.TH SINFO_REC_MFLAT "7" "2.5.2" "sinfo_rec_mflat" "sinfo recipes"
.SH NAME
sinfo_rec_mflat \- Master flat determination

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

.SH DESCRIPTION
This recipe reduce normal raw flat fields.
.PP
The input files are a set of flat fields with tag FLAT_LAMP
optionally one may have in input also several bad pixel maps to be coadded.
.PP
The main products are a master flat field (PRO.CATG=MASTER_FLAT_LAMP) image
a bad pixel map (PRO.CATG=BP_MAP_NO), a master bad pixel map (PRO.CATG=MASTER_BP_MAP) resulting by the coaddition
of all bad pixel maps.
.PP



.SH OPTIONS
.TP
\fB\-\-gen\-overpar\fR \fI<bool>\fR
Overwrite DRS ini parameters:  (bool; default: True). The full name of this option for the EsoRex configuration
file is \fBsinfoni.general.overwrite_parameters\fR [default = \fITrue\fR].
.TP
\fB\-\-lc_sw\fR \fI<bool>\fR
Correct for bad lines introduced by instrument software:  (bool;
default: False). The full name of this option for the EsoRex configuration
file is \fBsinfoni.general.lc_sw\fR [default = \fIFalse\fR].
.TP
\fB\-\-lc_kappa\fR \fI<long>\fR
Kappa sigma value (long; default: 18). The full name of this option for the EsoRex configuration
file is \fBsinfoni.general.lc_kappa\fR [default = \fI18\fR].
.TP
\fB\-\-lc_filt_rad\fR \fI<long>\fR
Filtering radii applied during median filter. Should be small (long;
default: 3). The full name of this option for the EsoRex configuration
file is \fBsinfoni.general.lc_filt_rad\fR [default = \fI3\fR].
.TP
\fB\-\-product\-density\fR \fI<long>\fR
Density of pipeline products: 0 (low), 1 (low+skycor), 2 (med\-QC), 3
(high\-debug+skycor) (long; default: 2). The full name of this option for the EsoRex configuration
file is \fBsinfoni.product.density\fR [default = \fI2\fR].
.TP
\fB\-\-bp_norm\-s_factor\fR \fI<float>\fR
Threshold Sigma Factor: to remove the column intensity tilt only
pixels which lie within a defined noiselimit are used to fit a
straight line (float; default: 5.0). The full name of this option for the EsoRex configuration
file is \fBsinfoni.bp_norm.sigma_factor\fR [default = \fI5.0\fR].
.TP
\fB\-\-bp_norm\-method_ind\fR \fI<long>\fR
Bad pixel Method Index1: median of nearest neighbors,2: absolute
distances check, 3: mean of nearest spectral neighbors (long; default:
1). The full name of this option for the EsoRex configuration
file is \fBsinfoni.bp_norm.method_index\fR [default = \fI1\fR].
.TP
\fB\-\-bp_norm\-fct\fR \fI<float>\fR
Factor: if |pixel \- median| > factor * standard deviation \-> then the
pixel value is replaced by the median of the 8 nearest neighbors
(float; default: 10.0). The full name of this option for the EsoRex configuration
file is \fBsinfoni.bp_norm.factor\fR [default = \fI10.0\fR].
.TP
\fB\-\-bp_norm\-it\fR \fI<long>\fR
Iterations: number of iterations to of median filtering to find bad
pixel clusters (long; default: 8). The full name of this option for the EsoRex configuration
file is \fBsinfoni.bp_norm.iterations\fR [default = \fI8\fR].
.TP
\fB\-\-bp_norm\-lo_rej\fR \fI<float>\fR
low_rejection: percentage of rejected low intensity pixels before
averaging (float; default: 0.1). The full name of this option for the EsoRex configuration
file is \fBsinfoni.bp_norm.low_rejection\fR [default = \fI0.1\fR].
.TP
\fB\-\-bp_norm\-hi_rej\fR \fI<float>\fR
