Index

A

add_brightness_noise() (in module cr_mech_coli.crm_gen.bacteria) add_darker_spots() (in module cr_mech_coli.crm_gen.background) add_fine_texture() (in module cr_mech_coli.crm_gen.background) add_gaussian_blur() (in module cr_mech_coli.crm_gen.background) add_gaussian_noise() (in module cr_mech_coli.crm_gen.filters) add_ident_divided() (CellContainer method) add_lighter_spots() (in module cr_mech_coli.crm_gen.background) add_poisson_noise() (in module cr_mech_coli.crm_gen.filters) agent (FixedRod attribute) AgentSettings (class in cr_mech_coli.simulation)

ambient (RenderSettings attribute) apply_age_based_brightness() (in module cr_mech_coli.crm_gen.bacteria) apply_gaussian_blur() (in module cr_mech_coli.crm_gen.filters) apply_halo_effect() (in module cr_mech_coli.crm_gen.filters) apply_microscope_effects() (in module cr_mech_coli.crm_gen.filters) apply_original_brightness() (in module cr_mech_coli.crm_gen.bacteria) apply_phase_contrast_pipeline() (in module cr_mech_coli.crm_gen.filters) apply_psf_blur() (in module cr_mech_coli.crm_gen.filters) apply_synthetic_effects() (in module cr_mech_coli.crm_gen.scene) area_diff_mask() (in module cr_mech_coli.fitting)

B

bg_brightness (RenderSettings attribute)

block_size (FixedRod attribute) (Parameters attribute)

C

calculate_profiles() (in module cr_mech_coli.crm_divide.optimize) 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) compute_age_based_brightness() (in module cr_mech_coli.crm_gen.bacteria) compute_all_metrics() (in module cr_mech_coli.crm_gen.metrics) compute_cell_ages() (in module cr_mech_coli.crm_gen.pipeline) compute_color_distribution() (in module cr_mech_coli.crm_gen.metrics) compute_final_metrics() (in module cr_mech_coli.crm_gen.optimization) compute_psnr() (in module cr_mech_coli.crm_gen.metrics) compute_ssim() (in module cr_mech_coli.crm_gen.metrics) compute_weighted_loss() (in module cr_mech_coli.crm_gen.optimization) 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_divide.main module cr_mech_coli.crm_divide.optimize module cr_mech_coli.crm_fit module

cr_mech_coli.crm_gen module cr_mech_coli.crm_gen.background module cr_mech_coli.crm_gen.bacteria module cr_mech_coli.crm_gen.config module cr_mech_coli.crm_gen.filters module cr_mech_coli.crm_gen.metrics module cr_mech_coli.crm_gen.optimization module cr_mech_coli.crm_gen.pipeline module cr_mech_coli.crm_gen.scene module cr_mech_coli.crm_gen.visualization 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 create_airy_psf() (in module cr_mech_coli.crm_gen.filters) create_base_background() (in module cr_mech_coli.crm_gen.background) create_gaussian_psf() (in module cr_mech_coli.crm_gen.filters) create_halo_gradient() (in module cr_mech_coli.crm_gen.filters) create_halo_mask() (in module cr_mech_coli.crm_gen.filters) create_synthetic_brightness_map() (in module cr_mech_coli.crm_gen.bacteria) create_synthetic_scene() (in module cr_mech_coli.crm_gen.scene)

D

damping (Parameters attribute) (RodMechanicsSettings attribute) DECheckpointManager (class in cr_mech_coli.crm_gen.optimization) default_parameters() (in module cr_mech_coli.crm_divide.main) deserialize() (CellContainer static method) (Configuration static method) DifferentialEvolution (class in cr_mech_coli.crm_fit) diffuse (RenderSettings attribute) diffusion_constant (RodMechanicsSettings attribute)

Division (CellIdentifier attribute) domain_height (Configuration attribute) domain_height() (Settings method) domain_size (Configuration attribute) (FixedRod attribute) (Parameters attribute) drag_force (Parameters attribute) dt (Configuration attribute) (Parameters attribute)

E

Explicit (GrowthRateSetter attribute) (SpringLengthThresholdSetter attribute) extract_masked_region() (in module cr_mech_coli.crm_gen.optimization) (in module cr_mech_coli.crm_gen.visualization)

extract_original_brightness() (in module cr_mech_coli.crm_gen.bacteria) extract_positions() (in module cr_mech_coli.fitting)

F

find_latest_checkpoint() (DECheckpointManager method) find_real_images() (in module cr_mech_coli.crm_gen.optimization) 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_all_synthetics() (in module cr_mech_coli.crm_gen.optimization) generate_comparison_plot() (in module cr_mech_coli.crm_gen.visualization) generate_detailed_plots() (in module cr_mech_coli.crm_gen.visualization) generate_phase_contrast_background() (in module cr_mech_coli.crm_gen.background) 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_default_config() (in module cr_mech_coli.crm_gen.config) get_default_config_path() (in module cr_mech_coli.crm_gen.config) get_parent() (CellContainer method) get_parent_map() (CellContainer method) growth_rate (AgentSettings attribute) (Parameters attribute) (RodAgent attribute) growth_rate_setter (AgentSettings attribute) (RodAgent attribute) GrowthRateSetter (class in cr_mech_coli.simulation)

