Utility tools ============= In addition to helper scripts (:ref:`helper_scripts:Helper scripts`), HemoCell provides different utility tools under the ``tools/`` directory. Typically these provide more extensive functionality compared to the more simple helper scripts in ``scripts/``. .. _pos_to_vtk: Viewing of cell packings ------------------------ When you are willing to inspect a distribution of cells, for instance as result of running the ``packCell`` tool, the ``pos_to_vtk`` command-line utility provides direct visualisation using using the corresponding cell position ``pos``-files only. Default usage illustrates the cells positions, considering red blood cells, platelets, or a combination thereof, in a small GUI window. This allows to explore the cell distributions in an easy manner up to 100000s of cells. Furthermore, the script can convert the ``pos``-files towards output files readable by Paraview, for when the cell counts are not properly handled anymore by the simple GUI display. The utility is easily installed within a virtual Python environment .. code:: pip install . # or when editing the source code pip install --editable . Usage is straightforward, for instance .. code:: # Show full usage and documentation pos_to_vtk --help # Show a RBC distribution pos_to_vtk /path/to/RBC.pos # Or pass through a pipe (the dash (-) is required) cat /path/to/RBC.pos | pos_to_vtk - # Combine RBC distributions pos_to_vtk /path/to/RBC.pos /other/path/to/RBC.pos # Show RBC and PLT pos_to_vtk /path/to/RBC.pos --plt /path/to/PLT.pos # Export to XDMF for visualisation in, for example, Paraview pos_to_vtk /path/to/RBC.pos --output /path/to/output.xdmf # Clip cells to a bounding box pos_to_vtk /path/to/RBC.pos --bounding-box 100 50 50 --clip # Clip cells to a surface mesh (STL) pos_to_vtk /path/to/RBC.pos --stl /path/to/mesh.stl --clip