VERSION:

P81.1 (May 2008)

April 2008: ThAr lamp exposures with fibre bundle.
April 2008: Reduced effective slit length.

DATA PACKAGES: GENERAL

Once a VLT/VLTI observing run is finished, the QC Group creates a data package which is then delivered by the Science Archive Group to the PI. Currently, data packages are created for the following cases:

• VLT/VLTI: all instruments, Service Mode runs only
• La Silla: most La Silla instruments, Service Mode runs only

Data packages for VLT pre-imaging runs are created and delivered just as ordinary Service Mode run packages (in addition to the ftp package delivered on the fast track).

The data packages are currently delivered on DVDs.

Science data have been processed by the pipeline with the best available calibration data. Please note that ESO is not assuming any responsibility in respect to the usefulness of the reduced data. The adopted reduction strategy may not be suitable for the scientific purpose of the observations.

The top-level structure of the data package is as follows:

For each observation block (OB) that has been executed on Paranal, you find all measured raw data (FITS files) in a directory named by the OB number (FITS key HIERARCH.ESO.OBS.ID). If pipeline products exist, these are also added in the OB directory.

The GEN_CALIB directory collects all those calibration files (raw and products) that have been measured as part of the regular calibration plan, and calibration frames of a general nature (like static line tables). The GEN_INFO directory has general information, like data reports and night logs.

The tree shown above is the logical structure, which means that this is the way the data have been organized before they have been put onto media. Depending on the size of your package, the directories may be distributed across several media. It is a good idea to create the original tree on your local disk and then copy all files from the media into this tree.

<OBS_ID> (e.g. 179211)

For each executed observation block of your run, the package contains a directory with all measured data from that OB. All data under <OBS_ID> carry your run ID.

Note that some of your OBs may have been executed more than once. In particular, if time permitted, observatory staff try to re-execute OBs which produced data clearly out of the specified constraints. Check out the NIGHTLOG.html file for details (go to "OB information"). All data from OBs that have been executed multiple times are found in the same directory.

Each OB directory is further subdivided into subdirectories for science frames, calibration frames, and log files. In many cases, there will be science data only, but there may also be OBs with attached calibration data:

<OBS_ID>

acq sci_raw sci_proc cal_raw cal_proc logs

<OBS_ID>/acq

All acquisition frames (DPR.CATG=ACQUISITION) from the OB are contained in this directory. This directory only exists if such data exist.

<OBS_ID>/sci_raw

All raw science frames (DPR.CATG=SCIENCE) from the OB are contained in this directory.

<OBS_ID>/sci_proc

Here you find the pipeline-processed science data. The naming scheme can be found here.

<OBS_ID>/cal_raw

If measured, raw calibration frames (DPR.CATG=CALIB) produced by the OB are contained in this directory ("attached calibrations"). These are the ones which have been taken upon user's request in addition to the ones from the calibration plan.

Calibrations measured as part of the regular calibration plan are stored under the GEN_CALIB directory.

<OBS_ID>/cal_proc

The pipeline products of the raw attached calibrations are delivered here.

The CALIB products are renamed. The naming scheme can be found here.

<OBS_ID>/logs

This directory has logging information about processing and packing of your data:

• logs of the pipeline processing (extension .rblog)
• Association Blocks (extension .ab)
• association logs (extension (.alog)

Association Blocks (ABs) are text files which contain all the information required to pipeline-process and pack data. This information includes the reduction recipe, the input raw file(s), the calibration products needed for processing, and the names of the final products. They are described here.

Association logs are delivered since P80. They are a simplified version of ABs, designed to provide the association information essential for the user. More ...

The pipeline processing log is a record of the science reduction process, with a detailed log of reduction steps, results etc.

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GEN_CALIB

This directory collects all calibration frames from the regular calibration plan that are associated to your science data. It also contains their pipeline products, and calibration frames of a general nature (like static line tables). Calibrations that have been measured by user-defined OBs and that have been used for pipeline processing of science data may be included here in addition.

