MUSE

Getting Started with EsoReflex for MUSE

Last Updated October 19, 2022 by J. Suherli.

This document is created to help MUSE Science users to get started with the setup of EsoReflex (latest public version is 2.11.5) and MUSE pipeline (latest version is 2.8.7).

Table of Contents

  1. About EsoReflex
    1.1. Instrument Pipelines
  2. Installation
    2.1. System Requirements
    2.2. Automatic Installation
    2.3. Pipeline Updates
  3. Execution
  4. Citing EsoReflex
  5. References

1. About EsoReflex

EsoReflex (ESO Recipe Flexible Execution Workbench) is the recommended workflow engine to automate the standard data reduction of ESO VLT/VLTI (Very Large Telescope / VLT Interferometer) data (Freudling et al. 2013). It is built on the open source workflow engine Kepler (a java-based application; see The Kepler Project for more information). EsoReflex visualizes the data reduction sequences graphically for intuitive understanding and makes the pipelines recipes accessible to the general science user.

For further information, please go to the EsoReflex’s official page or the latest manual. For even further information, browse the ESO data reduction FAQ page and EsoReflex public ftp.

1.1. Instrument Pipelines

EsoReflex supports any of the Common Pipeline Library (CPL)-based instrument pipelines or known as “recipes”. Users can choose to install all the instrument pipelines or any specific ones during the automatic installation of EsoReflex. For the complete list of supported instrument pipelines, please refer to this page, which also includes the information of the latest version, the user manual, the tutorial, and the demo data of each pipeline.

For the Multi-Unit Spectroscopic Explorer (MUSE) pipeline:

Release Notes Source Kit User Manual Tutorial Demo Data Reference
May 19, 2022 2.8.7 2.8.7 17.0 1.6 Weilbacher et al. 2020

2. Installation

There are two ways to install EsoReflex: the manual method and the automatic installation with installation script. This document will only go through the steps to do the automatic installation.

2.1. System Requirements

EsoReflex ver.2.11.5 requires:

To check the versions of your installed Python packages do: $ pip list

2.2. Automatic Installation

ESO provides a shell script that takes care of all the steps to install ESOReflex, including downloading and installing the instrument pipeline kits and the associated test data.

Steps:

  1. Download the install_esoreflex script.
  2. Run the script and follow the instructions (setting up the installation directories and choosing the pipelines to be installed) 
    $ sh install_esoreflex

    Or, the script could also be made executable:

    $ chmod u+x install_esoreflex
$ ./install_esoreflex

2.3. Pipeline Updates

To install and/or update the specific instrument pipeline, do:

  1. Download the pipeline source kit(s) from the instrument pipeline page (.tar.gz file).
  2. Download the install_pipelinekit shell script.
  3. Run the script 
    $ sh install_pipelinekit *-kit-*.tar.gz

3. Execution

To run EsoReflex, do:

$ install_dir/bin/esoreflex

Users could update the configuration file that located at install_dir/etc/esoreflex.rc, for example to change the python path to be used by ESO Reflex. If users choose to save the changes into a new .rc file, ESOReflex could be ran using:

$ install_dir/bin/esoreflex -config new_esoreflex.rc

More about the configuration file, esoreflex.rc, can be found in the EsoReflex User Manual section 8.2. (p.26).

The brief (and somewhat comprehensive) how-to guide on how to do the standard data reduction of MUSE data is available here.

4. Citing EsoReflex

Acknowledge EsoReflex by citing the Freudling et al. 2013 paper (BibTeX entry).

References

Automated Data Reduction Workflows for Astronomy: The ESO Reflex Environment, Freudling, W., Romaniello, M., Bramich, D. M., et al. 2013a, A&A, 559, A96.
The data processing pipeline for the MUSE instrument, Weilbacher, P. M., Palsa, R., Streicher, O., et al. 2020, A&A, 641, A28.