.TH XSH_SCIRED_SLIT_STARE "7" "3.5.3" "xsh_scired_slit_stare" "xshoo recipes" .SH NAME xsh_scired_slit_stare \- Reduce science exposure in SLIT configuration and stare mode .SH SYNOPSIS esorex .B xsh_scired_slit_stare [OPTIONS] FILE.sof .SH 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). .PP If both master and individual response are provided the individual response is preferred. .PP 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 .SH OPTIONS .TP \fB\-\-keep\-temp\fR \fI\fR If \'no\', temporary files are deleted. (str; default: \'no\'). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_scired_slit_stare.keep\-temp\fR [default = \fIno\fR]. .TP \fB\-\-debug\-level\fR \fI\fR 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 \fBxsh.xsh_scired_slit_stare.debug\-level\fR [default = \fInone\fR]. .TP \fB\-\-time\-stamp\fR \fI\fR Add timestamp to product file name. (bool; default: False). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_scired_slit_stare.time\-stamp\fR [default = \fIFalse\fR]. .TP \fB\-\-decode\-bp\fR \fI\fR 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 \fBxsh.xsh_scired_slit_stare.decode\-bp\fR [default = \fI2144337919\fR]. .TP \fB\-\-pre\-overscan\-corr\fR \fI\fR 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 \fBxsh.xsh_scired_slit_stare.pre\-overscan\-corr\fR [default = \fI1\fR]. .TP \fB\-\-stack\-method\fR \fI\fR Method used to build master frame. (str; default: \'median\'). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_scired_slit_stare.stack\-method\fR [default = \fImedian\fR]. .TP \fB\-\-klow\fR \fI\fR 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 \fBxsh.xsh_scired_slit_stare.klow\fR [default = \fI5.0\fR]. .TP \fB\-\-khigh\fR \fI\fR 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 \fBxsh.xsh_scired_slit_stare.khigh\fR [default = \fI5.0\fR]. .TP \fB\-\-background\-edges\-margin\fR \fI\fR 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 \fBxsh.xsh_scired_slit_stare.background\-edges\-margin\fR [default = \fI1\fR]. .TP \fB\-\-background\-poly\-deg\-y\fR \fI\fR Poly mode fit deg along Y. (int; default: 9). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_scired_slit_stare.background\-poly\-deg\-y\fR [default = \fI9\fR]. .TP \fB\-\-background\-poly\-deg\-x\fR \fI\fR Poly mode fit deg along X. (int; default: 9). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_scired_slit_stare.background\-poly\-deg\-x\fR [default = \fI9\fR]. .TP \fB\-\-background\-poly\-kappa\fR \fI\fR 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 \fBxsh.xsh_scired_slit_stare.background\-poly\-kappa\fR [default = \fI10.0\fR]. .TP \fB\-\-removecrhsingle\-sigmalim\fR \fI\fR 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 \fBxsh.xsh_scired_slit_stare.removecrhsingle\-sigmalim\fR [default = \fI20.0\fR]. .TP \fB\-\-removecrhsingle\-flim\fR \fI\fR 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 \fBxsh.xsh_scired_slit_stare.removecrhsingle\-flim\fR [default = \fI2.0\fR]. .TP \fB\-\-removecrhsingle\-niter\fR \fI\fR Max number of iterations (int; default: 4). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_scired_slit_stare.removecrhsingle\-niter\fR [default = \fI4\fR]. .TP \fB\-\-rectify\-kernel\fR \fI\fR 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 \fBxsh.xsh_scired_slit_stare.rectify\-kernel\fR [default = \fItanh\fR]. .TP \fB\-\-rectify\-radius\fR \fI\fR Rectify Interpolation radius [bin units]. (float; default: 2.0). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_scired_slit_stare.rectify\-radius\fR [default = \fI2.0\fR]. .TP \fB\-\-rectify\-bin\-lambda\fR \fI\fR Wavelength step in the output spectrum [nm] (float; default: \-1.0). