.TH XSH_MBIAS "7" "2.5.2" "xsh_mbias" "xshoo recipes"
.SH NAME
xsh_mbias \- Create the master bias frame

.SH SYNOPSIS
esorex
.B xsh_mbias
[OPTIONS] FILE.sof

.SH DESCRIPTION
This recipe creates a master bias frame by computing the median of all input bias frames.
.PP
Input Frames : 
  \- A set of n RAW frames (Format=RAW, n >=3, Tag = 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 bias frame (Format=PRE, PRO.CATG = MASTER_BIAS_arm)


.SH OPTIONS
.TP
\fB\-\-keep\-temp\fR \fI<str>\fR
If \'no\', temporary files are deleted. (str; default: \'no\'). The full name of this option for the EsoRex configuration
file is \fBxsh.xsh_mbias.keep\-temp\fR [default = \fIno\fR].
.TP
\fB\-\-debug\-level\fR \fI<str>\fR
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 \fBxsh.xsh_mbias.debug\-level\fR [default = \fInone\fR].
.TP
\fB\-\-time\-stamp\fR \fI<bool>\fR
Add timestamp to product file name. (bool; default: False). The full name of this option for the EsoRex configuration
file is \fBxsh.xsh_mbias.time\-stamp\fR [default = \fIFalse\fR].
.TP
\fB\-\-decode\-bp\fR \fI<long>\fR
Integer representation of the bits to be considered bad when decoding
the bad pixel mask pixel values. (long; default: 2144337919). The full name of this option for the EsoRex configuration
file is \fBxsh.xsh_mbias.decode\-bp\fR [default = \fI2144337919\fR].
.TP
\fB\-\-stack\-method\fR \fI<str>\fR
Method used to build master frame. (str; default: \'median\'). The full name of this option for the EsoRex configuration
file is \fBxsh.xsh_mbias.stack\-method\fR [default = \fImedian\fR].
.TP
\fB\-\-klow\fR \fI<float>\fR
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 \fBxsh.xsh_mbias.klow\fR [default = \fI5.0\fR].
.TP
\fB\-\-khigh\fR \fI<float>\fR
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 \fBxsh.xsh_mbias.khigh\fR [default = \fI5.0\fR].
.TP
\fB\-\-fpn_llx\fR \fI<long>\fR
Lower left reference area X coordinate for Fixed Pattern Noise
computation (long; default: 10). The full name of this option for the EsoRex configuration
file is \fBxsh.xsh_mbias.fpn_llx\fR [default = \fI10\fR].
.TP
\fB\-\-fpn_lly\fR \fI<long>\fR
Lower left reference area Y coordinate for Fixed Pattern Noise
computation (long; default: 10). The full name of this option for the EsoRex configuration
file is \fBxsh.xsh_mbias.fpn_lly\fR [default = \fI10\fR].
.TP
\fB\-\-fpn_urx\fR \fI<long>\fR
Upper right reference area X coordinate for Fixed Pattern Noise
computation (long; default: 1024). The full name of this option for the EsoRex configuration
file is \fBxsh.xsh_mbias.fpn_urx\fR [default = \fI1024\fR].
.TP
\fB\-\-fpn_ury\fR \fI<long>\fR
Upper right reference area Y coordinate for Fixed Pattern Noise
computation (long; default: 1024). The full name of this option for the EsoRex configuration
file is \fBxsh.xsh_mbias.fpn_ury\fR [default = \fI1024\fR].
.TP
\fB\-\-fpn_hsize\fR \fI<long>\fR
Sample size for Fixed Pattern Noise computation (long; default: 10). The full name of this option for the EsoRex configuration
file is \fBxsh.xsh_mbias.fpn_hsize\fR [default = \fI10\fR].
.TP
\fB\-\-fpn_nsamples\fR \fI<long>\fR
Number of sampling points for Fixed Pattern Noise computation (long;
default: 100). The full name of this option for the EsoRex configuration
file is \fBxsh.xsh_mbias.fpn_nsamples\fR [default = \fI100\fR].
.TP
\fB\-\-ron_method\fR \fI<str>\fR
RON computation method (str; default: \'ALL\'). The full name of this option for the EsoRex configuration
file is \fBxsh.xsh_mbias.ron_method\fR [default = \fIALL\fR].
.TP
\fB\-\-random_sizex\fR \fI<long>\fR
Region X size for random computation (long; default: 10). The full name of this option for the EsoRex configuration
file is \fBxsh.xsh_mbias.random_sizex\fR [default = \fI10\fR].
.TP
\fB\-\-random_nsamples\fR \fI<long>\fR
Number of random samples (long; default: 100). The full name of this option for the EsoRex configuration
file is \fBxsh.xsh_mbias.random_nsamples\fR [default = \fI100\fR].
.TP
\fB\-\-ref1_llx\fR \fI<long>\fR
Lower left X of reference region (long; default: \-1). The full name of this option for the EsoRex configuration
file is \fBxsh.xsh_mbias.ref1_llx\fR [default = \fI\-1\fR].
.TP
\fB\-\-ref1_lly\fR \fI<long>\fR
Lower left Y of reference region (long; default: \-1). The full name of this option for the EsoRex configuration
file is \fBxsh.xsh_mbias.ref1_lly\fR [default = \fI\-1\fR].
.TP
\fB\-\-ref1_urx\fR \fI<long>\fR
Upper right X of reference region (long; default: \-1). The full name of this option for the EsoRex configuration
file is \fBxsh.xsh_mbias.ref1_urx\fR [default = \fI\-1\fR].
.TP
\fB\-\-ref1_ury\fR \fI<long>\fR
Upper right Y of reference region (long; default: \-1). The full name of this option for the EsoRex configuration
file is \fBxsh.xsh_mbias.ref1_ury\fR [default = \fI\-1\fR].
.TP
\fB\-\-ref2_llx\fR \fI<long>\fR
Lower left X of reference region (long; default: \-1). The full name of this option for the EsoRex configuration
file is \fBxsh.xsh_mbias.ref2_llx\fR [default = \fI\-1\fR].
.TP
\fB\-\-ref2_lly\fR \fI<long>\fR
Lower left Y of reference region (long; default: \-1). The full name of this option for the EsoRex configuration
file is \fBxsh.xsh_mbias.ref2_lly\fR [default = \fI\-1\fR].
.TP
\fB\-\-ref2_urx\fR \fI<long>\fR
Upper right X of reference region (long; default: \-1). The full name of this option for the EsoRex configuration
file is \fBxsh.xsh_mbias.ref2_urx\fR [default = \fI\-1\fR].
.TP
\fB\-\-ref2_ury\fR \fI<long>\fR
Upper right Y of reference region (long; default: \-1). The full name of this option for the EsoRex configuration
file is \fBxsh.xsh_mbias.ref2_ury\fR [default = \fI\-1\fR].
.TP
\fB\-\-stacking_ks_low\fR \fI<long>\fR
Lower value of kappa\-sigma clip in stacking (long; default: 3). The full name of this option for the EsoRex configuration
file is \fBxsh.xsh_mbias.stacking_ks_low\fR [default = \fI3\fR].
.TP
\fB\-\-stacking_ks_iter\fR \fI<long>\fR
Number of iterations in kappa\-sigma clip in stacking (long; default:
25). The full name of this option for the EsoRex configuration
file is \fBxsh.xsh_mbias.stacking_ks_iter\fR [default = \fI25\fR].
.TP
\fB\-\-struct_refx\fR \fI<long>\fR
Reference X value to compute structure (long; default: \-1). The full name of this option for the EsoRex configuration
file is \fBxsh.xsh_mbias.struct_refx\fR [default = \fI\-1\fR].
.TP
\fB\-\-struct_refy\fR \fI<long>\fR
Reference Y value to compute structure (long; default: \-1). The full name of this option for the EsoRex configuration
file is \fBxsh.xsh_mbias.struct_refy\fR [default = \fI\-1\fR].

