nipoppy.config.main.Config

class nipoppy.config.main.Config(/, **data)

Schema for dataset configuration.

Parameters:

data (Any)

apply_substitutions_to_json(json_obj)

Apply substitutions to a JSON object.

Parameters:

json_obj (dict | list)

Return type:

dict | list

classmethod check_input(data)

Validate the raw input.

Specifically: - If session_ids is not given, set to be the same as visit_ids

Parameters:

data (Any)

classmethod load(path, apply_substitutions=True)

Load a dataset configuration from a file.

Parameters:

path (nipoppy.env.StrOrPathLike)

Return type:

typing_extensions.Self

propagate_container_config()

Propagate the container config to all pipelines.

Return type:

typing_extensions.Self

save(fpath, **kwargs)

Save the config to a JSON file.

Parameters:

fpath (nipoppy.env.StrOrPathLike) – Path to the JSON file to write

validate_and_process()

Validate and process the configuration.

Return type:

typing_extensions.Self

BIDS_PIPELINES: list[nipoppy.config.pipeline.BidsPipelineConfig] = None

CUSTOM: dict = None

DATASET_NAME: str = None

DICOM_DIR_MAP_FILE: pathlib.Path | None = None

DICOM_DIR_PARTICIPANT_FIRST: bool | None = None

EXTRACTION_PIPELINES: list[nipoppy.config.pipeline.ExtractionPipelineConfig] = None

PROC_PIPELINES: list[nipoppy.config.pipeline.ProcPipelineConfig] = None

SESSION_IDS: list[str] | None = None

SUBSTITUTIONS: dict[str, str] = None

VISIT_IDS: list[str] = None

model_config

Configuration for the model, should be a dictionary conforming to [ConfigDict][pydantic.config.ConfigDict].