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Molecfit

Correcting Observations for Telluric Absorption

Molecfit is a software tool to correct astronomical observations for atmospheric absorption features, based on fitting synthetic transmission spectra to the astronomical data. It can also estimate molecular abundances, especially the water vapour content of the Earth’s atmosphere.

The tool has been developed for ESO by a team of astronomers at the Institute for Astro- and Particle Physics at the University of Innsbruck, as one of three sky modeling and correction tools in an Austrian in-kind contribution to ESO.

Correcting for telluric absorption features usually requires supplementary calibration data which are very expensive in terms of telescope time. In addition, the scheduling flexibility is restricted as these data have to be taken usually directly before/after the science observations due to the high variability of the telluric absorption which depends on the state and the chemical composition of the atmosphere at the time of observations. A tool for telluric absorption correction like Molecfit that is based on synthetic transmission spectra calculated by a radiative transfer code does not require these supplementary calibration data if the science data can directly be fitted. This can save a significant amount of valuable telescope time and increases the instrumental efficiency.

The user must be aware that Molecfit has some limitations and observation of a telluric standard star may be better suited in some conditions. For instance, Molecfit might perform poorly with:

  • large number of intrinsic features,
  • little or no continuum,
  • low S/N
  • large airmass observations with high water vapor content.

The tool can be run from a command-line or more conveniently through a GUI.

Documentation

Manuals

Molecfit User Manual
Molecfit Tutorial

Publications

Users of Molecfit are requested to cite the following papers:

Molecfit: A general tool for telluric absorption correction I. Method and application to ESO instruments
A. Smette, H. Sana, S. Noll, H. Horst, W. Kausch, S. Kimeswenger, M.Barden, C. Szyszka, A. M. Jones, A. Gallene, J. Vinther, P. Ballester and J. Taylor (2015, A&A 576, A77)

Molecfit: A general tool for telluric absorption correction II. Quantitative evaluation on ESO-VLT/X-Shooter spectra
W. Kausch, S. Noll, A. Smette, S. Kimeswenger, M. Barden, C. Szyszka, A. M. Jones, H. Sana, H. Horst, and F. Kerber, (2015, A&A 576, A78).

Download

Installation packages

The latest version of the installers:

GNU/Linux 32 bit x86
GNU/Linux 64 bit x86
MacOS 64 bit x86

The installers include example data and configurations for CRIRES, FLAMES, KMOS, MUSE, SINFONI, VISIR and XSHOOTER instruments.

Older versions are available on the FTP server

Installation instructions

The installation procedure is described here.

Source code

Source code required to build Molecfit and its dependencies:

Molecfit source files
Third-party sources

GDAS weather profiles

In case the automatic download of weather profiles fails, a weekly updated local database can be downloaded here. It contains all available profiles for several different locations from December 2004 up the last week. See this list for the names of the available locations. When the longitude and latitude in the configuration files are setup correctly the files will be downloaded automatically by Molecfit, otherwise place the files into <INST_DIR>/data/profiles/gdas/.

Known Issues

  • If the data have pixels with unusually high values, Molecfit may fail since the underlying algorithm uses single precision floats. A solution is to apply a scale factor to the data before the fit.

History:

13. April 2018: New Molecfit release 1.5.1
  • The API was adapted to the requirements of the ESO pipelines group.
  • The folder structure of the installation was modified.
  • For the paths: TMPDIR, MOLECFITDIR and MOLECFITDIR_DATA environment variables can be used at runtime.
  • Various bug fixes in the code and the GUI.
22. December 2017: New Molecfit release 1.4.0
  • The basedir parameter was removed from the parameter file.
  • Paths are relative to the current directory. Of course, it is still possible to give absolute paths.
  • Molecfit no longer writes in installation directory and can therefore be installed systemwide.
  • Major upgrade of the third party applications and libraries: LNFL v3.1, LBLRTM v12.8 and aer v3.6.
  • Within the inclusion regions, the GUI now shows the fit also in the excluded regions.
  • Two additional executables have been created to allow one to access the two functionalities of calctrans separately:
    • calctrans_lblrtm for the radiative transfer computation, and
    • calctrans_convolution for convolving the spectra produced by calctrans_lblrtm with the instrument kernel.
  • New examples for CRIRES, FLAMES, KMOS, MUSE, SINFONI, VISIR and X-SHOOTER instruments.
  • Improved documentation.
  • Various minor bug fixes.
20. September 2016
  • Added several more locations to the GDAS weather profiles. The available locations are listed here. The files are downloaded automatically if the longitude and latitude are setup correctly in the configuration file.
23. Februrary 2016: New Molecfit release 1.2.0
  • Molecfit now uses the 3-hour interval GDAS data files in the local database. Previously it only used the 6-hour interval files despite the finer granularity being available for Paranal. This means the interpolation of pressure and humidity values to the observation time should be more accurate. Thanks to Leonard Burtscher for the report and testing.
  • When no GDAS data is available in the local database for the requested Paranal or La Silla observation it will check an ESO server for a new version of the database. Currently the database on the server only contains the data for Paranal and La Silla.
  • In this version the automatic download of GDAS profiles for arbitrary locations on earth is disabled as the server is not available anymore. Instead manual retrieval of the GDAS profiles can be carried out following this procedure.
  • Fix possible crash when no GDAS data is available and the averaged profile has to be used.
  • Updated bundled GDAS data to include data up to 21.02.2016
11. August 2015: New Molecfit release 1.1.1
  • Support ESO science data products standard (SDP) format for one-dimensional (1D) spectra Note the use of units stored in this format is not yet supported, wlgtomicron still needs to be set correctly in the parameter file.
  • support astropy.io.fits in addition to pyfits for GUI
  • Some more wxWidgets 3.0 fixes
  • Updated bundled gdas data to include data up to 07.08.2015
10. April 2015: New Molecfit release 1.1.0
  • Improved convolution with a wavelength-dependent synthetic kernel, which does not produce weak periodic glitches anymore.
  • User-defined kernels can also be provided for each pixel separately. The required matrix of kernel elements has to be written into an ASCII file.
  • Removed input wavelength range limit. This allows usage with instrument data covering larger ranges.
  • Improved compatibility with wxWidgets 3.0
  • Updated bundled gdas data to include data up to 07.04.2015
22. October 2014: NCEP Central Operations (NCO) has unexpectedly turned off the server nomad3.ncep.noaa.gov from where molecfit automatically retrieves the atmospheric profiles.
  • Molecfit will not be able to automatically determine atmospheric profiles for observations done at Cerro Paranal after the 31. July 2014 or any observations not done at Cerro Paranal.
  • For any location on Earth, manual retrieval of the GDAS profiles can be carried out following this procedure.
  • For Cerro Paranal observations obtained after 31 July 2014 the profile database can be updated manually as described here, or following Section 7.2.4 of the Molecfit User Manual.
  • We are working on an alternative procedure for automatic retrieval of GDAS profiles.
7. August 2014: Minor bugfix release of Molecfit 1.0.2.
  • Avoid pseudo-line at 2.069 µm in calctrans results of X-Shooter NIR-arm spectra due to an additional overlap of adjacent LBLRTM spectra. Only relevant for wide wavelength ranges, where LBLRTM has to be run several times.
  • Improved robustness to invalid parameter inputs
  • Updated bundled gdas data to include data up to 31.07.2014
11. April 2014: Minor bugfix release of Molecfit 1.0.1.
  • Fixes a wrong path in an example configuration file and issues with versions 1.1.0 and 1.2.0 of matplotlib used by the GUI.
1. April 2014: First release of Molecfit 1.0.0.