I

Initial (CellIdentifier attribute)

Inserted (CellIdentifier attribute) interaction (AgentSettings attribute)

J

jitter_synthetic_params() (in module cr_mech_coli.crm_gen.pipeline)

K

kernel_size (RenderSettings attribute)

L

lighting (RenderSettings attribute) load_checkpoint() (DECheckpointManager method) load_config() (in module cr_mech_coli.crm_gen.config)

load_from_storage() (CellContainer static method) load_image() (in module cr_mech_coli.crm_gen.metrics) load_parameter_sets() (in module cr_mech_coli.crm_gen.pipeline)

M

mechanics (AgentSettings attribute) Memory (StorageOption attribute) metallic (RenderSettings attribute) MiePotentialF32 (class in cr_mech_coli.simulation) minimize_de() (in module cr_mech_coli.crm_divide.optimize) minimize_lhs() (in module cr_mech_coli.crm_divide.optimize) module cr_mech_coli.__init__ cr_mech_coli.crm_amir cr_mech_coli.crm_divide cr_mech_coli.crm_divide.main cr_mech_coli.crm_divide.optimize cr_mech_coli.crm_fit cr_mech_coli.crm_gen cr_mech_coli.crm_gen.background cr_mech_coli.crm_gen.bacteria cr_mech_coli.crm_gen.config cr_mech_coli.crm_gen.filters cr_mech_coli.crm_gen.metrics cr_mech_coli.crm_gen.optimization cr_mech_coli.crm_gen.pipeline cr_mech_coli.crm_gen.scene cr_mech_coli.crm_gen.visualization 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)

N

n_saves (Configuration attribute) n_threads (Configuration attribute) n_vertices (Parameters attribute) n_voxels (Configuration attribute) neighbor_reduction (AgentSettings attribute) (RodAgent attribute)

new_initial() (CellIdentifier static method) new_inserted() (CellIdentifier static method) noise (RenderSettings attribute) NormalDistr (GrowthRateSetter attribute) (SpringLengthThresholdSetter attribute)

O

ObjectiveFunction (class in cr_mech_coli.crm_gen.optimization) optimization() (Settings method) OptimizationMethod (class in cr_mech_coli.crm_fit)

OptimizationResult (class in cr_mech_coli.crm_fit) optimize_parameters() (in module cr_mech_coli.crm_gen.optimization) Others (class in cr_mech_coli.crm_fit) others() (Settings method)

P

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_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) plot_growth_rate_distribution() (in module cr_mech_coli.crm_divide.main) plot_mask_adjustment() (in module cr_mech_coli.crm_divide.main)

plot_metrics() (in module cr_mech_coli.crm_gen.metrics) plot_profiles() (in module cr_mech_coli.crm_divide.main) plot_snapshots() (in module cr_mech_coli.crm_divide.main) plot_time_evolution() (in module cr_mech_coli.crm_divide.main) plot_timings() (in module cr_mech_coli.crm_divide.main) 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) preprocessing() (in module cr_mech_coli.crm_divide.main) process_frame_for_synthetic() (in module cr_mech_coli.crm_gen.pipeline) progressbar (Configuration attribute) (Parameters attribute)

R

radius (PhysicalInteraction attribute) (RodAgent attribute) render_and_save_frame() (in module cr_mech_coli.crm_gen.pipeline) 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) 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) run_optimizer() (in module cr_mech_coli.crm_divide.main) (in module cr_mech_coli.crm_fit) run_pipeline() (in module cr_mech_coli.crm_gen.pipeline) run_sim() (in module cr_mech_coli.crm_amir) (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) (in module cr_mech_coli.crm_gen.pipeline) run_simulation_with_agents() (in module cr_mech_coli.simulation)

S

sample_range() (in module cr_mech_coli.crm_gen.pipeline) sample_simulation_params() (in module cr_mech_coli.crm_gen.pipeline) SampledFloat (class in cr_mech_coli.crm_fit) save_checkpoint() (DECheckpointManager method) save_interval (Parameters attribute) save_metrics_json() (in module cr_mech_coli.crm_gen.metrics) save_results() (in module cr_mech_coli.crm_gen.optimization) SerdeJson (StorageOption attribute) serialize() (CellContainer 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) 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) tube_width (Parameters attribute)

V

validate_checkpoint() (DECheckpointManager method) vel (RodAgent attribute) (RodMechanicsSettings attribute)

VoxelPlainIndex (class in cr_mech_coli.datatypes)