coord2region.config

Structured configuration handling for Coord2Region pipelines.

Classes

Coord2RegionConfig

Pydantic model capturing all CLI-facing configuration options.

Module Contents

class coord2region.config.Coord2RegionConfig(/, **data: Any)

Bases: pydantic.BaseModel

Pydantic model capturing all CLI-facing configuration options.

model_config

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

input_type: Literal['coords', 'region_names'] = 'coords'

inputs: list[Any] | None = None

coordinates: list[CoordinateTriple] | None = None

coordinates_file: str | None = None

region_names: list[str] | None = None

legacy_config: dict[str, Any] | None = None

outputs: list[Literal['region_labels', 'summaries', 'images', 'raw_studies', 'mni_coordinates']] = None

output_format: Literal['json', 'pickle', 'csv', 'pdf', 'directory'] | None = None

output_name: str | None = None

image_backend: Literal['ai', 'nilearn', 'both'] = 'ai'

batch_size: conint(ge=0) = 0

working_directory: str | None = None

email_for_abstracts: str | None = None

use_cached_dataset: bool = True

sources: list[str] | None = None

study_search_radius: confloat(ge=0) = 0.0

region_search_radius: confloat(ge=0) | None = None

atlas_names: list[str] | None = None

atlas_configs: dict[str, dict[str, Any]] = None

max_atlases: conint(gt=0) | None = None

image_model: str | None = None

image_prompt_type: str | None = None

image_custom_prompt: str | None = None

gemini_api_key: str | None = None

openrouter_api_key: str | None = None

openai_api_key: str | None = None

anthropic_api_key: str | None = None

huggingface_api_key: str | None = None

providers: dict[str, dict[str, Any]] = None

summary_models: list[str] | None = None

prompt_type: str | None = None

custom_prompt: str | None = None

summary_max_tokens: conint(gt=0) | None = None

collect_inputs(*, load_coords_file: Callable[[str], Sequence[Sequence[float]]]) → list[Any]

Resolve configured inputs into data consumable by the pipeline.

build_pipeline_config() → dict[str, Any]

Construct the keyword arguments passed to run_pipeline’s config.

to_pipeline_runtime(inputs: Sequence[Any]) → dict[str, Any]

Return arguments expected by coord2region.pipeline.run_pipeline().