Provided by: cpl-plugin-xshoo-doc_3.5.3+dfsg-1build1_all 
NAME
xsh_scired_slit_nod - Reduce science frames in SLIT configuration and nod mode
SYNOPSIS
esorex xsh_scired_slit_nod [OPTIONS] FILE.sof
DESCRIPTION
This recipe reduces science exposure in SLIT configuration and NOD mode Input Frames :
- A set of n Science frames ( n even ), Tag = OBJECT_SLIT_NOD_arm
- Spectral format table (Tag = SPECTRAL_FORMAT_TAB_arm)
- [UVB,VIS] A master bias frame (Tag = MASTER_BIAS_arm)
- A master flat frame (Tag = MASTER_FLAT_SLIT_arm)
- An order table frame(Tag = ORDER_TABLE_EDGES_SLIT_arm)
- [poly mode] A wave solution frame(Tag = WAVE_TAB_2D_arm)
- [poly mode] A wave map frame(Tag = WAVE_MAP_arm)
- [poly mode] A disp table frame(Tag = DISP_TAB_arm)
- [physical model mode]A model cfg table (Format = TABLE, Tag = XSH_MOD_CFG_TAB_arm)
- [OPTIONAL] A non-linear badpixel map (Tag = BP_MAP_NL_arm)
- [OPTIONAL] A reference badpixel map (Tag = BP_MAP_RP_arm)
- [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 (2 dimension)
- PREFIX_ORDER1D_arm (1 dimension)
- PREFIX_MERGE2D_arm (2 dimension)
- PREFIX_MERGE1D_arm (1 dimension)
- PREFIX_WAVE_MAP_arm, wave map image
- PREFIX_SLIT_MAP_arm, slit map image
- [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)
- where PREFIX is SCI, FLUX, TELL if input raw DPR.TYPE contains OBJECT or FLUX or
TELLURIC
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_nod.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_nod.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_nod.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: 1741684735). The full name of
this option for the EsoRex configuration file is xsh.xsh_scired_slit_nod.decode-bp
[default = 1741684735].
--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_nod.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_nod.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_nod.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_nod.khigh [default = 5.0].
--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_nod.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_nod.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_nod.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_nod.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_nod.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_nod.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_nod.rectify-bin-slit [default = -1.0].
--rectify-fast <bool>
Fast if TRUE (Rect[B-A] = -Rect[A-B]), in that case only entire pixel shifts are
applied. (bool; default: True). The full name of this option for the EsoRex
configuration file is xsh.xsh_scired_slit_nod.rectify-fast [default = True].
--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_nod.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_nod.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_nod.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_nod.localize-deg-lambda
[default = 0].
--localize-slit-position <float>
Object position on the slit for MANUAL localization [arcsec]. It refers to the
object position in the first frame of the nodding sequence (float; default: 0.0).
The full name of this option for the EsoRex configuration file is
xsh.xsh_scired_slit_nod.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_nod.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_nod.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_nod.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_nod.localize-use-skymask [default = False].
--localize-nod-throw <float>
Step (arcsec) between A and B images in nodding mode. (float; default: 0.0). The
full name of this option for the EsoRex configuration file is
xsh.xsh_scired_slit_nod.localize-nod-throw [default = 0.0].
--extract-method <str>
Method used for extraction (LOCALIZATION, NOD) (str; default: ´NOD´). The full name
of this option for the EsoRex configuration file is
xsh.xsh_scired_slit_nod.extract-method [default = NOD].
--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_nod.stdextract-interp-hsize [default = 30].
--combinenod-throwlist <str>
Name of ascii file containing the list of throw shifts with respect to the first
exposure (str; default: ´throwlist.asc´). The full name of this option for the
EsoRex configuration file is xsh.xsh_scired_slit_nod.combinenod-throwlist [default
= throwlist.asc].
--combinenod-method <str>
Combination method for nodded frames (MEDIAN, MEAN) (str; default: ´MEAN´). The
full name of this option for the EsoRex configuration file is
xsh.xsh_scired_slit_nod.combinenod-method [default = MEAN].
--max-slit <float>
Lower Slit Limit (localize and extract (float; default: 5.7). The full name of this
option for the EsoRex configuration file is xsh.xsh_scired_slit_nod.max-slit
[default = 5.7].
--min-slit <float>
Upper Slit Limit (localize and extract (float; default: -5.3). The full name of
this option for the EsoRex configuration file is xsh.xsh_scired_slit_nod.min-slit
[default = -5.3].
--correct-sky-by-median <bool>
TRUE if the resampled spectrum at each wavelength is median subtracted to remove
sky lines (bool; default: True). The full name of this option for the EsoRex
configuration file is xsh.xsh_scired_slit_nod.correct-sky-by-median [default =
True].
--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_nod.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_nod.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_nod.dummy-association-keys [default = 0].
--scale-combine-nod-method <int>
frame scaling when nod frames are combined: 0 (no-scaling); 1 (scaling) (int;
default: 1). The full name of this option for the EsoRex configuration file is
xsh.xsh_scired_slit_nod.scale-combine-nod-method [default = 1].
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_offset(7), xsh_scired_slit_stare(7), xsh_util_physmod(7), xsh_wavecal(7)
VERSION
xsh_scired_slit_nod 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