high_rejection: percentage of rejected high intensity pixels before
averaging (float; default: 0.1). The full name of this option for the EsoRex configuration
file is \fBsinfoni.bp_norm.high_rejection\fR [default = \fI0.1\fR].
.TP
\fB\-\-bp_norm\-llx\fR \fI<long>\fR
llx: to compute image statistics on a rectangularzone of the image the
coordinates of the rectangle are needed:lower left x coordinate (long;
default: 270). The full name of this option for the EsoRex configuration
file is \fBsinfoni.bp_norm.llx\fR [default = \fI270\fR].
.TP
\fB\-\-bp_norm\-lly\fR \fI<long>\fR
lly: to compute image statistics on a rectangularzone of the image the
coordinates of the rectangle are needed:lower left y coordinate (long;
default: 1000). The full name of this option for the EsoRex configuration
file is \fBsinfoni.bp_norm.lly\fR [default = \fI1000\fR].
.TP
\fB\-\-bp_norm\-urx\fR \fI<long>\fR
urx: to compute image statistics on a rectangularzone of the image the
coordinates of the rectangle are needed:upper right x coordinate
(long; default: 310). The full name of this option for the EsoRex configuration
file is \fBsinfoni.bp_norm.urx\fR [default = \fI310\fR].
.TP
\fB\-\-bp_norm\-ury\fR \fI<long>\fR
ury: to compute image statistics on a rectangularzone of the image the
coordinates of the rectangle are needed:upper right y coordinate
(long; default: 1200). The full name of this option for the EsoRex configuration
file is \fBsinfoni.bp_norm.ury\fR [default = \fI1200\fR].
.TP
\fB\-\-bp_norm\-thr_ind\fR \fI<bool>\fR
Threshold Index: indicator that indicates if the values beyond a
threshold deviation from the mean are flagged as bad pixels (bool;
default: True). The full name of this option for the EsoRex configuration
file is \fBsinfoni.bp_norm.threshold_index\fR [default = \fITrue\fR].
.TP
\fB\-\-bp_norm\-mean_fct\fR \fI<float>\fR
Mean Factor: factor to the clean standard deviation to define the
threshold deviation from the clean mean (float; default: 100.0). The full name of this option for the EsoRex configuration
file is \fBsinfoni.bp_norm.mean_factor\fR [default = \fI100.0\fR].
.TP
\fB\-\-bp_norm\-min_cut\fR \fI<float>\fR
the minimum value of real data (float; default: 0.0). The full name of this option for the EsoRex configuration
file is \fBsinfoni.bp_norm.min_cut\fR [default = \fI0.0\fR].
.TP
\fB\-\-bp_norm\-max_cut\fR \fI<float>\fR
the minimum value of real data (float; default: 50000.0). The full name of this option for the EsoRex configuration
file is \fBsinfoni.bp_norm.max_cut\fR [default = \fI50000.0\fR].
.TP
\fB\-\-lamp_flats\-lo_rej\fR \fI<float>\fR
lower rejection: percentage of rejected low intensity pixels before
averaging (float; default: 0.1). The full name of this option for the EsoRex configuration
file is \fBsinfoni.lamp_flats.low_rejection\fR [default = \fI0.1\fR].
.TP
\fB\-\-lamp_flats\-hi_rej\fR \fI<float>\fR
high rejection: percentage of rejected high intensity pixels before
averaging (float; default: 0.1). The full name of this option for the EsoRex configuration
file is \fBsinfoni.lamp_flats.high_rejection\fR [default = \fI0.1\fR].
.TP
\fB\-\-lamp_flats\-interpol_index\fR \fI<bool>\fR
Interpolation index switch: indicator if the bad pixels of the
flatfield should be interpolated (bool; default: False). The full name of this option for the EsoRex configuration
file is \fBsinfoni.lamp_flats.interpol_index\fR [default = \fIFalse\fR].
