Index

A

agent (FixedRod attribute) agent_settings (MultilayerConfig attribute) AgentSettings (class in cr_mech_coli.simulation)

ambient (RenderSettings attribute) approx_eq() (MultilayerConfig method) area_diff_mask() (in module cr_mech_coli.fitting)

B

bg_brightness (RenderSettings attribute)

block_size (FixedRod attribute) (Parameters attribute)

C

cell_brightness (RenderSettings attribute) cell_identifier_to_counter() (CellContainer method) cell_to_color (CellContainer attribute) CellContainer (class in cr_mech_coli.datatypes) CellIdentifier (class in cr_mech_coli.datatypes) cells (CellContainer attribute) cells_are_siblings() (CellContainer method) child_map (CellContainer attribute) clone_with_args() (MultilayerConfig method) color_to_cell (CellContainer attribute) color_to_counter() (in module cr_mech_coli) config (MultilayerConfig attribute) Configuration (class in cr_mech_coli.simulation) Constants (class in cr_mech_coli.crm_fit) convert_cell_pos_to_pixels() (in module cr_mech_coli.fitting) convert_pixel_to_position() (in module cr_mech_coli.fitting) copy() (CellIdentifier method) counter_to_cell_identifier() (CellContainer method) counter_to_color() (in module cr_mech_coli) cr_mech_coli.__init__ module

cr_mech_coli.crm_amir module cr_mech_coli.crm_fit module cr_mech_coli.crm_multilayer module cr_mech_coli.crm_perf_plots module cr_mech_coli.datatypes module cr_mech_coli.fitting module cr_mech_coli.imaging module cr_mech_coli.simulation module crm_amir_main() (in module cr_mech_coli.crm_amir) crm_multilayer_main() (in module cr_mech_coli.crm_multilayer) crm_perf_plots_main() (in module cr_mech_coli.crm_perf_plots)

D

damping (RodMechanicsSettings attribute) deserialize() (CellContainer static method) (Configuration static method) diffuse (RenderSettings attribute) diffusion_constant (RodMechanicsSettings attribute) domain_height (Configuration attribute)

domain_size (Configuration attribute) (FixedRod attribute) (Parameters attribute) dt (Configuration attribute) (Parameters attribute) dx (MultilayerConfig attribute)

E

extract_positions() (in module cr_mech_coli.fitting)

F

FixedRod (class in cr_mech_coli.crm_amir) from_json() (Configuration static method)

from_toml() (Configuration static method) from_toml_string() (Configuration static method)

G

gel_pressure (Configuration attribute) generate_agents() (in module cr_mech_coli.simulation) generate_positions() (in module cr_mech_coli.simulation) get_all_identifiers() (CellContainer method) get_all_identifiers_unsorted() (CellContainer method) get_all_iterations() (CellContainer method) get_cell_from_color() (CellContainer method) get_cell_history() (CellContainer method) get_cells() (CellContainer method)

get_cells_at_iteration() (CellContainer method) get_child_map() (CellContainer method) get_children() (CellContainer method) get_color() (CellContainer method) get_parent() (CellContainer method) get_parent_map() (CellContainer method) growth_rate (AgentSettings attribute) (RodAgent attribute) growth_rate_distr (AgentSettings attribute) (RodAgent attribute)

I

inner() (PhysicalInteraction method)

interaction (AgentSettings attribute)

K

kernel_size (RenderSettings attribute)

L

lighting (RenderSettings attribute) load_from_storage() (CellContainer static method)

load_from_toml_file() (MultilayerConfig static method) load_from_toml_str() (MultilayerConfig static method)

M

mechanics (AgentSettings attribute) Memory (StorageOption attribute) metallic (RenderSettings attribute) MiePotentialF32 (class in cr_mech_coli.simulation) module cr_mech_coli.__init__ cr_mech_coli.crm_amir cr_mech_coli.crm_fit cr_mech_coli.crm_multilayer cr_mech_coli.crm_perf_plots cr_mech_coli.datatypes cr_mech_coli.fitting cr_mech_coli.imaging cr_mech_coli.simulation

MorsePotentialF32 (class in cr_mech_coli.simulation) MultilayerConfig (class in cr_mech_coli.crm_multilayer)

N

n_saves (Configuration attribute) n_threads (Configuration attribute) n_vertices (MultilayerConfig attribute) (Parameters attribute)

n_voxels (Configuration attribute) neighbor_reduction (AgentSettings attribute) (RodAgent attribute) noise (RenderSettings attribute)

O

Optimization (class in cr_mech_coli.crm_fit)

P

Parameter (class in cr_mech_coli.crm_fit) Parameters (class in cr_mech_coli.crm_amir) (class in cr_mech_coli.crm_fit) parent_map (CellContainer attribute) parents_diff_mask() (in module cr_mech_coli.fitting) path (CellContainer attribute) pbr (RenderSettings attribute)

penalty_area_diff() (in module cr_mech_coli.fitting) penalty_area_diff_account_parents() (in module cr_mech_coli.fitting) PhysicalInteraction (class in cr_mech_coli.simulation) pixel_per_micron (RenderSettings attribute) points_along_polygon() (in module cr_mech_coli.fitting) pos (RodAgent attribute) (RodMechanicsSettings attribute) prepare_for_masks() (RenderSettings method)

R

radius (PhysicalInteraction attribute) (RodAgent attribute) randomize_positions (MultilayerConfig attribute) render_image() (in module cr_mech_coli.imaging) render_mask (RenderSettings attribute) render_mask() (in module cr_mech_coli.imaging) render_pv_image() (in module cr_mech_coli.imaging) RenderSettings (class in cr_mech_coli.imaging) rigidity (RodMechanicsSettings attribute)

rng_seed (Configuration attribute) (MultilayerConfig attribute) rod_length (Parameters attribute) rod_rigiditiy (Parameters attribute) RodAgent (class in cr_mech_coli.simulation) RodMechanicsSettings (class in cr_mech_coli.simulation) Ron (StorageOption attribute) run_sim() (in module cr_mech_coli.crm_amir) (in module cr_mech_coli.crm_perf_plots) run_simulation_with_agents() (in module cr_mech_coli.simulation)

S

save_interval (Parameters attribute) SerdeJson (StorageOption attribute) serialize() (CellContainer method) Settings (class in cr_mech_coli.crm_fit) show_progressbar (Configuration attribute) Sled (StorageOption attribute) SledTemp (StorageOption attribute) sort_cellular_identifiers() (in module cr_mech_coli.simulation) specular (RenderSettings attribute) specular_power (RenderSettings attribute) spring_length (RodMechanicsSettings attribute)

spring_length_threshold (AgentSettings attribute) (RodAgent attribute) spring_tension (RodMechanicsSettings attribute) ssao_radius (RenderSettings attribute) storage_location (Configuration attribute) storage_options (Configuration attribute) storage_suffix (Configuration attribute) StorageOption (class in cr_mech_coli.simulation) store_all_images() (in module cr_mech_coli.imaging) strength (PhysicalInteraction attribute) surface_friction (Configuration attribute) surface_friction_distance (Configuration attribute)

T

t0 (Configuration attribute) t_max (Configuration attribute) (Parameters attribute) to_hash() (Configuration method)

to_json() (Configuration method) to_rod_agent_dict() (AgentSettings method) to_toml_file() (MultilayerConfig method) to_toml_string() (MultilayerConfig method)

V

vel (RodAgent attribute) (RodMechanicsSettings attribute)