The GIRAFFE pipeline recipes 2.12.1 have been released!

This is a maintenance release of the GIRAFFE pipeline recipes.

Changes:

2.12.1:
  • Update to CPL 6.4.x. This version will not work with older releases of the CPL!
  • The origin of the WCS for IFU cubes has been fixed. The right ascension and the declination given in the OzPoz table for each IFU button is now used as origin of the WCS.
2.11.1:
  • Invalid WCS keywords are removed from the reconstructed FOV images.
  • Fixes wrong offset of the WCS of the data cube products.
2.11:
  • The fiber setup table attached to the pipeline product files provides now also the object type column from the raw data OzPoz table.
  • The recipes giscience and gistandard can produce data cubes in ESO3D format, which can be visualized using the ESO 3D Visualization Tool (CASA 3D Viewer).
  • World Coordinate System information has been added to data cube products. The coordinate information is constructed from observations setup information (file headers, and setup tables)!
  • A new option to provide the list of fibers to process has been introduced in the gimasterflat recipe. The method serves as shortcut for specifying the list of fiber explicitly, as long as a valid, setup specific slit geometry is available.
2.9.2:
  • The pipeline has been ported to CPL 6. This release will not work with older versions of CPL!
  • Bug fixes to improve robustness of the HORNE extraction algorithm in the case that all pixels in the extraction slit are bad pixels.
  • Bug fixed in the HORNE extraction method which could lead to negative variances.
2.8.9:
  • giscience: The computation of the barycentric, heliocentric and the geocentric corrections is now also done for observations which did not use the simultaneous calibration fibers.


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 2.12.1, and it is included in the pipeline distribution kit giraf-kit-2.12.1.tar.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 5.3 (x86_64), using gcc 4.7.2
  • Linux Scientific Linux 5.5 (x86, x86_64), using gcc 4.4.0
  • Linux Scientific Linux 6.3 (x86, x86_64), using gcc 4.4.6
  • Linux Fedora 17 (x86_64), using gcc 4.7.2
  • Linux Fedora 20 (x86_64), using gcc 4.8.2
In addition the GIRAFFE pipeline has been built successfully on the following systems:
  • Linux openSUSE 13.1 (x86,x86_64), using gcc 4.8.1
  • Linux openSUSE 12.3 (x86,x86_64), using gcc 4.7.2
  • Linux openSUSE 12.2 (x86,x86_64), using gcc 4.7.1
  • Linux openSUSE 12.1 (x86,x86_64), using gcc 4.6.2
  • Linux Ubuntu 12.04 (x86,x86_64), using gcc 4.6
  • Linux Ubuntu 12.10 (x86,x86_64), using gcc 4.7
  • Mac OS X 10.6 (x86), using gcc 4.2
  • Mac OS X 10.7 (x86), using gcc 4.2
  • Mac OS X 10.8 (x86_64), using gcc 4.2

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 2.4.5 a Java Development Kit (JDK) version 1.7 or later must be available on your system. You may use either OpenJDK, or Oracle JDK. Most likely, OpenJDK is already part of your Linux distribution and can be installed from its software repositories. 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-2.12.1.tar.gz

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

        cd giraf-kit-2.12.1

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

        ./install_pipeline
    This may take a few minutes. Please be patient!

    Note for Mac OS X users:
    On Mac OS X the environment variable JAVA_HOME should be set to JAVA_HOME=/System/Library/Frameworks/JavaVM.framework/Versions/CurrentJDK/Home prior to running the installation script in order to avoid compilation errors during the installation.


    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-2.4.5.tar.gz
      cfitsio3350.tar.gz
      wcslib-4.16.tar.bz2
      fftw-3.3.3.tar.gz
      cpl-6.4.1tar.gz
      esorex-3.10.2.tar.gz
      giraf-2.12.1.tar.gz

    - with the following pipeline calibration file(s):
      giraf-calib-2.12.1.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-2.12.1

    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.

While these data sets are useful to get a first glance on the processed data, it is recommended to use the calibrations which have been specifically prepared for a given observation, in order to obtain the best possible results. Such calibrations may be obtained from the ESO archive using the CalSelector service.

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:

The latest release of the standard calibration data sets is still version 2.8.7. However, these data sets can be used together with the GIRAFFE pipeline version 2.12.1.

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-2.12.1
    $ tar -zxvf giraf-data-medusa1-2.8.7.tar.gz
The files will be copied to the
    cal
subdirectory of the directory
    /home/dummy/calibrations/calib/giraf-2.12.1



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 2.4.5 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 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 EsoRex web page for details about the related features and options.

Documentation

The GIRAFFE Pipeline User Manual (ca. 956 kB, 94 pages), is available here for download. Note that the manual is also included in the GIRAFFE 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 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