nipoppy.layout.DatasetLayout

class nipoppy.layout.DatasetLayout(dpath_root, fpath_config=None)

File/directory structure for a specific dataset.

Parameters:

• dpath_root (nipoppy.env.StrOrPathLike)

• fpath_config (Optional[nipoppy.env.StrOrPathLike])

get_dpath_bids_db(pipeline_name, pipeline_version, participant_id=None, session_id=None)

Return the path to a pipeline’s BIDS database directory.

Parameters:

• pipeline_name (str)

• pipeline_version (str)

• participant_id (Optional[str])

• session_id (Optional[str])

Return type:

pathlib.Path

get_dpath_pipeline(pipeline_name, pipeline_version)

Return the path to a pipeline’s directory.

Parameters:

• pipeline_name (str)

• pipeline_version (str)

Return type:

pathlib.Path

get_dpath_pipeline_output(pipeline_name, pipeline_version)

Return the path to a pipeline’s output directory.

Note: This path is the same given a pipeline name and version (i.e. does not depend on participant or session).

Parameters:

• pipeline_name (str)

• pipeline_version (str)

Return type:

pathlib.Path

get_dpath_pipeline_work(pipeline_name, pipeline_version, participant_id=None, session_id=None)

Return the path to a pipeline’s working directory.

Parameters:

• pipeline_name (str)

• pipeline_version (str)

• participant_id (Optional[str])

• session_id (Optional[str])

Return type:

pathlib.Path

get_full_path(path)

Build a full path from a relative path.

Parameters:

path (nipoppy.env.StrOrPathLike)

Return type:

pathlib.Path

get_paths(directory=True, include_optional=False)

Return a list of all directory or file paths.

Return type:

list[pathlib.Path]

validate()

Validate that all the expected paths exist.

Return type:

bool

config

dname_pipeline_output = 'output'

dname_pipeline_work = 'work'

dpath_assessments: pathlib.Path

dpath_bids: pathlib.Path

dpath_bids_db: pathlib.Path

dpath_bids_ignore_patterns: pathlib.Path

dpath_containers: pathlib.Path

dpath_demographics: pathlib.Path

dpath_derivatives: pathlib.Path

property dpath_descriptions: list[Tuple[pathlib.Path, str]]

Return a list of directory paths and associated description strings.

Return type:

list[Tuple[pathlib.Path, str]]

dpath_descriptors: pathlib.Path

dpath_downloads: pathlib.Path

dpath_invocations: pathlib.Path

dpath_logs: pathlib.Path

dpath_proc: pathlib.Path

dpath_pybids: pathlib.Path

dpath_raw_imaging: pathlib.Path

dpath_releases: pathlib.Path

dpath_root

dpath_scratch: pathlib.Path

dpath_sourcedata: pathlib.Path

dpath_tabular: pathlib.Path

dpath_tracker_configs: pathlib.Path

property dpaths: list[pathlib.Path]

Return a list of all required directory paths.

Return type:

list[pathlib.Path]

fpath_config: pathlib.Path

fpath_doughnut: pathlib.Path

fpath_imaging_bagel: pathlib.Path

fpath_manifest: pathlib.Path

fpath_spec

property fpaths: list[pathlib.Path]

Return a list of all required file paths.

Return type:

list[pathlib.Path]