Utility tools

In addition to 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/.

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

pip install .

# or when editing the source code

pip install --editable .

Usage is straightforward, for instance

# 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