fnndsc/pl-pyvista-volume repository overview

⁠pl-pyvista-volume

pl-pyvista-volume is a ChRIS⁠ ds plugin which calculates the volume enclosed by a polygonal mesh. It accepts an input directory containing MNI .obj surface files, and writes outputs to both stdout and text files in an output directory.

PyVista⁠ is used for calculating volume from a polygonal mesh.

⁠Installation

pl-pyvista-volume is a ChRIS⁠ plugin, meaning it can run from either within ChRIS or the command-line.

⁠Local Usage

To get started with local command-line usage, use Apptainer⁠ (a.k.a. Singularity) to run pl-pyvista-volume as a container:

apptainer exec docker://fnndsc/pl-pyvista-volume surfvol input/ output/

To print its available options, run:

apptainer exec docker://fnndsc/pl-pyvista-volume surfvol --help

See examples⁠ for sample data.

⁠Local Installation

For development, use pip to install the package locally.

python -m venv venv
source venv/bin/activate
pip install -e .

⁠Testing

pytest

⁠Notes

⁠Multiprocessing

vtk and pyvista require multiprocessing (instead of multithreading) for concurrency. On 8 cores:

multiprocessing:

real    0m38.632s
user    2m31.680s
sys     0m7.660s

multithreading:

real    2m43.133s
user    2m28.311s
sys     0m5.364s