.TH XSH_GEOM_IFU "7" "2.5.2" "xsh_geom_ifu" "xshoo recipes" .SH NAME xsh_geom_ifu \- Produces the spatial geometry of the IFU pattern on the sky .SH SYNOPSIS esorex .B xsh_geom_ifu [OPTIONS] FILE.sof .SH DESCRIPTION This recipe Produces the spatial geometry of the IFU pattern on the sky Input Frames : \- A set of n science frames ( n == 1 or >=3, Tag = TRACE_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_IFU_arm) \- An AFC corrected model order edges table for IFU frame (Tag = ORDER_TAB_AFC_IFU_arm) \- [PHYSMOD] An AFC corrected model cfg frame (Tag = XSH_MOD_CFG_OPT_AFC_arm) \- [POLY] An AFC corrected model wavesol frame (Tag = WAVE_TAB_AFC_arm) \- An AFC corrected dispersion solution frame (Tag = DISP_TAB_AFC_arm) \- [OPTIONAL] A badpixel map (Tag = BADPIXEL_MAP_arm) Products : \- A set of shift offset tables (Tag = OFFSET_TAB_slitlet_IFU_arm) .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_geom_ifu.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_geom_ifu.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_geom_ifu.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. (long; default: 2144337919). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_geom_ifu.decode\-bp\fR [default = \fI2144337919\fR]. .TP \fB\-\-pre\-overscan\-corr\fR \fI\fR pre\-overscan correction.0: no correction1: mean overscan correction2: mean prescan correction3: (mean pre+mean overscan)/2 correction (long; default: 1). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_geom_ifu.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_geom_ifu.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_geom_ifu.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_geom_ifu.khigh\fR [default = \fI5.0\fR]. .TP \fB\-\-crh\-clip\-kappa\fR \fI\fR Kappa value in sigma clipping during CRH rejection using multiple frames (float; default: 5.0). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_geom_ifu.crh\-clip\-kappa\fR [default = \fI5.0\fR]. .TP \fB\-\-crh\-clip\-niter\fR \fI\fR Number of iterations in sigma clipping during CRH rejection using multiple frames (long; default: 5). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_geom_ifu.crh\-clip\-niter\fR [default = \fI5\fR]. .TP \fB\-\-crh\-clip\-frac\fR \fI\fR Minimal ratio of points accepted / total in sigma clipping during CRH rejection using multiple frames (float; default: 0.7). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_geom_ifu.crh\-clip\-frac\fR [default = \fI0.7\fR]. .TP \fB\-\-background\-edges\-margin\fR \fI\fR X margin to order edge to define background sampling points (long; default: 1). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_geom_ifu.background\-edges\-margin\fR [default = \fI1\fR]. .TP \fB\-\-background\-poly\-deg\-y\fR \fI\fR Poly mode fit deg along Y. (long; default: 9). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_geom_ifu.background\-poly\-deg\-y\fR [default = \fI9\fR]. .TP \fB\-\-background\-poly\-deg\-x\fR \fI\fR Poly mode fit deg along X. (long; default: 9). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_geom_ifu.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_geom_ifu.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: 5.0). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_geom_ifu.removecrhsingle\-sigmalim\fR [default = \fI5.0\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_geom_ifu.removecrhsingle\-flim\fR [default = \fI2.0\fR]. .TP \fB\-\-removecrhsingle\-niter\fR \fI\fR Max number of iterations (long; default: 4). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_geom_ifu.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_geom_ifu.rectify\-kernel\fR [default = \fItanh\fR]. .TP \fB\-\-rectify\-radius\fR \fI\fR Rectify Interpolation radius [bin units]. (float; default: 4.0). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_geom_ifu.rectify\-radius\fR [default = \fI4.0\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_geom_ifu.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_geom_ifu.rectify\-bin\-slit\fR [default = \fI\-1.0\fR]. .TP \fB\-\-localizeifu\-bckg\-deg\fR \fI\fR Degree (<=2) of the polynomial component in the cross\-dispersion profile fit (long; default: 50). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_geom_ifu.localizeifu\-bckg\-deg\fR [default = \fI50\fR]. .TP \fB\-\-localizeifu\-smooth\-hsize\fR \fI\fR Half\-size of the median filter for smoothing the cross\-dispersion profile prior to localization (long; default: 3). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_geom_ifu.localizeifu\-smooth\-hsize\fR [default = \fI3\fR]. .TP \fB\-\-localizeifu\-wavelet\-nscales\fR \fI\fR Number of scales used for wavelet a trous algorithm (long; default: 5). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_geom_ifu.localizeifu\-wavelet\-nscales\fR [default = \fI5\fR]. .TP \fB\-\-localizeifu\-wavelet\-hf\-skip\fR \fI\fR Number of high frequency scales skipped from the wavelet decomposition (long; default: 2). