giscience (7)

esorex giscience [OPTIONS] FILE.sof

For detailed information please refer to the GIRAFFE pipeline user manual.

It is available at http://www.eso.org/pipelines.

--remove-bias <bool>

Enable bias removal (bool; default: True). The full name of this option for the EsoRex configuration file is giraffe.biasremoval.remove [default = True].

--bsremove-method <str>

Bias removal method (str; default: \'PROFILE\'). The full name of this option for the EsoRex configuration file is giraffe.biasremoval.method [default = PROFILE].

--bsremove-areas <str>

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 giraffe.biasremoval.areas [default = 5:40:0:4095].

--bsremove-sigma <float>

Sigma Clipping: sigma threshold factor (float; default: 2.5). The full name of this option for the EsoRex configuration file is giraffe.biasremoval.sigma [default = 2.5].

--bsremove-niter <long>

Sigma Clipping: maximum number of iterations (long; default: 5). The full name of this option for the EsoRex configuration file is giraffe.biasremoval.iterations [default = 5].

--bsremove-mfrac <float>

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 giraffe.biasremoval.fraction [default = 0.8].

--bsremove-xorder <long>

Order of X polynomial fit (CURVE method only) (long; default: 1). The full name of this option for the EsoRex configuration file is giraffe.biasremoval.xorder [default = 1].

--bsremove-yorder <long>

Order of Y polynomial fit (CURVE method only) (long; default: 1). The full name of this option for the EsoRex configuration file is giraffe.biasremoval.yorder [default = 1].

--bsremove-xstep <long>

Sampling step along X (CURVE method only) (long; default: 1). The full name of this option for the EsoRex configuration file is giraffe.biasremoval.xstep [default = 1].

--bsremove-ystep <long>

Sampling step along Y (CURVE method only) (long; default: 1). The full name of this option for the EsoRex configuration file is giraffe.biasremoval.ystep [default = 1].

--extr-method <str>

Extraction method: \'SUM\', \'HORNE\' or \'OPTIMAL\' (str; default: \'SUM\'). The full name of this option for the EsoRex configuration file is giraffe.extraction.method [default = SUM].

--extr-ron <float>

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 giraffe.extraction.ron [default = -1.0].

--extr-psfmodel <str>

PSF profile model: `psfexp\', `psfexp2\' (str; default: \'psfexp2\'). The full name of this option for the EsoRex configuration file is giraffe.extraction.psf.model [default = psfexp2].

--extr-psfsigma <float>

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 giraffe.extraction.psf.sigma [default = 7.0].

--extr-psfniter <long>

Maximum number of iterations used for fitting the PSF profile. (long; default: 2). The full name of this option for the EsoRex configuration file is giraffe.extraction.psf.iterations [default = 2].

--extr-hewidth <long>

Horne extraction method: Number of extra pixels added to the fiber half-width. (long; default: 2). The full name of this option for the EsoRex configuration file is giraffe.extraction.horne.extrawidth [default = 2].

--extr-hmingood <long>

Horne extraction method: Minimum number of points used for the profile fit. It sets the lower limit of data points for the pixel rejection. (long; default: 3). The full name of this option for the EsoRex configuration file is giraffe.extraction.horne.mingood [default = 3].

--extr-omfrac <float>

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 giraffe.extraction.optimal.fraction [default = 0.9].

--extr-owfactor <float>

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 giraffe.extraction.optimal.wfactor [default = 3.0].

--extr-obkgorder <long>

Optimal extraction method: Order of the polynomial background model, which is fitted for each wavelength bin along the spatial direction. (long; default: 2). The full name of this option for the EsoRex configuration file is giraffe.extraction.optimal.bkgorder [default = 2].

--flat-apply <bool>

Controls the flat field correction. (bool; default: True). The full name of this option for the EsoRex configuration file is giraffe.flat.apply [default = True].

--transmission-apply <bool>

Controls the fiber to fiber transmission correction. (bool; default: False). The full name of this option for the EsoRex configuration file is giraffe.flat.transmission [default = False].

--rbin-method <str>

Method to use : `linear\' or `spline\' (str; default: \'linear\'). The full name of this option for the EsoRex configuration file is giraffe.rebinning.method [default = linear].

