sovabids.rules#

Module dealing with the rules for bids conversion.

Module Contents#

Functions#

get_info_from_path(path, rules)

Parse information from a given path, given a set of rules.

get_files(source_path, rules)

Recursively scan the directory for valid files, returning a list with the full-paths to each.

load_rules(rules)

Load rules if given a path, bypass if given a dict.

apply_rules_to_single_file(file, rules, bids_path[, ...])

Apply rules to a single file.

apply_rules(source_path, bids_path, rules[, mapping_path])

Apply rules to a set of files.

sovapply()

Console script usage for applying rules.

Attributes#

sovabids.rules.LOGGER[source]#
sovabids.rules.get_info_from_path(path, rules)[source]#

Parse information from a given path, given a set of rules.

Parameters
  • path (str) – The path from where we want to extract information.

  • rules (dict) – A dictionary following the “Rules File Schema”.

Notes

See the Rules File Schema documentation for the expected schema of the dictionary.

sovabids.rules.get_files(source_path, rules)[source]#

Recursively scan the directory for valid files, returning a list with the full-paths to each.

The valid files are given by the ‘non-bids.eeg_extension’ rule. See the “Rules File Schema”.

Parameters
  • source_path (str) – The path we want to obtain the files from.

  • rules (str|dict) – The path to the rules file, or the rules dictionary.

Returns

filepaths – A list containing the path to each valid file in the source_path.

Return type

list of str

sovabids.rules.load_rules(rules)[source]#

Load rules if given a path, bypass if given a dict.

Parameters

rules (str|dict) – The path to the rules file, or the rules dictionary.

Returns

The rules dictionary.

Return type

dict

sovabids.rules.apply_rules_to_single_file(file, rules, bids_path, write=False, preview=False)[source]#

Apply rules to a single file.

Parameters
  • file (str) – Path to the file.

  • rules (str|dict) – Path to the rules file or rules dictionary.

  • bids_path (str) – Path to the bids directory

  • write (bool, optional) – Whether to write the converted files to disk or not.

  • preview (bool, optional) – Whether to return a dictionary with a “preview” of the conversion. This dict will have the same schema as the “Mapping File Schema” but may have flat versions of its fields. UNDER CONSTRUCTION

Returns

  • mapping (dict) – The mapping obtained from applying the rules to the given file

  • preview (bool|dict) – If preview = False, then False. If True, then the preview dictionary.

sovabids.rules.apply_rules(source_path, bids_path, rules, mapping_path='')[source]#

Apply rules to a set of files.

Parameters
  • source_path (str | list of str) – If str, the path with the files we want to convert to bids. If list of str with the paths of the files we want to convert (ie the output of get_files).

  • bids_path (str) – The path we want the converted files in.

  • rules (str|dict) – The path to the rules file, or a dictionary with the rules.

  • mapping_path (str, optional) – The fullpath where we want to write the mappings file. If ‘’, then bids_path/code/sovabids/mappings.yml will be used.

Returns

A dictionary following: {

‘General’: rules given, ‘Individual’:list of mapping dictionaries for each file

}

Return type

dict

sovabids.rules.sovapply()[source]#

Console script usage for applying rules.