.TH GIMASTERFLAT "7" "2.16.7" "gimasterflat" "giraf recipes"
.SH NAME
gimasterflat \- Create the fiber master flat field and the localization mask.

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

.SH DESCRIPTION
For detailed information please refer to the GIRAFFE pipeline user manual.
.PP
It is available at http://www.eso.org/pipelines.

.SH OPTIONS
.TP
\fB\-\-fiber\-splist\fR \fI<str>\fR
Index list of spectra to use for localization (e.g. 2,10,30\-40,55).
(str; default: \'\'). The full name of this option for the EsoRex configuration
file is \fBgiraffe.fibers.spectra\fR [default = \fI\fR].
.TP
\fB\-\-fiber\-nspec\fR \fI<int>\fR
Number of spectra to localize. (int; default: 0). The full name of this option for the EsoRex configuration
file is \fBgiraffe.fibers.nspectra\fR [default = \fI0\fR].
.TP
\fB\-\-remove\-bias\fR \fI<bool>\fR
Enable bias removal (bool; default: True). The full name of this option for the EsoRex configuration
file is \fBgiraffe.biasremoval.remove\fR [default = \fITrue\fR].
.TP
\fB\-\-bsremove\-method\fR \fI<str>\fR
Bias removal method (str; default: \'PROFILE\'). The full name of this option for the EsoRex configuration
file is \fBgiraffe.biasremoval.method\fR [default = \fIPROFILE\fR].
.TP
\fB\-\-bsremove\-areas\fR \fI<str>\fR
Bias areas to use (Xl0:Xr0:Yl0:Yr0, ... ,Xln:Xrn:Yln:Yrn) (str;
default: \'5:40:0:4095\'). The full name of this option for the EsoRex configuration
file is \fBgiraffe.biasremoval.areas\fR [default = \fI5:40:0:4095\fR].
.TP
\fB\-\-bsremove\-sigma\fR \fI<float>\fR
Sigma Clipping: sigma threshold factor (float; default: 2.5). The full name of this option for the EsoRex configuration
file is \fBgiraffe.biasremoval.sigma\fR [default = \fI2.5\fR].
.TP
\fB\-\-bsremove\-niter\fR \fI<int>\fR
Sigma Clipping: maximum number of iterations (int; default: 5). The full name of this option for the EsoRex configuration
file is \fBgiraffe.biasremoval.iterations\fR [default = \fI5\fR].
.TP
\fB\-\-bsremove\-mfrac\fR \fI<float>\fR
Sigma Clipping: minimum fraction of points accepted/total [0.0..1.0]
(float; default: 0.8). The full name of this option for the EsoRex configuration
file is \fBgiraffe.biasremoval.fraction\fR [default = \fI0.8\fR].
.TP
\fB\-\-bsremove\-xorder\fR \fI<int>\fR
Order of X polynomial fit (CURVE method only) (int; default: 1). The full name of this option for the EsoRex configuration
file is \fBgiraffe.biasremoval.xorder\fR [default = \fI1\fR].
.TP
\fB\-\-bsremove\-yorder\fR \fI<int>\fR
Order of Y polynomial fit (CURVE method only) (int; default: 1). The full name of this option for the EsoRex configuration
file is \fBgiraffe.biasremoval.yorder\fR [default = \fI1\fR].
.TP
\fB\-\-bsremove\-xstep\fR \fI<int>\fR
Sampling step along X (CURVE method only) (int; default: 1). The full name of this option for the EsoRex configuration
file is \fBgiraffe.biasremoval.xstep\fR [default = \fI1\fR].
.TP
\fB\-\-bsremove\-ystep\fR \fI<int>\fR
Sampling step along Y (CURVE method only) (int; default: 1). The full name of this option for the EsoRex configuration
file is \fBgiraffe.biasremoval.ystep\fR [default = \fI1\fR].
.TP
\fB\-\-sloc\-mode\fR \fI<str>\fR
Localization mode: Use all spectra or the 5 SIWC spectra (str;
default: \'all\'). The full name of this option for the EsoRex configuration
file is \fBgiraffe.localization.mode\fR [default = \fIall\fR].
