.TH GIWAVECALIBRATION "7" "2.16.7" "giwavecalibration" "giraf recipes"
.SH NAME
giwavecalibration \- Compute dispersion solution from an arc\-lamp spectrum.

.SH SYNOPSIS
esorex
.B giwavecalibration
[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\-\-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\-\-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\-\-wcal\-lswidth\fR \fI<str>\fR
List of window widths [pxl] used for line detection and fit (e.g.
\'60,40,15\'). (str; default: \'10,10,10,10,10\'). The full name of this option for the EsoRex configuration
file is \fBgiraffe.wlcalibration.line.widths\fR [default = \fI10,10,10,10,10\fR].
.TP
\fB\-\-wcal\-lssep\fR \fI<float>\fR
Factor used to compute the minimum line separation from the window
width. (float; default: 0.9). The full name of this option for the EsoRex configuration
file is \fBgiraffe.wlcalibration.line.separation\fR [default = \fI0.9\fR].
.TP
\fB\-\-wcal\-lsfxratio\fR \fI<float>\fR
Selects only lines whose neighbours have a relative intensity less
than 1. / fluxratio. (float; default: 50.0). The full name of this option for the EsoRex configuration
file is \fBgiraffe.wlcalibration.line.fluxratio\fR [default = \fI50.0\fR].
.TP
\fB\-\-wcal\-lsbright\fR \fI<float>\fR
Selects lines having an intensity greater or equal to the given
intensity. (float; default: 0.0). The full name of this option for the EsoRex configuration
file is \fBgiraffe.wlcalibration.line.brightness\fR [default = \fI0.0\fR].
.TP
\fB\-\-wcal\-lscount\fR \fI<int>\fR
Sets the minimum number of lines to select; selected are lines with
the highest nominal intensity. A value of 0 turns this selection off.
If the value is less than 0 the selection is skipped if the line list
does not contain enough lines. (int; default: \-80). The full name of this option for the EsoRex configuration
file is \fBgiraffe.wlcalibration.line.count\fR [default = \fI\-80\fR].
.TP
\fB\-\-wcal\-lswrange\fR \fI<str>\fR
Selects only lines within the given wavelength range [nm]. (str;
default: \'0.,0.\'). The full name of this option for the EsoRex configuration
file is \fBgiraffe.wlcalibration.line.wrange\fR [default = \fI0.,0.\fR].
.TP
\fB\-\-wcal\-lfmodel\fR \fI<str>\fR
Line profile model. (str; default: \'psfexp\'). The full name of this option for the EsoRex configuration
file is \fBgiraffe.wlcalibration.line.model\fR [default = \fIpsfexp\fR].
.TP
\fB\-\-wcal\-lfres\fR \fI<str>\fR
Use optical model residuals for line detection. (str; default: \'auto\'). The full name of this option for the EsoRex configuration
file is \fBgiraffe.wlcalibration.line.residuals\fR [default = \fIauto\fR].
.TP
\fB\-\-wcal\-lfthreshold\fR \fI<float>\fR
Line detection threshold during the line fitting (multiple of bias
sigma) (float; default: 1.0). The full name of this option for the EsoRex configuration
file is \fBgiraffe.wlcalibration.line.threshold\fR [default = \fI1.0\fR].
.TP
\fB\-\-wcal\-lfoffset\fR \fI<float>\fR
Maximum allowed difference between the fitted and raw line peak
position. (float; default: 10.0). The full name of this option for the EsoRex configuration
file is \fBgiraffe.wlcalibration.line.offset\fR [default = \fI10.0\fR].
.TP
\fB\-\-wcal\-lfniter\fR \fI<int>\fR
Line detection fit maximum number of iterations. (int; default: 50). The full name of this option for the EsoRex configuration
file is \fBgiraffe.wlcalibration.line.iterations\fR [default = \fI50\fR].
