MUSE pipeline recipes v2.4.2 are available!

This release is a maintenance release and addresses two Reflex workflow related issues. It supports AO assisted WFM observations, it provides an optional, improved illumination correction, slice autocalibration (ported from MPDAF), and the possibility to correct for Raman scattered light in AO mode observations. The software distribution can be obtained here!

The current version of the MUSE Data Reduction Software supports the processing of all MUSE data, and has been thoroughly tested. At the time of this release there are a few known issues, which are summarized in section 4 of the MUSE Pipeline User Manual. The MUSE Data Reduction Software is still actively being worked on. Improvements and updates addressing the known issues will be made available on the download page as soon as they are available and validated.

Users should note that processing of MUSE data is quite demanding in terms of computer equipment. Please have a look at the system requirements before using the MUSE Data Reduction Software!

In order to further improve the MUSE Data Reduction Software we encourage all users, and in particular the PIs of an observing program to provide feedback to the ESO User Support Department

Changes:

Version 2.4.2 (2018-07-20)

  • Bugfixes for the interactive actor for the exposure alignment step:
    Fixed update of the image display with the selected field-of-view background image in the MUSE Workflow.
    Fixed offset of the detected source when drawn onto the field-of-view image.

Version 2.4.1 (2018-04-20)

  • Improved Reflex workflows: added interactive actor for the exposure alignment step.

    Known issue: In the MUSE Workflow the GUI does not update the image display correctly with the selected field-of-view background image. This will be fixed in the next release! The MUSE Exposure Combination Workflow is not affected!

Version 2.4 (2018-03-15)

  • Implement slice autocalibration, ported from MPDAF (see manual for details).

  • Add possibility to correct for Raman scattered light in AO mode observations (see manual for details).

  • Add list of detected sources as a product to muse_exp_align.

  • Do not save ARC_RED images by default in muse_wavecal.

  • Do not compute throughput at 6000 Angstrom in muse_standard.

  • List the saturated pixels in QC parameter of the WAVECAL_TABLE.

  • Fixed detection threshold parameter of muse_exp_align, and document it correctly.

  • Various (minor) corrections to the documentation.

  • Updated set of static calibrations (standard response and LSF profiles) for the WFM-AO modes.

Version 2.2 (2017-10-01)

  • Initial support for WFM-AO observations: default crop wavelength ranges for the new modes were added, and masking of the NaD region depending on the instrument mode.

  • Improved arc-line selection in the common wavelength range of all instrument modes

  • The pixel down-scaling factor of the drizzle resampling method (recipe parameter pixfrac) accepts now a list of 3 values, one for each cube axis.

  • The calculation of the QC parameters measuring the source FWHM on the final data cube was fixed.

  • The units of the offset related QC parameters generated by muse_exp_align were changed from degrees to arcseconds.

  • The standard response static calibration were updated to include initial versions for the WFM-AO modes. The lsf-profiles for the WFM-AO modes will be added in a following release.


Known Issues

Recently a user reported that installing the MUSE pipeline on a parallel file system (OrangeFS) causes the MUSE recipes to fail (independent on the version of the MUSE pipeline being used), while installations on a standard Linux file system work as expected. Currently ESO does not use parallel file systems for running VLT instrument pipelines and does not recommend it at this point due to the lack of testing on such systems.

Users having experience with using the MUSE pipeline together with a parallel file system (as installation target and/or for data storage) are kindly asked to provide feedback to the ESO User Support Department. Please include which file system is used, how it is used (installation target, data storage), and, whether you could use it successfully or experienced any problems. In the latter case please also report your issues.


Legacy Static Calibrations

The pipeline distribution contains the latest set of static calibration files which is available at the time of the package release. However these calibration files may not suitable for processing data taken during previous periods, for instance if an instrument maintenance took place. In particular this applies to the geometric calibration and the associated astrometric calibration.

Therefore, the geometric calibration and the associated astrometric calibration to be used with datasets from previous periods (including Commissioning and Science Verification) are available as a legacy calibration dataset from the download page.

The necessary information on which calibrations should be used for data from the different periods is available in the README file included in the data set.


EsoReflex support

With the release of version 1.0 of the MUSE pipeline package the standard EsoReflex support is available, and covers the complete reduction chain. In addition, the support for aligning and co-adding multiple exposures is available. It can be obtained from the download section.

The workflow is distributed with a demo data package, which will be downloaded by the installer. Note that the size of the demo data set is about 12GB!

A list of scenarios for which the workflow has been successfully used can be found in Section 9 of the MUSE EsoReflex Tutorial. We encourage all users to provide feedback on the workflow to the ESO User Support Department


Recovery procedure for vignetted SV data sets

During the first MUSE Science Verifiaction run data sets taken at low temperatures may be affected by vignetting. The cause has been fixed before the last commissioning run and thus will not affect data taken after this last commissioning run. However for the affected SV data sets the pipeline may fail to produce a valid tracing of the slice edges of IFU 6 (most likely slice no. 10). At very low temperatures even the wavelength calibration may fail due to a complete loss of flux in these slices.

