API Reference

bids.layout: Querying BIDS datasets

bids.layout

bids.layout.BIDSLayout([root, validate, ...])

Layout class representing an entire BIDS dataset.

bids.layout.BIDSValidator([index_associated])

Object for BIDS (Brain Imaging Data Structure) verification.

bids.layout.BIDSFile(filename)

Represents a single file or directory in a BIDS dataset.

bids.layout.BIDSDataFile(filename)

Represents a single data file in a BIDS dataset.

bids.layout.BIDSJSONFile(filename)

Represents a single JSON metadata file in a BIDS dataset.

bids.layout.Config(name[, entities, ...])

Container for BIDS configuration information.

bids.layout.Entity(name[, pattern, ...])

Represents a single entity defined in the JSON config.

bids.layout.Tag(file, entity, value[, dtype])

Represents an association between a File and an Entity.

bids.layout.parse_file_entities(filename[, ...])

Parse the passed filename for entity/value pairs.

bids.layout.add_config_paths(**kwargs)

Add to the pool of available configuration files for BIDSLayout.

bids.layout.index.BIDSLayoutIndexer([...])

Indexer class for BIDSLayout.

bids.layout.writing

Contains helper functions that involve writing operations.

bids.analysis: Model specification for BIDS datasets

bids.reports: Data acquisition report generation

bids.reports

bids.reports.BIDSReport(layout[, config])

Generates publication-quality data acquisition methods section from BIDS dataset.

bids.reports.utils

Generate publication-quality data acquisition methods section from BIDS dataset.

bids.variables: Variables

bids.config: PyBIDS Configuration utilities

bids.config

Utilities for manipulating package-level settings.

bids.config.set_option(key, value)

Set a package-wide option.

bids.config.set_options(**kwargs)

Set multiple package-wide options.

bids.config.get_option(key)

Retrieve the current value of a package-wide option.

bids.config.from_file(filenames[, ...])

Load package-wide settings from specified file(s).

bids.config.reset_options([update_from_file])

Reset all options to the package defaults.

bids.utils: Utility functions

bids.utils

Utility functions.

bids.utils.listify(obj)

Wraps all non-list or tuple objects in a list; provides a simple way to accept flexible arguments.

bids.utils.matches_entities(obj, entities[, ...])

Checks whether an object's entities match the input.

bids.utils.convert_JSON(j)

Recursively convert CamelCase keys to snake_case.

bids.utils.make_bidsfile(filename)

Create a BIDSFile instance of the appropriate class.