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VIMOS pipeline recipes
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A new patch release of the VIMOS pipeline recipes is now available !
A new release of the
VIMOS pipeline recipes
is now available for the reduction of data obtained in the Direct Imaging,
MOS, and IFU instrument modes. Here is an overview of
what's new
with respect to the previous release (1.0, July 2004).
The current patch release just adds support for gcc compiler
4.0 or later.
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.
VIMOS pipeline recipes latest public version:
The latest public version of the VIMOS pipeline recipes is
2.0.14, and it is included in the pipeline
distribution kit vimos-kit-1.1.tar
together with
the following packages:
VIMOS pipeline recipes System Requirements
At present, the VIMOS pipeline recipes package is certified only for:
- Linux RedHat 9.0
- Scientific Linux 4.0
You may anyway try to install and run the VIMOS pipeline recipes
package on other distributions assuming that you have the gcc
compiler version 3.2 or newer, or 4.0 or newer available. In this
case, however, Gasgano will not be installed, and only EsoRex
would be available for launching the VIMOS pipeline recipes.
Installing and running the VIMOS pipeline
recipes 2.0.14
To install the VIMOS pipeline recipes 2.0.14 you will need to retrieve
the pipeline distribution kit, unpack and install it.
- 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 2.2.4
the
Java Runtime Environment (JRE) for Linux
version 1.4.1 must be available on your system.
If not, you may download it
from
ftp://ftp.eso.org/pub/usg/ohs/jre1.4.1-Linux.tar.gz.
Furthermore, the related java executable must be in your
PATH.
You may install and run Gasgano under other operating systems
(find the corresponding JREs in the
Gasgano web
page), or use a different JRE 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., tar files (
.tar
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:
- Change directory to where you want to retrieve the VIMOS pipeline
recipes 2.0.14 package. It can be any directory of your
choice but not:
- $HOME/gasgano
- $HOME/.esorex
- Download the software and the static calibration data
(line catalogs, extinction tables, etc.) necessary for running
the pipeline recipes:
- Verify the checksum value of the tar file with the
cksum
command. It should be:
2487727346 45977600 vimos-kit-1.1.tar
- Unpack using the following command:
tar -xvf vimos-kit-1.1.tar
Note that the size of the installed software (including Gasgano)
together with the static calibration data is about 90Mb.
- Install: after moving to the top installation directory,
cd vimos-kit-1.1
it is possible to perform a simple installation using the
available installer script (recommended):
./install_pipeline
(BEWARE: the execution may take a few minutes).
By default the script will install the VIMOS 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:
qfits-6.1.0.tar.gz
cpl-3.0.tar.gz
esorex-3.6.tar.gz
gasgano-2.2.4-Linux.tar.gz
vimos-2.0.14.tar.gz
- with the following pipeline calibration file(s):
vimos-calib-2.0.14.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/vimos
.
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
(experienced users only): the README file located in the
top installation directory contains more detailed information
about a step-by-step installation.
-
Executing the VIMOS pipeline recipes 2.0.14
Using Gasgano
- 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
- If the Gasgano main panel appears, then you have successfully
installed Gasgano. Make sure, however, that the expected
Gasgano 2.2.4 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
VIMOS Pipeline User Manual for detailed information about
the recipes usage.
Using EsoRex
-
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.
Testing the VIMOS pipeline recipes 2.0.14 (optional)
It is possible to test each pipeline recipe by running a number of
scripts on a set of test data. To do this you need to do the following:
- Download the
VIMOS Pipeline Verification tar file. This file includes
the data and the procedures (based on EsoRex) used for the
verification of the VIMOS pipeline: its size is about 1.4Gb,
that would expand to 2.4Gb of disk space.
- Run the available test scripts. There is at least one
test script for each VIMOS pipeline recipe, and running all of
the scripts would perform a complete data reduction for each main
instrument mode (Direct Imaging, MOS, and IFU). However, the
scripts are independent from each others, and it's not important
in what order they are run because all products are already
available (for reference). With few exceptions, the scripts have
the same name of the recipe that they are testing. A README file
located at the top of the created directory tree contains detailed
instructions about running the verification scripts.
- Compare the obtained products with the reference products,
as indicated during the execution of each verification script.
The
VIMOS Pipeline User Manual (2.0) (~1.6 Mb, 190 pages),
is available here for download. Note that the manual is also
included in the VIMOS pipeline kit, in the file
vimos-pipeline-manual-2.0.pdf
.
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 VIMOS pipeline
recipes package, please, first refer to the list of
known problems
in the current VIMOS pipeline release.
For any other issues or requests, please, send a report to the
ESO User Support Department, describing:
- the VIMOS 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