Index

A

add_frame_scalebar() (in module arcade_collection.convert.convert_to_projection) add_frame_timestamp() (in module arcade_collection.convert.convert_to_projection) approximate_radius_from_voxels() (in module arcade_collection.convert.convert_to_simularium_shapes) arcade_collection.convert module arcade_collection.convert.convert_to_contours module arcade_collection.convert.convert_to_images module arcade_collection.convert.convert_to_meshes module arcade_collection.convert.convert_to_projection module arcade_collection.convert.convert_to_simularium module arcade_collection.convert.convert_to_simularium_objects module arcade_collection.convert.convert_to_simularium_shapes module arcade_collection.convert.convert_to_tfe module arcade_collection.input module

arcade_collection.input.convert_to_cells_file module arcade_collection.input.convert_to_locations_file module arcade_collection.input.generate_setup_file module arcade_collection.input.group_template_conditions module arcade_collection.input.merge_region_samples module arcade_collection.output module arcade_collection.output.convert_model_units module arcade_collection.output.extract_tick_json module arcade_collection.output.get_location_voxels module arcade_collection.output.parse_cells_file module arcade_collection.output.parse_growth_file module arcade_collection.output.parse_locations_file module

C

calculate_patch_size() (in module arcade_collection.convert.convert_to_simularium_shapes) calculate_sample_bounds() (in module arcade_collection.input.generate_setup_file) CAMERA_LOOK_AT (in module arcade_collection.convert.convert_to_simularium) CAMERA_POSITIONS (in module arcade_collection.convert.convert_to_simularium) CELL_STATES (in module arcade_collection.convert.convert_to_simularium_shapes) (in module arcade_collection.output.parse_growth_file) CELLS_COLUMNS (in module arcade_collection.output.parse_cells_file) convert_hexagonal_to_rectangular_coordinates() (in module arcade_collection.convert.convert_to_simularium_shapes) convert_model_units() (in module arcade_collection.output.convert_model_units) convert_spatial_units() (in module arcade_collection.output.convert_model_units) convert_temporal_units() (in module arcade_collection.output.convert_model_units) convert_to_cell() (in module arcade_collection.input.convert_to_cells_file)

convert_to_cell_region() (in module arcade_collection.input.convert_to_cells_file) convert_to_cells_file() (in module arcade_collection.input.convert_to_cells_file) convert_to_contours() (in module arcade_collection.convert.convert_to_contours) convert_to_images() (in module arcade_collection.convert.convert_to_images) convert_to_location() (in module arcade_collection.input.convert_to_locations_file) convert_to_locations_file() (in module arcade_collection.input.convert_to_locations_file) convert_to_meshes() (in module arcade_collection.convert.convert_to_meshes) convert_to_projection() (in module arcade_collection.convert.convert_to_projection) convert_to_simularium() (in module arcade_collection.convert.convert_to_simularium) convert_to_simularium_objects() (in module arcade_collection.convert.convert_to_simularium_objects) convert_to_simularium_shapes() (in module arcade_collection.convert.convert_to_simularium_shapes) convert_to_tfe() (in module arcade_collection.convert.convert_to_tfe) convert_value_distribution() (in module arcade_collection.input.convert_to_cells_file)

D

DEFAULT (MeshType attribute)

DEFAULT_POPULATION_ID (in module arcade_collection.input.generate_setup_file)

E

EDGE_TYPES (in module arcade_collection.convert.convert_to_simularium_shapes) estimate_spatial_resolution() (in module arcade_collection.output.convert_model_units)

estimate_temporal_resolution() (in module arcade_collection.output.convert_model_units) extract_tick_json() (in module arcade_collection.output.extract_tick_json)

F

filter_border_voxels() (in module arcade_collection.convert.convert_to_simularium_shapes) filter_cell_reference() (in module arcade_collection.input.convert_to_cells_file) filter_valid_samples() (in module arcade_collection.input.merge_region_samples) find_seed_ranges() (in module arcade_collection.input.group_template_conditions) FLAT_BINARY_BY_FRAME (ImageType attribute) FLAT_BY_FRAME (ImageType attribute) FLAT_RGBA_BY_FRAME (ImageType attribute)

flatten_array_chunk() (in module arcade_collection.convert.convert_to_images) format_patch_for_shapes() (in module arcade_collection.convert.convert_to_simularium_shapes) format_potts_for_objects() (in module arcade_collection.convert.convert_to_simularium_objects) format_potts_for_shapes() (in module arcade_collection.convert.convert_to_simularium_shapes) FULL (ImageType attribute) FULL_BINARY (ImageType attribute) FULL_BINARY_BY_FRAME (ImageType attribute) FULL_BY_FRAME (ImageType attribute)

