Provided by: cpl-plugin-xshoo-doc_3.5.3+dfsg-1build1_all 
NAME
xsh_geom_ifu - Produces the spatial geometry of the IFU pattern on the sky
SYNOPSIS
esorex xsh_geom_ifu [OPTIONS] FILE.sof
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)
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_geom_ifu.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_geom_ifu.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_geom_ifu.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_geom_ifu.decode-bp
[default = 2144337919].
--pre-overscan-corr <int>
pre-overscan correction. 0: no correction 1: mean overscan correction 2: mean
prescan correction 3: (mean pre+mean overscan)/2 correction (int; default: 1). The
full name of this option for the EsoRex configuration file is
xsh.xsh_geom_ifu.pre-overscan-corr [default = 1].
--stack-method <str>
Method used to build master frame. (str; default: ´median´). The full name of this
option for the EsoRex configuration file is xsh.xsh_geom_ifu.stack-method [default
= median].
--klow <float>
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
xsh.xsh_geom_ifu.klow [default = 5.0].
--khigh <float>
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
xsh.xsh_geom_ifu.khigh [default = 5.0].
--crh-clip-kappa <float>
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
xsh.xsh_geom_ifu.crh-clip-kappa [default = 5.0].
--crh-clip-niter <int>
Number of iterations in sigma clipping during CRH rejection using multiple frames
(int; default: 5). The full name of this option for the EsoRex configuration file
is xsh.xsh_geom_ifu.crh-clip-niter [default = 5].
--crh-clip-frac <float>
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 xsh.xsh_geom_ifu.crh-clip-frac [default = 0.7].
--background-edges-margin <int>
X margin to order edge to define background sampling points (int; default: 1). The
full name of this option for the EsoRex configuration file is
xsh.xsh_geom_ifu.background-edges-margin [default = 1].
--background-poly-deg-y <int>
Poly mode fit deg along Y. (int; default: 9). The full name of this option for the
EsoRex configuration file is xsh.xsh_geom_ifu.background-poly-deg-y [default = 9].
--background-poly-deg-x <int>
Poly mode fit deg along X. (int; default: 9). The full name of this option for the
EsoRex configuration file is xsh.xsh_geom_ifu.background-poly-deg-x [default = 9].
--background-poly-kappa <float>
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
xsh.xsh_geom_ifu.background-poly-kappa [default = 10.0].
--removecrhsingle-sigmalim <float>
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 xsh.xsh_geom_ifu.removecrhsingle-sigmalim [default = 5.0].
--removecrhsingle-flim <float>
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 xsh.xsh_geom_ifu.removecrhsingle-flim [default = 2.0].
--removecrhsingle-niter <int>
Max number of iterations (int; default: 4). The full name of this option for the
EsoRex configuration file is xsh.xsh_geom_ifu.removecrhsingle-niter [default = 4].
--rectify-kernel <str>
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 xsh.xsh_geom_ifu.rectify-kernel [default = tanh].
--rectify-radius <float>
Rectify Interpolation radius [bin units]. (float; default: 4.0). The full name of
this option for the EsoRex configuration file is xsh.xsh_geom_ifu.rectify-radius
[default = 4.0].
--rectify-bin-lambda <float>
Wavelength step in the output spectrum [nm] (float; default: -1.0). The full name
of this option for the EsoRex configuration file is
xsh.xsh_geom_ifu.rectify-bin-lambda [default = -1.0].
--rectify-bin-slit <float>
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
xsh.xsh_geom_ifu.rectify-bin-slit [default = -1.0].
--localizeifu-bckg-deg <int>
Degree (<=2) of the polynomial component in the cross-dispersion profile fit (int;
default: 50). The full name of this option for the EsoRex configuration file is
xsh.xsh_geom_ifu.localizeifu-bckg-deg [default = 50].
--localizeifu-smooth-hsize <int>
Half-size of the median filter for smoothing the cross-dispersion profile prior to
localization (int; default: 3). The full name of this option for the EsoRex
configuration file is xsh.xsh_geom_ifu.localizeifu-smooth-hsize [default = 3].
--localizeifu-wavelet-nscales <int>
Number of scales used for wavelet a trous algorithm (int; default: 5). The full
name of this option for the EsoRex configuration file is
xsh.xsh_geom_ifu.localizeifu-wavelet-nscales [default = 5].
--localizeifu-wavelet-hf-skip <int>
Number of high frequency scales skipped from the wavelet decomposition (int;
default: 2). The full name of this option for the EsoRex configuration file is
xsh.xsh_geom_ifu.localizeifu-wavelet-hf-skip [default = 2].
--localizeifu-sigma-low <float>
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 xsh.xsh_geom_ifu.localizeifu-sigma-low [default = 0.05].
--localizeifu-sigma-up <float>
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 xsh.xsh_geom_ifu.localizeifu-sigma-up [default = 0.95].
--localizeifu-snr-low <float>
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 xsh.xsh_geom_ifu.localizeifu-snr-low [default = 0.05].
--localizeifu-snr-up <float>
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 xsh.xsh_geom_ifu.localizeifu-snr-up [default = 0.95].
--localizeifu-slitlow-edges-mask <float>
in arsec (float; default: 0.0). The full name of this option for the EsoRex
configuration file is xsh.xsh_geom_ifu.localizeifu-slitlow-edges-mask [default =
0.0].
--localizeifu-slitup-edges-mask <float>
in arsec (float; default: 0.0). The full name of this option for the EsoRex
configuration file is xsh.xsh_geom_ifu.localizeifu-slitup-edges-mask [default =
0.0].
--localizeifu-use-skymask <bool>
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
xsh.xsh_geom_ifu.localizeifu-use-skymask [default = False].
--localizeifu-chunk-hsize <int>
Half size of chunk [bin] (int; default: 0). The full name of this option for the
EsoRex configuration file is xsh.xsh_geom_ifu.localizeifu-chunk-hsize [default =
0].
--correctifu-niter <int>
Number of iterations in computing the localization shifts of the IFU slitlets (int;
default: 3). The full name of this option for the EsoRex configuration file is
xsh.xsh_geom_ifu.correctifu-niter [default = 3].
--correctifu-lambdaref <float>
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
xsh.xsh_geom_ifu.correctifu-lambdaref [default = -1.0].
--correctifu-lambdaref-hsize <float>
HAlf size in nm to estimate reference wavelength (float; default: 2.5). The full
name of this option for the EsoRex configuration file is
xsh.xsh_geom_ifu.correctifu-lambdaref-hsize [default = 2.5].
--do-cube <bool>
if TRUE creates a data cube (bool; default: False). The full name of this option
for the EsoRex configuration file is xsh.xsh_geom_ifu.do-cube [default = False].
--compute-map <bool>
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
xsh.xsh_geom_ifu.compute-map [default = True].
--check-afc <bool>
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 xsh.xsh_geom_ifu.check-afc [default = True].
--flat-method <str>
method adopted for flat: (str; default: ´blaze´). The full name of this option for
the EsoRex configuration file is xsh.xsh_geom_ifu.flat-method [default = blaze].
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_cfg_recover(7),
xsh_flexcomp(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_geom_ifu 3.5.3
AUTHOR
P.Goldoni, L.Guglielmi, R. Haigron, F. Royer <regis.haigron@obspm.fr>
BUG REPORTS
Please report any problems to regis.haigron@obspm.fr. 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