A release of the SOFI pipeline recipes is now available !

A release of the SOFI pipeline recipes is now available.

Together with the data processing modules, we also provide 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.

SOFI pipeline recipes public version:

The public version of the SOFI pipeline recipes is 1.5.6, and it is included in the pipeline distribution kit sofi-kit-1.5.6.tar.gz together with the following packages:


SOFI pipeline recipes System Requirements

The SOFI pipeline kit version 1.5.6 is verified and supported on the VLT target platform:
  • Scientific Linux 5.3 (Intel), using gcc v. 4.2.4
Additionally the pipeline kit version is known to build and to produce correct output with esorex on these platforms:
  • Scientific Linux 5.3 32-bit (Intel Xeon), using gcc v. 4.2.4
The pipeline is known to build and pass unit testing on these platforms (using their default compiler):
  • CentOS 6.4 (32- and 64-bit Intel)
  • Debian 7 (32- and 64-bit Intel)
  • Debian 6.0 (32- and 64-bit Intel)
  • Fedora 18.0 (32- and 64-bit Intel)
  • Fedora 17.0 (32- and 64-bit Intel)
  • Fedora 16.0 (32- and 64-bit Intel)
  • Ubuntu 13.10 (32- and 64-bit Intel)
  • Ubuntu 13.04 (32- and 64-bit Intel)
  • Ubuntu 12.10 (32- and 64-bit Intel)
  • Ubuntu 12.04 (32- and 64-bit Intel)
  • Ubuntu 11.10 (32- and 64-bit Intel)
  • Ubuntu 10.04 (32- and 64-bit Intel)
  • OpenSUSE 12.3 (64-bit Intel)
  • OpenSUSE 13.1 (64-bit Intel)
  • Scientific Linux 6.3 (64-bit Intel)
  • Scientific Linux 5.5 (64-bit Intel)
  • Scientific Linux 5.3 (32-bit Intel)
  • OSX 10.6 (32-bit Intel)

Installing and running the SOFI pipeline recipes 1.5.6

Installation using the public pipeline kit

To install the SOFI pipeline recipes 1.5.6 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 install the latest graphical front-end Gasgano version 2.4.5 and configure it properly the Java Developer Kit (JDK) version 1.7.0 must be available on your system. If it is not, you may download it from the official Sun Java page distribution, for example http://developer.apple.com/java/download/ for a Mac installation or http://java.sun.com/javase/downloads/ for Solaris and Linux platforms installations. On some modern Linux distributions like Ubuntu you may install the JDK simply by choosing it from the software installer. Furthermore, the related java executable must be in your PATH. You may install and run Gasgano under other operating systems or use a different JDK version, but ESO cannot guarantee that Gasgano will work correctly in such case. 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, i.e. gzipped tar files (.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. Change directory to where you want to retrieve the SOFI pipeline recipes 1.5.6 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 etc.) necessary for running the pipeline recipes:
  3. Unpack using for example the following command:     tar xzf sofi-kit-1.5.6.tar.gz
  4. Install: after moving into the installation directory,     cd sofi-kit-1.5.6 it is recommended to perform the installation using the supplied installer script:     ./install_pipeline (BEWARE: The installation may take several minutes). By default the script will install the SOFI 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:
    • cfitsio3350.tar.gz
    • cpl-6.4.1.tar.gz
    • esorex-3.10.2.tar.gz
    • gasgano-2.4.5.tar.gz
    • sofi-kit-1.5.6.tar.gz
    with the following pipeline calibration file(s):
    • sofi-calib-1.5.6.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/userid] /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/sofi 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.
    Alternatively, it is possible to perform a manual installation (experienced users only): the README file located in the top installation directory contains more detailed information about a step-by-step installation.

Executing the pipeline 1.5.6

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 2.4.5 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 Pipeline User Manual(s) 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.

Documentation

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 SOFI 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 pipeline manual of the current SOFI pipeline release.

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

  • the SOFI pipeline version (currently 1.5.6), 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