Provided by: cpl-plugin-xshoo-doc_3.5.3+dfsg-1build1_all 
NAME
xsh_scired_slit_stare - Reduce science exposure in SLIT configuration and stare mode
SYNOPSIS
esorex xsh_scired_slit_stare [OPTIONS] FILE.sof
DESCRIPTION
This recipe reduces science exposure in SLIT configuration and stare mode Input Frames :
- A set of n Science frames ( n == 1 or >=3, Tag = OBJECT_SLIT_STARE_UVB)
- A spectral format table (Tag = SPECTRAL_FORMAT_TAB_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_SLIT_arm)
- An order table frame(Tag = ORDER_TAB_EDGES_SLIT_arm)
- [OPTIONAL] A table with dispersion coefficients (Tag = DISP_TAB_arm,
required in poly mode
- [poly mode] A wave solution frame(Tag = WAVE_TAB_2D_arm)
- [physical model mode] A model cfg table (Format = TABLE, Tag = XSH_MOD_CFG_TAB_arm)
- [OPTIONAL] A table specifying multiplying factor for break points
(Tag = SKY_SUB_BKPTS_arm) to generate
- [OPTIONAL] A non-linear badpixel map (Tag = BP_MAP_NL_arm)
- [OPTIONAL] A reference badpixel map (Tag = BP_MAP_RP_arm)
- [OPTIONAL,physmod mode] A table listing sky line positions (Tag = SKY_LINE_LIST_arm)
this is used to be able to control quality of sky subtraction, for example
projecting guess positions on the product SCI_SLIT_STARE_SUB_SKY_arm
and is required if sky-method=BSPLINE
- [OPTIONAL] The instrument response table (Tag = RESPONSE_MERGE1D_SLIT_arm)
- [OPTIONAL] An atmospheric extinction table (Tag = ATMOS_EXT_arm)
- [OPTIONAL] A telluric mask (Tag = TELL_MASK_arm)
- [OPTIONAL] The instrument master response table (Tag = MRESPONSE_MERGE1D_SLIT_arm).
If both master and individual response are provided the individual response is
preferred.
Products :
- PREFIX_ORDER2D_arm extracted spectrum, order-by-order, 2D
- PREFIX_ORDER1D_arm extracted spectrum, order-by-order, 1D
- PREFIX_MERGE2D_arm merged spectrum, 2D
- PREFIX_MERGE1D_arm merged spectrum, 1D
- SKY_SLIT_MERGE2D_arm merged spectrum sky, 2D
- PREFIX_SUB_BACK_SLIT_arm sci frame bias, (dark), inter-order bkg subtracted
- PREFIX_WAVE_MAP_arm, wave map image
- PREFIX_SLIT_MAP_arm, slit map image
- PREFIX_DIVFF_arm as PREFIX_SUB_BACK_SLIT_arm, flat fielded
- PREFIX_SUB_SKY_arm, as PREFIX_DIVFF_arm, sky subtracted
- PREFIX_SKY_arm, 2D sky frame
- PREFIX_SKY_ORD1D_arm, 1D sky image (order-by-order)
- PREFIX_BACK_SLIT_arm, inter order background image
- where PREFIX is SCI, FLUX, TELL if input raw DPR.TYPE contains OBJECT or FLUX or
TELLURIC
- [OPTIONAL, if response and atm ext are provided] PREFIX_FLUX_ORDER2D_arm (2
dimension)
- [OPTIONAL, if response and atm ext are provided] PREFIX_FLUX_ORDER1D_arm (1
dimension)
- [OPTIONAL, if response and atm ext are provided] PREFIX_FLUX_MERGE2D_arm (2
dimension)
- [OPTIONAL, if response and atm ext are provided] PREFIX_FLUX_MERGE1D_arm (1
dimension)
- PREFIX_ON_arm bias (dark) subtracted sci frame
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_scired_slit_stare.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_scired_slit_stare.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_scired_slit_stare.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_scired_slit_stare.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_scired_slit_stare.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_scired_slit_stare.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_scired_slit_stare.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_scired_slit_stare.khigh [default = 5.0].
--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_scired_slit_stare.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_scired_slit_stare.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_scired_slit_stare.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_scired_slit_stare.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: 20.0). The full name of this option for the EsoRex configuration
file is xsh.xsh_scired_slit_stare.removecrhsingle-sigmalim [default = 20.0].
--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_scired_slit_stare.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_scired_slit_stare.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_scired_slit_stare.rectify-kernel [default
= tanh].
--rectify-radius <float>
Rectify Interpolation radius [bin units]. (float; default: 2.0). The full name of
this option for the EsoRex configuration file is
xsh.xsh_scired_slit_stare.rectify-radius [default = 2.0].
