The GIRAFFE pipeline recipes 2.8.1 have been released!

2009-09-02:
The GIRAFFE pipeline recipes 2.8.1 package has been replaced. The contents of the package is unchanged, but the directory name in the giraf-calib-2.8.1.tar.gz, which prevented a successful installation using the installation script, has been fixed.

This is a maintenance release of the GIRAFFE pipeline recipes. It fixes a problem that can occur during the IFU cube construction if not all IFU buttons are in use.

The distributed recipes can be used for all three observing modes of the GIRAFFE spectrograph:

  • Medusa
  • IFU
  • Argus

Together with the data processing modules, we also provide two standalone applications for running them:

  • Gasgano, a GUI for data browsing and organisation, providing an intuitive and comprehensive interface to pipeline recipes that are based on the ESO Common Pipeline Library (CPL).
  • EsoRex, a command-line driven utility to launch pipeline recipes, which can be used either as an interactive tool, or can be embedded into scripts for automating some of the data reduction tasks.

GIRAFFE pipeline recipes public version:

The public version of the GIRAFFE pipeline recipes is 2.8.1, and it is included in the pipeline distribution kit giraf-kit-2.8.1tar.gz together with the following packages:

System Requirements

This release of the GIRAFFE pipeline kit is verified and supported on the VLT target platforms:
  • Linux Scientific Linux 4.0 (x86), using gcc 3.3.4
  • Linux Scientific Linux 4.1 (x86), using gcc 3.3.4
  • Linux Scientific Linux 4.3 (x86), using gcc 3.3.4
  • Linux Scientific Linux 5.2 (x86), using gcc 4.2.4
  • Linux Red Hat 9 (x86), using gcc 3.2.2, 3.3
  • Linux Fedora Core 6 (x86), using gcc 4.1.2
  • Sun Solaris 2.8 (SPARC), using gcc 3.3
In addition the GIRAFFE pipeline has been built successfully on the following systems:
  • SuSE Linux 9.3 (x86, AMD64), using gcc 3.3.5, 4.1
  • openSUSE 10.0 (x86), using gcc 4.0.1
  • openSUSE 10.2 (x86), using gcc 4.1.2
  • openSUSE 11.0 (x86), using gcc 4.3.1
  • openSUSE 11.1 (x86), using gcc 4.3.2

Installing and running the GIRAFFE pipeline recipes

To use the GIRAFFE pipeline recipes you will need to retrieve the pipeline distribution kit, unpack and install it.

Prerequisites:
  • One of the C compilers listed above, and standard GNU tools including make
  • To use the latest graphical front-end Gasgano version 2.3.0 the Java Development Kit (JDK) version 1.5 or later must be available on your system. If not, you may download it from http://java.sun.com/javase/downloads/index.jsp. The environment variable JAVA_HOME must be set correctly, and the related java executable must be in your PATH.

    Gasgano is known to be resource-intensive: see details of memory and CPU usage in Appendix A of the Gasgano User's Manual.
Note:
In order to retrieve the distribution kit, you may need to configure your Web browser so that it knows how to deal with the files we distribute, which usually are gzip compressed tar archives (.tar.gz filename extension). If you click on one of the links below, your browser should display a file selection panel; if you end up instead with a page full of strange characters, you may try clicking on the link while holding the Shift key down, or configure your browser.


Installation procedure:

  1. Download the GIRAFFE pipeline kit to a directory on your computer. This may be any directory with the exception of $HOME/gasgano and $HOME/.esorex!
  1. Unpack the distribution file, using the following command:

        tar -zxvf giraf-kit-2.8.1.tar.gz

  2. Install: after moving into the top level directory of the unpacked distribution,

        cd giraf-kit-2.8.1

    it is recommended to perform the installation using the supplied installation script:

        ./install_pipeline

    Note that this may take a few minutes. Please be patient!

    By default the script will install the GIRAFFE recipes, Gasgano, EsoRex, all the necessary libraries, and the static calibration tables, into a directory tree rooted at $HOME A different path may be specified as soon as the script is run. For instance (user input is boldfaced):
    $ ./install_pipeline
    I am about to install the following software packages:
    gasgano-2.3.0.tar.gz
    cfitsio3090.tar.gz
    cpl-5.0.1.tar.gz
    esorex-3.7.2.tar.gz
    giraf-2.8.1.tar.gz

    - with the following pipeline calibration file(s):
    giraf-calib-2.8.1.tar.gz

    The software installation will be organised in bin/, lib/ and include/
    directories, while the calibration files will be installed in a calib/ directory.

