cellmap_flow.config.yaml

Reading a cellmap_flow yaml or blockwise YAML file.

load_config reads and checks the file’s top level, filling charge_group and queue from the dashboard’s saved settings (then the site’s default queues) when the file leaves them out, reading queue as a list (one queue, queue: gpu_h200, is a list of one) and data_path as pasted (portable/pasted.py: one copied from Neuroglancer without the format it names); the model entries under models are built by models.registry.build_models. Every problem is a ConfigError. resolve_data_path is the one rule for a model’s data_path and scale, used by every launcher. Every model’s input is resampled to its voxel size when the data has no level at it (cellmap_flow yaml passes --resample to each server; blockwise opens the raw with io.raw.open_raw(..., resample=True)) unless the YAML says resample: false.

Attributes

logger

Exceptions

ConfigError

The YAML configuration is not usable; the message says why.

Functions

resolve_data_path(data_path, scale) → str	The dataset a model reads: data_path, with scale applied.
load_config(path) → Dict[str, Any]	Load and validate the YAML configuration.

Module Contents

cellmap_flow.config.yaml.logger

exception cellmap_flow.config.yaml.ConfigError

The YAML configuration is not usable; the message says why.

Raised rather than calling sys.exit: this code also runs inside the dashboard (the blockwise precheck, a finetuned model’s base config), where SystemExit slips past except Exception and the request thread dies without sending a response. The CLIs catch it and exit non-zero.

cellmap_flow.config.yaml.resolve_data_path(data_path: str, scale: str | None) → str

The dataset a model reads: data_path, with scale applied.

The one rule every launcher uses (cellmap_flow infer, yaml and blockwise), so the same YAML reads the same data in each:

• data_path is an array: it is used as it is. A scale naming a different level is ignored, with a warning.

• otherwise (a multiscale group, or a path that cannot be inspected here, such as a URL): scale selects the level under it.

cellmap_flow.config.yaml.load_config(path: str) → Dict[str, Any]

Load and validate the YAML configuration.

Parameters:

path – Path to YAML configuration file: a str, bytes or os.PathLike. Anything else is refused, because open() takes an int as a file descriptor: it would read through whatever the process has open under that number, and then close it.

Returns:

Validated configuration dictionary

Raises:

ConfigError – path is not a path, or a required field is missing or malformed