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_geom_ifu.localizeifu\-wavelet\-hf\-skip\fR [default = \fI2\fR]. .TP \fB\-\-localizeifu\-sigma\-low\fR \fI\fR Gaussian fits of the cross\-dispersion profile whose FWHM is lower than this value are rejected (float; default: 0.05). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_geom_ifu.localizeifu\-sigma\-low\fR [default = \fI0.05\fR]. .TP \fB\-\-localizeifu\-sigma\-up\fR \fI\fR Gaussian fits of the cross\-dispersion profile whose FWHM is larger than this value are rejected (float; default: 0.95). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_geom_ifu.localizeifu\-sigma\-up\fR [default = \fI0.95\fR]. .TP \fB\-\-localizeifu\-snr\-low\fR \fI\fR Gaussian fits of the cross\-dispersion profile whose SNR is lower than this value are rejected (float; default: 0.05). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_geom_ifu.localizeifu\-snr\-low\fR [default = \fI0.05\fR]. .TP \fB\-\-localizeifu\-snr\-up\fR \fI\fR Gaussian fits of the cross\-dispersion profile whose SNR is larger than this value are rejected (float; default: 0.95). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_geom_ifu.localizeifu\-snr\-up\fR [default = \fI0.95\fR]. .TP \fB\-\-localizeifu\-slitlow\-edges\-mask\fR \fI\fR in arsec (float; default: 0.0). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_geom_ifu.localizeifu\-slitlow\-edges\-mask\fR [default = \fI0.0\fR]. .TP \fB\-\-localizeifu\-slitup\-edges\-mask\fR \fI\fR in arsec (float; default: 0.0). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_geom_ifu.localizeifu\-slitup\-edges\-mask\fR [default = \fI0.0\fR]. .TP \fB\-\-localizeifu\-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_geom_ifu.localizeifu\-use\-skymask\fR [default = \fIFalse\fR]. .TP \fB\-\-localizeifu\-chunk\-hsize\fR \fI\fR Half size of chunk [bin] (long; default: 0). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_geom_ifu.localizeifu\-chunk\-hsize\fR [default = \fI0\fR]. .TP \fB\-\-correctifu\-niter\fR \fI\fR Number of iterations in computing the localization shifts of the IFU slitlets (long; default: 3). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_geom_ifu.correctifu\-niter\fR [default = \fI3\fR]. .TP \fB\-\-correctifu\-lambdaref\fR \fI\fR Reference wavelength where the reference localization on the slit is chosen (float; default: \-1.0). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_geom_ifu.correctifu\-lambdaref\fR [default = \fI\-1.0\fR]. .TP \fB\-\-correctifu\-lambdaref\-hsize\fR \fI\fR HAlf size in nm to estimate reference wavelength (float; default: 2.5). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_geom_ifu.correctifu\-lambdaref\-hsize\fR [default = \fI2.5\fR]. .TP \fB\-\-do\-cube\fR \fI\fR if TRUE creates a data cube (bool; default: False). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_geom_ifu.do\-cube\fR [default = \fIFalse\fR]. .TP \fB\-\-compute\-map\fR \fI\fR if TRUE recompute (wave and slit) maps from the dispersion solution. (bool; default: True). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_geom_ifu.compute\-map\fR [default = \fITrue\fR]. .TP \fB\-\-check\-afc\fR \fI\fR Input AFC corrected model/wave solution and science frame check.If TRUE the recipe verify that the input mode/wave solution is AFC corrected, its INS.OPTIi.NAME is \'Pin_0.5 \', and its OBS.ID and OBS.TARG.NAME values matches with the corresponding values of the science frame. (bool; default: True). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_geom_ifu.check\-afc\fR [default = \fITrue\fR]. .TP \fB\-\-flat\-method\fR \fI\fR method adopted for flat: (str; default: \'blaze\'). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_geom_ifu.flat\-method\fR [default = \fIblaze\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 \fBhttp://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 \fBhttp://packages.python.org/python\-cpl/index.html\fR for further information. .PP The other recipes of the xshoo pipeline are .IR xsh_cfg_recover (7), .IR xsh_lingain (7), .IR xsh_wavecal (7), .IR xsh_scired_slit_nod (7), .IR xsh_respon_slit_nod (7), .IR xsh_mdark (7), .IR xsh_respon_slit_offset (7), .IR xsh_orderpos (7), .IR xsh_scired_ifu_stare_drl (7), .IR xsh_scired_ifu_stare (7), .IR xsh_flexcomp (7), .IR xsh_scired_ifu_offset_drl (7), .IR xsh_util_physmod (7), .IR xsh_respon_slit_stare (7), .IR xsh_2dmap (7), .IR xsh_mflat (7), .IR xsh_mbias (7), .IR xsh_predict (7), .IR xsh_scired_ifu_offset (7), .IR xsh_scired_slit_stare (7), .IR xsh_scired_slit_offset (7) .SH VERSION xsh_geom_ifu 2.5.2 .SH AUTHOR P.Goldoni, L.Guglielmi, R. Haigron, F. Royer .SH BUG REPORTS Please report any problems to regis.haigron@obspm.fr. 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