The MUSE Instrument Pipeline Code and Supporting Data

The MUSE pipeline — also called data reduction software (DRS) or data reduction library (DRL) — of MUSE was developed at AIP. For the general user, it is distributed by ESO, but within the MUSE collaboration it is used to reduce data from the guaranteed time. We package the code slightly differently, to ensure its use within the MUSE-WISE data handling system. We also distribute data for automated testing.

ESO provides both the EsoRex command-line tool and the Reflex GUI as interfaces for the pipeline. Another interface, written by Ole Streicher at AIP is python-cpl, it can be used to script the MUSE reductions in Python.

If you use the pipeline for your research, please cite the pipeline paper Weilbacher et al. 2020. The MUSE pipeline also has a citable entry in the ascl:1610.004Astrophysics Source Code Library (ASCL) (see ADS).

MUSE pipeline v2.8.3

released on 2020-06-04 (tarballs created on 2020-05-20)

The changes from v2.8.1 are:

  • Changed the order of the Raman contamination correction and the auto-calibration.
  • Added the SPECSYS FITS keyword to the data cube headers.
  • ESO Phase 3 format updates to comply with their unit string requirements.


Complete Pipeline Kit v2.8.3 (135 MB)
This is the tarball packaged by ESO, it includes the code tarball, the tarball of calibrations, all required libraries, the ESO pipeline manual, and an installation script. For installation just run the included script ./install_pipeline and follow the instructions.

Code tarball (4.8 MB)
This tarball contains only the pipeline code, also packaged by ESO.

Corresponding test data 2018-02-28 (1.5 GB, optional, unchanged since v2.6)
Only useful for automated testing (see README inside pipeline kit) not as pipeline input data.

User Manual and Cookbook v2.8.3 as PDF (5.1 MB)
This is the consortium version of the manual. Different from the ESO manual it contains usage instructions for EsoRex and the python-cpl interface.

MUSE pipeline v2.8.1

released on 2019-10-25

The only changes from v2.8 are:

  • Fixed computation of the extraction radius of the circular aperture flux extraction method for NFM standards.
  • Add missing XML files for MUSE-Wise integration.


Complete Pipeline Kit v2.8.1 (135 MB), packaged by ESO

Corresponding test data 2018-02-28 (1.5 GB, optional, unchanged since v2.6)

User Manual and Cookbook v2.8.1 as PDF (4.9 MB)

MUSE pipeline v2.8

released on 2019-10-02

The main changes since v2.6.x are:

  • Multi-step flux extraction for standard stars:
    • for Moffat fits, the first step fits parameters in all planes
    • the 2nd step fits low-order polynomials to all parameters (except flux)
    • the 3rd step runs constrained Moffat fits to extract the flux
    • this is now the default flux extraction mechanism for WFM
  • For NFM, the default flux extraction uses the circular aperture.
  • Updated Raman line list, based on better physical understanding.
  • Improvements to the astrometric calibration
    • kd-tree matching detected sources to astrometric catalog
    • works with WFM and NFM astrometric fields
    • the detections are now saved as binary table extension to the ASTROMETRY_WCS output file
    • the computed solution is saved as secondary FITS WCS to the DATACUBE_ASTROMETRY product
  • Optimize default parameters of overscan modeling, for cleaner bias subtraction
  • Add possibility to compute a smoothed model of the MASTER_DARK
  • Save multi-extension images with the INHERIT keyword, so that viewers display the OBJECT header.
  • Add preview image of the combined field-of-view as a product to the exposure alignment.
  • Update documentation.


Complete Pipeline Kit v2.8 (135 MB, packaged by ESO)

Corresponding test data 2018-02-28 (1.5 GB, optional, unchanged since v2.6)

User Manual and Cookbook v2.8 as PDF (5.1 MB)

MUSE pipeline v2.6.2

released on 2019-05-23

The main changes since v2.6 are:

  • Improved flux integration in muse_standard for NFM (with circular aperture).
  • Various improvements to muse_exp_align:
    • add possibility to create simple exposure map
    • clean sources near the edge of the field
    • allow to input SOURCE_LIST table
  • New QC parameter to muse_geometry to track invalid entries.
  • Updated STD_FLUX_TABLE to include EG 21


