cellpack.bin package

Submodules

cellpack.bin.analyze module

Run analysis code

cellpack.bin.analyze.analyze(analysis_config_path, recipe_path, packing_results_path, output_path=None)

Runs specified analyses based on the config :param analysis_config_path: string argument, path to analysis config file :param recipe_path: string argument, path to recipe file :param packing_results_path: string argument path to packing results

Returns:

void

cellpack.bin.analyze.main()

cellpack.bin.clean module

cellpack.bin.clean.clean()

Cleans the local cache directory :return: void

cellpack.bin.clean.main()

cellpack.bin.cleanup_tasks module

cellpack.bin.cleanup_tasks.run_cleanup(db_id=DATABASE_IDS.FIREBASE)

Performs cleanup operations on expired database entries. This function is executed as part of a scheduled task defined in .github/workflows/cleanup-firebase.yml

Args:

db_id(str): The database id to use

cellpack.bin.get-pdb-offset module

cellpack.bin.pack module

cellpack.bin.pack.main()

cellpack.bin.pack.pack(recipe, config_path=None, analysis_config_path=None)

Initializes an autopack packing from the command line :param recipe: string argument, path to recipe :param config_path: string argument, path to packing config file :param analysis_config_path: string argument, path to analysis config file

Returns:

void

cellpack.bin.simularium_converter module

class cellpack.bin.simularium_converter.ConvertToSimularium(total_steps=1)

Bases: Namespace

DEFAULT_GEO_TYPE = 'PDB'

DEFAULT_INPUT_RECIPE = '/Users/meganriel-mehan/dev/allen-inst/cellPack/cellpack/examples/recipes/v1/NM_Analysis_FigureC1.json'

DEFAULT_OUTPUT_DIRECTORY = '/Users/meganriel-mehan/Dropbox/cellPack/'

DEFAULT_PACKING_RESULT = '/Users/meganriel-mehan/Dropbox/cellPack/NM_Analysis_C_rapid/results_seed_0.json'

DEFAULT_SCALE_FACTOR = 0.01

fill_in_empty_fiber_data(time_step_index)

get_bounding_box(recipe_data)

get_euler(data_in)

get_euler_from_matrix(data_in)

get_euler_from_quat(data_in)

get_ingredient_data(cytoplasm, main_container, ingredient)

get_ingredient_display_data(ingredient_data)

static get_mesh_data(ingredient_data)

get_positions_per_ingredient(all_ingredients, results_data_in, time_step_index)

is_matrix(data_in)

process_one_ingredient(ingredient_data, time_step_index)

unpack_curve(data, time_step_index, ingredient_name, index, agent_id)

unpack_positions(data, time_step_index, ingredient_name, index, agent_id, comp_id=0, left_hand=False)

cellpack.bin.simularium_converter.main()

cellpack.bin.upload module

cellpack.bin.upload.get_recipe_metadata(loader)

Extracts and returns essential metadata from a recipe for uploading

cellpack.bin.upload.main()

cellpack.bin.upload.upload(recipe_path, db_id=DATABASE_IDS.FIREBASE)

Uploads a recipe to the database

Returns:

void

Module contents

Bin scripts package for cellpack.