BidsFileDictionary¶
- class BidsFileDictionary(collection_name, files, entities=('sub', 'ses', 'task', 'run'))[source]
A dictionary of BidsFile keyed by entity pairs.
The keys are simplified entity key-value pairs and the values are BidsFile objects.
Methods
Attributes
|
Dictionary of keys and paths. |
|
Paths of the files in the list. |
|
The dictionary keys. |
Name of this dictionary |
- BidsFileDictionary.__init__(collection_name, files, entities=('sub', 'ses', 'task', 'run'))[source]¶
Create the dictionary keyed to entities.
- Parameters:
collection_name (str) – Name of this collection.
files (list or dict) – Full paths of files to include.
entities (tuple) – Entity names to use in creating the keys.
- Raises:
If files has inappropriate values.
Notes
This function is used for cross listing BIDS style files for different studies.
Examples
If entities is (‘sub’, ‘ses’, ‘task’, ‘run’), a typical key might be sub-001_ses-01_task-memory_run-01.
- BidsFileDictionary.create_file_dict(file_list, key_indices, separator)¶
Create new dict based on key indices.
- Parameters:
file_list (list) – Paths of the files to include.
key_indices (tuple) – A tuple of integers representing order of entities for key.
separator (str) – The separator used between entities to form the key.
- BidsFileDictionary.get_file_path(key)[source]¶
Return the file path corresponding to key.
- Parameters:
key (str) – The key to use to look up the file in this dictionary.
- Returns:
The real path of the file being looked up.
- Return type:
str
Notes
None is returned if the key is not present.
- BidsFileDictionary.get_new_dict(name, files)[source]¶
Create a dictionary with these files.
- Parameters:
name (str) – Name of this dictionary
files (list or dict) – List or dictionary of files. These could be paths or objects.
- Returns:
The newly created dictionary.
- Return type:
BidsFileDictionary
Notes
The new dictionary uses the same type of entities for keys as this dictionary.
- BidsFileDictionary.iter_files()[source]¶
Iterator over the files in this dictionary.
- Yields:
tuple – - str: The next entity-based key. - BidsFile: The next BidsFile.
- BidsFileDictionary.key_diffs(other_dict)[source]¶
Return the symmetric key difference with other.
- Parameters:
other_dict (FileDictionary) –
- Returns:
The symmetric difference of the keys in this dictionary and the other one.
- Return type:
list
- BidsFileDictionary.make_dict(files, entities)[source]¶
Make a dictionary from files or a dict.
- Parameters:
files (list or dict) – List or dictionary of file-like objs to use.
entities (tuple) – Tuple of entity names to use as keys, e.g. (‘sub’, ‘run’).
- Returns:
A dictionary whose keys are entity keys and values are BidsFile objects.
- Return type:
dict
- Raises:
If incorrect format is passed or something not recognizable as a Bids file.
- static BidsFileDictionary.make_file_dict(file_list, key_indices=(0, 2), separator='_')¶
Return a dictionary of files using entity keys.
- Parameters:
file_list (list) – Paths to files to use.
key_indices (tuple) – Positions of entities to use for key.
separator (str) – Separator character used to construct key.
- Returns:
Key is based on key indices and value is a full path.
- Return type:
dict
- static BidsFileDictionary.make_key(key_string, indices=(0, 2), separator='_')¶
Create a key from specified entities.
- Parameters:
key_string (str) – The string from which to extract the key (usually a filename or path).
indices (tuple) – Positions of entity pairs to use as key.
separator (str) – Separator between entity pairs in the created key.
- Returns:
The created key.
- Return type:
str
- BidsFileDictionary.make_query(query_dict={'sub': '*'})[source]¶
Return a dictionary of files matching query.
- Parameters:
query_dict (dict) – A dictionary whose keys are entities and whose values are entity values to match.
- Returns:
A dictionary entries in this dictionary that match the query.
- Return type:
dict
Notes
A query dictionary key a valid BIDS entity name such as sub or task.
A query dictionary value may be a string or a list.
A query value string should contain a specific value of the entity or a ‘*’ indicating any value matches.
A query value list should be a list of valid values for the corresponding entity.
- static BidsFileDictionary.match_query(query_dict, entity_dict)[source]¶
Return True if query has a match in dictionary.
- Parameters:
query_dict (dict) – A dictionary representing a query about entities.
entity_dict (dict) – A dictionary containing the entity representation for a BIDS file.
- Returns:
True if the query matches the entities representing the file.
- Return type:
bool
Notes
A query is a dictionary whose keys are entity names and whose values are specific entity values or ‘*’.
Examples
{‘sub’, ‘001’, ‘run’, ‘*’} requests all runs from subject 001.
- BidsFileDictionary.output_files(title=None, logger=None)¶
Return a string with the output of the list.
- Parameters:
title (None, str) – Optional title.
logger (HedLogger) – Optional HED logger for recording.
- Returns:
The dictionary in string form.
- Return type:
str
Notes
The logger is updated if available.
- BidsFileDictionary.split_by_entity(entity)[source]¶
Split this dictionary based on an entity.
- Parameters:
entity (str) – Entity name (for example task).
- Returns:
dict: A dictionary unique values of entity as keys and BidsFileDictionary objs as values.
dict: A BidsFileDictionary containing the files that don’t have entity in their names.
- Return type:
tuple
Notes
This function is used for analysis where a single subject or single type of task is being analyzed.
- BidsFileDictionary.file_dict¶
Dictionary of keys and paths.
- BidsFileDictionary.file_list¶
Paths of the files in the list.
- BidsFileDictionary.key_list¶
The dictionary keys.
- BidsFileDictionary.name¶
Name of this dictionary