topostats.processing#

Functions for procesing data.

Attributes#

LOGGER

Functions#

process_scan(→ None)

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

check_run_steps(→ None)

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

completion_message(→ None)

Print a completion message summarising images processed.

Module Contents#

topostats.processing.LOGGER#
topostats.processing.process_scan(img_path_px2nm: Dict[str, numpy.ndarray | pathlib.Path | float], base_dir: str | pathlib.Path, filter_config: dict, grains_config: dict, grainstats_config: dict, dnatracing_config: dict, plotting_config: dict, output_dir: str | pathlib.Path = 'output') → None#

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

Parameters:

  • img_path_px2nm (Dict[str, Union[np.ndarray, Path, float]]) – 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.

  • base_dir (Union[str, Path]) – Directory to recursively search for files, if not specified the current directory is scanned.

  • filter_config (dict) – Dictionary of configuration options for running the Filter stage.

  • grains_config (dict) – Dictionary of configuration options for running the Grain detection stage.

  • grainstats_config (dict) – Dictionary of configuration options for running the Grain Statistics stage.

  • dnatracing_config (dict) – Dictionary of configuration options for running the DNA Tracing stage.

  • plotting_config (dict) – Dictionary of configuration options for plotting figures.

  • output_dir (Union[str, Path]) – 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.

topostats.processing.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.

Parameters:

  • filter_run (bool) – Flag for running Filtering.

  • grains_run (bool) – Flag for running Grains.

  • grainstats_run (bool) – Flag for running GrainStats.

  • dnatracing_run (bool) – Flag for running DNA Tracing.

Return type:

None

topostats.processing.completion_message(config: Dict, img_files: List, summary_config: Dict, images_processed: int) → None#

Print a completion message summarising images processed.

Parameters:

  • config (dict) – Configuration dictionary.

  • img_files (list()) – List of found image paths.

  • summary_config (dict() – Configuration for plotting summary statistics.

  • images_processed (int) – Pandas DataFrame of results.

  • Results

  • -------

  • None