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simple_vessel's Introduction

Model to test handshake between PhysiCell and SimVascular

Clone this repo (or use a release). From the root directory:

Generate the desired config file (.xml):

cd data  # from root dir
python generate_simple_vessel.py
# select the "simple_network.csv" in this same dir
# script will generate "simple_test.xml"
cp simple_test.xml simple_vessel.xml

Build the model's executable:

cd src   # from root dir
make -j2

To test in /src:

cp ../data/simple_vessel.xml .
simple_vessel simple_vessel.xml

# kill (ctl-c) the sim after the first 1 or 2 time steps

# analyze, visualize the output files
cd output/
cp ../../examples/pyMCDS_cells.py .
cp ../../examples/info_cells3D.py .
cp ../../examples/fury_cells.py .

python info_cells3D.py

python fury_cells.py   # assuming you have done "pip install fury"

To use the Model Builder (+ Studio) GUI:

From the root directory (if you are in /src, just cd ..)

mv src/simple_vessel .    # don't just copy it, move it!
python bin/pmb.py --studio

Click the Run tab then click Run Simulation (might take a few secs to start). Click the Plot tab and Play output results.

simple_vessel's People

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