Complete Pipeline Kit v2.6.2 (32.5 MB)

Corresponding test data 2018-02-28 (1.5 GB, optional, unchanged since v2.6)

User Manual and Cookbook v2.6.2 as PDF (4.9 MB)

MUSE pipeline v2.6

released on 2018-12-21

The main changes since v2.4 are:

  • correct wiggles in AO modes, visible in high S/N data
  • make muse_scipost autocalibration more robust
  • allow muse_astrometry to more likely find a solution
  • do not crash in Raman module when fed data of partial wavelength coverage
  • update calibrations for all runs including GTO-29 (MUSE release only)
  • updates for NFM (these were already available in the SV pre-release v2.5.2 distributed by ESO):
    • adapt wavelength ranges used for cropping and NaD masking
    • fix data vignetting at top of frame
    • somewhat improve standard star flux extraction for bad external seeing


Complete Pipeline Kit v2.6 (32.3 MB)

Corresponding test data 2018-02-28 (1.5 GB, optional)

User Manual and Cookbook v2.6 as PDF (4.9 MB)

MUSE pipeline v2.4

released on 2018-03-05

Main changes since v2.2:

  • Implement slice autocalibration, ported from MPDAF.
  • Add possibility to correct for Raman scattered light in AO mode observations.
  • Do not save ARC_RED images by default in muse_wavecal and instead list the saturated pixels in QC parameter of the WAVECAL_TABLE.
  • Add list of detected sources as a product to muse_exp_align and fix threshold parameter.
  • Various updates to the documentation.
  • Update calibrations for all runs including GTO-22 (MUSE release only).


Complete Pipeline Kit v2.4 (31.6 MB)

Corresponding test data 2018-02-28 (1.5 GB, optional)

User Manual and Cookbook v2.4 as PDF (4.9 MB)

MUSE pipeline v2.2

released on 2017-10-01

Main changes since v1.6.x:

  • revised handling of the flat-field spectrum:
    • divide all (on-sky) data by the average flat-field spectrum at the start of post-processing (muse_scipost, muse_standard, etc.)
    • compute the throughput of instrument + telescope + sky in muse_standard
    • add throughput-related QC parameters to muse_standard
  • speed up cube creation by parallelizing the grid contruction
  • improve headers and documentation of the STD_FLUXES data product
  • update default FILTER_LIST with photometric zeropoints (Vega and AB)
  • propagate the photometric zeropoints from the filter list to the IMAGE_FOV products
  • add more infos about recipe parameters and variables to debug-level output
  • hide some rarely used recipe parameters in the recipe help output and show them only in expert mode.
  • various improvements for processing of AO mode data:
    • add default crop wavelength ranges for new mode
    • masking of NaD region depending on instrument mode
    • fix response calculation in NaD region
  • improve arc line selection in common wavelength range of all instrument modes
  • the pixel down-scaling factor of the ‘drizzle’ resampling method (recipe parameter ‘pixfrac’) now accepts a list of up to 3 values, one for each dimension
  • fix QC FWHM calculation of sources in final data cube
  • units of offset related QC parameters created by muse_exp_align were changed from degrees to arcsec
  • update calibrations for all runs including GTO-19 (MUSE release only)


Complete Pipeline Kit v2.2 (31.6 MB)

Corresponding test data 2015-09-03 (911 MB, optional, unchanged since v1.2)

User Manual and Cookbook v2.2 as PDF (4.9 MB)

MUSE pipeline v1.6.4

released on 2017-01-25

Main changes since v1.6:

  • fix smoothing problem of STD_RESPONSE curve
  • work around tracing in IFU 24 problems for 2017 (and all following years)
  • improve documentation and messages regarding OFFSET_LIST
  • make wavelength calibration more robust for extreme cases
  • updated astrometric catalog, including NGC 1851
  • update calibrations for all GTO runs to date (MUSE release only)
  • minor improvements to the muse_product_split tool
  • load SKY_MASK also for simple sky subtraction


Complete Pipeline Kit v1.6.4 (31 MB)

Corresponding test data 2015-09-03 (911 MB, optional, unchanged since v1.2)

