Release 2.2.2 of the EFOSC pipeline recipes is available!

This is a patch to the public release of the EFOSC pipeline recipes, now available for the reduction of data obtained with the EFOSC2 instrument in the spectroscopic and direct imaging instrument modes.

This release is compatible with the latest CPL 5.3.1 release.

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 the data reduction tasks.

EFOSC pipeline recipes public version:

The public version of the EFOSC pipeline recipes is 2.2.2, and it is included in the pipeline distribution kit efosc-kit-2.2.2.tar.gz together with the following packages:


System Requirements

This release of the EFOSC pipeline kit is verified on the VLT target platforms:
  • Linux Scientific Linux 5.3 (x86), using gcc 4.2.4
  • Linux Fedora Core 11 (x86_64), using gcc 4.4.1

You may anyway try to install and run the EFOSC pipeline on other distributions assuming that you have the gcc compiler version 3.2 or newer, or 4.0 or newer available. Gasgano will only be installed if the Java Development Kit (JDK 1.5 or later) is found in your machine (follow the instructions in the efosc-kit-2.2.2.tar.gz README file about how to download and install the JDK). If Gasgano is not installed, only EsoRex would be available for launching the EFOSC pipeline recipes.


Installing and running the EFOSC pipeline recipes 2.2.2

To install the EFOSC pipeline recipes 2.2.2 you will need to retrieve the pipeline distribution kit, unpack and run the installation script.

Prerequisites:
  • To install this software package, the GNU C compiler (gcc) version 3.2 or newer, or 4.0 or newer, must be available on your system.

  • To use the latest graphical front-end Gasgano version 2.4.0 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.

Installation procedure:

  1. Change directory to where you want to retrieve the EFOSC pipeline recipes 2.2.2 package. It can be any directory of your choice but not:

    • $HOME/gasgano
    • $HOME/.esorex

  2. Download the software and the static calibration data (line catalogs, extinction tables, etc.) necessary for running the pipeline recipes:


  3. Verify the checksum value of the tar file with the cksum command. It should be:

        1607323357 69637992 efosc-kit-2.2.2.tar.gz

  4. Unpack using the following command:

        tar -xvf efosc-kit-2.2.2.tar

    The size of the installed software (including Gasgano) together with the static calibration data is about 70 Mb.

  5. Install: after moving to the top installation directory,

        cd efosc-kit-2.2.2

    it is possible to install the package using the available installer script:

        ./install_pipeline

    By default the script will install the EFOSC 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-2.4.0.tar.gz
    cfitsio3090.tar.gz
    wcslib-4.4.4.tar.bz2
    fftw-3.1.2.tar.gz
    cpl-5.3.1.tar.gz
    esorex-3.9.0.tar.gz
    efosc-2.2.2.tar.gz
    - with the following pipeline calibration file(s):
    efosc-calib-2.2.2.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/efosc-2.2.2.

    The pipeline specific software is installed in a separate subdirectory /home/dummy/pipelines/efosc, to prevent conflicts with other pipelines installed in the same machine. 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).

    Please follow the instructions shown at the end of a successful installation script: they will indicate how to set your PATH and CPLDIR variables in your machine in order to run the pipeline.



Executing the EFOSC pipeline recipes 2.2.2

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. The instructions displayed at the end of a successful installation script will indicate how to set your PATH and CPLDIR variables in your machine in order to run the pipeline. 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 2.4.0 release is running: the version number is listed at the top of the main Gasgano panel.

  3. If Gasgano doesn't start at all, a JDK version 1.5 or later is not available on your system.
  4. Refer to the Gasgano User's Manual to learn how to browse data and run pipeline recipes. Refer to the EFOSC2 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 EsoRex web page for details about the related features and options.

Testing the EFOSC2 pipeline recipes 2.2.2 (optional)

It is possible to test each pipeline recipe by applying them to a set of test data. To do this you need to download the EFOSC2 test data tar file. This file includes data to play with the EFOSC pipeline: its size is about 100 Mb, that would expand to 160 Mb of disk space.


Documentation

The EFOSC2 Pipeline User Manual (1.0) (~1.5 Mb, 132 pages), is available here for download. Note that the manual is also included in the EFOSC pipeline kit.

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 EFOSC pipeline, please send a report to the ESO User Support Department, describing:        

  • the EFOSC pipeline recipes package release, and the release of other components (e.g., Gasgano, EsoRex, ...) you are using
  • the version of your OS
  • 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