.TP
\fB\-\-sloc\-start\fR \fI<int>\fR
Bin along x\-axis (int; default: \-1). The full name of this option for the EsoRex configuration
file is \fBgiraffe.localization.start\fR [default = \fI\-1\fR].
.TP
\fB\-\-sloc\-retries\fR \fI<int>\fR
Initial localization detection xbin retries. (int; default: 10). The full name of this option for the EsoRex configuration
file is \fBgiraffe.localization.retries\fR [default = \fI10\fR].
.TP
\fB\-\-sloc\-binsize\fR \fI<int>\fR
Initial localization detection xbin size. (int; default: \-1). The full name of this option for the EsoRex configuration
file is \fBgiraffe.localization.binsize\fR [default = \fI\-1\fR].
.TP
\fB\-\-sloc\-ewidth\fR \fI<float>\fR
Localization detection extra width. (float; default: 1.0). The full name of this option for the EsoRex configuration
file is \fBgiraffe.localization.ewidth\fR [default = \fI1.0\fR].
.TP
\fB\-\-sloc\-ywidth\fR \fI<int>\fR
Full width [pxl] of the equilizing filter (distance between two
adjacent fibers). (int; default: \-1). The full name of this option for the EsoRex configuration
file is \fBgiraffe.localization.ywidth\fR [default = \fI\-1\fR].
.TP
\fB\-\-sloc\-center\fR \fI<str>\fR
Method used for mask center computation. (str; default: \'centroid\'). The full name of this option for the EsoRex configuration
file is \fBgiraffe.localization.center\fR [default = \fIcentroid\fR].
.TP
\fB\-\-sloc\-norm\fR \fI<bool>\fR
Enable spectrum normalization along the dispersion axis. (bool;
default: False). The full name of this option for the EsoRex configuration
file is \fBgiraffe.localization.normalize\fR [default = \fIFalse\fR].
.TP
\fB\-\-sloc\-noise\fR \fI<float>\fR
Threshold multiplier. (float; default: 7.0). The full name of this option for the EsoRex configuration
file is \fBgiraffe.localization.noise\fR [default = \fI7.0\fR].
.TP
\fB\-\-sloc\-threshold\fR \fI<str>\fR
Selects thresholding algorithm: local, row or global (str; default:
\'local\'). The full name of this option for the EsoRex configuration
file is \fBgiraffe.localization.threshold\fR [default = \fIlocal\fR].
.TP
\fB\-\-sloc\-ron\fR \fI<float>\fR
New bias sigma (RON) value for dark subtraction (float; default: \-1.0). The full name of this option for the EsoRex configuration
file is \fBgiraffe.localization.ron\fR [default = \fI\-1.0\fR].
.TP
\fB\-\-sloc\-yorder\fR \fI<int>\fR
Order of Chebyshev polynomial fit. (int; default: 4). The full name of this option for the EsoRex configuration
file is \fBgiraffe.localization.yorder\fR [default = \fI4\fR].
.TP
\fB\-\-sloc\-worder\fR \fI<int>\fR
Order of Chebyshev 2D polynomial fit. (int; default: 2). The full name of this option for the EsoRex configuration
file is \fBgiraffe.localization.worder\fR [default = \fI2\fR].
.TP
\fB\-\-sloc\-sigma\fR \fI<float>\fR
Localization clipping: sigma threshold factor (float; default: 2.5). The full name of this option for the EsoRex configuration
file is \fBgiraffe.localization.sigma\fR [default = \fI2.5\fR].
.TP
\fB\-\-sloc\-niter\fR \fI<int>\fR
Localization clipping: number of iterations (int; default: 5). The full name of this option for the EsoRex configuration
file is \fBgiraffe.localization.iterations\fR [default = \fI5\fR].
.TP
\fB\-\-sloc\-mfrac\fR \fI<float>\fR
Localization clipping: minimum fraction of points accepted/total.
