topostats.run_topostats#
Run TopoStats
This provides an entry point for running TopoStats as a command line programme.
Attributes#
Functions#
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Create a parser for reading options. |
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Process a single image, filtering, finding grains and calculating their statistics. |
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Run processing. |
Module Contents#
- topostats.run_topostats.LOGGER#
- topostats.run_topostats.create_parser() argparse.ArgumentParser#
Create a parser for reading options.
- topostats.run_topostats.process_scan(image_path: str | pathlib.Path, base_dir: str | pathlib.Path, loading_config: dict, filter_config: dict, grains_config: dict, grainstats_config: dict, dnatracing_config: dict, plotting_config: dict, output_dir: str | pathlib.Path = 'output') None[source]#
Process a single image, filtering, finding grains and calculating their statistics.
- Parameters:
image_path (Union[str, Path]) – Path to image to process.
base_dir (Union[str, Path]) – Directory to recursively search for files, if not specified the current directory is scanned.
loading_config (dict) – Dictionary of configuration options for running the Load Scan stage.
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.run_topostats.main()#
Run processing.