nipoppy.config.pipeline_step

Pipeline step configuration.

Module Contents

class nipoppy.config.pipeline_step.AnalysisLevelType

Bases: str, enum.Enum

Pipeline step types.

group = 'group'

participant = 'participant'

participant_session = 'participant_session'

session = 'session'

class nipoppy.config.pipeline_step.BasePipelineStepConfig(/, **data)

Bases: nipoppy.config.container.SchemaWithContainerConfig, abc.ABC

Schema for processing pipeline step configuration.

Parameters:

data (Any)

ANALYSIS_LEVEL: AnalysisLevelType

DESCRIPTOR_FILE: pathlib.Path | None

INVOCATION_FILE: pathlib.Path | None

NAME: str | None

classmethod validate_before(data)

Validate the pipeline step configuration before instantiation.

Specifically: - Apply substitutions for step name in the config

Parameters:

data (Any)

Return type:

Any

class nipoppy.config.pipeline_step.BidsPipelineStepConfig(/, **data)

Bases: BasePipelineStepConfig

Schema for BIDS pipeline step configuration.

Parameters:

data (Any)

UPDATE_DOUGHNUT: bool | None

model_config

class nipoppy.config.pipeline_step.ProcPipelineStepConfig(/, **data)

Bases: BasePipelineStepConfig

Schema for processing pipeline step configuration.

Parameters:

data (Any)

PYBIDS_IGNORE_FILE: pathlib.Path | None

model_config