.TH XSH_CFG_RECOVER "7" "2.5.2" "xsh_cfg_recover" "xshoo recipes" .SH NAME xsh_cfg_recover \- Optimizes a model configuration to match data taken after a major format change .SH SYNOPSIS esorex .B xsh_cfg_recover [OPTIONS] FILE.sof .SH DESCRIPTION This recipe creates a wavelength solution and an order table. .PP Input Frames : \- [UVB, VIS] A RAW frame (Format = RAW, Tag = FMTCHK_arm) \- [NIR] Two RAW frames (Format = RAW, Tag = FMTCHK_arm_ON,FMTCHK_arm_OFF) \- The old model cfg table (Format = TABLE, Tag = XSH_MOD_CFG_TAB_arm) \- A ref. line list. The model computes corresponding positions (Format = TABLE, Tag = ARC_LINE_LIST_arm) \- [UVB,VIS,OPTIONAL] A master bias (Format = PRE, Tag = MASTER_BIAS_arm) \- [UVB,VIS,OPTIONAL] A master dark (Format = PRE, Tag = MASTER_DARK_arm) \- [OPTIONAL\-Required if method=pm,peaks] An order table (Format = TABLE, Tag = ORDER_TAB_CENTR_arm) \- [OPTIONAL\-Required if first\-anneal=TRUE] A table with measured line positions (Format = TABLE, Tag = XSH_MEASCOORD_arm) Products : \- if first\-anneal=FALSE & last\-step=FALSE nothing \- if first\-anneal=TRUE & last\-step=FALSE an optimized model configuration, PRO.CATG=XSH_MOD_CFG_arm \- if last\-step=TRUE an optimized model configuration, PRO.CATG=XSH_MOD_FAN_arm an optimized model configuration, PRO.CATG=XSH_MOD_CFG_OPT_arm an quality control table, PRO.CATG=MODEL_GUESS_XY_arm the model theoretical map corresponding to the optimized model config, PRO.CATG=THEO_TAB_MULT_arm, THEO_TAB_IFU_arm, and THEO_TAB_SING_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_cfg_recover.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_cfg_recover.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_cfg_recover.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_cfg_recover.decode\-bp\fR [default = \fI2144337919\fR]. .TP \fB\-\-first\-anneal\fR \fI\fR Run first annealing (TRUE) or not (FALSE)See recipe man\-page % Input frames (bool; default: False). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_cfg_recover.first\-anneal\fR [default = \fIFalse\fR]. .TP \fB\-\-arm\fR \fI\fR Arm setting: (str; default: \'vis\'). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_model_compute.arm\fR [default = \fIvis\fR]. .TP \fB\-\-name_i\fR \fI\fR Filename with wavelength,x,y,order: (str; default: \'line_xy_ord.txt\'). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_model_compute.name_i\fR [default = \fIline_xy_ord.txt\fR]. .TP \fB\-\-niter\fR \fI\fR No of iterations for first anneal (long; default: 100000). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_model_compute.niter\fR [default = \fI100000\fR]. .TP \fB\-\-coord_frame\fR \fI\fR Co\-ordinate frame for centroids (0=raw,1=pre) (long; default: 1). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_model_compute.coord_frame\fR [default = \fI1\fR]. .TP \fB\-\-last\-step\fR \fI\fR Run last step (TRUE) or not (FALSE)See recipe man\-page % Input frames (bool; default: False). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_cfg_recover.last\-step\fR [default = \fIFalse\fR]. .TP \fB\-\-plot\fR \fI\fR Display plot (TRUE) or not (FALSE) (bool; default: False). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_cfg_recover.plot\fR [default = \fIFalse\fR]. .TP \fB\-\-ima_tresh_min\fR \fI\fR Min thresh raw image. (float; default: 40.0). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_cfg_recover.ima_thresh_min\fR [default = \fI40.0\fR]. .TP \fB\-\-cor_prescan\fR \fI\fR Correct for prescan (bool; default: False). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_cfg_recover.cor_prescan\fR [default = \fIFalse\fR]. .TP \fB\-\-method\fR \fI\fR Model predictions correction method. safefit: safe fitgfit: 2D Gaussian line fitpeaks: line peaks detectionpm: line peaks detection & pattern match (str; default: \'safefit\'). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_cfg_recover.method\fR [default = \fIsafefit\fR]. .TP \fB\-\-offx\fR \fI\fR X offset to model predictions (float; default: 0.0). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_cfg_recover.offx\fR [default = \fI0.0\fR]. .TP \fB\-\-offy\fR \fI\fR Y offset to model predictions (float; default: 0.0). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_cfg_recover.offy\fR [default = \fI0.0\fR]. .TP \fB\-\-slit\fR \fI\fR Extraction slit (long; default: 5). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_cfg_recover.slit\fR [default = \fI5\fR]. .TP \fB\-\-gfit_box_sy\fR \fI\fR Gauss fit Y search box size for lines on actual frame (long; default: 20). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_cfg_recover.gfit_box_sy\fR [default = \fI20\fR]. .TP \fB\-\-peak_line_fwhm\fR \fI\fR The FWHM used in line convolution, in pixel units (long; default: 4). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_cfg_recover.peak_line_fwhm\fR [default = \fI4\fR]. .TP \fB\-\-peak_kappa\fR \fI\fR The kappa value, used to identify line peaks if max>kappa*stdev+median, max is a valid peak where max, stdev,median are computed on the extracted spectrum (float; default: 5.0). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_cfg_recover.peak_kappa\fR [default = \fI5.0\fR]. .TP \fB\-\-peak_factor\fR \fI\fR Relative Intensity threshold factor for line peaks detection (float; default: 10.0). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_cfg_recover.peak_factor\fR [default = \fI10.0\fR]. .TP \fB\-\-peak_match_x\fR \fI\fR Radii for line peaks matches (long; default: 10). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_cfg_recover.peak_match_x\fR [default = \fI10\fR]. .TP \fB\-\-peak_match_y\fR \fI\fR Radii for line peaks matches (long; default: 20). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_cfg_recover.peak_match_y\fR [default = \fI20\fR]. .TP \fB\-\-pm_ord_sel\fR \fI\fR From guess line and peaks positions are extracted the ones in the range [ord_min,ord_min+pm_ord_sel] (long; default: 1). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_cfg_recover.pm_ord_sel\fR [default = \fI1\fR]. .TP \fB\-\-pm_radius\fR \fI\fR Search radius applied in final pattern matching (data units). (float; default: 20.0). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_cfg_recover.pm_radius\fR [default = \fI20.0\fR]. .TP \fB\-\-pm_tolerance\fR \fI\fR Max relative difference of angles and scales from their median value for match acceptance. (float; default: 0.1). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_cfg_recover.pm_tolerance\fR [default = \fI0.1\fR]. .TP \fB\-\-anneal_niter\fR \fI\fR Simulated annealing iterations (long; default: 1000). The full name of this option for the EsoRex configuration file is \fBxsh.xsh_cfg_recover.anneal_niter\fR [default = \fI1000\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_lingain (7), .IR xsh_geom_ifu (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_cfg_recover 2.5.2 .SH AUTHOR A. Modigliani, P. Bristow .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