The directory has four subdirectories (gen, logs, proc, raw), two of which have further fine-structure:

GEN_CALIB
raw	proc	gen	logs
cal1 cal2 cal3 cal4	cal1 cal2 cal3 cal4

GEN_CALIB/raw

Raw calibration files. These divide into raw file types (e.g. BIAS, FLAT etc.; see instrument specific section below).

GEN_CALIB/proc

Calibration products derived from the raw calibrations. These divide into file types like the raw calibration files, see instrument specific section below.

The CALIB products are renamed. The naming scheme can be found here.

GEN_CALIB/logs

Association Blocks, association logs and processing logs for the calibration files under GEN_CALIB.

GEN_CALIB/gen

General calibration data of static nature.

Additional or missing raw calibration files may be retrieved anytime from the generic ESO Archive form, or from the instrument specific forms.

Calibration data are public immediately while SCIENCE data normally have a proprietary period of one year.

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GEN_INFO

This directory hosts some general information. It has the following subdirectories:

DIRECTORY	CONTENT
ObservingReports	nightlogs, OB report (HTML files), association report
scripts	executable scripts (presently one: print_all_reports)

 

The data package contains the following report files:

FILE	CONTENT	WHERE
README.html	the package portal page: point your browser here to find all information	top
ServiceMode.html	this file	top
product_codes.html	a table describing the naming scheme for product files	top
archive_<RUN_ID.txt	list of all proprietary files (SCIENCE, attached CALIBs) as read from the archive	GEN_INFO
qc0_<RUN_ID>.txt	list of all SCIENCE files, containing the comparison between the user constraint set and the actual values	GEN_INFO
NIGHTLOG.html	set of html files with nightlog, OB and association information	GEN_INFO/ObservingReports
list_sciRaw_<OBS_ID>.txt etc.	summary report of the fits files in each directory (these files are provided in text [*.txt] and PostScript format)	all data directories

The executable script print_all_reports under GEN_INFO/scripts can be used to print all postscript files in your package.

Archive report: archive_<RUN_ID>

While the above listings are about files in the package, the archive report is the result of a query to the ESO Archive. It is useful as a check on the completeness of the data package. All files created by OBs which have been generated by the PI are listed here. The list includes all SCIENCE files, and the attached calibrations, and acquisitions, if applicable.

archive report
keyword table
sample file

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QC0 report: qc0_<RUN_ID>

This file contains a report of quality control parameters ('QC level 0' where level 0 stands for Quality Control without pipeline processing) for your raw SCIENCE files. These parameters are airmass, seeing, moon distance, and fractional lunar illumination. They have been measured on site (column 'msrd'). They are compared to the required values as defined in your OBs ('targt') and flagged (OK/NOK).

The list is intended to give a rough indication of whether or not the required constraints have been fulfilled. They should not be interpreted in a too formal way, however. E.g., there may be cases where the seeing was worse than required, but this was compensated by a longer exposure time. Check the night reports for details.

Note that the seeing values reported here are DIMM seeing values, they are not measured on the frame. If the alarm flag ("NOK") is set in the SEEING column, the DIMM seeing value was larger than your seeing constraint during the indicated obseration. However, in many cases, the delivered seeing in the instrument focal plane is better than the DIMM seeing. Whenever possible, the on-site astronomer has measured the focal plane immediately after or during execution to determine the success or failure of your observation. Thus, your observation may have been completed within your specifications, even if the SEEING alarm flag is set. Please review the affected observation carefully and check the night reports for details.

QC0 report
keyword table
sample file (.txt)

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Night logs, OB logs and Association report

This is a set of HTML files with night log information, OB grading information and data association information. All relevant information about the nights contained in your package is included here, as well as information about each OB in your delivery.

Point your browser to GEN_INFO/ObservingReports/NIGHTLOG.html (or start from the package portal page, README.html) and navigate per night (labeled as 1), per OB (2) or per set of files (3).

