Note: Until the end of P87 (September 2011) science data have been processed by QC Garching with the best possible (certified) calibrations solutions. The products were ingested into the Science Archive and delivered to the PIs. This service has been terminated with the begin of October 2011.
The documentation of the GIRAFFE science recipe is kept here for its heritage value. All statements about science processing by QC refer to the status before October 2011.
DPR CATG = SCIENCE, DPR TYPE = OBJECT,OzPoz or OBJECT,SimCal
Recipe. The pipeline recipe giscience performs the full reduction of GIRAFFE science frames.
Scheme. The following steps are performed:
The GIRAFFE pipeline run by QC Garching on science data until October 2011 used certified and closest-in-time calibration solutions, mostly taken during daytime following the science night. As of 2008-01-18, the recipe took into account the signal in the simultaneous calibration fibres (OBJECT,SimCal data). Data taken earlier do not have this correction enabled.
Extraction. The fibre signal is extracted by summing up (average extraction) the signal based on the localization solution of the flat field (PLOC file, pro.catg = FF_LOCCENTROID). Note: the signal from the last one or two fibres does usually not fall completely onto the chip. The pipeline suppresses these fibres completely.
The pipeline version 2.5 and later can provide optimum extraction and average extraction. For operational reasons, science data delivered by QC always used the average extraction. That extraction mode is operationally more stable but cannot suppress cosmic rays. The optimum extraction mode requires a modified calibration product scheme.
Flat-fielding. The extracted spectra are divided by the corresponding spectra of the flat field (PFEX file, pro.catg = FF_EXTSPECTRA). The flat-field signal is normalized such that the collapsed spectrum of the object fibre with the highest transmission is set to 1, and all other object fibres are scaled relative to that fibre signal. SIMCAL fibres in the flat-field are excluded from the statistics and always set to 1, while the SKY fibres get scaled like the object fibres. The extracted spectrum has the instrument response curve removed (at the price of now being affected by the lamp continuum which is however very smooth), and to a large extent also the fringing. The figure below demonstrates the effect of flattening: the 20nm scale ondulations are caused by the instrument response, while the ripples on the 1-2 nm scale are due to fringing. Both effects have disappeared after flattening.
Response. There is no response correction done by the pipeline, nor is it currently foreseen. In Medusa mode, no standard stars are taken, in IFU mode only on request of the user. In Argus mode, spectrophotometric standard stars are measured routinely. These are presently processed like science data. Their products are included in the data packages and can be used to derive an approximate flux calibration, using the fibres with the STD signal to derive the response curve, while the transmission scaling of the other fibres is provided by the flat field data.
Transmission. The fibre-to-fibre response differences are corrected using information from the fibre flats (the normalized factors from the above section "Flat-fielding"). Their values are stored as column TRANSMISSION in the fibre_setup table (extension 2 of the product files) and can be used to undo the correction.
Sky correction. The sky signal is recorded in the dedicated SKY fibres in the IFU and Argus modes. In Medusa mode, the user is completely free to record the sky signal in any object fibre. Since the pipeline recipe in general does not know exactly which fibres correctly record the sky signal, the sky signal is extracted by the recipe just as for any other fibre, and sky subtraction is left to the user.
Background subtraction. For data taken between October 2007 and March 2008, the recipe has subtracted the background as recorded in a master dark frame. For data later than that, there is no need for subtraction (no glow in the new CCD).
The master dark is constructed from at least 3 input raw darks (one hour exposure time each) and scaled properly for exposure time.
SimCal fibre correction. If the simultaneous calibration fibres have been used, their signal is used to incrementally correct the wavelength scale. The amount of the correction is available as column WLRES in the fibre_setup table (extension 2 of the product files) and can be used to undo the correction.
Since 2008-04-01, all SimCal science data also have information provided (in their product binary table) about barycentric, heliocentric and geocentric RV corrections (in km/s) per fibre. These corrections have not been applied by the pipeline.
Products. The following science products are created by the pipeline:
* coded as HIERARCH.ESO.PRO.CATG in the fits header
The error files (PRO.CATG = SCIENCE_EXTERRORS etc.) contain the calculated standard deviation per pixel of the SCIENCE_EXTSPECTRA file (containing: photon noise, read noise; the flat-field extraction errors is not included here). This error is propagated to the error files of the rebinned spectrum (SCIENCE_RBNERRORS) and, for IFU and Argus, of the recombined spectro-image, SCIENCE_RCERRORS, and the datacube, SCIENCE_CUBE_ERRORS (Argus only).
Data format. All products come as FITS files with the product pixels in the first extension, and a binary table in the second extension. That fibre_setup table is described here.
Medusa. The first QC plot for the Medusa setups has the following elements:
The lower panel displays, among other things, the delta in temperature ("deg") and time ("day"), resp., between the science exposure and the wavelength calibration; these values should be small in order to be sure to have no thermal or non-thermal drifts of the temperature-sensitive grating between science and calibration exposures.
For spectra above 585 nm, sky emission lines are marked in #4a (red vertical lines), and telluric absorption lines are marked in #4b (blue vertical lines). The emission lines (at UVES resolution) are taken from Hanuschik (2003). The list of telluric lines at the UVES resolution is not yet published.
Three more QC plots for the Medusa modes display all extracted spectra, along with their user-provided target name and magnitude:
IFU, Argus. The Argus and IFU settings also have a set of QC plots. The first one is very similar to the Medusa case, with the faintest object fibre showed under #4a, the integrated signal from all fibres of subslit #6 under 4b, and the S/N for the first fibre from #6. This selection has been made since Argus and IFU spectra are not independent of each other. The guess of the faintest object may fail under the same conditions as described in the Medusa case. The S/N comparison (plot #3) is not active for Argus/IFU since there is no brightest fibre. The histogram checks in plot #5 are the same as for Medusa.
Instead of a preview of all fibres, for Argus and IFU the reconstructed image (RCSPECTRA) is available as preview. It has been obtained by collapsing the spectra into a single number per fibre and display that value on a relative spatial grid. The mapping between fibre index and spatial coordinates has been provided by the pipeline (Fig. 2.7 of the FLAMES manual). Note this is a collapse of the whole spectrum. A narrow-band image in an emission-line can look rather different. Also note that this image is not sky subtracted (but the sky signal is available).