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Sen2mosaic

Sen2mosaic is a tool to download, preprocess and mosaic Sentinel-2 data.

Available

Sen2mosaic is available in Puhti with following versions:

  • 0.2

Dependencies

The sen2mosaic module depends on geoconda/3.8.8 and sen2cor/2.9 modules which are loaded automatically.

Usage

Sen2mosaic is included in the sen2mosaic module and can be loaded with

module load sen2mosaic

On Puhti, you run the tools with 

s2m_download <arguments>
s2m_preprocess <arguments>
s2m_mosaic <arguments>

More information on the available arguments for each tool can be displayed with

s2m_mosaic --help

or from the sen2mosaic user manual. (Note the _ in tool names on Puhti!)

For s2m_preprocess and s2m_mosaic you can use the argument --n_processes to set the number of available CPU cores to the number of computing cores of your job.

Advanced usage

Further configuration of s2m_preprocess can be done via the L2A_GIPP.xml file (part of Sen2cor). You can find the default GIPP file in /appl/soft/geo/sen2cor/2.9/Sen2Cor-02.09.00-Linux64/lib/python2.7/site-packages/sen2cor/cfg/L2A_GIPP.xml. Copy it to your $HOME directory, adjust it to your needs and add it to the call: s2m_preprocess --gipp $HOME/L2A_GIPP.xml <other arguments>

License

Sen2mosaic is published under the GNU,GPL v3 license.

Citation

Sen2mosaic does not provide any preferred citation information.

Samuel Bowers: Sen2mosaic v.0.2. https://github.com/smfm-project/sen2mosaic , last accessed on {date}.

Acknowledgement

Please acknowledge CSC and Geoportti in your publications, it is important for project continuation and funding reports. As an example, you can write "The authors wish to thank CSC - IT Center for Science, Finland (urn:nbn:fi:research-infras-2016072531) and the Open Geospatial Information Infrastructure for Research (Geoportti, urn:nbn:fi:research-infras-2016072513) for computational resources and support".

Installation

Almost all dependencies for Sen2mosaic are available from the sen2cor and geoconda modules, so Sen2mosaic was installed on top of them using pip install --user opencv-python git+https://github.com/smfm-project/sen2mosaic.git, while both modules were loaded (remember to set the installation directory first with export PYTHONUSERBASE=/path/to/sen2mosaic/install/directory. For shorter command line calls, the commands s2m_download ,s2m_preprocess and s2m_mosaic were created to shorten the original python3 /path/to/sen2mosaic/cli/download.py commands. This last step is not necessary for usability.

References