The UVES-MOS pipeline is designed to reduce raw SCIENCE spectra taken in fibre mode (FLAMES-UVES) to a level almost free from instrumental signature.

On Paranal, the quick-look pipeline makes an attempt to automatically reduce all science data. The reduction is performed using standard calibration solutions from a local calibration database which is refreshed a few times a year. All settings currently offered for FLAMES-UVES in Service and Visitor Mode are supported. Generally, any pipeline processing on the site is done on a best-effort basis.

At QC Garching, all SCIENCE data taken in Service Mode are pipeline-reduced, using the best available calibration solutions (quality-checked and closest in time, following the calibration cascade). The products of science reduction are also quality-checked. If any irregularity in the reduced data is found, an attempt is made to improve on this. If not possible, information about the poor quality is made available in the SM package. Present policy is to not suppress these data.

Two types of raw science files exist:

Recipe. A science raw file is pipeline-processed by the pipeline recipe flames_obs_scired. In short, the bias level and the interorder background are subtracted. Every order of the spectrum is extracted, flat-fielded, de-convolved for fibre cross talk, wavelength calibrated, and corrected for differences in fibre transparency. Finally, the orders are merged.

Extraction. The UVES-MOS pipeline knows two extraction modes:

• optimum (OPT)
• average (AVG)

Optimum extraction is the default extraction mode. It provides an optimized signal-to-noise ratio. Average (or standard) extraction is an alternative mode which simply averages any signal along the slit and above the sky background level. It may be a good choice in case of failure of the optimum extraction, e.g. at high exposure level. More information about optimum extraction can be found on the UVES sciende recipe pages.

Optimum extraction. Science data reduced for Service Mode programmes are processed in optimal extraction mode (OPT). The pipeline assumes a Gaussian profile for the cross-dispersion flux distribution. This procedure

• yields optimum S/N,
• automatically discriminates against any non-Gaussian components in the cross-dispersion profile.
  

This means specifically

• automatic sky subtraction (since the sky background is treated as a pedestal),
• automatic cosmic ray rejection (whenever the hit has a non-Gaussian distribution),
• automatic sky emission line removal (since these fill up the whole slit and have a rectangular profile).

Simultaneous calibration. UVES-MOS offers the possibility to use one fibre for measuring a ThAr spectrum simultaneously with the science observations. Since pipeline version 2.4, the science recipe can cross-correlate the simultaneous ThAr spectrum with a template spectrum and determines a velocity shift of the observation with respect to the template. The same calculation is performed with the day-time ThAr calibration.

The cross-correlation is calculated on each order separately. The results are written in the CORVEL_TAB file. The average velocity shift (in km/s) with respect to the template is written in the QC.CCF.POSAVG header keyword; QC.CCF.POSRMS contains the rms of the average and QC.CCF.POSOFF the shift of the day-time ThAr spectrum with respect to the template.

Important note: The cross-correlation results are not yet fully explored and should be regarded only as an indication for the stability of the instrument. Comments on this are highly welcome.

Products. Service Mode programmes receive the following reduction products:

• one FIB_SCI_INFO_TAB tfits table containing information about the fibre positions
• one MWXB_SCI file per CCD (i.e. two files); this is the merged and wavelength-calibrated extracted spectrum that has been corrected for different throughputs of the fibres; it is a 2D image with wavelength on x-axis and fibre on y-axis
• one ERR_MWXB_SCI file per CCD; this is the errorbar file corresponding to MWXB_SCI
• one XB_SCI file per CCD; this is a 3D data cube containing the extracted and throughput-corrected spectrum for each order
• one MWXB_SCI_RAW file per CCD; similar to MWXB_SCI but without correction for fibre throughput
• one ERR_MWXB_SCI_RAW file per CCD; the corresponding errorbar file
• one XB_SCI_RAW per CCD; extracted and not throughput-corrected spectra for each order
• in case of SimCal data, one CORVEL_TAB table per CCD containing the results of the cross-correlation.

All pipeline results delivered within Service Mode packages are renamed since P75. Please look here for details of the scheme. The naming scheme for older packages was:

The 3D files can be assessed within MIDAS with the commands:

midas> indisk/fits XB_file.fits XB_file.bdf
midas> plot XB_file.bdf[<,@order,@fibre:>,@order,@fibre]

where XB_file is the filename of the XB_SCI file without extension, order is the order number to be plotted, and fibre is the fibre number (1-8 for 580 and 860 settings, 1-6 for 520).

The UVES pipeline, running on Service Mode data in optimum extraction mode, implicitly makes the following assumptions on the raw spectra:

• the object is a point source,
• the object is centred on the fibre,
• the object has some continuum, i.e. is not a pure emission line object,
• the signal-to-noise ratio is not too high ( < 50 approximately).

