fishdist.automated_analysis_pipeline

get_channel_indices()

Prompt the user for channel indices with default values.

get_valid_folder(prompt)

Prompt the user for a folder path and validate it exists.

load_config(config_path)

Load configuration from a JSON file.

merge_args_with_config(args)

Merge command line arguments with configuration file settings.

move_to_DONE_when_DONE(lst, add_extras=False)

Move a list of files (and optionally associated extra files) into a 'DONE' subdirectory.

Parameters:
  • lst (list of str) –

    List of file paths to move.

  • add_extras (bool, default=False, default: False ) –

    If True, also move additional files in the same parent directory with extensions .png, .npy, or .pdf.
Returns:
  • None –

    Files are moved to a 'DONE' folder; the function does not return a value.
Example 
move_to_DONE_when_DONE(['/path/to/file1.txt', '/path/to/file2.txt'], add_extras=True)

parse_arguments()

Parse command line arguments with all required options.

print_folder_logic_with_values()

Prints the folder structure and workflow logic with actual values.

validate_paths(args)

Validate and set up the paths based on user input.