topostats.config#

Functions and tools for working with configuration files.

Attributes#

MutableMappingType

LOGGER

Functions#

reconcile_config_args(→ dict)

Reconcile command line arguments with the default configuration.

update_module() → None)

Update the args.module argument if processing TopoStats objects.

merge_mappings(→ MutableMappingType)

Merge two mappings (dictionaries), with priority given to the second mapping.

write_config_with_comments(→ None)

Write a sample configuration with in-line comments.

update_config(→ dict)

Update the configuration with any arguments.

update_plotting_config(→ dict)

Update the plotting config for each of the plots in plot_dict.

Module Contents#

topostats.config.MutableMappingType#
topostats.config.LOGGER#
topostats.config.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 (Namespace) – Command line arguments passed into TopoStats.

Returns:

The configuration dictionary.

Return type:

dict

topostats.config.update_module(args: argparse.Namespace, topostats_modules: tuple = ('bruker-rename', 'curvature', 'disordered_tracing', 'filter', 'grains', 'grainstats', 'nodestats', 'ordered_tracing', 'process', 'splining')) → None[source]#

Update the args.module argument if processing TopoStats objects.

This function allows the sub-parser command to map to the pipeline we wish to use. For now TopoStats has sub-parsers but it is the intention to introduce sub-sub-parsers for other modules such that eventually we invoke topostats` with a module argument followed by the step of processing.

>>> topostats topostats filter
>>> topostats topostats process
>>> topostats afmslicer slice
>>> topostats afmslicer process
>>> topostats perovstats process
Parameters:

  • args (Namespace) – Default arguments that need parsing and updating.

  • topostats_modules (tuple) – List of module names that are unique to TopoStats.

topostats.config.merge_mappings(map1: MutableMappingType, map2: MutableMappingType) → MutableMappingType[source]#

Merge two mappings (dictionaries), with priority given to the second mapping.

Note: Using a Mapping should make this robust to any mapping type, not just dictionaries. MutableMapping was needed as Mapping is not a mutable type, and this function needs to be able to change the dictionaries.

Parameters:

  • map1 (MutableMapping) – First mapping to merge, with secondary priority.

  • map2 (MutableMapping) – Second mapping to merge, with primary priority.

Returns:

Merged dictionary.

Return type:

dict

topostats.config.write_config_with_comments(args: argparse.Namespace = None) → None[source]#

Write a sample configuration with in-line comments.

This function is not designed to be used interactively but can be, just call it without any arguments and it will write a configuration to ‘./config.yaml’.

Parameters:

args (Namespace) – A Namespace object parsed from argparse with values for ‘filename’.

topostats.config.update_config(config: dict, args: dict | argparse.Namespace) → dict[source]#

Update the configuration with any arguments.

Parameters:

  • config (dict) – Dictionary of configuration (typically read from YAML file specified with ‘-c/–config <filename>’).

  • args (Namespace) – Command line arguments.

Returns:

Dictionary updated with command arguments.

Return type:

dict

topostats.config.update_plotting_config(plotting_config: dict) → dict[source]#

Update the plotting config for each of the plots in plot_dict.

Ensures that each entry has all the plotting configuration values that are needed.

Parameters:

plotting_config (dict) – Plotting configuration to be updated.

Returns:

Updated plotting configuration.

Return type:

dict