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
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