Only if these assumptions are readily met by the nature of the observations, can useful results be expected. While some of these assumptions are checked as part of the QC checks done for assessment of the pipeline products, there is no alternative approach chosen (e.g. average extraction). This is the sole responsibility of the user.

UVES-MOS calibration and reduction scheme

The successful execution of science reduction requires a complete set of calibration products available.

All science data processed by QC Garching are reduced with a quality-checked set of calibration files which are usually generated from day-time calibrations taken immediately after the science night. Attached calibrations (Nasmyth FLATs taken during night-time) and simultaneous wavelength calibrations are currently not used.

QC Garching checks on the quality of the reduced science data. The following items are checked:

• proper selection of calibration data
  
  
• any peculiarities in the raw data
  e.g. unusual bias level.
  
  
• the cross-dispersion profile
  Here the exposure level and the sky background are controlled.
  
  
• the mean intensity per fibre
  This gives an indication whether the complete fibre has been extracted correctly
  
  
• proper dispersion solution
  A comparison to the expected positions of frequent lines, e.g. the Balmer lines, reveals at least larger errors in wavelength calibration.
  
  
• proper extraction
  The full spectrum and its variance are plotted and checked visually for anomalies in the extraction
  

Extensive QC1 reports about SCIENCE reduction and signal tracing are delivered as part of the Service Mode package.

Wavelength calibration. The precision of the wavelength calibration in the course of science reduction is determined by

• the precision of the dispersion solution used for resampling,
• the difference of temperature between the science observation and the calibration solution used.

Typical values for the standard deviation are of the order of 3-9 milli-Angstroem.

The overall UVES spectrum shifts on the detector mainly depend on the air temperature in the UVES enclosure. The shift in the red arm is, in first approximation, 0.35 pixels/Degree C in the dispersion direction. One pixel is ~1.2 km/sec. These drifts are actively compensated.

The temperature information is recorded in the file headers and reported in the 'TEMP' columns of the list files. By comparing the temperatures at the times of the science exposure and of the wavelength calibration applied to the data, the magnitude of the possible shift can be estimated from the gradients given above.

CCD defects. The UVES-MOS pipeline does not apply any correction for cosmetic defects of the CCDs. These are minimal because of the good cosmetic quality of the devices. However, there are a few defects which show up, notably in long integrations on faint objects on the two CCDs of the red arm.

There are four trails of hot pixels which appear in long exposures in the blue-side quadrant of the EEV chip (bluer side of the red arm mosaic, X coordinates 3896,3963, 4052 and 4140 in an unbinned fits file, middle of the chip in y). They occupy a single column and are almost parallel to the orders. They appear as broadish emission in the bluer part of the extracted spectrum of a faint object.

In the MIT-LL chip (red side of the CCD mosaic of the red arm) there is a trap in the column X1609 which might show up as a slight depression over ~130 pixels in the extracted spectrum of one order. In long, binned exposures this chip shows also an emission band starting on the red side and extending over the rows 2790-2850 with decreasing intensity toward the blue side of the echelle format. Since this band is perpendicular to the spectrum, it is usually well subtracted in the sky subtraction step of the optimal extraction.

High signal. Optimum extraction may face problems in cases of high signal, i.e. when the differences between the true shape of the instrumental profile and the assumed Gaussian start to become systematic rather than random.

Two kinds of artifacts may show up then:

• ripple-like patterns repeating with the orders. These are due to the non-Gaussian shape effect being stronger in the centre of an order than at the edges. Hence optimum extraction loses more flux in the centre of an order. Since usually flattening removes these order-period ripples completely, their occurrence is a good indicator of the "high-signal" problem. In such cases, average extraction will produce better results.
• Small-scale scatter with a period of about 20-30 pixels. This problem is due to problems in the order-tracing algorithm which become stronger in case of high signal and good seeing, hence small FWHM. Since the echelle orders are inclined by a few degree, their centre "jumps" vertically by one pixel every 20-30 pixels. This affect degrades the S/N ratio of the spectrum considerably. Again, average extraction will produce better results.
  

Some of these cases are detected by quality check procedures, and a short note is included in the Service Mode package. However, this is not generally true, and we strongly recommend to carefully check the results if they could be affected by this problem.

See also the tutorial on optimum extraction for UVES-Echelle.

Sky emission lines. Optimum extraction may over/under-corrected bright sky emission lines by 5% or more.

Artificial lines. Series of artificial lines are occasionally seen around 607 nm and 638 nm in spectra reduced with optimum extraction. These features may be mistaken as telluric or real physical lines.

Errorbar values. The values in the ERR_MWXB_SCI files are about a factor of two higher than the statistical 1sigma errors.