A release of the FORS pipeline recipes is now available !
A release of the FORS pipeline recipes is now available.
Together with the data processing modules, we also provide standalone applications for running them:
- Reflex, 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.
Version 5.3.11 (Public release)
- The fors_science recipe now computes the sky coordinates of the extracted spectra which helps the identification of the science objects. This applies to modes LSS, MOS and MXU.
- A non-recoverable crash of recipe fors_pmos_calib running under macOS environment has been fixed.
FORS pipeline recipes public version:
The public version of the FORS pipeline recipes is
5.3.11, and it is included in the pipeline
fors-kit-5.3.11.tar.gz together with
the following packages:
- the CFITSIO library, version 3360
- the Common Pipeline Library (CPL), version 7.0
- Gasgano version 2.4.8
- EsoRex, version 3.12.3
- Third-party libraries used by CPL (wcslib, fftw)
FORS pipeline documentationUser Manual: 5.4
Reflex Tutorial: 1.1 (FORS-IMG)
Reflex Tutorial: 1.1 (FORS-PMOS)
Reflex Tutorial: 1.10 (FORS-SPEC)
FORS pipeline recipes System RequirementsThe FORS pipeline kit version 5.3.11 is verified and supported on the VLT target platform:
- Scientific Linux 6.3 (x86_64), using gcc v. 4.4.6
- Fedora 18 (Intel Core 2 64 bits), using gcc v. 4.6.3
- Scientific Linux 5.3 (Athlon), using gcc v. 4.1.2
- SLC 5.3, i386, gcc4.4
- SLC 5.5, amd64, gcc4.4
- SLC 6.3, amd64, gcc4.4
- Ubuntu 10.04, i386, gcc4.4
- Ubuntu 10.04, amd64, gcc4.4
- Ubuntu 10.10, amd64, gcc4.6
- Ubuntu 12.04, i386, gcc4.6
- Ubuntu 12.04, amd64, gcc4.6
- Ubuntu 12.10, i386, gcc4.7
- Ubuntu 12.10, amd64, gcc4.7
- Ubuntu 13.04, i386, gcc4.7
- Ubuntu 13.04, amd64, gcc4.7
- Debian 6 (Squeeze), i386, gcc4.4
- Debian 6 (Squeeze), amd64, gcc4.4
- Fedora 11, i386, gcc4.4
- Fedora 16, i386, gcc4.6
- Fedora 16, x86_64, gcc4.6
- Fedora 17, i386, gcc4.7
- Fedora 17, x86_64, gcc4.7
- Fedora 18, i386, gcc4.7
- Fedora 18, x86_64, gcc4.7
- Intel Mac 10.6, i386, gcc4.2, Apple clang 1.7
- Intel Mac 10.8, amd64, gcc4.2, Apple clang 4.2
- OpenSuse 12.1, amd64, gcc4.6
Installing and running the FORS pipeline recipes 5.3.11There 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 20/21/22/23, 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 Reflex workflow, demo data and the Reflex tool itself.
Please refer to the instructions provided here.
Installation using MacPorts repositories
For Apple Mac OS X 10.9 or newer, 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 Reflex workflow, demo data and the Reflex tool itself.
Please refer to the instructions provided here.
Installation using the Reflex installation procedure
Please refer to Reflex Software Prerequisites and Installation Instructions for detailed instructions
Installation using the public pipeline kit
To install the FORS pipeline recipes 5.3.11 you will need to retrieve the pipeline distribution kit, unpack and install it.
- One of the C++ compilers listed above, and standard GNU tools including make.
- To install the latest graphical front-end Gasano version 2.4.8 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.
- 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.
- Change directory to where you want to retrieve the FORS pipeline
recipes 5.3.11 package. It can be any directory of your
choice but not:
- Download the software and the static calibration data (line catalogs etc.) necessary for running the pipeline recipes:
- Unpack using for example the following command:
tar xzf fors-kit-5.3.11.tar.gz
- Install: after moving into the installation directory,
cd fors-kit-5.3.11it 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 FORS 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_pipelineIn this case the software is installed under the directory
I am about to install the following software packages:
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
/home/dummy/pipelinesand the static calibration tables under
/home/dummy/calibrations/forsThe only exception to all this is the Gasgano tool, that will always be installed under the directory
$HOME/gasganoNote that the installer will move an existing
$HOME/gasgano.oldbefore 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 5.3.11
- To run the Reflex workflow, please refer to the FORS workflow tutorial available in this table under column Documentation.
- To run the Gasgano GUI, just add
$HOME/gasgano/binto your PATH environment variable:
export PATH="$HOME/gasgano/bin:"$PATHYou should also define an environment variable CPLDIR to point to the same path specified for the installation. Possible files to update are:
$HOME/.profileFinally, enter the command
- 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.
- 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.
- 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).
- Refer to the EsoRex web page for details about the related features and options.
The Reflex 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.
If you experience an unexpected behavior of any component of the FORS 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 FORS pipeline release.
For any other issues or requests, please, send a report to the ESO User Support Department, describing:
- the FORS pipeline version (currently 5.3.11), 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