topostats.run_topostats
=======================

.. py:module:: topostats.run_topostats

.. autoapi-nested-parse::

   Run TopoStats

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

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Attributes
----------

.. autoapisummary::

   topostats.run_topostats.LOGGER


Functions
---------

.. autoapisummary::

   topostats.run_topostats.create_parser
   topostats.run_topostats.process_scan
   topostats.run_topostats.main


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

.. py:data:: LOGGER

.. py:function:: create_parser() -> argparse.ArgumentParser

   
   Create a parser for reading options.
















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.. py:function:: process_scan(image_path: Union[str, pathlib.Path], base_dir: Union[str, pathlib.Path], loading_config: dict, filter_config: dict, grains_config: dict, grainstats_config: dict, dnatracing_config: dict, plotting_config: dict, output_dir: Union[str, pathlib.Path] = 'output') -> None

   
   Process a single image, filtering, finding grains and calculating their statistics.

   :param image_path: Path to image to process.
   :type image_path: Union[str, Path]
   :param base_dir: Directory to recursively search for files, if not specified the current directory is scanned.
   :type base_dir: Union[str, Path]
   :param loading_config: Dictionary of configuration options for running the Load Scan stage.
   :type loading_config: dict
   :param filter_config: Dictionary of configuration options for running the Filter stage.
   :type filter_config: dict
   :param grains_config: Dictionary of configuration options for running the Grain detection stage.
   :type grains_config: dict
   :param grainstats_config: Dictionary of configuration options for running the Grain Statistics stage.
   :type grainstats_config: dict
   :param dnatracing_config: Dictionary of configuration options for running the DNA Tracing stage.
   :type dnatracing_config: dict
   :param plotting_config: Dictionary of configuration options for plotting figures.
   :type plotting_config: dict
   :param output_dir: Directory to save output to, it will be created if it does not exist. If it already exists then it is possible
                      that output will be over-written.
   :type output_dir: Union[str, Path]















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.. py:function:: main()

   
   Run processing.
















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