The HTML files also come as stripped-down, printer-friendly versions. The files are organized to have a summary on top, and details below.

You can use either the navigation bar to jump to a specific night/OB/set of files, or use the up/down arrows (night logs only) to browse sequentially. The OB navigation bar (2) uses colour coding to give you a quick impression about OB grading. There are additional links to ambient condition information.

The association report (3) organizes your data and their association. It has two main levels: the OB (observing block), and the AB (association block) which collects raw file(s) and associated information like product files, calibration files, log files etc. This report gives you an impression how the data in your package are logically linked, while the listings in each directory give you a table of contents. File names in the association report may show up several times, e.g when a calibration file has been used for processing more than one science file.

NOTE:

• The external links (like the ASM links: seeing, sky transparency etc.) will only work with network connection.
• The ASM links require java-enabled browsers.
• The navigation bars read best with style-sheets and java-enabled browsers.

Sample nightlog files
NIGHTLOG.html

Known IRAF problems

• Filename Length. To display or manipulate the FITS files with older versions of IRAF (before 2.11), you can:
  - copy these FITS files to your hard-disk and rename them with filenames <= 32 characters in length;
  - create symbolic links with filenames <= 32 characters in length to your DVD files.
  
  
• Header Interpretation. ESO FITS files use the ESO HIERARCH FITS keyword extensions standard to all ESO telescopes. Note that IRAF treats all ESO HIERARCH header lines as COMMENT lines, i.e. IRAF and IDL cannot automatically interpret the information provided in ESO HIERARCH header lines. The problem may be solved using the tool hierarch28. Find information about this tool here.
  
  
• RA, DEC. Please note that the RA and DEC keywords are recorded in degrees. To translate these keywords so that they can be used by IRAF you have to use the asthedit task in the noao.astutil package. The help file for this task gives an example of how to translate the ESO format to the IRAF format.

Stand-alone FITS handling tools

 

CRIRES INFORMATION

For further information about CRIRES please look at:

• CRIRES Quality Control and Data Flow Operations Homepage
• General description of CRIRES data management with a list of FAQs
• CRIRES pipeline processing
• CRIRES data types: science raw | science products | calibration raw | calibration products

 

CRIRES GEN_CALIB DIRECTORY

GEN_CALIB

The GEN_CALIB directory for CRIRES has the following structure:

GEN_CALIB
gen	logs	proc	raw
		DET FLAT WAVE STD	DET FLAT WAVE STD

All calibration frames are divided into a few general types. These types can be found as subdirectories of the proc and raw directories:

TYPE/SUBDIRECTORY	CONTENT	DPR.TYPE
DET	Detector dark frames	DARK
FLAT	Lamp flat field exposures	FLAT
WAVE	Wavelength calibration exposures	WAVE,LAMP WAVE,ABSORPTION-CELL WAVE,SKY
STD	Telluric and spectroscopic standard star exposures	STD

GEN_CALIB/gen

General calibration data of static nature. You may expect the following files:

FILE NAME	PRO.CATG	DESCRIPTION
lines_thar.fits	CALPRO_THAR_CATALOG	catalog of ThAr lines
lines_n2o.fits	CALPRO_N2O_CATALOG	catalog of N2O lines
lines_hitran.fits	CALPRO_HITRAN_CATALOG	catalog of sky lines (for > 1800nm)
lines_oh.fits	CALPRO_OH_CATALOG	catalog of OH sky lines (for < 1800nm)
stdstars.fits	CALPRO_STD_PHOTOFLUX	table of photometric standard star fluxes
model_conf.fits	CALPRO_MODEL_CONFIG	configuration for physical model

Wavelength calibration

New with P81: In April 2008, a fibre bundle has been mounted to the ThAr lamp carriage. The fibres are projected on the slit. ThAr wavelength calibration exposures now have three separate light traces on the detector.