--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_scired_slit_stare.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_scired_slit_stare.rectify-bin-slit [default = -1.0].
--localize-method <str>
Localization method (MANUAL, MAXIMUM, GAUSSIAN) used to detect the object centroid
and height on the slit (str; default: ´MANUAL´). The full name of this option for
the EsoRex configuration file is xsh.xsh_scired_slit_stare.localize-method [default
= MANUAL].
--localize-chunk-nb <int>
Number of chunks in the full spectrum to localize the object (int; default: 10).
The full name of this option for the EsoRex configuration file is
xsh.xsh_scired_slit_stare.localize-chunk-nb [default = 10].
--localize-thresh <float>
Threshold relative to the peak intensity below which the edges of the object are
detected for MAXIMUM localization (float; default: 0.1). The full name of this
option for the EsoRex configuration file is
xsh.xsh_scired_slit_stare.localize-thresh [default = 0.1].
--localize-deg-lambda <int>
Degree in lambda in the localization polynomial expression slit=f(lambda), used
only for MAXIMUM and GAUSSIAN (int; default: 0). The full name of this option for
the EsoRex configuration file is xsh.xsh_scired_slit_stare.localize-deg-lambda
[default = 0].
--localize-slit-position <float>
Object position on the slit for MANUAL localization [arcsec] (float; default: 0.0).
The full name of this option for the EsoRex configuration file is
xsh.xsh_scired_slit_stare.localize-slit-position [default = 0.0].
--localize-slit-hheight <float>
Object half height on the slit for MANUAL localization [arcsec] (float; default:
2.0). The full name of this option for the EsoRex configuration file is
xsh.xsh_scired_slit_stare.localize-slit-hheight [default = 2.0].
--localize-kappa <float>
Kappa value for sigma clipping in the localization polynomial fit (float; default:
3.0). The full name of this option for the EsoRex configuration file is
xsh.xsh_scired_slit_stare.localize-kappa [default = 3.0].
--localize-niter <int>
Number of iterations for sigma clipping in the localization polynomial fit (int;
default: 3). The full name of this option for the EsoRex configuration file is
xsh.xsh_scired_slit_stare.localize-niter [default = 3].
--localize-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_scired_slit_stare.localize-use-skymask [default = False].
--sky-subtract <bool>
TRUE to use subtract sky single. (bool; default: True). The full name of this
option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.sky-subtract
[default = True].
--sky-bspline-nbkpts-first <int>
Nb of break points for Bezier curve fitting (without localization) (int; default:
3000). The full name of this option for the EsoRex configuration file is
xsh.xsh_scired_slit_stare.sky-bspline-nbkpts-first [default = 3000].
--sky-bspline-nbkpts-second <int>
Nb of break points for Bezier curve fitting (with localization) (int; default:
3000). The full name of this option for the EsoRex configuration file is
xsh.xsh_scired_slit_stare.sky-bspline-nbkpts-second [default = 3000].
--sky-bspline-order <int>
Bezier spline order (int; default: 7). The full name of this option for the EsoRex
configuration file is xsh.xsh_scired_slit_stare.sky-bspline-order [default = 7].
--sky-bspline-niter <int>
Nb of iterations (int; default: 20). The full name of this option for the EsoRex
configuration file is xsh.xsh_scired_slit_stare.sky-bspline-niter [default = 20].
--sky-bspline-kappa <float>
Kappa value used to kappa-sigma-clip object (float; default: 5.0). The full name of
this option for the EsoRex configuration file is
xsh.xsh_scired_slit_stare.sky-bspline-kappa [default = 5.0].
--sky-method <str>
Sky subtract Method (BSPLINE, BSPLINE1, BSPLINE2 MEDIAN). BSPLINE is equivalent to
BSPLINE1 (str; default: ´MEDIAN´). The full name of this option for the EsoRex
configuration file is xsh.xsh_scired_slit_stare.sky-method [default = MEDIAN].
--bspline-sampling <str>
BSPLINE sampling. UNIFORM-uses the user defined nbkpts value, corrected for
binning, for all orders. FINE: multiplies the user defined nbkpts value, corrected
for binning, by a hard coded coefficient optimized on each arm-order) (str;
default: ´FINE´). The full name of this option for the EsoRex configuration file is
xsh.xsh_scired_slit_stare.bspline-sampling [default = FINE].
--sky-median-hsize <int>
Half size of the running median. If sky-method=MEDIAN . (int; default: 20). The
full name of this option for the EsoRex configuration file is
xsh.xsh_scired_slit_stare.sky-median-hsize [default = 20].
