giscience - Process a science observation.

Giraffe Pipeline <https://support.eso.org/>

Please report any problems to https://support.eso.org/. Alternatively, you may send a report to the ESO User Support Department <usd-help@eso.org>.

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

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 giscience 2.16.10 GISCIENCE(7)

giscience - Process a science observation.

--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<int> Sigma Clipping: maximum number of iterations (int; 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<int> Order of X polynomial fit (CURVE method only) (int; default: 1). The full name of this option for the EsoRex configuration file is giraffe.biasremoval.xorder [default = 1]. --bsremove-yorder<int> Order of Y polynomial fit (CURVE method only) (int; default: 1). The full name of this option for the EsoRex configuration file is giraffe.biasremoval.yorder [default = 1]. --bsremove-xstep<int> Sampling step along X (CURVE method only) (int; default: 1). The full name of this option for the EsoRex configuration file is giraffe.biasremoval.xstep [default = 1]. --bsremove-ystep<int> Sampling step along Y (CURVE method only) (int; 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<int> 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 giraffe.extraction.psf.iterations [default = 2]. --extr-hewidth<int> 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 giraffe.extraction.horne.extrawidth [default = 2]. --extr-hmingood<int> 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 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<int> 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 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<int> 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 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<int> Slit geometry calibration maximum number of iterations. (int; 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<int> Maximum number of iterations used for the RV determination. (int; 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<int> Peak model fit maximum number of iterations. (int; default: 50). The full name of this option for the EsoRex configuration file is giraffe.sgcalibration.peak.iterations [default = 50]. --scal-pfntest<int> Cross-correlation peak fit maximum number of tests (int; 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<int> Sets the number of dummy (empty) ASSONi, ASSOCi and ASSOMi keywords to create. (int; 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.

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 https://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 https://packages.python.org/python-cpl/index.html for further information. The other recipes of the giraf pipeline are giframestack(7), gimasterbias(7), gimasterdark(7), gimasterflat(7), gistandard(7), giwavecalibration(7)

esorex giscience [OPTIONS] FILE.sof

giscience 2.16.10