Documentation

• crm.simulation
• crm.datatypes
• crm.imaging
• crm.fitting

This package performs numerical simulations of rod-shaped bacterial cells. It can also visualize the results of these simulations and perform parameter estimations.

Performing a simulation and storing the corresponding images is straightforward. All settings needed to run a single simulation are contained in the Configuration class. The routine is executed via the run_simulation() function.

>>> import cr_mech_coli as crm
>>> config = crm.Configuration()
>>> config.n_agents = 8
>>> sim_result = crm.run_simulation(config)

To adjust visualization settings, we provide the RenderSettings class.

>>> render_settings = RenderSettings()
>>> render_settings.noise = 30
>>> crm.store_all_images(config, sim_result, save_dir="out")

Note

This package is based on the f32 floating point type. All numerical calculations performed by cellular_raza are done in this format. However the same can not be guaranteed for calculations involving any of the python packages.