.TP
\fB\-\-wcal\-lfntest\fR \fI<int>\fR
Line detection fit maximum number of tests. (int; default: 7). The full name of this option for the EsoRex configuration
file is \fBgiraffe.wlcalibration.line.tests\fR [default = \fI7\fR].
.TP
\fB\-\-wcal\-lfdchisq\fR \fI<float>\fR
Line detection fit minimum chi\-square difference. (float; default:
0.0001). The full name of this option for the EsoRex configuration
file is \fBgiraffe.wlcalibration.line.dchisquare\fR [default = \fI0.0001\fR].
.TP
\fB\-\-wcal\-lfreswid\fR \fI<float>\fR
Line width/resolution width factor. (float; default: 0.5). The full name of this option for the EsoRex configuration
file is \fBgiraffe.wlcalibration.line.rwidthratio\fR [default = \fI0.5\fR].
.TP
\fB\-\-wcal\-lfexpwid\fR \fI<float>\fR
Exponential line profile exponent; it will not be fitted if it is
larger than 0. (float; default: \-3.0). The full name of this option for the EsoRex configuration
file is \fBgiraffe.wlcalibration.line.exponent\fR [default = \fI\-3.0\fR].
.TP
\fB\-\-wcal\-soffset\fR \fI<str>\fR
Initial slit position offsets along the x and y direction and rotation
angle. (str; default: \'setup\'). The full name of this option for the EsoRex configuration
file is \fBgiraffe.wlcalibration.slit.offset\fR [default = \fIsetup\fR].
.TP
\fB\-\-wcal\-ommodel\fR \fI<str>\fR
Optical model. (str; default: \'xoptmod2\'). The full name of this option for the EsoRex configuration
file is \fBgiraffe.wlcalibration.opt.model\fR [default = \fIxoptmod2\fR].
.TP
\fB\-\-wcal\-omdir\fR \fI<int>\fR
Dispersion direction flag. (int; default: 1). The full name of this option for the EsoRex configuration
file is \fBgiraffe.wlcalibration.opt.direction\fR [default = \fI1\fR].
.TP
\fB\-\-wcal\-omsol\fR \fI<bool>\fR
Controls optical model parameter fitting. (bool; default: True). The full name of this option for the EsoRex configuration
file is \fBgiraffe.wlcalibration.opt.solution\fR [default = \fITrue\fR].
.TP
\fB\-\-wcal\-omflags\fR \fI<str>\fR
List of flags defining the set of free parameters used for fitting the
optical model. Possible values are: fcoll, gcam, theta, sdx, sdy, sphi
(str; default: \'sdx,sdy,sphi\'). The full name of this option for the EsoRex configuration
file is \fBgiraffe.wlcalibration.opt.flags\fR [default = \fIsdx,sdy,sphi\fR].
.TP
\fB\-\-wcal\-omsslits\fR \fI<bool>\fR
Controls subslit geometry usage in the optical model fit; subslits are
used if set to `true\'. (bool; default: False). The full name of this option for the EsoRex configuration
file is \fBgiraffe.wlcalibration.opt.subslits\fR [default = \fIFalse\fR].
.TP
\fB\-\-wcal\-omniter\fR \fI<int>\fR
Optical model fit maximum number of iterations. (int; default: 50). The full name of this option for the EsoRex configuration
file is \fBgiraffe.wlcalibration.opt.iterations\fR [default = \fI50\fR].
.TP
\fB\-\-wcal\-omntest\fR \fI<int>\fR
Optical model fit maximum number of tests (int; default: 7). The full name of this option for the EsoRex configuration
file is \fBgiraffe.wlcalibration.opt.tests\fR [default = \fI7\fR].
.TP
\fB\-\-wcal\-omdchisq\fR \fI<float>\fR
Optical model fit minimum chi\-square difference. (float; default:
0.0001). The full name of this option for the EsoRex configuration
file is \fBgiraffe.wlcalibration.opt.dchisquare\fR [default = \fI0.0001\fR].
