Index

A

absolute() (Path method) add_ident_divided() (CellContainer method) agent (FixedRod attribute) agent_settings (MultilayerConfig attribute) AgentSettings (class in cr_mech_coli.simulation) ambient (RenderSettings attribute)

anchor (Path property) Any (class in cr_mech_coli.crm_multilayer) approx_eq() (MultilayerConfig method) area_diff_mask() (in module cr_mech_coli.fitting) as_posix() (Path method) as_uri() (Path method)

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) chmod() (Path method) clear() (tqdm method) clone_with_args() (MultilayerConfig method) close() (tqdm 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) constants() (Settings method) 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_divide 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) cwd() (Path class method)

D

damping (Parameters attribute) (RodMechanicsSettings attribute) deserialize() (CellContainer static method) (Configuration static method) DifferentialEvolution (class in cr_mech_coli.crm_fit) diffuse (RenderSettings attribute) diffusion_constant (RodMechanicsSettings attribute) display() (tqdm method) Division (CellIdentifier attribute)

domain_height (Configuration attribute) domain_height() (Settings method) domain_size (Configuration attribute) (FixedRod attribute) (Parameters attribute) drag_force (Parameters attribute) drive (Path property) dt (Configuration attribute) (Parameters attribute) dx (MultilayerConfig attribute)

E

exists() (Path method) expanduser() (Path method) Explicit (GrowthRateSetter attribute), [1] (SpringLengthThresholdSetter attribute)

external_write_mode() (tqdm class method) extract_positions() (in module cr_mech_coli.fitting)

F

find_ml_config_path() (in module cr_mech_coli.crm_multilayer) FixedRod (class in cr_mech_coli.crm_amir) format_dict (tqdm property) format_interval() (tqdm static method) format_meter() (tqdm static method)

format_num() (tqdm static method) format_sizeof() (tqdm static method) 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_daughter_map() (CellContainer method) get_lock() (tqdm class method) get_parent() (CellContainer method) get_parent_map() (CellContainer method) glob() (in module cr_mech_coli.crm_multilayer) (Path method) group() (Path method) growth_rate (AgentSettings attribute) (Parameters attribute) (RodAgent attribute) growth_rate_setter (AgentSettings attribute) (RodAgent attribute) GrowthRateSetter (class in cr_mech_coli.crm_multilayer) (class in cr_mech_coli.simulation)

H

hardlink_to() (Path method)

home() (Path class method)

I

Initial (CellIdentifier attribute) Inserted (CellIdentifier attribute) interaction (AgentSettings attribute) is_absolute() (Path method) is_block_device() (Path method) is_char_device() (Path method) is_dir() (Path method) is_fifo() (Path method)

is_file() (Path method) is_junction() (Path method) is_mount() (Path method) is_relative_to() (Path method) is_reserved() (Path method) is_socket() (Path method) is_symlink() (Path method) iterdir() (Path method)

J

joinpath() (Path method)

K

kernel_size (RenderSettings attribute)

L

lchmod() (Path method) lighting (RenderSettings attribute) load_from_storage() (CellContainer static method) load_from_toml_file() (MultilayerConfig static method)

load_from_toml_str() (MultilayerConfig static method) load_or_compute_container() (in module cr_mech_coli.crm_multilayer) load_or_compute_ydata() (in module cr_mech_coli.crm_multilayer) load_or_compute_ydata_samples() (in module cr_mech_coli.crm_multilayer) lstat() (Path method)

M

match() (Path method) mechanics (AgentSettings attribute) Memory (StorageOption attribute) metallic (RenderSettings attribute) MiePotentialF32 (class in cr_mech_coli.simulation) mkdir() (Path method) module cr_mech_coli.__init__ cr_mech_coli.crm_amir cr_mech_coli.crm_divide 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

monitor (tqdm attribute) monitor_interval (tqdm attribute) MorsePotentialF32 (class in cr_mech_coli.simulation) moveto() (tqdm method) 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) name (Path property)

neighbor_reduction (AgentSettings attribute) (RodAgent attribute) new_initial() (CellIdentifier static method) new_inserted() (CellIdentifier static method) noise (RenderSettings attribute) NormalDistr (GrowthRateSetter attribute), [1] (SpringLengthThresholdSetter attribute)