User Manual and Cookbook v1.6.4 as PDF (4.9 MB)

MUSE pipeline v1.6

released on 2016-03-23

Main changes since v1.4:

  • improve robustness of wavelength alignment using sky lines
  • correct computation of log-lambda axes


Complete Pipeline Kit v1.6 (30 MB)

Corresponding test data 2015-09-03 (911 MB, optional, unchanged since v1.2)

User Manual and Cookbook v1.6 as PDF (4.9 MB)

MUSE pipeline v1.4

released on 2016-02-19

Main changes since v1.2:

  • allow creation of cubes in vacuum wavelengths (using CTYPE3='WAVE' in an OUTPUT_WCS)
  • new (experimental) recipe muse_lingain to compute the gain and the residual non-linearity for each detector of each IFU
  • give correct sky continuum output from the muse_scipost recipe
  • limit number of iterations when fitting the sky spectrum
  • correct handling of OUTPUT_WCS in the muse_scipost recipe
  • full integration of ESO IDP keywords, when using --format=sdbCube
  • add and correct QC parameters for muse_geometry and muse_lsf
  • improve header keywords for static calibrations and add calibrations suitable for data taken since Oct. 2015
  • correct listing of inputs in the ESO.PRO.RECi keywords, for several recipes
  • improve stability of the muse_geometry recipe


Complete Pipeline Kit v1.4 (30 MB)

Corresponding test data 2015-09-03 (911 MB, optional, unchanged since v1.2)

User Manual and Cookbook v1.4 as PDF (4.9 MB)

MUSE pipeline v1.2

released on 2015-10-01

Main changes since v1.0.x:

  • two LSF descriptions (old parameter table, new cube format):
    • muse_lsf by default computes the new cube format
    • model-base sky subtraction can use both formats
  • new recipe muse_exp_align to compute exposure alignment (wobble correction)
    • create OFFSET_LIST from individual IMAGE_FOVs
    • input OFFSET_LIST into muse_exp_combine to correct offsets
  • allow use of ILLUMs in muse_twilight
  • reject lowest (5%) of regions in white-light image for sky spectrum
  • improve FWHM-based exposure weighting (use auto-guider measurements if possible)
  • new “simple” sky subtraction (no LSF, no model)
  • allow CR rejection in both cube and spectrum when creating the sky spectrum
  • ignore INFs and NANs when creating sky spectrum (MPDAF #374)
  • add possibility to offset single exposures (in muse_scipost; MPDAF #324; uses OFFSET_LIST)
  • allow flux-scaling of exposures, both single and multiple, in muse_scipost and muse_exp_combine (MPDAF #347; uses OFFSET_LIST)
  • create functions to smooth geometrical solution
    • active if --smooth of the muse_geometry recipe is positive
    • also supplied in tool muse_geo_smooth, for quicker post-processing
  • add useful recipe info at start of processing
  • fix muse_cube_combine tool to work again
  • tools muse_product_split and muse_products_merge
  • adapt tools muse_trace_plot_samples, muse_trace_plot_widths, muse_wave_plot_column, and muse_wave_plot_residuals to be able to select extension names, so that they can be used on merged data


Complete Pipeline Kit v1.2 (30 MB)

Corresponding test data 2015-09-03 (911 MB, optional)

User Manual and Cookbook v1.2 as PDF (4.9 MB)

MUSE pipeline v1.0.3

released on 2015-04-07

Main changes since v1.0:

  • make flux response calculation more robust
  • fixed memory leak when loading incomplete pixel table
  • improvements to tool muse_crop_pixtable
  • fixed typo in save parameters of muse_scipost
  • minor improvements to the documentation of muse_wavecal


Complete Pipeline Kit v1.0 (27 MB)

Corresponding test data 2014-09-09 (908 MB, optional, unchanged since v1.0)

User Manual and Cookbook v1.0 as PDF (5.2 MB)

MUSE pipeline v1.0

released on 2014-12-05

First public release in conjunction with ESO, for observing period 94.


Complete Pipeline Kit v1.0 (27 MB)

Corresponding test data 2014-09-09 (908 MB, optional)

User Manual and Cookbook v1.0 as PDF (5.2 MB)