anndict.AdataDict.fapply

AdataDict.fapply(func, *, use_multithreading=True, num_workers=None, max_retries=0, catch_errors=True, return_as_adata_dict=False, **kwargs_dicts)

Applies func to each AnnData in adata_dict, with error handling, retry mechanism, and the option to use either threading or sequential execution. The return behaviour is based on the return behaviour of func.

kwargs can be Any. if a kwarg is a dict with keys that match adata_dict, then values are broadcast to the func call on the corresponding key-value of adata_dict. Otherwise, the kwarg is directly broadcast to all calls of func.

Parameters:

adata_dict AdataDict

An AdataDict.

func callable

Function to apply to each AnnData object in adata_dict.

use_multithreading bool (default: True)

If True, use ThreadPoolExecutor; if False, execute sequentially. Default is True.

num_workers int | None (default: None)

Number of worker threads to use. If None, defaults to the number of CPUs available.

max_retries int (default: 0)

Maximum number of retry attempts after the first failure. (i.e. 0 means no retries, 1 means one retry after the first failure, for a total of 2 attempts)

catch_errors bool (default: True)

If False, raise exceptions instead of catching errors.

return_as_adata_dict bool (default: False)

Whether to return the results as a dict (if False) or AdataDict (if True).

kwargs_dicts Any

Additional keyword arguments to pass to the function.

Return type:

dict | AdataDict | None

Returns:

• If all results are None: None

• Otherwise: A dict or AdataDict (based on return_as_adata_dict) containing all results of func applied to each AnnData

Notes

Be careful when setting max_retries != 0. If retries are used, the same function will be called again on whatever the current data is, which may not be the original data. For example, if func log-transform the data, then does something that fails, the second time func is called, the already log-transformed data will have another log transform applied.