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_scired_slit_stare.rectify\-bin\-lambda\fR [default = \fI\-1.0\fR]. .TP \fB\-\-rectify\-bin\-slit\fR \fI\fR 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 \fBxsh.xsh_scired_slit_stare.rectify\-bin\-slit\fR [default = \fI\-1.0\fR]. .TP \fB\-\-localize\-method\fR \fI\fR 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 \fBxsh.xsh_scired_slit_stare.localize\-method\fR [default = \fIMANUAL\fR]. .TP \fB\-\-localize\-chunk\-nb\fR \fI\fR 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 \fBxsh.xsh_scired_slit_stare.localize\-chunk\-nb\fR [default = \fI10\fR]. .TP \fB\-\-localize\-thresh\fR \fI\fR 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 \fBxsh.xsh_scired_slit_stare.localize\-thresh\fR [default = \fI0.1\fR]. .TP \fB\-\-localize\-deg\-lambda\fR \fI\fR 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 \fBxsh.xsh_scired_slit_stare.localize\-deg\-lambda\fR [default = \fI0\fR]. .TP \fB\-\-localize\-slit\-position\fR \fI\fR 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 \fBxsh.xsh_scired_slit_stare.localize\-slit\-position\fR [default = \fI0.0\fR]. .TP \fB\-\-localize\-slit\-hheight\fR \fI\fR 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 \fBxsh.xsh_scired_slit_stare.localize\-slit\-hheight\fR [default = \fI2.0\fR]. .TP \fB\-\-localize\-kappa\fR \fI\fR 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 \fBxsh.xsh_scired_slit_stare.localize\-kappa\fR [default = \fI3.0\fR]. .TP \fB\-\-localize\-niter\fR \fI\fR 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 \fBxsh.xsh_scired_slit_stare.localize\-niter\fR [default = \fI3\fR]. .TP \fB\-\-localize\-use\-skymask\fR \fI\fR 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 \fBxsh.xsh_scired_slit_stare.localize\-use\-skymask\fR [default = \fIFalse\fR]. .TP \fB\-\-sky\-subtract\fR \fI\fR TRUE to use subtract sky single. (bool; default: True). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_scired_slit_stare.sky\-subtract\fR [default = \fITrue\fR]. .TP \fB\-\-sky\-bspline\-nbkpts\-first\fR \fI\fR 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 \fBxsh.xsh_scired_slit_stare.sky\-bspline\-nbkpts\-first\fR [default = \fI3000\fR]. .TP \fB\-\-sky\-bspline\-nbkpts\-second\fR \fI\fR 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 \fBxsh.xsh_scired_slit_stare.sky\-bspline\-nbkpts\-second\fR [default = \fI3000\fR]. .TP \fB\-\-sky\-bspline\-order\fR \fI\fR Bezier spline order (int; default: 7). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_scired_slit_stare.sky\-bspline\-order\fR [default = \fI7\fR]. .TP \fB\-\-sky\-bspline\-niter\fR \fI\fR Nb of iterations (int; default: 20). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_scired_slit_stare.sky\-bspline\-niter\fR [default = \fI20\fR]. .TP \fB\-\-sky\-bspline\-kappa\fR \fI\fR Kappa value used to kappa\-sigma\-clip object (float; default: 5.0). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_scired_slit_stare.sky\-bspline\-kappa\fR [default = \fI5.0\fR]. .TP \fB\-\-sky\-method\fR \fI\fR 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 \fBxsh.xsh_scired_slit_stare.sky\-method\fR [default = \fIMEDIAN\fR]. .TP \fB\-\-bspline\-sampling\fR \fI\fR 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 \fBxsh.xsh_scired_slit_stare.bspline\-sampling\fR [default = \fIFINE\fR]. .TP \fB\-\-sky\-median\-hsize\fR \fI\fR 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 \fBxsh.xsh_scired_slit_stare.sky\-median\-hsize\fR [default = \fI20\fR]. .TP \fB\-\-sky\-slit\-edges\-mask\fR \fI\fR Size of edges mask in arcsec (float; default: 0.5). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_scired_slit_stare.sky\-slit\-edges\-mask\fR [default = \fI0.5\fR]. .TP \fB\-\-sky\-position1\fR \fI\fR Central position of the sky window #1 [arcsec] (float; default: 0.0). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_scired_slit_stare.sky\-position1\fR [default = \fI0.0\fR]. .TP \fB\-\-sky\-hheight1\fR \fI\fR Half size of sky window #1 [arcsec] (float; default: 0.0). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_scired_slit_stare.sky\-hheight1\fR [default = \fI0.0\fR]. .TP \fB\-\-sky\-position2\fR \fI\fR Central position of the sky window #2 [arcsec] (float; default: 0.0). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_scired_slit_stare.sky\-position2\fR [default = \fI0.0\fR]. .TP \fB\-\-sky\-hheight2\fR \fI\fR Half size of the sky window #2 [arcsec] (float; default: 0.0). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_scired_slit_stare.sky\-hheight2\fR [default = \fI0.0\fR]. .TP \fB\-\-stdextract\-interp\-hsize\fR \fI\fR 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 \fBxsh.xsh_scired_slit_stare.stdextract\-interp\-hsize\fR [default = \fI30\fR]. .TP \fB\-\-do\-optextract\fR \fI\fR TRUE if we do the optimal extraction (bool; default: False). