SimuCell3D saves three different types of files.
First, it saves the cell statistics in a csv file named simulation_statistics.csv located in the output simulation folder. This file contains statistics about the cells as a function of time (cell volumes, areas, pressures, kinetic energies..). The python script located in:
path/to/SimuCell3D/scripts/data_plotting/
can be called in the following way:
python3 plot_data.py path/to/simulation_output_folder
To generate from this CSV file the following plots:
To save additional statistics, the user can add a new function in the vector named file_data_mapper_lst of the file path\to\SimuCell3D\include\io\mesh_data.hpp.
Example:
cell_data_mapper("cell_nb_nodes", "int", [](cell_ptr c) -> std::string {
return format_number(c->get_node_lst().size(), "%d");
}),
After that you should recompile the code otherwise your new function will not be taken into account:
cd path\to\SimuCell3D\build
make
This new function would generate a new column named cell_nb_nodes in the simulation_statistics.csv file where the number of nodes of each cell would be saved.
Cell meshes are meshes where all the faces of a given cell are regrouped in one vtkCell entity. This type of mesh can be used to visualize the attributes of the cells (ex: volume, pressure etc).
Similarly, new attributes can be added to the cell meshes, by adding a new function in the vector named cell_data_mapper_lst of the file path\to\SimuCell3D\include\io\mesh_data.hpp.
Face meshes are meshes where all the faces are stored as individual cells. Then can be used to visualize the attributes of the faces of the cells (triangle area, adhesion energy etc).
