topostats.run_modules
=====================

.. py:module:: topostats.run_modules

.. autoapi-nested-parse::

   Run TopoStats modules.

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

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Attributes
----------

.. autoapisummary::

   topostats.run_modules.LOGGER


Functions
---------

.. autoapisummary::

   topostats.run_modules.reconcile_config_args
   topostats.run_modules._set_logging
   topostats.run_modules._log_setup
   topostats.run_modules._parse_configuration
   topostats.run_modules.process
   topostats.run_modules.filters
   topostats.run_modules.grains
   topostats.run_modules.grainstats
   topostats.run_modules.disordered_tracing
   topostats.run_modules.nodestats
   topostats.run_modules.ordered_tracing
   topostats.run_modules.splining


Module Contents
---------------

.. py:data:: LOGGER

.. py:function:: reconcile_config_args(args: argparse.Namespace | None) -> dict

   
   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.

   :param args: Command line arguments passed into TopoStats.
   :type args: argparse.Namespace

   :returns: The configuration dictionary.
   :rtype: dict















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.. py:function:: _set_logging(log_level: str | None) -> None

   
   Set the logging level.

   :param log_level: String for the desired log-level.
   :type log_level: str















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.. py:function:: _log_setup(config: dict, args: argparse.Namespace | None, img_files: dict) -> None

   
   Log the current configuration.

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















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.. py:function:: _parse_configuration(args: argparse.Namespace | None = None) -> tuple[dict, dict]

   
   Load configurations, validate and check run steps are consistent.

   :param args: Arguments.
   :type args: None

   :returns: Returns the dictionary of configuration options and a dictionary of image files found on the input path.
   :rtype: tuple[dict, dict]















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.. py:function:: process(args: argparse.Namespace | None = None) -> None

   
   Find and process all files.

   :param args: Arguments.
   :type args: None















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.. py:function:: filters(args: argparse.Namespace | None = None) -> None

   
   Load files from disk and run filtering.

   :param args: Arguments.
   :type args: None















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.. py:function:: grains(args: argparse.Namespace | None = None) -> None

   
   Load files from disk and run grain finding.

   :param args: Arguments.
   :type args: None















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.. py:function:: grainstats(args: argparse.Namespace | None = None) -> None

   
   Load files from disk and run grainstats.

   :param args: Arguments.
   :type args: None















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.. py:function:: disordered_tracing(args: argparse.Namespace | None = None) -> None

   
   Load files from disk and run grainstats.

   :param args: Arguments.
   :type args: None















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.. py:function:: nodestats(args: argparse.Namespace | None = None) -> None

   
   Load files from disk and run grainstats.

   :param args: Arguments.
   :type args: None















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.. py:function:: ordered_tracing(args: argparse.Namespace | None = None) -> None

   
   Load files from disk and run grainstats.

   :param args: Arguments.
   :type args: None















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.. py:function:: splining(args: argparse.Namespace | None = None) -> None

   
   Load files from disk and run grainstats.

   :param args: Arguments.
   :type args: None















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