one.alf.cache

Construct Parquet database from local file system.

NB: If using a remote Alyx instance it is advisable to generate the cache via the Alyx one_cache management command, otherwise the resulting cache UUIDs will not match those on the database.

Examples

>>> from one.api import One
>>> cache_dir = 'path/to/data'
>>> make_parquet_db(cache_dir)
>>> one = One(cache_dir=cache_dir)

Functions

make_parquet_db

Given a data directory, index the ALF datasets and save the generated cache tables.

remove_missing_datasets

Remove dataset files and session folders that are not in the provided cache.
make_parquet_db(root_dir, out_dir=None, hash_ids=True, hash_files=False, lab=None)[source]

Given a data directory, index the ALF datasets and save the generated cache tables.

Parameters:

  • root_dir (str, pathlib.Path) – The file directory to index.

  • out_dir (str, pathlib.Path) – Optional output directory to save cache tables. If None, the files are saved into the root directory.

  • hash_ids (bool) – If True, experiment and dataset IDs will be UUIDs generated from the system and relative paths (required for use with ONE API).

  • hash_files (bool) – If True, an MD5 hash is computed for each dataset and stored in the datasets table. This will substantially increase cache generation time.

  • lab (str) – An optional lab name to associate with the data. If the folder structure contains ‘lab/Subjects’, the lab name will be taken from the folder name.

Returns:

  • pathlib.Path – The full path of the saved sessions parquet table.

  • pathlib.Path – The full path of the saved datasets parquet table.

remove_missing_datasets(cache_dir, tables=None, remove_empty_sessions=True, dry=True)[source]

Remove dataset files and session folders that are not in the provided cache.

NB: This does not remove entries from the cache tables that are missing on disk. Non-ALF files are not removed. Empty sessions that exist in the sessions table are not removed.

Parameters:

  • cache_dir (str, pathlib.Path) –

  • tables (dict[str, pandas.DataFrame], optional) – A dict with keys (‘sessions’, ‘datasets’), containing the cache tables as DataFrames.

  • remove_empty_sessions (bool) – Attempt to remove session folders that are empty and not in the sessions table.

  • dry (bool) – If true, do not remove anything.

Returns:

A sorted list of paths to be removed.

Return type:

list