.TP
\fB\-\-lamp_flats\-max_rad\fR \fI<long>\fR
Max Rad: maximal pixel distance from bad pixel to take valid pixels
(long; default: 4). The full name of this option for the EsoRex configuration
file is \fBsinfoni.lamp_flats.max_rad\fR [default = \fI4\fR].
.TP
\fB\-\-lamp_flats\-bad_ind\fR \fI<bool>\fR
indicator if a bad pixel mask should be generated or not (bool;
default: False). The full name of this option for the EsoRex configuration
file is \fBsinfoni.lamp_flats.bad_ind\fR [default = \fIFalse\fR].
.TP
\fB\-\-lamp_flats\-sigma_factor\fR \fI<float>\fR
Sigma Factor: factor of the sigma noise limit; to remove the column
intensity tilt only pixels which lie within a defined noise limit are
used to fit a straight line (float; default: 5.0). The full name of this option for the EsoRex configuration
file is \fBsinfoni.lamp_flats.sigma_factor\fR [default = \fI5.0\fR].
.TP
\fB\-\-lamp_flats\-factor\fR \fI<float>\fR
Factor: if |pixel \- median| > factor * standard deviation \-> then the
pixel value is replaced by the median of the 8 nearest neighbors
(float; default: 3.0). The full name of this option for the EsoRex configuration
file is \fBsinfoni.lamp_flats.factor\fR [default = \fI3.0\fR].
.TP
\fB\-\-lamp_flats\-iterations\fR \fI<long>\fR
Iterations: number of iterations to of median filtering to find bad
pixel clusters (long; default: 8). The full name of this option for the EsoRex configuration
file is \fBsinfoni.lamp_flats.iterations\fR [default = \fI8\fR].
.TP
\fB\-\-lamp_flats\-bad_lo_rej\fR \fI<float>\fR
low rejection: Percentage for bad pixel low rejection (float; default:
10.0). The full name of this option for the EsoRex configuration
file is \fBsinfoni.lamp_flats.bad_low_rejection\fR [default = \fI10.0\fR].
.TP
\fB\-\-lamp_flats\-bad_hi_rej\fR \fI<float>\fR
high rejection: Percentage for bad pixel high rejection (float;
default: 10.0). The full name of this option for the EsoRex configuration
file is \fBsinfoni.lamp_flats.bad_high_rejection\fR [default = \fI10.0\fR].
.TP
\fB\-\-lamp_flats\-llx\fR \fI<long>\fR
Lower Lext X corner (long; default: 1350). The full name of this option for the EsoRex configuration
file is \fBsinfoni.lamp_flats.llx\fR [default = \fI1350\fR].
.TP
\fB\-\-lamp_flats\-lly\fR \fI<long>\fR
Lower Lext Y corner (long; default: 1000). The full name of this option for the EsoRex configuration
file is \fBsinfoni.lamp_flats.lly\fR [default = \fI1000\fR].
.TP
\fB\-\-lamp_flats\-rrx\fR \fI<long>\fR
Upper right X corner (long; default: 1390). The full name of this option for the EsoRex configuration
file is \fBsinfoni.lamp_flats.urx\fR [default = \fI1390\fR].
.TP
\fB\-\-lamp_flats\-ury\fR \fI<long>\fR
Upper right Y corner (long; default: 1200). The full name of this option for the EsoRex configuration
file is \fBsinfoni.lamp_flats.ury\fR [default = \fI1200\fR].
.TP
\fB\-\-lamp_flats\-tresh_ind\fR \fI<bool>\fR
Treshold index:  (bool; default: False). The full name of this option for the EsoRex configuration
file is \fBsinfoni.lamp_flats.thresh_ind\fR [default = \fIFalse\fR].
.TP
\fB\-\-lamp_flats\-mean_factor\fR \fI<float>\fR
Mean Factor: factor to the clean standard deviation to define the
threshold deviation from the clean mean (float; default: 10.0). The full name of this option for the EsoRex configuration
file is \fBsinfoni.lamp_flats.mean_factor\fR [default = \fI10.0\fR].