CRIRES offers several options for obtaining a wavelength calibration (see User Manual). For pipeline-reduced science products in this package, the following strategy has been chosen:

• If an attached wavelength calibration (ThAr lamp or N2O gas cell) has been measured together with the science data then the wavelength solution from this calibration has been used for calibrating the science.
• If an attached wavelength calibration does not exist but a daytime wavelength calibration exists then the wavelength solution is obtained from the daytime measurement.
• If neither an attached nor a daytime wavelength calibration has been measured then the wavelength solution is obtained from sky lines present in the science exposures. This is usually the case for observations redward of 2500 nm where the density of sky emission lines is sufficiently high.

Pipeline wavelength calibration operates on each detector separately. Depending on the calibration source and the availability of appropriate spectral lines, it is possible that a wavelength solution is found for some but not for all 4 detectors. The success of the wavelength calibration is given by the fits header keyword HIERARCH ESO QC XCORR which is present in each of the four extensions of any science or wave pipeline product. In case of an arc lamp or gas cell exposure, a value of -1 indicates a failure of the wavelength calibration for this extension (i.e. detector). Then, the default linear solution for this spectral setting has been written to the output product. For science and standard star exposures, the QC XCORR keyword is meaningful only if sky lines have been used for obtaining a wavelength solution.

An alternative method is provided by the physical model of the CRIRES spectrograph. The model uses the actual state of the spectrograph and predicts a wavelength map (i.e. a wavelength for each pixel). This map is also included in the package and can be compared to the solution obtained from arc lamp or gas cell calibration sources. The predicted wavelengths usually have a small offset which can be determined from this comparison and then be used to calibrate detectors without a sufficient number of ThAr or N2O lines.

It cannot be guaranteed that the adopted strategy for wavelength calibration, that has been chosen for the pipeline reduction in this package, is appropriate for the scientific goal. A first check can be obtained from the XCORR header keyword. It is also highly recommended to cross-check the solutions obtained with different methods.

Reduced effective slit length

After the instrument upgrade early April 2008, the field-of-view along the slit (and therefore the effective slit length) is reduced to 12 arcsec. On the detector, only about 200 pixels in Y direction can be illuminated.

Vignetting on detectors 1 and 4

Adjacent echelle orders are isolated in the spectrograph by usage of an additional slit after the pre-dispersing prism (so-called intermediate slit). For settings below 1450 nm, the slit had to be set up in a way that the outer parts of detectors 1 and 4 are not fully exposed. See Sect. 14 of the User Manual or this listing for a detailed description of the usable wavelength ranges for each setting. Since October 2007, updated values for the wavelength range that is not affected by adjacent orders are written into the header keywords INS WLEN MIN and INS WLEN MAX.

Accurate positioning of the pre-disperser and the intermediate slit turned out to be difficult during the first weeks of CRIRES Service Mode operations. Although measures have been taken to stabilise these elements, some observations were affected by additional vignetting and/or contamination from adjacent orders on detectors 1 and 4. All observations have been checked for these effects and have been repeated where appropriate.

Fixed-pattern noise and detector non-linearity

The CRIRES detectors have significant gain variations from pixel to pixel which are strongest in dispersion direction on detectors 1 and 4 (and in cross-dispersion direction on detectors 2 and 3). This results in an odd-even column effect in the extracted spectra for these detectors. The gain variations can be corrected with flat fields but in several cases a small pattern remains present after flat-fielding. Since 7 June 2007, daily flat fields are measured with DIT = 2 sec (instead of 1 sec). This significantly improved correction for fixed-pattern noise.

The detectors also become non-linear for exposure levels above about 4000 ADUs. This effect is measured by a series of dedicated flats measured with increasing exposure level (so-called detlin flats). A quadratic function is fitted for each pixel and the coefficients are used later on in the reduction cascade for correcting raw frames.

Pipeline products in Service Mode packages have been reduced as follows:

• Flat fields are corrected for detector non-linearity
• Raw science and standard star frames are corrected for non-linearity and then flat-fielded.