giscience(7) Process a science observation.

SYNOPSIS

esorex giscience [OPTIONS] FILE.sof

DESCRIPTION

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

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

OPTIONS

--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].
--generate-SDP-format <bool>
TRUE if additional files should be generated in Science Data Product (SDP) format. (bool; default: False). The full name of this option for the EsoRex configuration file is giraffe.sdp.format.generate [default = False].
--dummy-association-keys <long>
Sets the number of dummy (empty) ASSONi, ASSOCi and ASSOMi keywords to create. (long; default: 0). The full name of this option for the EsoRex configuration file is giraffe.sdp.nassoc.keys [default = 0].

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.

VERSION

giscience 2.14.3

AUTHOR

Giraffe Pipeline <[email protected]>

BUG REPORTS

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

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