Provided by: cpl-plugin-xshoo-doc_3.5.3+dfsg-1build4_all 
NAME
xsh_cfg_recover - 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 <int>
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_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 <int>
No of iterations for first anneal (int; default: 100000). The full name of this
option for the EsoRex configuration file is xsh.xsh_model_compute.niter [default =
100000].
--coord_frame <int>
Co-ordinate frame for centroids (0=raw,1=pre) (int; 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 <int>
Extraction slit (int; default: 5). The full name of this option for the EsoRex
configuration file is xsh.xsh_cfg_recover.slit [default = 5].
--gfit_box_sy <int>
Gauss fit Y search box size for lines on actual frame (int; 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 <int>
The FWHM used in line convolution, in pixel units (int; 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 <int>
Radii for line peaks matches (int; 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 <int>
Radii for line peaks matches (int; 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 <int>
From guess line and peaks positions are extracted the ones in the range
[ord_min,ord_min+pm_ord_sel] (int; 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 <int>
Simulated annealing iterations (int; 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.
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_flexcomp(7),
xsh_geom_ifu(7), xsh_lingain(7), xsh_mbias(7), xsh_mdark(7), xsh_mflat(7),
xsh_orderpos(7), xsh_predict(7), xsh_respon_slit_nod(7), xsh_respon_slit_offset(7),
xsh_respon_slit_stare(7), xsh_scired_ifu_offset(7), xsh_scired_ifu_offset_drl(7),
xsh_scired_ifu_stare(7), xsh_scired_ifu_stare_drl(7), xsh_scired_slit_nod(7),
xsh_scired_slit_offset(7), xsh_scired_slit_stare(7), xsh_util_physmod(7), xsh_wavecal(7)
VERSION
xsh_cfg_recover 3.5.3
AUTHOR
A. Modigliani, P. Bristow <amodigli@eso.org>
BUG REPORTS
Please report any problems to amodigli@eso.org. Alternatively, you may send a report to
the ESO User Support Department <usd-help@eso.org>.
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