xsh_cfg_recover - Optimizes a model configuration to match data
taken after a major format change
esorex xsh_cfg_recover [OPTIONS] FILE.sof
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
- --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.
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)
A. Modigliani, P. Bristow <amodigli@eso.org>
Please report any problems to amodigli@eso.org. Alternatively, you
may send a report to the ESO User Support Department
<usd-help@eso.org>.
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