XSH_MFLAT(7)

📦 version 3.5.3, in ubuntu jammy, ubuntu noble

✨ XSH_MFLAT ✨

okay bestie, gather round — this is the xsh_mflat page from the xshoo recipes manual (section 7 of the manual, if you're keeping score 💅). It's a long one so buckle up, we're doing this in parts.

🌸 NAME 🌸

xsh_mflat — Create the master flat and the orders edges traces table frames.

🦋 SYNOPSIS 🦋

esorex xsh_mflat [OPTIONS] FILE.sof

🎀 DESCRIPTION 🎀

So like, this recipe makes the master flat and the orders edges traces table frames. That's the whole vibe. 💖

🌈 Input Frames :

  • [UVB] A set of n RAW frames (Format = RAW, n>=3, Tag = FLAT_D2_mode_UVB, mode=SLIT/IFU)
  • [UVB] A set of n RAW frames (Format = RAW, n>=3, Tag = FLAT_QTH_mode_UVB)
  • [VIS] A set of n RAW frames (Format = RAW, n>=3, Tag = FLAT_mode_VIS)
  • [NIR] A set of n x n RAW frames ((Format = RAW, n>=3, Tag = FLAT_mode_NIR_ON, FLAT_mode_NIR_OFF)
  • A spectral format table (Format = PRE, Tag = SPECTRAL_FORMAT_TAB_arm)
  • An order table (Format = TABLE, Tag = ORDER_TAB_CENTR_arm)
  • [UVB,VIS] A master bias (Format = PRE, Tag = MASTER_BIAS_arm)
  • [OPTIONAL] A map of reference bad pixel (Format = QUP,RAW, Tag = BP_MAP_RP_arm)
  • [OPTIONAL] A map of non linear pixel (Format = QUP,RAW, Tag = BP_MAP_NL_arm)
  • [OPTIONAL,UVB,VIS] A master dark (Format = PRE, Tag = MASTER_DARK_arm)

💫 Products :

  • An updated order table with edge UP and edge LOW (Format = TABLE, TAG = ORDER_TAB_EDGES_mode_arm)
  • A master flat (Format = PRE, PRO.CATG = MASTER_FLAT_mode_arm)
  • The inter-order background frame (Format = PRE, PRO.CATG = MFLAT_BACK_mode_arm)
  • The inter-order background sampling points grid table (Format = PRE, PRO.CATG = MFLAT_GRID_BACK_mode_arm)

and then the recipe does its little routine, in this order, no cap:

  • Prepare the flat frames.
  • Stack and sigma clip all the flat frames.
  • Subtract master bias.
  • Subtract master dark.
  • Detect order edge.
  • Subtract background.
  • Create the Master Flat.

💅 OPTIONS 💅

every single one of them, bestie, we are NOT skipping any:

  • --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_mflat.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_mflat.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_mflat.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_mflat.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_mflat.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_mflat.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_mflat.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_mflat.khigh [default = 5.0].
  • --detectorder-edges-search-win-hsize <int> — During extraction the local spatial profile (=cross-order) of the spectrum is determined by collapsing the 2-dimensional spectrum along the dispersion axis. This parameter defines the half size of the region across which the spectrum is collapsed. This parameter affects flagged pixels interpolation. In case of spectrum gaps the recommended optimal value is: (size_of_gap [nm]/(2*size_of_pixel [nm])+1) (int; default: 50). The full name of this option for the EsoRex configuration file is xsh.xsh_mflat.detectorder-edges-search-win-hsize [default = 50].
  • --detectorder-edges-flux-thresh <float> — Threshold in relative flux (compared to the central flux) below which the order edges are defined (float; default: 0.4). The full name of this option for the EsoRex configuration file is xsh.xsh_mflat.detectorder-edges-flux-thresh [default = 0.4].
  • --detectorder-min-sn <float> — Minimum signal-to-noise ratio at the centroid of the orders (60 for SLIT-UVB,VIS,NIR, 20 for IFU-UVB,VIS, 4 for IFU-NIR (float; default: -1.0). The full name of this option for the EsoRex configuration file is xsh.xsh_mflat.detectorder-min-sn [default = -1.0].
  • --detectorder-min-order-size-x <int> — Minimum order size in pixels along X direction [60 for UVB,VIS, 40 for NIR] (int; default: -1). The full name of this option for the EsoRex configuration file is xsh.xsh_mflat.detectorder-min-order-size-x [default = -1].
  • --detectorder-chunk-half-size <int> — Half size in pixels of the chunks in Y direction (int; default: 1). The full name of this option for the EsoRex configuration file is xsh.xsh_mflat.detectorder-chunk-half-size [default = 1].
  • --detectorder-slitlet-low-factor <float> — Factor for slitlet on lower edge slitlet (IFU) (float; default: 1.0). The full name of this option for the EsoRex configuration file is xsh.xsh_mflat.detectorder-slitlet-low-factor [default = 1.0].
  • --detectorder-slitlet-up-factor <float> — Factor for slitlet on upper edge (IFU) (float; default: 1.0). The full name of this option for the EsoRex configuration file is xsh.xsh_mflat.detectorder-slitlet-up-factor [default = 1.0].
  • --detectorder-fixed-slice <bool> — If true the size of slitlet is fixed (IFU) (bool; default: True). The full name of this option for the EsoRex configuration file is xsh.xsh_mflat.detectorder-fixed-slice [default = True].
  • --detectorder-slice-trace-method <str> — method adopted for IFU slice tracing (´fixed´ for SLIT and ´sobel´ for IFU): (str; default: ´auto´). The full name of this option for the EsoRex configuration file is xsh.xsh_mflat.detectorder-slice-trace-method [default = auto].
  • --detectorder-qc-mode <bool> — If true allows one to skip edge detection on orders below detectorder- min-sn (oly for QC mode, not to be set by normal users) (bool; default: False). The full name of this option for the EsoRex configuration file is xsh.xsh_mflat.detectorder-qc-mode [default = False].
bestie this one literally says "not to be set by normal users" — so if you're a normal user, do NOT touch it. 🙈
  • --detectorder-d2-min-sn <float> — minimum signal noise ratio in D2 lamp frame in order (float; default: 60.0). The full name of this option for the EsoRex configuration file is xsh.xsh_mflat.detectorder-d2-min-sn [default = 60.0].
  • --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_mflat.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_mflat.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_mflat.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_mflat.background-poly-kappa [default = 10.0].

okay and heads up 🫶 — 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 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_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_scired_slit_stare(7), xsh_util_physmod(7), xsh_wavecal(7)

⭐ VERSION ⭐

xsh_mflat 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>.

💖 LICENSE 💖

Okay bestie, this is the legal tea and we're keeping it exactly as written, because lawyers do not play 💅

This file is part of the X-shooter Instrument Pipeline Copyright (C) 2006 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., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA

fr fr, read that warranty bit twice. "Without any warranty" is not a vibe, it's a legally binding mood 😭

And that's the whole page, bestie — you made it to the end 🫶 The footer says this is xsh_mflat, version 3.5.3, living its life as page XSH_MFLAT(7) 💫 No cap, that's the source and the version, right at the bottom where the manpage keeps its little signature. Go forth and flat-field your spectra, you absolute icon 👑✨

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