photon_mosaic.rules.suite2p_run#

Snakemake rule for running Suite2P.

Functions

get_edited_options(input_path, save_folder)

Generate a dictionary of options for Suite2P by loading the default options and then modifying them with user-provided options.

run_suite2p(stat_path, dataset_folder[, ...])

This function runs Suite2P on a given dataset folder and saves the results in the specified paths.
photon_mosaic.rules.suite2p_run.run_suite2p(stat_path, dataset_folder, user_ops_dict=None)[source]#

This function runs Suite2P on a given dataset folder and saves the results in the specified paths. It also handles any exceptions that may occur during the process and logs them in an error file.

Parameters:

  • stat_path (str) – The path where the Suite2P statistics will be saved.

  • dataset_folder (Path) – The path to the folder containing the dataset.

  • user_ops_dict (dict, optional) – A dictionary containing user-provided options to override the default Suite2P options. The default is None.

Returns:

The function runs Suite2P and saves results to the specified paths. If an error occurs, it logs the error to an error.txt file in the dataset folder.

Return type:

None

photon_mosaic.rules.suite2p_run.get_edited_options(input_path, save_folder, user_ops_dict=None)[source]#

Generate a dictionary of options for Suite2P by loading the default options and then modifying them with user-provided options.

The function also sets the required runtime paths for saving the results.

Parameters:

  • input_path (Path) – The path to the input data folder.

  • save_folder (Path) – The path to the folder where the results will be saved.

  • user_ops_dict (dict, optional) – A dictionary containing user-provided options to override the default options. The default is None.

Returns:

A dictionary containing the Suite2P options, including the user-provided options and the required runtime paths.

Return type:

dict

Raises:

ValueError – If a user-provided option is not valid for Suite2P.