topostats.run_modules#

Run TopoStats modules.

This provides an entry point for running TopoStats as a command line programme.

Attributes#

LOGGER

Functions#

`reconcile_config_args`(→ dict)	Reconcile command line arguments with the default configuration.
`_set_logging`(→ None)	Set the logging level.
`_log_setup`(→ None)	Log the current configuration.
`_parse_configuration`(→ tuple[dict, dict])	Load configurations, validate and check run steps are consistent.
`process`(→ None)	Find and process all files.
`filters`(→ None)	Load files from disk and run filtering.
`grains`(→ None)	Load files from disk and run grain finding.
`grainstats`(→ None)	Load files from disk and run grainstats.
`disordered_tracing`(→ None)	Load files from disk and run grainstats.
`nodestats`(→ None)	Load files from disk and run grainstats.
`ordered_tracing`(→ None)	Load files from disk and run grainstats.
`splining`(→ None)	Load files from disk and run grainstats.

Module Contents#

topostats.run_modules.LOGGER#

topostats.run_modules.reconcile_config_args(args: argparse.Namespace | None) → dict[source]#

Reconcile command line arguments with the default configuration.

Command line arguments take precedence over the default configuration. If a partial configuration file is specified (with ‘-c’ or ‘–config-file’) the defaults are over-ridden by these values (internally the configuration dictionary is updated with these values). Any other command line arguments take precedence over both the default and those supplied in a configuration file (again the dictionary is updated).

The final configuration is validated before processing begins.

Parameters:: args (argparse.Namespace) – Command line arguments passed into TopoStats.
Returns:: The configuration dictionary.
Return type:: dict

topostats.run_modules._set_logging(log_level: str | None) → None[source]#

Set the logging level.

Parameters:: log_level (str) – String for the desired log-level.

topostats.run_modules._log_setup(config: dict, args: argparse.Namespace | None, img_files: dict) → None[source]#

Log the current configuration.

Parameters:

config (dict) – Dictionary of configuration options.
args (argparse.Namespace | None) – Arguments function was invoked with.
img_files (dict) – Dictionary of image files that have been found.

topostats.run_modules._parse_configuration(args: argparse.Namespace | None = None) → tuple[dict, dict][source]#

Load configurations, validate and check run steps are consistent.

Parameters:: args (None) – Arguments.
Returns:: Returns the dictionary of configuration options and a dictionary of image files found on the input path.
Return type:: tuple[dict, dict]

topostats.run_modules.process(args: argparse.Namespace | None = None) → None[source]#

Find and process all files.

Parameters:: args (None) – Arguments.

topostats.run_modules.filters(args: argparse.Namespace | None = None) → None[source]#

Load files from disk and run filtering.

Parameters:: args (None) – Arguments.

topostats.run_modules.grains(args: argparse.Namespace | None = None) → None[source]#

Load files from disk and run grain finding.

Parameters:: args (None) – Arguments.

topostats.run_modules.grainstats(args: argparse.Namespace | None = None) → None[source]#