Provided by: cpl-plugin-xshoo-doc_3.3.5+dfsg-2_all 
NAME
xsh_scired_ifu_offset - Reduce science IFU on-off exposures and build a 3D cube
SYNOPSIS
esorex xsh_scired_ifu_offset [OPTIONS] FILE.sof
DESCRIPTION
This recipe Reduce science IFU on-off exposures and build a 3D cube Input Frames :
- A set of 2xn Science frames, Tag = OBJECT_IFU_OFFSET_arm, SKY_IFU_arm
- A spectral format table (Tag = SPECTRAL_FORMAT_TAB_arm)
- A master flat frame (Tag = MASTER_FLAT_IFU_arm)
- An order table frame(Tag = ORDER_TABLE_EDGES_IFU_arm)
- 3 wave solution frames, one per slitlet (Tag = WAVE_TAB_ARC_IFU_slitlet_arm)
where ´slitlet´ is DOWN, CEN or UP
- [OPTIONAL] A dispersion table (Tag = DISP_TAB_IFU_arm)
- [OPTIONAL] A non-linear badpixel map (Tag = BP_MAP_NL_arm)
- [OPTIONAL] A reference badpixel map (Tag = BP_MAP_RP_arm) Products :
- Merged 3D data cube (PREFIX_MERGE3D_DATA_OBJ_arm)
- QC Traces of 3D data cube (PREFIX_MERGE3D_TRACE_OBJ_arm)
- Order by order 3D data cube (PREFIX_ORDER3D_DATA_OBJ_arm)
- Order by order 3D qual cube (IFU_CFG_COR_arm)
- Order by order 3D qual cube (PREFIX_MERGE3D_DATA_SKY_arm)
- where PREFIX is SCI, FLUX, TELL if input raw DPR.TYPE contains OBJECT or FLUX or TELLURIC
- 1 Spectrum merge 3D, PRO.CATG=MERGE3D_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_scired_ifu_offset.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_ifu_offset.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_ifu_offset.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_ifu_offset.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_ifu_offset.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_ifu_offset.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_ifu_offset.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_ifu_offset.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_scired_ifu_offset.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_scired_ifu_offset.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_scired_ifu_offset.crh-clip-frac [default = 0.7].
--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_scired_ifu_offset.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_scired_ifu_offset.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_ifu_offset.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_ifu_offset.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_ifu_offset.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_ifu_offset.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_ifu_offset.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_ifu_offset.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_ifu_offset.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_ifu_offset.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_ifu_offset.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_ifu_offset.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_ifu_offset.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_ifu_offset.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_ifu_offset.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_ifu_offset.localize-use-skymask
[default = False].
--compute-map <bool>
if TRUE recompute (wave and slit) maps from the dispersion solution. If sky-subtract is set to
TRUE this must be set to TRUE. (bool; default: False). The full name of this option for the EsoRex
configuration file is xsh.xsh_scired_ifu_offset.compute-map [default = False].
--trace-obj <bool>
if TRUE trace object position on each IFU slice. In this case order TAB edges is required (bool;
default: False). The full name of this option for the EsoRex configuration file is
xsh.xsh_scired_ifu_offset.trace-obj [default = False].
--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_scired_ifu_offset.check-afc [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_ifu_offset.cut-uvb-spectrum
[default = True].
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_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_scired_ifu_offset 3.3.5
AUTHOR
A.Modigliani, J.Vernet, P. Bristow <Andrea.Modigliani@eso.org>
BUG REPORTS
Please report any problems to Andrea.Modigliani@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