Provided by: cpl-plugin-xshoo-doc_3.5.3+dfsg-1build1_all 
NAME
xsh_mdark - Create the master dark frame
SYNOPSIS
esorex xsh_mdark [OPTIONS] FILE.sof
DESCRIPTION
This recipe creates a master dark frame Input Frames :
- A set of n RAW frames (Format=RAW, n >=3, Tag = DARK_arm)
- [UVB,VIS] A master bias frame (Format=PRE, Tag = MASTER_BIAS_arm)
- [OPTIONAL] A map of non linear bad pixels (Format=QUP, Tag = BP_MAP_NL_arm)
- [OPTIONAL] A map of reference bad pixels (Format = QUP,RAW, Tag = BP_MAP_RP_arm)
Products :
- A master dark frame (Format=PRE, PRO.CATG = MASTER_DARK_arm)
A dark frame, (Format=PRE, PRO.CATG = DARK_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_mdark.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_mdark.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_mdark.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_mdark.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_mdark.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_mdark.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_mdark.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_mdark.khigh [default = 5.0].
--bp-output <bool>
Flag indicating whether the noise bad pixel map is to be computed (bool; default:
False). The full name of this option for the EsoRex configuration file is
xsh.xsh_mdark.bp-output [default = False].
--crh-clip-kappa <float>
Kappa value in sigma clipping during CRH rejection using multiple frames (float;
default: -1.0). The full name of this option for the EsoRex configuration file is
xsh.xsh_mdark.crh-clip-kappa [default = -1.0].
--crh-clip-niter <int>
Number of iterations in sigma clipping during CRH rejection using multiple frames
(int; default: 3). The full name of this option for the EsoRex configuration file
is xsh.xsh_mdark.crh-clip-niter [default = 3].
--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_mdark.crh-clip-frac [default = 0.7].
--noise-clip-kappa <float>
Multiple of sigma in sigma clipping (float; default: 9.0). The full name of this
option for the EsoRex configuration file is xsh.xsh_mdark.noise-clip-kappa [default
= 9.0].
--noise-clip-niter <int>
Number of iterations in sigma clipping (int; default: 5). The full name of this
option for the EsoRex configuration file is xsh.xsh_mdark.noise-clip-niter [default
= 5].
--noise-clip-frac <float>
Minimal fractions of bad pixel allowed (float; default: 0.7). The full name of this
option for the EsoRex configuration file is xsh.xsh_mdark.noise-clip-frac [default
= 0.7].
--noise-clip-diff <float>
Minimum relative change in sigma for sigma clipping (float; default: 0.0). The full
name of this option for the EsoRex configuration file is
xsh.xsh_mdark.noise-clip-diff [default = 0.0].
--noise-lower-rejection <float>
Lower rejection percentile to flag bad pixels via noise (float; default: 10.0). The
full name of this option for the EsoRex configuration file is
xsh.xsh_mdark.noise-lower-rejection [default = 10.0].
--noise-higher-rejection <float>
Upper rejection percentile to flag bad pixels via noise (float; default: 10.0). The
full name of this option for the EsoRex configuration file is
xsh.xsh_mdark.noise-higher-rejection [default = 10.0].
--ref1_llx <int>
Lower left X of reference region (int; default: -1). The full name of this option
for the EsoRex configuration file is xsh.xsh_mdark.ref1_llx [default = -1].
--ref1_lly <int>
Lower left Y of reference region (int; default: -1). The full name of this option
for the EsoRex configuration file is xsh.xsh_mdark.ref1_lly [default = -1].
--ref1_urx <int>
Upper right X of reference region (int; default: -1). The full name of this option
for the EsoRex configuration file is xsh.xsh_mdark.ref1_urx [default = -1].
--ref1_ury <int>
Upper right Y of reference region (int; default: -1). The full name of this option
for the EsoRex configuration file is xsh.xsh_mdark.ref1_ury [default = -1].
--ron_llx <int>
Lower left X of reference region to measure RON (int; default: -1). The full name
of this option for the EsoRex configuration file is xsh.xsh_mdark.ron_llx [default
= -1].
--ron_lly <int>
Lower left Y of reference region to measure RON (int; default: -1). The full name
of this option for the EsoRex configuration file is xsh.xsh_mdark.ron_lly [default
= -1].
--ron_urx <int>
Upper right X of reference region to measure RON (int; default: -1). The full name
of this option for the EsoRex configuration file is xsh.xsh_mdark.ron_urx [default
= -1].
--ron_ury <int>
Upper right Y of reference region to measure RON (int; default: -1). The full name
of this option for the EsoRex configuration file is xsh.xsh_mdark.ron_ury [default
= -1].
--ron_hsize <int>
Sampling area size (int; default: 4). The full name of this option for the EsoRex
configuration file is xsh.xsh_mdark.ron_hsize [default = 4].
--ron_nsamples <int>
Number of random samples (int; default: 100). The full name of this option for the
EsoRex configuration file is xsh.xsh_mdark.ron_nsamples [default = 100].
--fpn_llx <int>
Lower left reference area X coordinate for Fixed Pattern Noise computation (int;
default: -1). The full name of this option for the EsoRex configuration file is
xsh.xsh_mdark.fpn_llx [default = -1].
--fpn_lly <int>
Lower left reference area Y coordinate for Fixed Pattern Noise computation (int;
default: -1). The full name of this option for the EsoRex configuration file is
xsh.xsh_mdark.fpn_lly [default = -1].
--fpn_urx <int>
Upper right reference area X coordinate for Fixed Pattern Noise computation (int;
default: -1). The full name of this option for the EsoRex configuration file is
xsh.xsh_mdark.fpn_urx [default = -1].
--fpn_ury <int>
Upper right reference area Y coordinate for Fixed Pattern Noise computation (int;
default: -1). The full name of this option for the EsoRex configuration file is
xsh.xsh_mdark.fpn_ury [default = -1].
--fpn_hsize <int>
Sample size for Fixed Pattern Noise computation (int; default: 4). The full name of
this option for the EsoRex configuration file is xsh.xsh_mdark.fpn_hsize [default =
4].
--fpn_nsamples <int>
Number of sampling points for Fixed Pattern Noise computation (int; default: 100).
The full name of this option for the EsoRex configuration file is
xsh.xsh_mdark.fpn_nsamples [default = 100].
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_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_mdark 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