.TP
\fB\-\-lamp_flats\-qc_fpn_xmin1\fR \fI<long>\fR
qc_fpn_xmin1 (long; default: 512). The full name of this option for the EsoRex configuration
file is \fBsinfoni.lamp_flats.qc_fpn_xmin1\fR [default = \fI512\fR].
.TP
\fB\-\-lamp_flats\-qc_fpn_xmax1\fR \fI<long>\fR
qc_fpn_xmax1 (long; default: 1536). The full name of this option for the EsoRex configuration
file is \fBsinfoni.lamp_flats.qc_fpn_xmax1\fR [default = \fI1536\fR].
.TP
\fB\-\-lamp_flats\-qc_fpn_ymin1\fR \fI<long>\fR
qc_fpn_ymin1 (long; default: 512). The full name of this option for the EsoRex configuration
file is \fBsinfoni.lamp_flats.qc_fpn_ymin1\fR [default = \fI512\fR].
.TP
\fB\-\-lamp_flats\-qc_fpn_ymax1\fR \fI<long>\fR
qc_fpn_ymax1 (long; default: 1536). The full name of this option for the EsoRex configuration
file is \fBsinfoni.lamp_flats.qc_fpn_ymax1\fR [default = \fI1536\fR].
.TP
\fB\-\-lamp_flats\-qc_fpn_xmin2\fR \fI<long>\fR
qc_fpn_xmin2 (long; default: 1350). The full name of this option for the EsoRex configuration
file is \fBsinfoni.lamp_flats.qc_fpn_xmin2\fR [default = \fI1350\fR].
.TP
\fB\-\-lamp_flats\-qc_fpn_xmax2\fR \fI<long>\fR
qc_fpn_xmax2 (long; default: 1390). The full name of this option for the EsoRex configuration
file is \fBsinfoni.lamp_flats.qc_fpn_xmax2\fR [default = \fI1390\fR].
.TP
\fB\-\-lamp_flats\-qc_fpn_ymin2\fR \fI<long>\fR
qc_fpn_ymin2 (long; default: 1000). The full name of this option for the EsoRex configuration
file is \fBsinfoni.lamp_flats.qc_fpn_ymin2\fR [default = \fI1000\fR].
.TP
\fB\-\-lamp_flats\-qc_fpn_ymax2\fR \fI<long>\fR
qc_fpn_ymax2 (long; default: 1200). The full name of this option for the EsoRex configuration
file is \fBsinfoni.lamp_flats.qc_fpn_ymax2\fR [default = \fI1200\fR].
.TP
\fB\-\-lamp_flats\-qc_thresh_min\fR \fI<long>\fR
qc_thresh_min (long; default: 0). The full name of this option for the EsoRex configuration
file is \fBsinfoni.lamp_flats.qc_thresh_min\fR [default = \fI0\fR].
.TP
\fB\-\-lamp_flats\-qc_thresh_max\fR \fI<long>\fR
qc_thresh_max (long; default: 49000). The full name of this option for the EsoRex configuration
file is \fBsinfoni.lamp_flats.qc_thresh_max\fR [default = \fI49000\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 sinfo pipeline can be downloaded as 
a PDF file using the following URL:
.IP
.B ftp://ftp.eso.org/pub/dfs/pipelines/sinfoni/sinfo\-pipeline\-manual\-19.0.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 sinfo pipeline are
.IR sinfo_utl_cube2spectrum (7),
.IR sinfo_rec_jitter (7),
.IR sinfo_utl_ima_line_corr (7),
.IR sinfo_utl_cube_combine (7),
.IR sinfo_utl_bp_mask_add (7),
.IR sinfo_utl_skycor (7),
.IR sinfo_utl_spectrum_divide_by_blackbody (7),
.IR sinfo_utl_cube_create (7),
.IR sinfo_utl_line_oh_select (7),
.IR sinfo_utl_cube2ima (7),
.IR sinfo_utl_spectrum_wavelength_shift (7),
.IR sinfo_rec_distortion (7),
.IR sinfo_rec_pupil (7),
.IR sinfo_rec_wavecal (7),
.IR sinfo_utl_ima_arith (7),
.IR sinfo_utl_cube_arith (7),
.IR sinfo_rec_detlin (7),
.IR sinfo_utl_skymap (7),
.IR sinfo_rec_mdark (7)

.SH VERSION
sinfo_rec_mflat 2.5.2

.SH AUTHOR
Andrea Modigliani <Andrea.Modigliani@eso.org>

.SH 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>.

.SH LICENSE
This file is part of the SINFONI Instrument Pipeline
Copyright (C) 2002,2003 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