    Where should I install the software packages ? [/home/dummy] /home/dummy/pipelines
    Where should I install the pipeline calibration files ? [/home/dummy/pipelines] /home/dummy/calibrations
     In this case the software is installed under the directory /home/dummy/pipelines and the static calibration tables under /home/dummy/calibrations/calib/giraf-2.8.1

    The only exception to all this is the Gasgano tool, that will always be installed under the directory $HOME/gasgano Note that the installer will move an existing $HOME/gasgano directory to $HOME/gasgano.old before the new Gasgano version is installed.

    Important: the installation script would ensure that any existing Gasgano and EsoRex setup would be inherited into the newly installed configuration files (avoiding in this way any conflict with other installed instrument pipelines).

    Alternatively, it is possible to perform a manual installation of the individual components (experienced users only): the README file located in the top installation directory contains more detailed information about a step-by-step installation.

Setup of the GIRAFFE calibration files

In order to use the GIRAFFE pipeline recipes, you may want to download additional calibration files. The GIRAFFE Standard Calibration Data Sets contain all calibrations which are necessary run the GIRAFFE pipeline immediately on scientific observations.

However, a set of calibrations specifically prepared for your observation is usually part of the data packages prepared, and delivered to the PIs, by ESO. It is obvious that these calibrations should be prefered whenever possible.

If you decide to re-create the calibration using the GIRAFFE pipeline recipes, certain processing steps will still require some of these calibrations as an initial guess. Please check the GIRAFFE Pipeline User Manual for details.


Installing the GIRAFFE Standard Calibration Data Sets:

It is recommended to install these calibration in the same place where the static calibration tables are located and simply unpack the downloaded archive files. Continuing with the above example, you have to execute the following commands to install the calibration files for the Medusa1 fibre system:

    $ cd /home/dummy/calibrations/calib/giraf-2.8.1
    $ tar -zxvf giraf-data-medusa1-2.8.1.tar.gz
The files will be copied to the
    cal
subdirectory of the directory
    /home/dummy/calibrations/calib/giraf-2.8.1


Using the GIRAFFE pipeline recipes

Using Gasgano

  1. To run the Gasgano GUI, just add $HOME/gasgano/bin to your PATH environment variable:

        export PATH="$HOME/gasgano/bin:"$PATH

    You should also define an environment variable CPLDIR to point to the same path specified for the installation. Possible files to update are:

        $HOME/.bashrc
        $HOME/.profile

    Finally, enter the command

        gasgano

  2. If the Gasgano main panel appears, then you have successfully installed Gasgano. Make sure, however, that the expected Gasgano 2.3.0 release is running: the version number is listed at the top of the main Gasgano panel.

  3. Refer to the Gasgano User's Manual to learn how to browse data and run pipeline recipes. Refer to the GIRAFFE Pipeline User Manual for detailed information about the recipes usage.

Using EsoRex

  1. The EsoRex executable should be available in the bin directory under your installation path (see above). The $PATH environment variable should be upgraded accordingly (similarly as done for Gasgano).

  2. Refer to the EsoRexweb page for details about the related features and options.

Documentation

The GIRAFFE Pipeline User Manual (ca. 917 kB, 90 pages), is available here for download. Note that the manual is also included in the GIRAFFE pipeline kit.
Note: An update of the manual including the changes of version 2.8.1 is in preparation!

The GASGANO Users' Manual (~1.2 Mb, 66 pages) is available for download in the Gasgano web page.

On the EsoRex web page some online documentation about EsoRex can be found.

The CPL manuals are available on the CPL web pages.

In case of problems when opening the documents directly from your web browser, the files may be first saved on disk, and then opened with Acrobat Reader.

Bug Reports

If you experience an unexpected behavior of any component of the GIRAFFE pipeline recipes package, please, first verify that you are using one of the above mentioned supported platforms and refer to the list of known problems and limitations in the current GIRAFFE pipeline release, in chapter 5 of the pipeline manual.

For any other issues or requests, please, send a report to the ESO User Support Department, describing:        

  • the GIRAFFE pipeline version, and the version of other components (e.g., Gasgano, EsoRex, ...) you are using
  • the version of your OS and C compiler.
  • the exact sequence of actions that were performed before the problem occurred
  • what were precisely the symptoms and the possible error message(s)
  • whether the problem is repeatable