--- name: "xsh_scired_slit_stare" section: "7" platform: "linux" package: "cpl-plugin-xshoo-doc" version: "3.5.0+dfsg-4" release: "Debian 11 (Bullseye)" platforms: ["linux"] url: "https://new.carta.tech/xsh_scired_slit_stare" --- # xsh\_scired\_slit\_stare(7) Reduce science exposure in SLIT configuration and stare mode ## NAME xsh\_scired\_slit\_stare - Reduce science exposure in SLIT configuration and stare mode ## SYNOPSIS esorex **xsh\_scired\_slit\_stare** \[OPTIONS\] FILE.sof ## DESCRIPTION This recipe reduces science exposure in SLIT configuration and stare mode Input Frames : \ \- A set of n Science frames ( n == 1 or \>=3, Tag = OBJECT\_SLIT\_STARE\_UVB)\ \- 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 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. 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 - **--keep-temp** *\* 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** *\* 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** *\* 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** *\* 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** *\* 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** *\* 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** *\* 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** *\* 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** *\* 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** *\* 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** *\* 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** *\* 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** *\* 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** *\* 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** *\* 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** *\* 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** *\* 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** *\* 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** *\* 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** *\* 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** *\* 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** *\* 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** *\* 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** *\* 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** *\* 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** *\* 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** *\* Number of iterations for sigma clipping in the localization polynomial fit (int; default: 3). The full name of this option for the EsoRex configuration file is **xsh.xsh\_scired\_slit\_stare.localize-niter** \[default = *3*\]. - **--localize-use-skymask** *\* TRUE if we want to mask sky lines using SKY\_LINE\_LIST file. (bool; default: False). The full name of this option for the EsoRex configuration file is **xsh.xsh\_scired\_slit\_stare.localize-use-skymask** \[default = *False*\]. - **--sky-subtract** *\* TRUE to use subtract sky single. (bool; default: True). The full name of this option for the EsoRex configuration file is **xsh.xsh\_scired\_slit\_stare.sky-subtract** \[default = *True*\]. - **--sky-bspline-nbkpts-first** *\* Nb of break points for Bezier curve fitting (without localization) (int; default: 3000). The full name of this option for the EsoRex configuration file is **xsh.xsh\_scired\_slit\_stare.sky-bspline-nbkpts-first** \[default = *3000*\]. - **--sky-bspline-nbkpts-second** *\* Nb of break points for Bezier curve fitting (with localization) (int; default: 3000). The full name of this option for the EsoRex configuration file is **xsh.xsh\_scired\_slit\_stare.sky-bspline-nbkpts-second** \[default = *3000*\]. - **--sky-bspline-order** *\* Bezier spline order (int; default: 7). The full name of this option for the EsoRex configuration file is **xsh.xsh\_scired\_slit\_stare.sky-bspline-order** \[default = *7*\]. - **--sky-bspline-niter** *\* Nb of iterations (int; default: 20). The full name of this option for the EsoRex configuration file is **xsh.xsh\_scired\_slit\_stare.sky-bspline-niter** \[default = *20*\]. - **--sky-bspline-kappa** *\* Kappa value used to kappa-sigma-clip object (float; default: 5.0). The full name of this option for the EsoRex configuration file is **xsh.xsh\_scired\_slit\_stare.sky-bspline-kappa** \[default = *5.0*\]. - **--sky-method** *\* Sky subtract Method (BSPLINE, BSPLINE1, BSPLINE2 MEDIAN). BSPLINE is equivalent to BSPLINE1 (str; default: ´MEDIAN´). The full name of this option for the EsoRex configuration file is **xsh.xsh\_scired\_slit\_stare.sky-method** \[default = *MEDIAN*\]. - **--bspline-sampling** *\* BSPLINE sampling. 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´). The full name of this option for the EsoRex configuration file is **xsh.xsh\_scired\_slit\_stare.bspline-sampling** \[default = *FINE*\]. - **--sky-median-hsize** *\* Half size of the running median. If sky-method=MEDIAN . (int; default: 20). The full name of this option for the EsoRex configuration file is **xsh.xsh\_scired\_slit\_stare.sky-median-hsize** \[default = *20*\]. - **--sky-slit-edges-mask** *\* Size of edges mask in arcsec (float; default: 0.5). The full name of this option for the EsoRex configuration file is **xsh.xsh\_scired\_slit\_stare.sky-slit-edges-mask** \[default = *0.5*\]. - **--sky-position1** *\* Central position of the sky window #1 \[arcsec\] (float; default: 0.0). The full name of this option for the EsoRex configuration file is **xsh.xsh\_scired\_slit\_stare.sky-position1** \[default = *0.0*\]. - **--sky-hheight1** *\* Half size of sky window #1 \[arcsec\] (float; default: 0.0). The full name of this option for the EsoRex configuration file is **xsh.xsh\_scired\_slit\_stare.sky-hheight1** \[default = *0.0*\]. - **--sky-position2** *\* Central position of the sky window #2 \[arcsec\] (float; default: 0.0). The full name of this option for the EsoRex configuration file is **xsh.xsh\_scired\_slit\_stare.sky-position2** \[default = *0.0*\]. - **--sky-hheight2** *\* Half size of the sky window #2 \[arcsec\] (float; default: 0.0). The full name of this option for the EsoRex configuration file is **xsh.xsh\_scired\_slit\_stare.sky-hheight2** \[default = *0.0*\]. - **--stdextract-interp-hsize** *\* Half size of mask used to define object cross order profile (int; default: 30). The full name of this option for the EsoRex configuration file is **xsh.xsh\_scired\_slit\_stare.stdextract-interp-hsize** \[default = *30*\]. - **--do-optextract** *\* TRUE if we do the optimal extraction (bool; default: False). The full name of this option for the EsoRex configuration file is **xsh.xsh\_scired\_slit\_stare.do-optextract** \[default = *False*\]. - **--optextract-oversample** *\* Oversample factor for the science image (int; default: 5). The full name of this option for the EsoRex configuration file is **xsh.xsh\_scired\_slit\_stare.optextract-oversample** \[default = *5*\]. - **--optextract-box-half-size** *\* Extraction box \[pixel\] (int; default: 10). The full name of this option for the EsoRex configuration file is **xsh.xsh\_scired\_slit\_stare.optextract-box-half-size** \[default = *10*\]. - **--optextract-chunk-size** *\* Chunk size \[bin\] (int; default: 50). The full name of this option for the EsoRex configuration file is **xsh.xsh\_scired\_slit\_stare.optextract-chunk-size** \[default = *50*\]. - **--optextract-step-lambda** *\* Lambda step \[nm\] (float; default: 0.02). The full name of this option for the EsoRex configuration file is **xsh.xsh\_scired\_slit\_stare.optextract-step-lambda** \[default = *0.02*\]. - **--optextract-clip-kappa** *\* Kappa for cosmics ray hits rejection (float; default: 3.0). The full name of this option for the EsoRex configuration file is **xsh.xsh\_scired\_slit\_stare.optextract-clip-kappa** \[default = *3.0*\]. - **--optextract-clip-frac** *\* Maximum bad pixels fraction for cosmics ray hits rejection (float; default: 0.4). The full name of this option for the EsoRex configuration file is **xsh.xsh\_scired\_slit\_stare.optextract-clip-frac** \[default = *0.4*\]. - **--optextract-clip-niter** *\* Maximum number of iterations for cosmics ray hits rejection (int; default: 2). The full name of this option for the EsoRex configuration file is **xsh.xsh\_scired\_slit\_stare.optextract-clip-niter** \[default = *2*\]. - **--optextract-niter** *\* Number of iterations (int; default: 1). The full name of this option for the EsoRex configuration file is **xsh.xsh\_scired\_slit\_stare.optextract-niter** \[default = *1*\]. - **--optextract-method** *\* Extraction method GAUSSIAN \| GENERAL (str; default: ´GAUSSIAN´). The full name of this option for the EsoRex configuration file is **xsh.xsh\_scired\_slit\_stare.optextract-method** \[default = *GAUSSIAN*\]. - **--cut-uvb-spectrum** *\* TRUE if recipe cuts the UVB spectrum at 556 nm (dichroich) (bool; default: True). The full name of this option for the EsoRex configuration file is **xsh.xsh\_scired\_slit\_stare.cut-uvb-spectrum** \[default = *True*\]. - **--generate-SDP-format** *\* TRUE if additional files should be generated in Science Data Product (SDP) format. (bool; default: False). The full name of this option for the EsoRex configuration file is **xsh.xsh\_scired\_slit\_stare.generate-SDP-format** \[default = *False*\]. - **--dummy-association-keys** *\* Sets the number of dummy (empty) ASSONi, ASSOCi and ASSOMi keywords to create. (int; default: 0). The full name of this option for the EsoRex configuration file is **xsh.xsh\_scired\_slit\_stare.dummy-association-keys** \[default = *0*\]. Note that 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_2dmap/7.md), [*xsh\_cfg\_recover*(7)](/xsh_cfg_recover/7.md), [*xsh\_flexcomp*(7)](/xsh_flexcomp/7.md), [*xsh\_geom\_ifu*(7)](/xsh_geom_ifu/7.md), [*xsh\_lingain*(7)](/xsh_lingain/7.md), [*xsh\_mbias*(7)](/xsh_mbias/7.md), [*xsh\_mdark*(7)](/xsh_mdark/7.md), [*xsh\_mflat*(7)](/xsh_mflat/7.md), [*xsh\_orderpos*(7)](/xsh_orderpos/7.md), [*xsh\_predict*(7)](/xsh_predict/7.md), [*xsh\_respon\_slit\_nod*(7)](/xsh_respon_slit_nod/7.md), [*xsh\_respon\_slit\_offset*(7)](/xsh_respon_slit_offset/7.md), [*xsh\_respon\_slit\_stare*(7)](/xsh_respon_slit_stare/7.md), [*xsh\_scired\_ifu\_offset*(7)](/xsh_scired_ifu_offset/7.md), [*xsh\_scired\_ifu\_offset\_drl*(7)](/xsh_scired_ifu_offset_drl/7.md), [*xsh\_scired\_ifu\_stare*(7)](/xsh_scired_ifu_stare/7.md), [*xsh\_scired\_ifu\_stare\_drl*(7)](/xsh_scired_ifu_stare_drl/7.md), [*xsh\_scired\_slit\_nod*(7)](/xsh_scired_slit_nod/7.md), [*xsh\_scired\_slit\_offset*(7)](/xsh_scired_slit_offset/7.md), [*xsh\_util\_physmod*(7)](/xsh_util_physmod/7.md), [*xsh\_wavecal*(7)](/xsh_wavecal/7.md) ## VERSION xsh\_scired\_slit\_stare 3.5.0 ## AUTHOR P.Goldoni, L.Guglielmi, R. Haigron, F. Royer, D. Bramich, A. Modigliani \ ## BUG REPORTS Please report any problems to amodigli@eso.org. Alternatively, you may send a report to the ESO User Support Department \. ## LICENSE 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