.PP
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.

.SH SEE ALSO
The full documentation for the xshoo pipeline can be downloaded as 
a PDF file using the following URL:
.IP
.B ftp://ftp.eso.org/pub/dfs/pipelines/xshoo/xshoo\-pipeline\-manual\-12.1.pdf
.PP
An overview over the existing ESO pipelines can be found on the web page
\fBhttp://www.eso.org/sci/software/pipelines/\fR.
.PP
Basic documentation about the EsoRex program can be found at the esorex (1) 
man page.
.PP
It is possible to call the pipelines from python using the python\-cpl package.
See \fBhttp://packages.python.org/python\-cpl/index.html\fR for further
information.
.PP
The other recipes of the xshoo pipeline are
.IR xsh_cfg_recover (7),
.IR xsh_lingain (7),
.IR xsh_geom_ifu (7),
.IR xsh_wavecal (7),
.IR xsh_scired_slit_nod (7),
.IR xsh_respon_slit_nod (7),
.IR xsh_mdark (7),
.IR xsh_respon_slit_offset (7),
.IR xsh_orderpos (7),
.IR xsh_scired_ifu_stare_drl (7),
.IR xsh_scired_ifu_stare (7),
.IR xsh_flexcomp (7),
.IR xsh_scired_ifu_offset_drl (7),
.IR xsh_util_physmod (7),
.IR xsh_respon_slit_stare (7),
.IR xsh_2dmap (7),
.IR xsh_mflat (7),
.IR xsh_predict (7),
.IR xsh_scired_ifu_offset (7),
.IR xsh_scired_slit_stare (7),
.IR xsh_scired_slit_offset (7)

.SH VERSION
xsh_mbias 2.5.2

.SH AUTHOR
P.Goldoni, L.Guglielmi, R. Haigron, F. Royer, D. Bramich, A. Modigliani <amodigli@eso.org>

.SH 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>.

.SH 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