(float; default: 0.9). The full name of this option for the EsoRex configuration
file is \fBgiraffe.localization.fraction\fR [default = \fI0.9\fR].
.TP
\fB\-\-psf\-model\fR \fI<str>\fR
PSF profile model: `psfexp\', `psfexp2\' (str; default: \'psfexp2\'). The full name of this option for the EsoRex configuration
file is \fBgiraffe.psf.model\fR [default = \fIpsfexp2\fR].
.TP
\fB\-\-psf\-norm\fR \fI<bool>\fR
Use normalized pixel values. (bool; default: False). The full name of this option for the EsoRex configuration
file is \fBgiraffe.psf.normalize\fR [default = \fIFalse\fR].
.TP
\fB\-\-psf\-binsize\fR \fI<int>\fR
Size of bin along dispersion axis (int; default: 64). The full name of this option for the EsoRex configuration
file is \fBgiraffe.psf.binsize\fR [default = \fI64\fR].
.TP
\fB\-\-psf\-maxwidth\fR \fI<float>\fR
Maximum width of the PSF profile. (float; default: 16.0). The full name of this option for the EsoRex configuration
file is \fBgiraffe.psf.maxwidth\fR [default = \fI16.0\fR].
.TP
\fB\-\-psf\-width\fR \fI<float>\fR
Initial width of the PSF profile. (float; default: 0.0). The full name of this option for the EsoRex configuration
file is \fBgiraffe.psf.width\fR [default = \fI0.0\fR].
.TP
\fB\-\-psf\-exponent\fR \fI<float>\fR
Exponent of the exponential PSF profile (will not be fitted if > 0).
(float; default: \-3.0). The full name of this option for the EsoRex configuration
file is \fBgiraffe.psf.exponent\fR [default = \fI\-3.0\fR].
.TP
\fB\-\-psf\-pfniter\fR \fI<int>\fR
Maximum number of iterations used for the fit of the fiber PSF
profile. (int; default: 120). The full name of this option for the EsoRex configuration
file is \fBgiraffe.psf.profile.iterations\fR [default = \fI120\fR].
.TP
\fB\-\-psf\-pfntest\fR \fI<int>\fR
Maximum number of tests used for the fit of the fiber PSF profile
(int; default: 7). The full name of this option for the EsoRex configuration
file is \fBgiraffe.psf.profile.tests\fR [default = \fI7\fR].
.TP
\fB\-\-psf\-pfdchisq\fR \fI<float>\fR
Minimum chi\-square difference used for the fit of the fiber PSF
profile. (float; default: 0.001). The full name of this option for the EsoRex configuration
file is \fBgiraffe.psf.profile.dchisquare\fR [default = \fI0.001\fR].
.TP
\fB\-\-psf\-prmfit\fR \fI<bool>\fR
2D fit of the PSF profile parameters using a Chebyshev polynomial
model. (bool; default: False). The full name of this option for the EsoRex configuration
file is \fBgiraffe.psf.parameters.fit\fR [default = \fIFalse\fR].
.TP
\fB\-\-psf\-yorder\fR \fI<int>\fR
Order of Chebyshev polynomial fit. (int; default: 4). The full name of this option for the EsoRex configuration
file is \fBgiraffe.psf.parameters.yorder\fR [default = \fI4\fR].
.TP
\fB\-\-psf\-worder\fR \fI<int>\fR
Order of Chebyshev 2D polynomial fit. (int; default: 4). The full name of this option for the EsoRex configuration
file is \fBgiraffe.psf.parameters.worder\fR [default = \fI4\fR].
.TP
\fB\-\-psf\-sigma\fR \fI<float>\fR
PSF parameter fitting: sigma threshold factor (float; default: 3.5). The full name of this option for the EsoRex configuration
file is \fBgiraffe.psf.parameters.sigma\fR [default = \fI3.5\fR].
.TP
\fB\-\-psf\-niter\fR \fI<int>\fR
PSF parameter fitting: number of iterations (int; default: 10). The full name of this option for the EsoRex configuration
file is \fBgiraffe.psf.parameters.iterations\fR [default = \fI10\fR].
