xsh_cfg_recover(7) Optimizes a model configuration to match data taken after a major format change

SYNOPSIS

esorex xsh_cfg_recover [OPTIONS] FILE.sof

DESCRIPTION

This recipe creates a wavelength solution and an order table.


  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
      

OPTIONS

--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_cfg_recover.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_cfg_recover.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_cfg_recover.time-stamp [default = False].
--decode-bp <long>
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. (long; default: 2144337919). The full name of this option for the EsoRex configuration file is xsh.xsh_cfg_recover.decode-bp [default = 2144337919].
--first-anneal <bool>
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 xsh.xsh_cfg_recover.first-anneal [default = False].
--arm <str>
Arm setting: (str; default: 'vis'). The full name of this option for the EsoRex configuration file is xsh.xsh_model_compute.arm [default = vis].
--name_i <str>
Filename with wavelength,x,y,order: (str; default: 'line_xy_ord.txt'). The full name of this option for the EsoRex configuration file is xsh.xsh_model_compute.name_i [default = line_xy_ord.txt].
--niter <long>
No of iterations for first anneal (long; default: 100000). The full name of this option for the EsoRex configuration file is xsh.xsh_model_compute.niter [default = 100000].
--coord_frame <long>
Co-ordinate frame for centroids (0=raw,1=pre) (long; default: 1). The full name of this option for the EsoRex configuration file is xsh.xsh_model_compute.coord_frame [default = 1].
--last-step <bool>
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 xsh.xsh_cfg_recover.last-step [default = False].
--plot <bool>
Display plot (TRUE) or not (FALSE) (bool; default: False). The full name of this option for the EsoRex configuration file is xsh.xsh_cfg_recover.plot [default = False].
--ima_tresh_min <float>
Min thresh raw image. (float; default: 40.0). The full name of this option for the EsoRex configuration file is xsh.xsh_cfg_recover.ima_thresh_min [default = 40.0].
--cor_prescan <bool>
Correct for prescan (bool; default: False). The full name of this option for the EsoRex configuration file is xsh.xsh_cfg_recover.cor_prescan [default = False].
--method <str>
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 xsh.xsh_cfg_recover.method [default = safefit].
--offx <float>
X offset to model predictions (float; default: 0.0). The full name of this option for the EsoRex configuration file is xsh.xsh_cfg_recover.offx [default = 0.0].
--offy <float>
Y offset to model predictions (float; default: 0.0). The full name of this option for the EsoRex configuration file is xsh.xsh_cfg_recover.offy [default = 0.0].
--slit <long>
Extraction slit (long; default: 5). The full name of this option for the EsoRex configuration file is xsh.xsh_cfg_recover.slit [default = 5].
--gfit_box_sy <long>
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 xsh.xsh_cfg_recover.gfit_box_sy [default = 20].
--peak_line_fwhm <long>
The FWHM used in line convolution, in pixel units (long; default: 4). The full name of this option for the EsoRex configuration file is xsh.xsh_cfg_recover.peak_line_fwhm [default = 4].
--peak_kappa <float>
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 xsh.xsh_cfg_recover.peak_kappa [default = 5.0].
--peak_factor <float>
Relative Intensity threshold factor for line peaks detection (float; default: 10.0). The full name of this option for the EsoRex configuration file is xsh.xsh_cfg_recover.peak_factor [default = 10.0].
--peak_match_x <long>
Radii for line peaks matches (long; default: 10). The full name of this option for the EsoRex configuration file is xsh.xsh_cfg_recover.peak_match_x [default = 10].
--peak_match_y <long>
Radii for line peaks matches (long; default: 20). The full name of this option for the EsoRex configuration file is xsh.xsh_cfg_recover.peak_match_y [default = 20].
--pm_ord_sel <long>
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 xsh.xsh_cfg_recover.pm_ord_sel [default = 1].
--pm_radius <float>
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 xsh.xsh_cfg_recover.pm_radius [default = 20.0].
--pm_tolerance <float>
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 xsh.xsh_cfg_recover.pm_tolerance [default = 0.1].
--anneal_niter <long>
Simulated annealing iterations (long; default: 1000). The full name of this option for the EsoRex configuration file is xsh.xsh_cfg_recover.anneal_niter [default = 1000].

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.

VERSION

xsh_cfg_recover 2.7.1

AUTHOR

A. Modigliani, P. Bristow <[email protected]>

BUG REPORTS

Please report any problems to [email protected] Alternatively, you may send a report to the ESO User Support Department <[email protected]>.

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