--sky-slit-edges-mask <float>
Size of edges mask in arcsec (float; default: 0.5). The full name of this option
for the EsoRex configuration file is xsh.xsh_scired_slit_stare.sky-slit-edges-mask
[default = 0.5].
--sky-position1 <float>
Central position of the sky window #1 [arcsec] (float; default: 0.0). The full name
of this option for the EsoRex configuration file is
xsh.xsh_scired_slit_stare.sky-position1 [default = 0.0].
--sky-hheight1 <float>
Half size of sky window #1 [arcsec] (float; default: 0.0). The full name of this
option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.sky-hheight1
[default = 0.0].
--sky-position2 <float>
Central position of the sky window #2 [arcsec] (float; default: 0.0). The full name
of this option for the EsoRex configuration file is
xsh.xsh_scired_slit_stare.sky-position2 [default = 0.0].
--sky-hheight2 <float>
Half size of the sky window #2 [arcsec] (float; default: 0.0). The full name of
this option for the EsoRex configuration file is
xsh.xsh_scired_slit_stare.sky-hheight2 [default = 0.0].
--stdextract-interp-hsize <int>
Half size of mask used to define object cross order profile (int; default: 30). The
full name of this option for the EsoRex configuration file is
xsh.xsh_scired_slit_stare.stdextract-interp-hsize [default = 30].
--do-optextract <bool>
TRUE if we do the optimal extraction (bool; default: False). The full name of this
option for the EsoRex configuration file is xsh.xsh_scired_slit_stare.do-optextract
[default = False].
--optextract-oversample <int>
Oversample factor for the science image (int; default: 5). The full name of this
option for the EsoRex configuration file is
xsh.xsh_scired_slit_stare.optextract-oversample [default = 5].
--optextract-box-half-size <int>
Extraction box [pixel] (int; default: 10). The full name of this option for the
EsoRex configuration file is xsh.xsh_scired_slit_stare.optextract-box-half-size
[default = 10].
--optextract-chunk-size <int>
Chunk size [bin] (int; default: 50). The full name of this option for the EsoRex
configuration file is xsh.xsh_scired_slit_stare.optextract-chunk-size [default =
50].
--optextract-step-lambda <float>
Lambda step [nm] (float; default: 0.02). The full name of this option for the
EsoRex configuration file is xsh.xsh_scired_slit_stare.optextract-step-lambda
[default = 0.02].
--optextract-clip-kappa <float>
Kappa for cosmics ray hits rejection (float; default: 3.0). The full name of this
option for the EsoRex configuration file is
xsh.xsh_scired_slit_stare.optextract-clip-kappa [default = 3.0].
--optextract-clip-frac <float>
Maximum bad pixels fraction for cosmics ray hits rejection (float; default: 0.4).
The full name of this option for the EsoRex configuration file is
xsh.xsh_scired_slit_stare.optextract-clip-frac [default = 0.4].
--optextract-clip-niter <int>
Maximum number of iterations for cosmics ray hits rejection (int; default: 2). The
full name of this option for the EsoRex configuration file is
xsh.xsh_scired_slit_stare.optextract-clip-niter [default = 2].
--optextract-niter <int>
Number of iterations (int; default: 1). The full name of this option for the EsoRex
configuration file is xsh.xsh_scired_slit_stare.optextract-niter [default = 1].
--optextract-method <str>
Extraction method GAUSSIAN | GENERAL (str; default: ´GAUSSIAN´). The full name of
this option for the EsoRex configuration file is
xsh.xsh_scired_slit_stare.optextract-method [default = GAUSSIAN].
--cut-uvb-spectrum <bool>
TRUE if recipe cuts the UVB spectrum at 556 nm (dichroich) (bool; default: True).
The full name of this option for the EsoRex configuration file is
xsh.xsh_scired_slit_stare.cut-uvb-spectrum [default = True].
--generate-SDP-format <bool>
TRUE if additional files should be generated in Science Data Product (SDP) format.
(bool; default: False). The full name of this option for the EsoRex configuration
file is xsh.xsh_scired_slit_stare.generate-SDP-format [default = False].
--dummy-association-keys <int>
Sets the number of dummy (empty) ASSONi, ASSOCi and ASSOMi keywords to create.
(int; default: 0). The full name of this option for the EsoRex configuration file
is xsh.xsh_scired_slit_stare.dummy-association-keys [default = 0].
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_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_util_physmod(7), xsh_wavecal(7)
VERSION
xsh_scired_slit_stare 3.5.3
AUTHOR
P.Goldoni, L.Guglielmi, R. Haigron, F. Royer, D. Bramich, A. Modigliani <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