xsh_geom_ifu - Produces the spatial geometry of the IFU pattern on
the sky
esorex xsh_geom_ifu [OPTIONS] FILE.sof
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)
- --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.
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)
P.Goldoni, L.Guglielmi, R. Haigron, F. Royer
<regis.haigron@obspm.fr>
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>.
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