.TP
\fB\-\-wcal\-xwsigma\fR \fI<float>\fR
PSF width fit sigma clipping factor. (float; default: 1.25). The full name of this option for the EsoRex configuration
file is \fBgiraffe.wlcalibration.psf.sigma\fR [default = \fI1.25\fR].
.TP
\fB\-\-wcal\-xwniter\fR \fI<int>\fR
PSF width fit sigma clipping maximum number of iterations. (int;
default: 10). The full name of this option for the EsoRex configuration
file is \fBgiraffe.wlcalibration.psf.iterations\fR [default = \fI10\fR].
.TP
\fB\-\-wcal\-xwmfrac\fR \fI<float>\fR
PSF width fit sigma clipping minimum fraction of points
accepted/total. (float; default: 0.9). The full name of this option for the EsoRex configuration
file is \fBgiraffe.wlcalibration.psf.fraction\fR [default = \fI0.9\fR].
.TP
\fB\-\-wcal\-xworder\fR \fI<str>\fR
X and Y polynomial orders for PSF x\-width Chebyshev fit. (str;
default: \'2,2\'). The full name of this option for the EsoRex configuration
file is \fBgiraffe.wlcalibration.psf.order\fR [default = \fI2,2\fR].
.TP
\fB\-\-wcal\-wssigma\fR \fI<float>\fR
Chebyshev correction sigma clipping factor. (float; default: 150.0). The full name of this option for the EsoRex configuration
file is \fBgiraffe.wlcalibration.wsol.sigma\fR [default = \fI150.0\fR].
.TP
\fB\-\-wcal\-wsniter\fR \fI<int>\fR
Chebyshev correction sigma clipping maximum number of iterations (int;
default: 10). The full name of this option for the EsoRex configuration
file is \fBgiraffe.wlcalibration.wsol.iterations\fR [default = \fI10\fR].
.TP
\fB\-\-wcal\-wsmfrac\fR \fI<float>\fR
Chebyshev correction sigma clipping minimum fraction of points
accepted/total. (float; default: 0.9). The full name of this option for the EsoRex configuration
file is \fBgiraffe.wlcalibration.wsol.fraction\fR [default = \fI0.9\fR].
.TP
\fB\-\-wcal\-wsorder\fR \fI<str>\fR
X and Y polynomial orders for the wavelength solution Chebyshev
correction. (str; default: \'6,4\'). The full name of this option for the EsoRex configuration
file is \fBgiraffe.wlcalibration.wsol.order\fR [default = \fI6,4\fR].
.TP
\fB\-\-wcal\-rebin\fR \fI<bool>\fR
Rebin extracted arc\-lamp spectra. (bool; default: True). The full name of this option for the EsoRex configuration
file is \fBgiraffe.wcal.rebin\fR [default = \fITrue\fR].
.TP
\fB\-\-rbin\-method\fR \fI<str>\fR
Method to use : `linear\' or `spline\' (str; default: \'linear\'). The full name of this option for the EsoRex configuration
file is \fBgiraffe.rebinning.method\fR [default = \fIlinear\fR].
.TP
\fB\-\-rbin\-xresid\fR \fI<bool>\fR
Use x residuals during rebinning? `true\'/`false\' (bool; default: True). The full name of this option for the EsoRex configuration
file is \fBgiraffe.rebinning.xresiduals\fR [default = \fITrue\fR].
.TP
\fB\-\-rbin\-lstep\fR \fI<float>\fR
Lambda step size, only used if scaling method is \'linear\' (float;
default: 0.005). The full name of this option for the EsoRex configuration
file is \fBgiraffe.rebinning.lstep\fR [default = \fI0.005\fR].
.TP
\fB\-\-rbin\-scmethod\fR \fI<str>\fR
Scaling method: `log\' or `linear\' (str; default: \'linear\'). The full name of this option for the EsoRex configuration
file is \fBgiraffe.rebinning.scalemethod\fR [default = \fIlinear\fR].
