bids.variables.entities

Classes

Node(level, entities) Base class for objects that represent a single object in the BIDS hierarchy.
NodeIndex() Represents the top level in a BIDS hierarchy.
RunInfo(entities, duration, tr, image)
Attributes:
RunNode(entities, image_file, duration, …) Represents a single Run in a BIDS project.
class Node(level, entities)[source]

Base class for objects that represent a single object in the BIDS hierarchy.

Parameters:id (int, str) – A value uniquely identifying this node. Typically the entity value extracted from the filename via layout.

Methods

add_variable(variable) Adds a BIDSVariable to the current Node’s list.
add_variable(variable)[source]

Adds a BIDSVariable to the current Node’s list.

Parameters:variable (BIDSVariable) – The Variable to add to the list.
class NodeIndex[source]

Represents the top level in a BIDS hierarchy.

Methods

add_variable(variable) Adds a BIDSVariable to the current Node’s list.
get_collections(unit[, names, merge, …]) Retrieve variable data for a specified level in the Dataset.
get_or_create_node(level, entities, *args, …) Retrieves a child Node based on the specified criteria, creating a new Node if necessary.
get_nodes  
add_variable(variable)

Adds a BIDSVariable to the current Node’s list.

Parameters:variable (BIDSVariable) – The Variable to add to the list.
get_collections(unit, names=None, merge=False, sampling_rate=None, **entities)[source]

Retrieve variable data for a specified level in the Dataset.

Parameters:
  • unit (str) – The unit of analysis to return variables for. Must be one of ‘run’, ‘session’, ‘subject’, or ‘dataset’.
  • names (list) – Optional list of variables names to return. If None, all available variables are returned.
  • merge (bool) – If True, variables are merged across all observations of the current unit. E.g., if unit=’subject’ and return_type= ‘collection’, variablesfrom all subjects will be merged into a single collection. If False, each observation is handled separately, and the result is returned as a list.
  • sampling_rate (int, str) – If unit=’run’, the sampling rate to pass onto the returned BIDSRunVariableCollection.
  • entities – Optional constraints used to limit what gets returned.

Returns:

get_or_create_node(level, entities, *args, **kwargs)[source]

Retrieves a child Node based on the specified criteria, creating a new Node if necessary.

Parameters:
  • entities (dict) – Dictionary of entities specifying which Node to return.
  • kwargs (args,) – Optional positional or named arguments to pass onto class-specific initializers. These arguments are only used if a Node that matches the passed entities doesn’t already exist, and a new one must be created.
Returns:

A Node instance.

class RunInfo(entities, duration, tr, image)
Attributes:
duration

Alias for field number 1

entities

Alias for field number 0

image

Alias for field number 3

tr

Alias for field number 2

Methods

count($self, value, /) Return number of occurrences of value.
index($self, value[, start, stop]) Return first index of value.
count($self, value, /)

Return number of occurrences of value.

duration

Alias for field number 1

entities

Alias for field number 0

image

Alias for field number 3

index($self, value, start=0, stop=sys.maxsize, /)

Return first index of value.

Raises ValueError if the value is not present.

tr

Alias for field number 2

class RunNode(entities, image_file, duration, repetition_time)[source]

Represents a single Run in a BIDS project.

Parameters:
  • id (int) – The index of the run.
  • entities (dict) – Dictionary of entities for this Node.
  • image_file (str) – The full path to the corresponding nifti image.
  • duration (float) – Duration of the run, in seconds.
  • repetition_time (float) – TR for the run.
  • task (str) – The task name for this run.

Methods

add_variable(variable) Adds a BIDSVariable to the current Node’s list.
get_info  
add_variable(variable)

Adds a BIDSVariable to the current Node’s list.

Parameters:variable (BIDSVariable) – The Variable to add to the list.