--rbin-xresid <bool>

Use x residuals during rebinning? `true\'/`false\' (bool; default: True). The full name of this option for the EsoRex configuration file is giraffe.rebinning.xresiduals [default = True].

--rbin-lstep <float>

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 giraffe.rebinning.lstep [default = 0.005].

--rbin-scmethod <str>

Scaling method: `log\' or `linear\' (str; default: \'linear\'). The full name of this option for the EsoRex configuration file is giraffe.rebinning.scalemethod [default = linear].

--rbin-size <long>

Size of output rebinned spectra, 0 means calculate size based on wavelength range and lambda stepsize (long; default: 0). The full name of this option for the EsoRex configuration file is giraffe.rebinning.size [default = 0].

--rbin-range <str>

Rebinning range: `setup\' or `common\' (str; default: \'setup\'). The full name of this option for the EsoRex configuration file is giraffe.rebinning.range [default = setup].

--siwc-apply <bool>

Enable simultaneous wavelength calibration correction. (bool; default: True). The full name of this option for the EsoRex configuration file is giraffe.siwc.apply [default = True].

--scal-cniter <long>

Slit geometry calibration maximum number of iterations. (long; default: 1). The full name of this option for the EsoRex configuration file is giraffe.sgcalibration.iterations [default = 1].

--scal-zmax <float>

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 giraffe.sgcalibration.zmax [default = 10000.0].

--scal-cstep <float>

Cross-correlation step. (float; default: -0.005). The full name of this option for the EsoRex configuration file is giraffe.sgcalibration.cc.step [default = -0.005].

--scal-cdomain <str>

Restricts the cross-correlation to the given domain. (str; default: \'0.,0.\'). The full name of this option for the EsoRex configuration file is giraffe.sgcalibration.cc.domain [default = 0.,0.].

--scal-rvlimits <str>

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 giraffe.sgcalibration.rv.limits [default = -200.,200.].

--scal-rvniter <long>

Maximum number of iterations used for the RV determination. (long; default: 3). The full name of this option for the EsoRex configuration file is giraffe.sgcalibration.rv.iterations [default = 3].

--scal-rvwfactor <float>

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 giraffe.sgcalibration.rv.wfactor [default = 1.5].

--scal-pfniter <long>

Peak model fit maximum number of iterations. (long; default: 50). The full name of this option for the EsoRex configuration file is giraffe.sgcalibration.peak.iterations [default = 50].

--scal-pfntest <long>

Cross-correlation peak fit maximum number of tests (long; default: 7). The full name of this option for the EsoRex configuration file is giraffe.sgcalibration.peak.tests [default = 7].

--scal-pfdchisq <float>

Cross-correlation peak fit minimum chi-square difference. (float; default: 0.0001). The full name of this option for the EsoRex configuration file is giraffe.sgcalibration.peak.dchisquare [default = 0.0001].

--recon-min <float>

Minimum wavelength for image reconstruction (float; default: 0.0). The full name of this option for the EsoRex configuration file is giraffe.fov.range.minimum [default = 0.0].

--recon-max <float>

Maximum wavelength for image reconstruction (float; default: 0.0). The full name of this option for the EsoRex configuration file is giraffe.fov.range.maximum [default = 0.0].

--recon-cube <bool>

Turns data cube creation on and off (bool; default: True). The full name of this option for the EsoRex configuration file is giraffe.fov.cube [default = True].

--recon-format <str>

Selects the file format for cubes (str; default: \'single\'). The full name of this option for the EsoRex configuration file is giraffe.fov.cube.format [default = single].

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.

The full documentation for the giraf pipeline can be downloaded as a PDF file using the following URL:

• ftp://ftp.eso.org/pub/dfs/pipelines/giraffe/giraf-pipeline-manual-2.11.pdf

An overview over the existing ESO pipelines can be found on the web page http://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 http://packages.python.org/python-cpl/index.html for further information.

The other recipes of the giraf pipeline are gimasterbias(7), gistandard(7), gimasterflat(7), giwavecalibration(7), giframestack(7), gimasterdark(7)

giscience 2.12.1

Giraffe Pipeline <[email protected]>

Please report any problems to [email protected]. Alternatively, you may send a report to the ESO User Support Department <[email protected]>.

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