O

open() (Path method) optimization() (Settings method) OptimizationMethod (class in cr_mech_coli.crm_fit)

OptimizationResult (class in cr_mech_coli.crm_fit) Others (class in cr_mech_coli.crm_fit) others() (Settings method) owner() (Path method)

P

pandas() (tqdm class method) Parameter (class in cr_mech_coli.crm_fit) Parameters (class in cr_mech_coli.crm_amir) (class in cr_mech_coli.crm_fit) parameters() (Settings method) parent (Path property) parent_map (CellContainer attribute) parents (Path property) parents_diff_mask() (in module cr_mech_coli.fitting) parts (Path property) path (CellContainer attribute) Path (class in cr_mech_coli.crm_multilayer) 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) plot_colony_height_over_time() (in module cr_mech_coli.crm_multilayer) points_along_polygon() (in module cr_mech_coli.fitting) pos (RodAgent attribute) (RodMechanicsSettings attribute) PotentialType (class in cr_mech_coli.crm_fit) prepare_for_masks() (RenderSettings method) produce_ml_config() (in module cr_mech_coli.crm_multilayer) produce_ydata() (in module cr_mech_coli.crm_multilayer) progressbar (Configuration attribute) (Parameters attribute)

R

radius (PhysicalInteraction attribute) (RodAgent attribute) randomize_positions (MultilayerConfig attribute) read_bytes() (Path method) read_text() (Path method) readlink() (Path method) refresh() (tqdm method) relative_to() (Path method) rename() (Path method) render_image() (in module cr_mech_coli.crm_multilayer) (in module cr_mech_coli.imaging) render_image_helper() (in module cr_mech_coli.crm_multilayer) 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) replace() (Path method) reset() (tqdm method)

resolve() (Path method) rglob() (Path method) rigidity (RodMechanicsSettings attribute) rmdir() (Path method) rng_seed (Configuration attribute) (MultilayerConfig attribute) rod_length (Parameters attribute) rod_rigidity (Parameters attribute) RodAgent (class in cr_mech_coli.simulation) RodMechanicsSettings (class in cr_mech_coli.simulation) Ron (StorageOption attribute) root (Path property) run_optimizer() (in module cr_mech_coli.crm_fit) run_sim() (in module cr_mech_coli.crm_amir) (in module cr_mech_coli.crm_multilayer) (in module cr_mech_coli.crm_perf_plots) run_sim_with_relaxation() (in module cr_mech_coli.crm_amir) run_simulation() (in module cr_mech_coli.crm_fit) run_simulation_with_agents() (in module cr_mech_coli.simulation)

S

samefile() (Path method) sample_parameters() (in module cr_mech_coli.crm_multilayer) SampledFloat (class in cr_mech_coli.crm_fit) save_interval (Parameters attribute) SerdeJson (StorageOption attribute) serialize() (CellContainer method) set_description() (tqdm method) set_description_str() (tqdm method) set_lock() (tqdm class method) set_postfix() (tqdm method) set_postfix_str() (tqdm method) Settings (class in cr_mech_coli.crm_fit) 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_length_threshold_setter (AgentSettings attribute) (RodAgent attribute) spring_tension (Parameters attribute) (RodMechanicsSettings attribute) SpringLengthThresholdSetter (class in cr_mech_coli.simulation) ssao_radius (RenderSettings attribute) stat() (Path method) status_printer() (tqdm static method) stem (Path property) 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) suffix (Path property) suffixes (Path property) surface_friction (Configuration attribute) surface_friction_distance (Configuration attribute) symlink_to() (Path method)

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) touch() (Path method) tqdm (class in cr_mech_coli.crm_multilayer) tube_width (Parameters attribute)

U

unlink() (Path method)

unpause() (tqdm method) update() (tqdm method)

V

vel (RodAgent attribute) (RodMechanicsSettings attribute)

VoxelPlainIndex (class in cr_mech_coli.datatypes)

W

walk() (Path method) with_name() (Path method) with_segments() (Path method) with_stem() (Path method)

with_suffix() (Path method) wrapattr() (tqdm class method) write() (tqdm class method) write_bytes() (Path method) write_text() (Path method)