.TP
\fB\-\-rbin\-size\fR \fI<int>\fR
Size of output rebinned spectra, 0 means calculate size based on
wavelength range and lambda stepsize (int; default: 0). The full name of this option for the EsoRex configuration
file is \fBgiraffe.rebinning.size\fR [default = \fI0\fR].
.TP
\fB\-\-rbin\-range\fR \fI<str>\fR
Rebinning range: `setup\' or `common\' (str; default: \'setup\'). The full name of this option for the EsoRex configuration
file is \fBgiraffe.rebinning.range\fR [default = \fIsetup\fR].
.TP
\fB\-\-wcal\-slit\fR \fI<bool>\fR
Controls the slit geometry calibration. (bool; default: False). The full name of this option for the EsoRex configuration
file is \fBgiraffe.wcal.slitgeometry\fR [default = \fIFalse\fR].
.TP
\fB\-\-scal\-cniter\fR \fI<int>\fR
Slit geometry calibration maximum number of iterations. (int; default:
1). The full name of this option for the EsoRex configuration
file is \fBgiraffe.sgcalibration.iterations\fR [default = \fI1\fR].
.TP
\fB\-\-scal\-zmax\fR \fI<float>\fR
Maximum allowed pixel value. To be effective it must be larger than 0.
(float; default: 10000.0). The full name of this option for the EsoRex configuration
file is \fBgiraffe.sgcalibration.zmax\fR [default = \fI10000.0\fR].
.TP
\fB\-\-scal\-cstep\fR \fI<float>\fR
Cross\-correlation step. (float; default: \-0.005). The full name of this option for the EsoRex configuration
file is \fBgiraffe.sgcalibration.cc.step\fR [default = \fI\-0.005\fR].
.TP
\fB\-\-scal\-cdomain\fR \fI<str>\fR
Restricts the cross\-correlation to the given domain. (str; default:
\'0.,0.\'). The full name of this option for the EsoRex configuration
file is \fBgiraffe.sgcalibration.cc.domain\fR [default = \fI0.,0.\fR].
.TP
\fB\-\-scal\-rvlimits\fR \fI<str>\fR
Delta RV limits of the cross\-correlation window in km/s. (str;
default: \'\-200.,200.\'). The full name of this option for the EsoRex configuration
file is \fBgiraffe.sgcalibration.rv.limits\fR [default = \fI\-200.,200.\fR].
.TP
\fB\-\-scal\-rvniter\fR \fI<int>\fR
Maximum number of iterations used for the RV determination. (int;
default: 3). The full name of this option for the EsoRex configuration
file is \fBgiraffe.sgcalibration.rv.iterations\fR [default = \fI3\fR].
.TP
\fB\-\-scal\-rvwfactor\fR \fI<float>\fR
Data window width factor. The FWHM times this value determines the
window width. (float; default: 1.5). The full name of this option for the EsoRex configuration
file is \fBgiraffe.sgcalibration.rv.wfactor\fR [default = \fI1.5\fR].
.TP
\fB\-\-scal\-pfniter\fR \fI<int>\fR
Peak model fit maximum number of iterations. (int; default: 50). The full name of this option for the EsoRex configuration
file is \fBgiraffe.sgcalibration.peak.iterations\fR [default = \fI50\fR].
.TP
\fB\-\-scal\-pfntest\fR \fI<int>\fR
Cross\-correlation peak fit maximum number of tests (int; default: 7). The full name of this option for the EsoRex configuration
file is \fBgiraffe.sgcalibration.peak.tests\fR [default = \fI7\fR].
.TP
\fB\-\-scal\-pfdchisq\fR \fI<float>\fR
Cross\-correlation peak fit minimum chi\-square difference. (float;
default: 0.0001). The full name of this option for the EsoRex configuration
file is \fBgiraffe.sgcalibration.peak.dchisquare\fR [default = \fI0.0001\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 gimasterflat (7),
.IR giscience (7),
.IR gistandard (7)

.SH VERSION
giwavecalibration 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