clinicaio.path

clinicaio.path#

Path functions and classes.

Attributes#

`LOGGER`
`KEY_DELIMITER`
`COMPONENT_DELIMITER`
`PathArg`

Classes#

BIDSPath

BIDS path with parsed metadata.

Functions#

`get_path`(path)	Get the underlying Path object from a PathArg.
`check_name`(name)	Check entity and suffix names for invalid characters. This is used for keys

Module Contents#

clinicaio.path.LOGGER#

clinicaio.path.KEY_DELIMITER = '-'#

clinicaio.path.COMPONENT_DELIMITER = '_'#

clinicaio.path.get_path(path: PathArg)#: Get the underlying Path object from a PathArg.

clinicaio.path.check_name(name)#

Check entity and suffix names for invalid characters. This is used for keys and suffixes.

Raises:

ValueError:: The name is invalid.

class clinicaio.path.BIDSPath#

BIDS path with parsed metadata.

extensions: List[str]#

entities: collections.OrderedDict[str, str | int]#

suffix: str | None = None#

parent: BIDSDirectory | pathlib.Path | None = None#

__post_init__()#: Validate that the data is BIDS-compliant.

asdict()#

Get the dict of attributes for this dataclass.

Returns:: The shallow copy of dict of attributes that can be used to instantiate a new instance via unpacking.

property prime_entity#: The first entity in this path, or None if this path has no entities.

property path#: The pathlib.Path object for this BIDSPath.

check()#: Check for errors in this path. Override this in subclasses to add specific logic for that subclass, such as checking entity values in names or that required files exist in a directory. The method should raise BIDSPathError or a subclass thereof if the check fails.

__str__()#

__repr__()#

classmethod from_path(path: PathArg, parent: BIDSDirectory | None = None, is_root: bool = False)#

Create an instance of this class from a path and parent.

Args:

path:: The path.
parent:: An optional BIDSDirectory subclass to return when the parent directory is requested.
is_root:: If True, treat path as the root directory of a dataset and skip entity checking. The filename’s stem will be set to the suffix.

Returns:

An instance of this class.

classmethod from_bids_path(bids_path: BIDSPath)#

Create an instance of this class from another BIDSPath instance or subclass thereof.

Args:

bids_path:: The BIDSPath instance.

Returns:

An instance of this class. If the input argument is already a direct instance of this class then it will be returned unchanged. Otherwise a new instance of this class will be created with shallow copies of the attributes in the input path.

classmethod get_entities_and_suffix(path: pathlib.Path)#

Parse the entities and suffix from a path.

Args:

path:: The pathlib.Path object to parse.

Returns:

The OrderedDict of entities and the suffix.

get_entity_value(entity: clinicaio.entities.EntityArg)#

Get the value of an entity if it exits.

Args:

entity:: The entity name.

Returns:

The entity value as a string if present, else None.

has_entity(entity: clinicaio.entities.EntityArg)#

Check if this path contains the given entity.

Args:

entity:: The entity to check.

Returns:

True if this path contains the entity, else False.

matches_entity_value(entity: clinicaio.entities.EntityArg, value: clinicaio.entities.EntityValue)#

Check if this path matches the given entity value. If the value to match is an integer, the internal value will be converted to an integer before matching.

Args:

entity:: The entity to match.
value:: The value to match.

Returns:

True if the values match, else False. Missing entities will also return False.

is_dir()#: True if this path is a directory, else False.

resolve()#: Resolve the path (equivalent to pathlib.Path.resolve()).

maybe_convert_child(bids_path: BIDSPath)#

Optionally convert a child BIDSPath instance to a different BIDSPath type. This function is invoked by the __div__ operator and can be overridden in subclasses to customize child paths by e.g. entity.

When cnoverting types, it is recommended to invoke the from_bids_path() method of the target class with the given bids_path argument.

Args:

bids_path:: The child BIDSPath instance.

Returns:

A child BIDSPath instance.

__div__(value: PathArg)#

Emulate Path’s division operator.

Args:

value:: The value to join to the path.

Returns:

The joined path as a BIDSPath or subclass thereof.

property depth#: The depth of this path within a dataset’s file hierarchy, or None if it is not part of one.

clinicaio.path.PathArg#