A release of the EFOSC pipeline recipes is now available !

A release of the EFOSC pipeline recipes is now available.

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

  • EsoReflex, a GUI which provides an easy and flexible way of runing pipeline execution workflows.
  • 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.

Changes:

Version 2.3.1 public release (24 April 2018)

  • Fixed a crash in the pipeline when using non standard filters.
  • Note that the pipeline manual still refers to version 2.3.0. However the contents still apply to version 2.3.1.

Version 2.3.0 public release (12th January 2018)

  • Added support for simple EsoReflex workflows. As of version 2.3.0 the EFOSC pipeline includes two simple workflows, one for imaging and one for spectroscopy.

EFOSC pipeline recipes public version:

The public version of the EFOSC pipeline recipes is 2.3.1, and it is included in the pipeline distribution kit efosc-kit-2.3.1-2.tar.gz together with the following packages:


EFOSC pipeline documentation

User Manual: 1.1
EsoReflex Tutorial: 1.0 (EFOSC-IMG)
EsoReflex Tutorial: 1.0 (EFOSC-MOS)

EFOSC pipeline recipes System Requirements

The EFOSC pipeline kit version 2.3.1 is verified and supported on the VLT target platform:
  • CentOS 7 (x86_64), using gcc v. 4.4.6
Additionally the pipeline kit version is known to compile on these platforms using their default compiler:
  • CentOS 7
  • Fedora 24
  • Fedora 25
  • Fedora 26
  • Fedora 27
  • OSX 10.10
  • OSX 10.11
  • OSX 10.12
  • OSX 10.13
  • Scientific Linux 7
  • Ubuntu 16.04
  • Debian 8

Installing and running the EFOSC pipeline recipes 2.3.1

There are several ways to install the pipeline on your machine. The recommended installation procedure depends on whether you are working on a Mac OSX or on Linux.

Installation using RPM repositories

For Fedora 24/25/26/27, CentOS 7 and Scientific Linux 7, it is recommended to install the pipeline from our RPM repository. The RPM repositories include not only the pipeline recipes but also the library dependencies (CPL, etc..), the EsoReflex workflow, demo data and the EsoReflex tool itself.

Please refer to the instructions provided here.

Installation using MacPorts repositories

For Apple macOS 10.10/10.11/10.12/10.13, it is recommended to install the pipeline with MacPorts. The MacPorts repositories include not only the pipeline recipes but also the library dependencies (CPL, etc..), the EsoReflex workflow, demo data and the EsoReflex tool itself.

Please refer to the instructions provided here.

Installation using the EsoReflex installation procedure

Please refer to EsoReflex Software Prerequisites and Installation Instructions for detailed instructions

Installation using the public pipeline kit

To install the EFOSC pipeline recipes 2.3.1 you will need to retrieve the pipeline distribution kit, unpack and install it.

Prerequisites:
  • Please check the software prerequisites here.

Installation procedure:

  1. Change directory to where you want to retrieve the EFOSC pipeline recipes 2.3.1 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 efosc-kit-2.3.1-2.tar.gz
  4. Install: after moving into the installation directory,     cd efosc-kit-2.3.1-2 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 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:
    • cfitsio3360.tar.gz
    • cpl-7.1.tar.gz
    • esorex-3.13.1.tar.gz
    • gasgano-2.4.8.tar.gz
    • efosc-kit-2.3.1-2.tar.gz
    with the following pipeline calibration file(s):
    • efosc-calib-2.3.1.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/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/efosc 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 2.3.1

Using EsoReflex

  • To run the EsoReflex workflow, please refer to the EFOSC workflow tutorial available in this table under column Documentation.

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 2.4.8 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 EsoReflex Users' Manual is availale for download

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 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 EFOSC pipeline release.

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

  • the EFOSC pipeline version (currently 2.3.1), 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