Index

A

AgentSettings (class in cr_mech_coli.simulation)

ambient (RenderSettings attribute) area_diff_mask() (in module cr_mech_coli.fitting)

B

bg_brightness (RenderSettings 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) color_to_cell (CellContainer attribute) color_to_counter() (in module cr_mech_coli) Configuration (class in cr_mech_coli.simulation) 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.datatypes module cr_mech_coli.fitting module cr_mech_coli.imaging module cr_mech_coli.simulation module

D

damping (RodMechanicsSettings attribute) diffuse (RenderSettings attribute) diffusion_constant (RodMechanicsSettings attribute)

domain_height (Configuration attribute) domain_size (Configuration attribute) dt (Configuration attribute)

E

extract_positions() (in module cr_mech_coli.fitting)

F

from_json() (Configuration static method)

G

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)

I

interaction (AgentSettings attribute)

K

kernel_size (RenderSettings attribute)

L

lighting (RenderSettings attribute)

M

mechanics (AgentSettings attribute) metallic (RenderSettings attribute) module cr_mech_coli.__init__ cr_mech_coli.datatypes cr_mech_coli.fitting cr_mech_coli.imaging cr_mech_coli.simulation

MorsePotentialF32 (class in cr_mech_coli.simulation)

N

n_agents (Configuration attribute) n_threads (Configuration attribute)

n_vertices (AgentSettings attribute) n_voxels (Configuration attribute) noise (RenderSettings attribute)

P

parent_map (CellContainer attribute) parents_diff_mask() (in module cr_mech_coli.fitting) pbr (RenderSettings attribute) penalty_area_diff() (in module cr_mech_coli.fitting)

penalty_area_diff_account_parents() (in module cr_mech_coli.fitting) points_along_polygon() (in module cr_mech_coli.fitting) pos (RodAgent attribute) (RodMechanicsSettings attribute) prepare_for_masks() (RenderSettings method)

R

radius (RodAgent attribute) randomize_position (Configuration 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)

resolution (RenderSettings attribute) rigidity (RodMechanicsSettings attribute) rng_seed (Configuration attribute) RodAgent (class in cr_mech_coli.simulation) RodMechanicsSettings (class in cr_mech_coli.simulation) run_simulation() (in module cr_mech_coli.simulation) run_simulation_with_agents() (in module cr_mech_coli.simulation)

S

save_interval (Configuration attribute) show_progressbar (Configuration 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) store_all_images() (in module cr_mech_coli.imaging)

T

t0 (Configuration attribute) t_max (Configuration attribute)

to_hash() (Configuration method) to_json() (Configuration method)

V

vel (RodAgent attribute) (RodMechanicsSettings attribute)