.TP
\fB\-\-psf\-mfrac\fR \fI<float>\fR
PSF parameter fitting: minimum fraction of points accepted/total.
(float; default: 0.8). The full name of this option for the EsoRex configuration
file is \fBgiraffe.psf.parameters.fraction\fR [default = \fI0.8\fR].
.TP
\fB\-\-extr\-method\fR \fI<str>\fR
Extraction method: \'SUM\', \'HORNE\' or \'OPTIMAL\' (str; default: \'SUM\'). The full name of this option for the EsoRex configuration
file is \fBgiraffe.extraction.method\fR [default = \fISUM\fR].
.TP
\fB\-\-extr\-ron\fR \fI<float>\fR
New bias sigma (RON) value for bias and dark corrected image (float;
default: \-1.0). The full name of this option for the EsoRex configuration
file is \fBgiraffe.extraction.ron\fR [default = \fI\-1.0\fR].
.TP
\fB\-\-extr\-psfmodel\fR \fI<str>\fR
PSF profile model: `psfexp\', `psfexp2\' (str; default: \'psfexp2\'). The full name of this option for the EsoRex configuration
file is \fBgiraffe.extraction.psf.model\fR [default = \fIpsfexp2\fR].
.TP
\fB\-\-extr\-psfsigma\fR \fI<float>\fR
Sigma clippging threshold used for rejecting data points during PSF
fitting (Horne\'s sigma). It is used to reject bad pixels and cosmics.
(float; default: 7.0). The full name of this option for the EsoRex configuration
file is \fBgiraffe.extraction.psf.sigma\fR [default = \fI7.0\fR].
.TP
\fB\-\-extr\-psfniter\fR \fI<int>\fR
Maximum number of iterations used for fitting the PSF profile. (int;
default: 2). The full name of this option for the EsoRex configuration
file is \fBgiraffe.extraction.psf.iterations\fR [default = \fI2\fR].
.TP
\fB\-\-extr\-hewidth\fR \fI<int>\fR
Horne extraction method: Number of extra pixels added to the fiber
half\-width. (int; default: 2). The full name of this option for the EsoRex configuration
file is \fBgiraffe.extraction.horne.extrawidth\fR [default = \fI2\fR].
.TP
\fB\-\-extr\-hmingood\fR \fI<int>\fR
Horne extraction method: Minimum number of points used for the profile
fit. It sets the lower limit of data points for the pixel rejection.
(int; default: 3). The full name of this option for the EsoRex configuration
file is \fBgiraffe.extraction.horne.mingood\fR [default = \fI3\fR].
.TP
\fB\-\-extr\-omfrac\fR \fI<float>\fR
Optimal extraction method: Minimum fraction of the data points used
for fitting the fiber profiles. It sets the lower limit for the pixel
rejection. (float; default: 0.9). The full name of this option for the EsoRex configuration
file is \fBgiraffe.extraction.optimal.fraction\fR [default = \fI0.9\fR].
.TP
\fB\-\-extr\-owfactor\fR \fI<float>\fR
Optimal extraction method: Factor by which the fiber PSF half width is
multiplied. Adjacent spectra within this area are assumed to affect
the spectrum being extracted. (float; default: 3.0). The full name of this option for the EsoRex configuration
file is \fBgiraffe.extraction.optimal.wfactor\fR [default = \fI3.0\fR].
.TP
\fB\-\-extr\-obkgorder\fR \fI<int>\fR
Optimal extraction method: Order of the polynomial background model,
which is fitted for each wavelength bin along the spatial direction.
(int; default: 2). The full name of this option for the EsoRex configuration
file is \fBgiraffe.extraction.optimal.bkgorder\fR [default = \fI2\fR].
.TP
\fB\-\-transmission\fR \fI<bool>\fR
Controls the relative fiber transmission computation. (bool; default:
True). The full name of this option for the EsoRex configuration
file is \fBgiraffe.masterflat.transmission\fR [default = \fITrue\fR].
