nipoppy.layout

Dataset layout.

Module Contents

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

Bases: nipoppy.base.Base

File/directory structure for a specific dataset.

Parameters:

• dpath_root (nipoppy.env.StrOrPathLike)

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

dpath_descriptions()

Return a list of directory paths and associated description strings.

Return type:

list[Tuple[pathlib.Path, str]]

dpaths()

Return a list of all required directory paths.

Return type:

list[pathlib.Path]

fpaths()

Return a list of all required file paths.

Return type:

list[pathlib.Path]

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

class nipoppy.layout.DpathInfo(/, **data)

Bases: PathInfo

Relative path and description for a directory.

Parameters:

data (Any)

class nipoppy.layout.FpathInfo(/, **data)

Bases: PathInfo

Relative path and description for a file.

Parameters:

data (Any)

class nipoppy.layout.LayoutConfig(/, **data)

Bases: pydantic.BaseModel

Relative paths for the dataset layout.

Parameters:

data (Any)

dpath_assessments: DpathInfo

dpath_bids: DpathInfo

dpath_bids_db: DpathInfo

dpath_bids_ignore_patterns: DpathInfo

dpath_containers: DpathInfo

dpath_demographics: DpathInfo

dpath_derivatives: DpathInfo

dpath_descriptors: DpathInfo

dpath_downloads: DpathInfo

dpath_invocations: DpathInfo

dpath_logs: DpathInfo

dpath_proc: DpathInfo

dpath_pybids: DpathInfo

dpath_raw_imaging: DpathInfo

dpath_releases: DpathInfo

dpath_scratch: DpathInfo

dpath_sourcedata: DpathInfo

dpath_tabular: DpathInfo

dpath_tracker_configs: DpathInfo

fpath_config: FpathInfo

fpath_doughnut: OptionalFpathInfo

fpath_imaging_bagel: OptionalFpathInfo

fpath_manifest: FpathInfo

model_config

get_path_info(path_label)

Return the PathInfo object associated with the given path label.

Parameters:

path_label (str)

Return type:

PathInfo

path_infos()

Return a list of all PathInfo objects defined in the layout.

Return type:

list[PathInfo]

path_labels()

Return a list of all path labels defined in the layout.

Return type:

list[str]

class nipoppy.layout.OptionalFpathInfo(/, **data)

Bases: FpathInfo

Relative path and description for a file that is optional.

Parameters:

data (Any)

class nipoppy.layout.PathInfo(/, **data)

Bases: pydantic.BaseModel

Relative path and description for a directory or file.

Parameters:

data (Any)

description: str | None

path: pathlib.Path

nipoppy.layout.DEFAULT_LAYOUT_INFO