HemeLB python tools

These tools are a set of Python libraries and some command-line tools that use them, for tasks such as converting HemeLB input and output files into other formats.

Dependencies:

• Python >= 3.6
• setuptools
• Cython
• Numpy
• VTK (python bindings)
• C compiler

Install

1. Create and activate a virtual environment
2. Install with pip:

   cd hemelb/python-tools
   pip install .
   

Use

For now, please run the script with the -h option for help.

Available command line tools:

• hlb-gmy-decompress: decompress a geometry file.

• hlb-gmy-compress: compress an uncompressed geometry file.

• hlb-dump-extracted-properties: convert an extraction file (.xtr) to CSV. (Note: You may find another library HemeXtract, to be mentioned online for this, however, please note that it was developed for a fork of HemeLB and is not compatible with this version. So, instead of that, please use this to convert extraction files to CSV.)

• hlb-gmy-selfconsistent: check if a geometry file is self-consistent.

• hlb-gmy-countsites: print some basic information about how many sites in a geometry file

Runnable modules (run with python -m):

Convert an XML + geometry file to VTK unstructured grid (.vtu)

python -m hlb.converters.GmyUnstructuredGridReader path/to/config.xml

Convert an extracted property file to VTK unstructured grid (.vtu). Note you also require EITHER the .xml/.gmy used for the run OR the output of GmyUnstructuredGridReader to provide the geometry information needed:

python -m hlb.converters.ExtractedPropertyUnstructuredGridReader geometry.vtu data.xtr