.TP
\fB\-\-slight\fR \fI<bool>\fR
Controls the scattered light model computation. (bool; default: False). The full name of this option for the EsoRex configuration
file is \fBgiraffe.masterflat.slight\fR [default = \fIFalse\fR].
.TP
\fB\-\-slight\-model\fR \fI<str>\fR
Name of the scattered light model to use. (str; default: \'polynom\'). The full name of this option for the EsoRex configuration
file is \fBgiraffe.slight.model.name\fR [default = \fIpolynom\fR].
.TP
\fB\-\-slight\-order\fR \fI<str>\fR
Scattered light model fit X and Y order. (str; default: \'4,2\'). The full name of this option for the EsoRex configuration
file is \fBgiraffe.slight.model.order\fR [default = \fI4,2\fR].
.TP
\fB\-\-slight\-xstep\fR \fI<int>\fR
Interspectrum region sampling step along the dispersion direction.
(int; default: 10). The full name of this option for the EsoRex configuration
file is \fBgiraffe.slight.xstep\fR [default = \fI10\fR].
.TP
\fB\-\-slight\-ystep\fR \fI<int>\fR
Interspectrum region sampling step along the spatial direction. (int;
default: 1). The full name of this option for the EsoRex configuration
file is \fBgiraffe.slight.ystep\fR [default = \fI1\fR].
.TP
\fB\-\-slight\-xslice\fR \fI<str>\fR
Interspectrum region sampling step along the dispersion direction for
a specific region. This overrides \'xstep\' for the given region. (str;
default: \'none\'). The full name of this option for the EsoRex configuration
file is \fBgiraffe.slight.xslice\fR [default = \fInone\fR].
.TP
\fB\-\-slight\-ewidth\fR \fI<float>\fR
Extra width [pixels] added to both sides of a spectrum trace. (float;
default: 0.5). The full name of this option for the EsoRex configuration
file is \fBgiraffe.slight.ewidth\fR [default = \fI0.5\fR].
.TP
\fB\-\-slight\-iswidth\fR \fI<int>\fR
Minimum width [pixels] required for interspectrum regions. (int;
default: 2). The full name of this option for the EsoRex configuration
file is \fBgiraffe.slight.iswidth\fR [default = \fI2\fR].
.TP
\fB\-\-slight\-istrim\fR \fI<bool>\fR
Turn off using the first and last interspectrum region. (bool;
default: True). The full name of this option for the EsoRex configuration
file is \fBgiraffe.slight.istrim\fR [default = \fITrue\fR].
.TP
\fB\-\-slight\-phff\fR \fI<bool>\fR
Use photometric flat field correction. (bool; default: False). The full name of this option for the EsoRex configuration
file is \fBgiraffe.slight.phffcorrection\fR [default = \fIFalse\fR].
.TP
\fB\-\-slight\-remove\fR \fI<bool>\fR
Remove scattered light from the input frame. (bool; default: False). The full name of this option for the EsoRex configuration
file is \fBgiraffe.slight.remove\fR [default = \fIFalse\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 giraf pipeline can be downloaded as 
a PDF file using the following URL:
.IP
.B ftp://ftp.eso.org/pub/dfs/pipelines/giraffe/giraf\-pipeline\-manual\-2.11.pdf
.PP
An overview over the existing ESO pipelines can be found on the web page
\fBhttps://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 \fBhttps://packages.python.org/python\-cpl/index.html\fR for further
information.
.PP
The other recipes of the giraf pipeline are
.IR giframestack (7),
.IR gimasterbias (7),
.IR gimasterdark (7),
.IR giscience (7),
.IR gistandard (7),
.IR giwavecalibration (7)

.SH VERSION
gimasterflat 2.16.7

.SH AUTHOR
Giraffe Pipeline <usd\-help@eso.org>

.SH BUG REPORTS
Please report any problems to usd\-help@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 GIRAFFE Instrument Pipeline
 Copyright (C) 2002\-2014 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., 51 Franklin St, Fifth Floor, Boston, MA  02110\-1301  USA