Documentation

• crm.simulation
• crm.datatypes
• crm.imaging
• crm.fitting
• crm.gen
  • background
  • bacteria
  • configuration
  • filters
  • metrics
  • optimization
  • pipeline
  • scene
  • visualization

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

Running 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 and returns a CellContainer which contains all information of the cells at every stored time interval.

import cr_mech_coli as crm

# Contains settings regarding simulation domain, time increments etc.
config = crm.Configuration()

# Use predefined values for agents
agent_settings = crm.AgentSettings()

# Automatically generate agents
agents = crm.generate_agents(
    4,
    agent_settings,
    config
)

# Run simulation and return container
cell_container = crm.run_simulation_with_agents(config, agents)

# Plot individual results
crm.store_all_images(cell_container, config.domain_size)

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.