Simulation of brain tumor evolution

Simulation of the spread of a tumor in the brain using simple diffusion equations.

Running the solver

The solver needs to have install g++7 or more recent and cmake version 3.13 or more. In order to compile use:

mkdir build
cd build
cmake ..
make

This creates the executable run_simulation for running the solver. When running it, you will be prompted with several input parameters:

• Spacial step and temporal step: size of one step of the solver grid (use 1.0 if not known) and the size of one time step in the simulation.

• Total simulation time: how long the simulation must run. The number of diffusion equation solutions computed is determined by total simulation time/temporal step. If you wants to see the full tumor diffusion set a total time greater than 75.

• Every which number of steps printing the partial solution for visualization.

• The time step when the radiotherapy effect is activated for stopping the tumor growth.

• Method used to solve the diffusion equation. Select 0 for the Lie-Trotter method and 1 for the direct explicit method.

Visualize tumor evolution

The visualization folder contains a simple web application built using the Dash library. This allows to visualize the tumor evolution based on the solution of the diffusion equations.

Using your favorite virtual environment tool, install the requirements provided. You can use pipenv as follows:

cd visualization
pipenv shell
pipenv install

To run the application within the virtual environment, and copy inside the folder solution created after running the solver and run the application:

cd visualization
cp -r ../build/solution .
python plot_evolution.py

You can now open it within you browser.