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_scired_slit_stare.do\-optextract\fR [default = \fIFalse\fR]. .TP \fB\-\-optextract\-oversample\fR \fI\fR Oversample factor for the science image (int; default: 5). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_scired_slit_stare.optextract\-oversample\fR [default = \fI5\fR]. .TP \fB\-\-optextract\-box\-half\-size\fR \fI\fR Extraction box [pixel] (int; default: 10). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_scired_slit_stare.optextract\-box\-half\-size\fR [default = \fI10\fR]. .TP \fB\-\-optextract\-chunk\-size\fR \fI\fR Chunk size [bin] (int; default: 50). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_scired_slit_stare.optextract\-chunk\-size\fR [default = \fI50\fR]. .TP \fB\-\-optextract\-step\-lambda\fR \fI\fR Lambda step [nm] (float; default: 0.02). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_scired_slit_stare.optextract\-step\-lambda\fR [default = \fI0.02\fR]. .TP \fB\-\-optextract\-clip\-kappa\fR \fI\fR Kappa for cosmics ray hits rejection (float; default: 3.0). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_scired_slit_stare.optextract\-clip\-kappa\fR [default = \fI3.0\fR]. .TP \fB\-\-optextract\-clip\-frac\fR \fI\fR 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 \fBxsh.xsh_scired_slit_stare.optextract\-clip\-frac\fR [default = \fI0.4\fR]. .TP \fB\-\-optextract\-clip\-niter\fR \fI\fR Maximum number of iterations for cosmics ray hits rejection (int; default: 2). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_scired_slit_stare.optextract\-clip\-niter\fR [default = \fI2\fR]. .TP \fB\-\-optextract\-niter\fR \fI\fR Number of iterations (int; default: 1). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_scired_slit_stare.optextract\-niter\fR [default = \fI1\fR]. .TP \fB\-\-optextract\-method\fR \fI\fR Extraction method GAUSSIAN | GENERAL (str; default: \'GAUSSIAN\'). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_scired_slit_stare.optextract\-method\fR [default = \fIGAUSSIAN\fR]. .TP \fB\-\-cut\-uvb\-spectrum\fR \fI\fR 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 \fBxsh.xsh_scired_slit_stare.cut\-uvb\-spectrum\fR [default = \fITrue\fR]. .TP \fB\-\-generate\-SDP\-format\fR \fI\fR 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 \fBxsh.xsh_scired_slit_stare.generate\-SDP\-format\fR [default = \fIFalse\fR]. .TP \fB\-\-dummy\-association\-keys\fR \fI\fR 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 \fBxsh.xsh_scired_slit_stare.dummy\-association\-keys\fR [default = \fI0\fR]. .PP 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. .SH SEE ALSO The full documentation for the xshoo pipeline can be downloaded as a PDF file using the following URL: .IP .B ftp://ftp.eso.org/pub/dfs/pipelines/xshoo/xshoo\-pipeline\-manual\-12.1.pdf .PP An overview over the existing ESO pipelines can be found on the web page \fBhttps://www.eso.org/sci/software/pipelines/\fR. .PP Basic documentation about the EsoRex program can be found at the esorex (1) man page. .PP It is possible to call the pipelines from python using the python\-cpl package. See \fBhttps://packages.python.org/python\-cpl/index.html\fR for further information. .PP The other recipes of the xshoo pipeline are .IR xsh_2dmap (7), .IR xsh_cfg_recover (7), .IR xsh_flexcomp (7), .IR xsh_geom_ifu (7), .IR xsh_lingain (7), .IR xsh_mbias (7), .IR xsh_mdark (7), .IR xsh_mflat (7), .IR xsh_orderpos (7), .IR xsh_predict (7), .IR xsh_respon_slit_nod (7), .IR xsh_respon_slit_offset (7), .IR xsh_respon_slit_stare (7), .IR xsh_scired_ifu_offset (7), .IR xsh_scired_ifu_offset_drl (7), .IR xsh_scired_ifu_stare (7), .IR xsh_scired_ifu_stare_drl (7), .IR xsh_scired_slit_nod (7), .IR xsh_scired_slit_offset (7), .IR xsh_util_physmod (7), .IR xsh_wavecal (7) .SH VERSION xsh_scired_slit_stare 3.5.3 .SH AUTHOR P.Goldoni, L.Guglielmi, R. Haigron, F. Royer, D. Bramich, A. Modigliani .SH BUG REPORTS Please report any problems to amodigli@eso.org. Alternatively, you may send a report to the ESO User Support Department . .SH 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