organoid_tracker.config package

Module contents

With this package, you can read the organoid_tracker.ini config files.

This will read from the config section called “my_script_name”: >>> config = ConfigFile(“my_script_name”)

This will read an organoid_tracker.ini file from a different folder: >>> config = ConfigFile(“my_script_name”, folder_name=r”C:path o older”)

This will read some settings, or provide default values for them if not found: >>> config.get_or_default(“example_string”, “My default value”, comment=”Some helpful comment”) >>> config.get_or_default(“example_int”, “4”, comment=”Only accepts integers”, type=config_type_int) >>> config.save() # Saves to disk

You can also define custom config types. For that, you need to create a function that takes a string and returns some object. >>> def config_type_complex_number(input: str) -> complex: >>> input = input.replace(” “, “”) # Strip spaces, so that you can write “5 + 3j” instead of “5+3j” >>> input = input.replacE(“i”, “j”) # Allow writing “5+2i” instead of just “5+2j” >>> return complex(input) >>> >>> config.get_or_default(“example_complex”, “8+2j”, comment=”Oooh, complex!”, type=config_type_complex_number)

class organoid_tracker.config.ConfigFile(section_name: str, *, folder_name: str = './')

Bases: object

Simple wrapper around ConfigParser

FILE_NAME = 'organoid_tracker.ini'

get_or_default(key: str, default_value: ~typing.Any, *, comment: str = '', store_in_defaults: bool = False, type: ~typing.Callable[[str], ~typing.Any] = <function config_type_str>) → Any

Gets a string from the config file for the given key. If no such string exists, the default value is stored in the config first. If store_in_defaults is True, then the default value is stored in the DEFAULTS section, otherwise the default value is stored in the section given to __init__.

The default value can be supplied as a string or as the actual type. If it is a string, it will be stored as-is, but ran through the type function before being returned. If it is not a string, it will be stored as str(default_value), and returned as-is.

get_or_prompt(key: str, question: str, store_in_defaults: bool = False, *, type: ~typing.Callable[[str], ~typing.Any] = <function config_type_str>) → Any: Gets a string from the config file for the given key. If no such string exists, the user is asked for a default value, which is then stored in the configuration file. If store_in_defaults is True, then the default value is stored in the DEFAULTS section, otherwise the default value is stored in the section given to __init__.

made_value_changes: bool = False

save() → bool: Saves the configuration file if there are any changes made. Returns True if the config file was saved, False if no save was necessary.

save_and_exit_if_changed(): If the configuration file was changed, the changes are stored an then the program is exited. This allows the user to see what changes were made, and then restart the program.

set(key: str, value: str, *, comment: str = '', store_in_defaults: bool = False): Sets a string in the config file. Stores in the default section of store_in_defaults is True. Otherwise, the setting is saved in the section specified in __init__.

organoid_tracker.config.config_type_bool(input: str) → bool

organoid_tracker.config.config_type_csv_file(input: str) → str: A string that will automatically have “.csv” appended to it if it hasn’t already (except for empty strings).

organoid_tracker.config.config_type_float(input: str) → float: Parses values as floats.

organoid_tracker.config.config_type_image_shape(input: str) → Tuple[int, int, int]: Parses a string like “512, 512, 32” as the tuple (32, 512, 512). Note the inversion of order.

organoid_tracker.config.config_type_int(input: str) → int: Parses values as integers.

organoid_tracker.config.config_type_json_file(input: str) → str: A string that will automatically have “.json” appended to it if it hasn’t already (except for empty strings).

organoid_tracker.config.config_type_str(input: str) → str: Default type of settings in a configuration file.