A recovery procedure for such cases is available in Section 8.2 of the MUSE Pipeline User Manual. This procedure needs an additional utility, muse_pixtable_erase_slice, which has is available in the MUSE pipeline distribution since version 0.18.2.

In addition, a set of valid trace tables for IFU 6, for both, nominal and extended wavelength range has been prepared and is available here. They are ready to be used in the recovery procedure.


MUSE pipeline recipes version 2.4.2:

The current release version of the MUSE pipeline recipes is 2.4.2, and it is included in the pipeline distribution kit muse-kit-2.4.2.tar.gz together with the following packages:


System Requirements

The MUSE Data Reduction Software is only supported on 64-bit platforms and requires a 64-bit compiler to build correctly!

Minimum requirements:

  • 32 GB of memory
  • 4 (physical) CPU cores
  • 1 TB of free disk space (data storage)

Recommended requirements:

  • 64 GB of memory
  • 24 (physical) CPU cores
  • 4 TB of free disk space (data storage)

The minimum requirements are sufficient to process standard calibration sets (5 exposures) and create the final data cube from a single exposure.

This release of the MUSE pipeline kit is verified and supported on the VLT target platforms:

  • Linux CentOS 7.3 (x86_64), using gcc 4.8.5 (or newer)
In addition the MUSE pipeline has been built successfully on the following systems using the default system compiler:
  • Linux Fedora 24 (x86_64)
  • Linux Fedora 25 (x86_64)
  • Linux Fedora 26 (x86_64)
  • Linux Fedora 27 (x86_64)
  • Linux openSUSE Leap 42.3 (x86_64)
  • Linux openSUSE Leap 42.2 (x86_64)
  • Linux openSUSE Leap 42.1 (x86_64)
  • Linux Ubuntu 14.04 (x86_64)
  • Linux Ubuntu 16.04 (x86_64)
  • Linux Scientific Linux 7 (x86_64)
  • Linux CentOS 7 (x86_64)
  • macOS 10.10 (x86_64) (but see below!)
  • macOS 10.11 (x86_64) (but see below!)
  • macOS 10.12 (x86_64) (but see below!)
  • macOS 10.13 (x86_64) (but see below!)

Note for macOS Users:

The MUSE pipeline recipes can be built on the 64-bit Intel platform. However it lacks certain features compared the to a Linux installation, which lead to a degraded performance. In general it is recommended to run the MUSE pipeline recipes on Linux systems!


Installing and running the MUSE pipeline recipes

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

Installation using RPM repositories

For Fedora 24/25/26/27, 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.

General installation instructions for RPM packages are provided here.

User-contributed workflows are available for MUSE 2.4.2. The RPM packages of these workflows can be installed using:
dnf list esopipe-*contrib* # (Fedora 22 or newer)

Installation using MacPorts repositories

For Apple macOS 10.10 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 EsoReflex workflow, demo data and the EsoReflex tool itself.

General installation instructions for MacPorts packages are provided here.

User contributed workflows are available for MUSE 2.4.2. The MacPorts packages of these workflows can be installed using:
sudo port install esopipe-*contrib*

Installation using the EsoReflex installation procedure

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

User-contributed workflows are available for MUSE 2.4.2 and they are installed automatically with the standard instrument workflows when using the install_esoreflex script.
Please note that these user-contributed workflows may have additional, non-standard software dependencies! These must be installed by the users themselves. For detailed information on additional software dependencies please refer to the documentation of the individual workflows!

Installation using the public pipeline kit

To use the MUSE 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 2.4.8 a Java Development Kit (JDK) version 1.8.0 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.

    Using Gasgano to run MUSE recipes is not supported! It can however be used as a filebrowser.
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 MUSE pipeline kit to a directory on your computer. This may be any directory with the exception of
    • $HOME/gasgano
    • $HOME/.esorex
  1. Unpack the distribution file, using the following command:

        tar -zxvf muse-kit-2.4.2.tar.gz

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

        cd muse-kit-2.4.2

    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 macOS users:
    On macOS 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 MUSE 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-2.4.8.tar.gz
      cfitsio3360.tar.gz
      wcslib-4.24.tar.bz2
      fftw-3.3.4.tar.gz
      cpl-7.1.tar.gz
      esorex-3.13.1.tar.gz
      muse-2.4.2.tar.gz

    - with the following pipeline calibration file(s):
      muse-calib-2.4.2.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/muse-2.4.2

    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.


Using the MUSE pipeline recipes

Using EsoRex

  1. To run the EsoRex command line tool, just add the bin of the installation path (see above) to your PATH environment variable:     export PATH="$HOME/pipelines/bin:"$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     esorex --recipes
  2. If the list of MUSE recipes appears, then you have successfully installed EsoRex and the MUSE Data Reduction Software.
  3. Refer to the EsoRex web page for details about the related features and options.
  4. Refer to the MUSE Pipeline User Manual for detailed information about using the recipes.

Using Gasgano to run MUSE pipeline recipes is not supported!


Documentation

The MUSE Pipeline User Manual (ca. 3.5 MB, 152 pages), is available here for download. Note that the manual is also included in the MUSE 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 MUSE 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 MUSE pipeline release, in section 4 of the MUSE Pipeline User Manual.

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

  • the MUSE 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