (float; default: 0.0). full EsoRex config name: xsh.xsh_scired_ifu_offset.localize-slit-position [default = 0.0].
  • --localize-slit-hheight <float> — the object's half height on the slit for MANUAL localization, in arcsec (float; default: 2.0). full EsoRex config name: xsh.xsh_scired_ifu_offset.localize-slit-hheight [default = 2.0].
  • --localize-kappa <float> — the kappa value for sigma clipping in the localization polynomial fit (float; default: 3.0). full EsoRex config name: xsh.xsh_scired_ifu_offset.localize-kappa [default = 3.0].
  • --localize-niter <int> — number of iterations for sigma clipping in the localization polynomial fit (int; default: 3). full EsoRex config name: xsh.xsh_scired_ifu_offset.localize-niter [default = 3].
  • --localize-use-skymask <bool> — TRUE if we want to mask sky lines using the SKY_LINE_LIST file 🦋 (bool; default: False). full EsoRex config name: xsh.xsh_scired_ifu_offset.localize-use-skymask [default = False].
  • --compute-map <bool> — if TRUE, recompute the (wave and slit) maps from the dispersion solution. and heads up: if sky-subtract is set to TRUE, this must be set to TRUE too, no exceptions bestie (bool; default: False). full EsoRex config name: xsh.xsh_scired_ifu_offset.compute-map [default = False].
  • --trace-obj <bool> — if TRUE, trace the object position on each IFU slice. in that case the order TAB edges are required (bool; default: False). full EsoRex config name: xsh.xsh_scired_ifu_offset.trace-obj [default = False].
  • --check-afc <bool> — input AFC corrected model/wave solution and science frame check. if TRUE, the recipe verifies that the input mode/wave solution is AFC corrected, that its INS.OPTIi.NAME is ´Pin_0.5 ´, and that its OBS.ID and OBS.TARG.NAME values match the corresponding values of the science frame. (bool; default: True). full EsoRex config name: xsh.xsh_scired_ifu_offset.check-afc [default = True].
  • --cut-uvb-spectrum <bool> — TRUE if the recipe cuts the UVB spectrum at 556 nm (dichroich) (bool; default: True). full EsoRex config name: xsh.xsh_scired_ifu_offset.cut-uvb-spectrum [default = True].
💡 psst — you can totally make a configuration file holding all of these options with nice suitable default values. just go check the details from the 'esorex --help' command, she'll tell you everything.

🌈 SEE ALSO 🌈

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

ftp://ftp.eso.org/pub/dfs/pipelines/xshoo/xshoo-pipeline-manual-12.1.pdf

there's also an overview of all the existing ESO pipelines on the web page https://www.eso.org/sci/software/pipelines/ ✨

basic documentation about the EsoRex program lives at the esorex (1) man page.

and yes you can 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 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_drl(7), xsh_scired_ifu_stare(7), xsh_scired_ifu_stare_drl(7), xsh_scired_slit_nod(7), xsh_scired_slit_offset(7), xsh_scired_slit_stare(7), xsh_util_physmod(7), xsh_wavecal(7)

👑 VERSION 👑

xsh_scired_ifu_offset 3.5.3

🫶 AUTHOR 🫶

A.Modigliani, J.Vernet, P. Bristow <Andrea.Modigliani@eso.org>

💌 BUG REPORTS 💌

okay bestie, if something's acting up, don't suffer in silence 🫶 please report any problems to Andrea.Modigliani@eso.org.

or, like, alternatively — you can slide a report over to the ESO User Support Department <usd-help@eso.org>. either way works, we just wanna know 💅

📜 LICENSE 📜

so this file is part of the X-shooter Instrument Pipeline, Copyright (C) 2006 European Southern Observatory. periodt ✨

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. iconic behaviour honestly 👑

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. (yes this is the loud part. it's supposed to be loud. no cap.)

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 a wrap on this whole page, bestie 🦋 the footer down at the bottom is just the source name xsh_scired_ifu_offset, version 3.5.3, and the man page tag XSH_SCIRED_IFU_OFFSET(7) — that's the whole vibe check, we're done here 💖✨🌸

📦 where this page comes from