G

generate_setup_file() (in module arcade_collection.input.generate_setup_file) get_agent_data() (in module arcade_collection.convert.convert_to_simularium) get_cell_state() (in module arcade_collection.input.convert_to_cells_file) get_center_voxel() (in module arcade_collection.input.convert_to_locations_file) get_display_data() (in module arcade_collection.convert.convert_to_simularium) get_feature_from_data() (in module arcade_collection.convert.convert_to_tfe) get_location_voxels() (in module arcade_collection.input.convert_to_locations_file) (in module arcade_collection.output.get_location_voxels)

get_manifest_data() (in module arcade_collection.convert.convert_to_tfe) get_meta_data() (in module arcade_collection.convert.convert_to_simularium) get_resolution_voxels() (in module arcade_collection.convert.convert_to_simularium_shapes) get_times_from_data() (in module arcade_collection.convert.convert_to_tfe) get_tracks_from_data() (in module arcade_collection.convert.convert_to_tfe) group_condition_sets() (in module arcade_collection.input.group_template_conditions) group_seed_ranges() (in module arcade_collection.input.group_template_conditions) group_template_conditions() (in module arcade_collection.input.group_template_conditions) GROWTH_COLUMNS (in module arcade_collection.output.parse_growth_file)

I

ImageType (class in arcade_collection.convert.convert_to_images)

INVERTED (MeshType attribute)

L

LOCATIONS_COLUMNS (in module arcade_collection.output.parse_locations_file)

M

make_combined_mesh() (in module arcade_collection.convert.convert_to_meshes) make_individual_mesh() (in module arcade_collection.convert.convert_to_meshes) make_mesh_array() (in module arcade_collection.convert.convert_to_meshes) make_mesh_file() (in module arcade_collection.convert.convert_to_meshes) make_mesh_geometry() (in module arcade_collection.convert.convert_to_meshes) make_mesh_groups() (in module arcade_collection.convert.convert_to_meshes) make_setup_file() (in module arcade_collection.input.generate_setup_file) MAX_ARRAY_LEVEL (in module arcade_collection.convert.convert_to_meshes) merge_region_samples() (in module arcade_collection.input.merge_region_samples) MeshType (class in arcade_collection.convert.convert_to_meshes) module arcade_collection.convert arcade_collection.convert.convert_to_contours arcade_collection.convert.convert_to_images arcade_collection.convert.convert_to_meshes arcade_collection.convert.convert_to_projection arcade_collection.convert.convert_to_simularium arcade_collection.convert.convert_to_simularium_objects arcade_collection.convert.convert_to_simularium_shapes arcade_collection.convert.convert_to_tfe arcade_collection.input arcade_collection.input.convert_to_cells_file arcade_collection.input.convert_to_locations_file arcade_collection.input.generate_setup_file arcade_collection.input.group_template_conditions arcade_collection.input.merge_region_samples arcade_collection.output arcade_collection.output.convert_model_units arcade_collection.output.extract_tick_json arcade_collection.output.get_location_voxels arcade_collection.output.parse_cells_file arcade_collection.output.parse_growth_file arcade_collection.output.parse_locations_file

P

parse_cell_tick() (in module arcade_collection.output.parse_cells_file) parse_cells_file() (in module arcade_collection.output.parse_cells_file) parse_growth_file() (in module arcade_collection.output.parse_growth_file)

parse_growth_timepoint() (in module arcade_collection.output.parse_growth_file) parse_location_tick() (in module arcade_collection.output.parse_locations_file) parse_locations_file() (in module arcade_collection.output.parse_locations_file)

R

ROTATIONS (in module arcade_collection.convert.convert_to_contours)

S

shade_color() (in module arcade_collection.convert.convert_to_simularium)

split_array_chunks() (in module arcade_collection.convert.convert_to_images)

T

transform_sample_coordinates() (in module arcade_collection.input.merge_region_samples)