neurocarto.config

python -m neurocarto -h

usage: neurocarto [-h] [-C PATH] [-P NAME] [--selector MODULE:NAME] [--atlas NAME]
                  [--atlas-root PATH] [--config-file FILE] [--view MODULE:NAME]
                  [--server-address URL] [--server-port PORT] [--no-open-browser]
                  [FILE]

positional arguments:
  FILE                  open channelmap file.

options:
  -h, --help            show this help message and exit

Source:
  -C PATH, --chmap-dir PATH
                        channel saving directory

Probe:
  -P NAME, --probe NAME
                        use probe family. default use "npx" (Neuropixels probe family).
  --selector MODULE:NAME
                        use which electrode selection method

Atlas:
  --atlas NAME          atlas mouse brain name
  --atlas-root PATH     atlas mouse brain download path

Bokeh Application:
  --config-file FILE    global config file.
  --view MODULE:NAME    install extra views in right panel
  --server-address URL
  --server-port PORT
  --no-open-browser     do not open browser when server starts

class neurocarto.config.CartoConfig

Startup (command-line) configuration for CartoApp.

chmap_root: Path | None = None

probe_family: str = 'npx'

selector: str | None = None

atlas_name: int | str = 25

atlas_root: Path | None = None

config_file: Path | None = None

extra_view: list[str]

server_address: str | None = None

server_port: int | None = None

no_open_browser: bool = False

debug: bool = False

open_file: str | None = None

__init__(chmap_root=None, probe_family='npx', selector=None, atlas_name=25, atlas_root=None, config_file=None, extra_view=<factory>, server_address=None, server_port=None, no_open_browser=False, debug=False, open_file=None)

Parameters:

• chmap_root (Path | None)

• probe_family (str)

• selector (str | None)

• atlas_name (int | str)

• atlas_root (Path | None)

• config_file (Path | None)

• extra_view (list[str])

• server_address (str | None)

• server_port (int | None)

• no_open_browser (bool)

• debug (bool)

• open_file (str | None)

Return type:

None

neurocarto.config.new_parser()

Create a cli parse for CartoConfig.

Return type:

ArgumentParser

neurocarto.config.parse_cli(args=None)

Parse command-line arguments and return result.

Parameters:

args (list[str] | None) – command-line arguments list. use sys.argv if None.

Returns:

Return type:

CartoConfig

neurocarto.config.setup_logger(config)

setup logger

Parameters:

config (CartoConfig)