pyopia.cli

PyOPIA top-level code primarily for managing cmd line entry points

Functions

check_chunks(chunks, pipeline_config)
convert_raw_images(config_filename)	Convert raw images files to bitmap format (png).
docs()	Open browser at PyOPIA's readthedocs page
export_to_ecotaxa(stats_filename, ...[, ...])	EcoTaxa export: Create a zip file with particle images and statistics csv
generate_config(instrument, raw_files, ...)	Put an example config.toml file in the current directory
get_custom_progress_bar(description, disable)	Create a custom rich.progress.Progress object for displaying progress bars
init_project(project_name[, instrument, ...])	Initialize a PyOPIA processing project with a standard config file and folder layout
make_montage(stats_filename[, ...])	Create a montage of particles
merge_mfdata(path_to_data[, prefix, ...])	Combine a multi-file directory of STATS.nc files into a single '-STATS.nc' file that can then be loaded with {func}`pyopia.io.load_stats`
modify_config(existing_filename, ...[, ...])	Modify a existing config.toml file and write a new one to disc
process(config_filename[, num_chunks, strategy])	Run a PyOPIA processing pipeline based on given a config.toml
process_file_list(file_list, pipeline_config, c)	Run a PyOPIA processing pipeline for a chuncked list of files based on a given config.toml
process_realtime(config_filename[, watch_folder])	Run a PyOPIA processing pipeline in realtime by watching a folder.
setup_logging(pipeline_config)	Configure logging