topostats.processing
====================

.. py:module:: topostats.processing

.. autoapi-nested-parse::

   Functions for procesing data.

   ..
       !! processed by numpydoc !!


Attributes
----------

.. autoapisummary::

   topostats.processing.LOGGER


Functions
---------

.. autoapisummary::

   topostats.processing.process_scan
   topostats.processing.check_run_steps
   topostats.processing.completion_message


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

.. py:data:: LOGGER

.. py:function:: process_scan(img_path_px2nm: Dict[str, Union[numpy.ndarray, pathlib.Path, float]], base_dir: Union[str, pathlib.Path], 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 img_path_px2nm: A dictionary with keys 'image', 'img_path' and 'px_2_nm' containing a file or frames' image, it's path and it's pixel to namometre scaling value.
   :type img_path_px2nm: Dict[str, Union[np.ndarray, Path, float]]
   :param base_dir: Directory to recursively search for files, if not specified the current directory is scanned.
   :type base_dir: Union[str, Path]
   :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]















   ..
       !! processed by numpydoc !!

.. py:function:: check_run_steps(filter_run: bool, grains_run: bool, grainstats_run: bool, dnatracing_run: bool) -> None

   
   Check options for running steps (Filter, Grain, Grainstats and DNA tracing) are logically consistent.

   This checks that earlier steps required are enabled.

   :param filter_run: Flag for running Filtering.
   :type filter_run: bool
   :param grains_run: Flag for running Grains.
   :type grains_run: bool
   :param grainstats_run: Flag for running GrainStats.
   :type grainstats_run: bool
   :param dnatracing_run: Flag for running DNA Tracing.
   :type dnatracing_run: bool

   :rtype: None















   ..
       !! processed by numpydoc !!

.. py:function:: completion_message(config: Dict, img_files: List, summary_config: Dict, images_processed: int) -> None

   
   Print a completion message summarising images processed.

   :param config: Configuration dictionary.
   :type config: dict
   :param img_files: List of found image paths.
   :type img_files: list()
   :param summary_config: Configuration for plotting summary statistics.
   :type summary_config: dict(
   :param images_processed: Pandas DataFrame of results.
   :type images_processed: int
   :param Results:
   :param -------:
   :param None:















   ..
       !! processed by numpydoc !!