bids.analysis.analysis.Step¶
-
class
Step
(layout, level, index, name=None, transformations=None, model=None, contrasts=None, inputs=None, dummy_contrasts=False)[source]¶ Represents a single analysis step from a BIDS-Model specification.
- Parameters
layout (
bids.layout.BIDSLayout
) – The BIDSLayout containing all project files.level (str) – The BIDS keyword to use as the grouping variable; must be one of [‘run’, ‘session’, ‘subject’, or ‘dataset’].
index (int) – The numerical index of the current Step within the sequence of steps.
name (str) – Optional name to assign to the step. Must be specified in order to enable name-based indexing in the parent Analysis.
transformations (list) – List of BIDS-Model transformations to apply.
model (dict) – The ‘model’ part of the BIDS-StatsModels specification.
contrasts (list) – List of contrasts to apply to the parameter estimates generated when the model is fit.
inputs (list) – Optional list of BIDSVariableCollections to use as input to this Step (typically, the outputs from the preceding Step).
dummy_contrasts (dict) – Optional dictionary specifying which conditions to create indicator contrasts for. Dictionary must include a “type” key (‘t’ or ‘FEMA’), and optionally a subset of “conditions”. This parameter is over-written by the setting in setup() if the latter is passed.
Methods
add_collections
([drop_na])Add BIDSVariableCollections (i.e., predictors) to the current Step.
get_collections
(**filters)Returns BIDSVariableCollections at the current Step.
get_contrasts
(collection[, names, variables])Return contrast information at this step for the passed collection.
get_model_spec
(collection[, sampling_rate])Get a ModelSpec instance for the passed collection.
setup
([inputs])Set up the Step.
-
__init__
(layout, level, index, name=None, transformations=None, model=None, contrasts=None, inputs=None, dummy_contrasts=False)[source]¶ Initialize self. See help(type(self)) for accurate signature.
Methods
__init__
(layout, level, index[, name, …])Initialize self.
add_collections
([drop_na])Add BIDSVariableCollections (i.e., predictors) to the current Step.
get_collections
(**filters)Returns BIDSVariableCollections at the current Step.
get_contrasts
(collection[, names, variables])Return contrast information at this step for the passed collection.
get_model_spec
(collection[, sampling_rate])Get a ModelSpec instance for the passed collection.
setup
([inputs])Set up the Step.