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Increase the flexibility and modularity of the package. Implement bas…
…e classes (#35) Increase the flexibility and modularity of the package and reduce the need to manipulate collections of primitives. Provide the basis for being able to implement different types of plate and colony analysis (see #38). - Adds base classes to provide core functionality - Create a Plate class (and collection) to store information related to plates and hold a collection of Colony class instances - Create an ImageFile class (and collection) to store image file paths and timestamp information - Refactored most of the functions from `main` as static methods in the `plate` or `image_file` modules - Adds a command line argument, `plate_labels`, to allow labels to be attached to specific plates - Rename `save_plots` CLA to `plots` Closes #30 Closes #36
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,242 @@ | ||
| from typing import Type, TypeVar, Optional, List | ||
| from collections.abc import Collection | ||
| from datetime import datetime, timedelta | ||
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| class Identified: | ||
| """ | ||
| An object with a integer ID number | ||
| """ | ||
| def __init__(self, id: int): | ||
| self.id = id | ||
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| @property | ||
| def id(self) -> int: | ||
| return self.__id | ||
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| @id.setter | ||
| def id(self, val: int): | ||
| if self.__id_is_valid(val): | ||
| self.__id = val | ||
| else: | ||
| raise ValueError(f"'{val}' is not a valid id. An id must be a non-negative integer'") | ||
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| @staticmethod | ||
| def __id_exists(collection: Collection, id: int) -> bool: | ||
| """ | ||
| Verifies if an object in a collection matches the specified ID number | ||
| :param collection: a collection of objects (List, Dict etc) | ||
| :param id: an ID number to locate | ||
| :returns: True if an object with id exists in the collection | ||
| """ | ||
| return any(id == existing.id for existing in collection) | ||
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| @staticmethod | ||
| def __id_is_valid(id: int) -> bool: | ||
| """ | ||
| Verifies if a value conforms to the requirements for an ID number | ||
| An ID number is an integer with a value greater than zero | ||
| :param id: an ID number to verify | ||
| :returns: True if the value conforms to the requirements for an ID number | ||
| """ | ||
| return isinstance(id, int) and id > 0 | ||
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| class IdentifiedCollection: | ||
| """ | ||
| An collection of Identified objects with generic methods for modifying the collection | ||
| """ | ||
| T = TypeVar("T", bound = Identified) | ||
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| def __init__(self, items: Collection = None): | ||
| self.items = items | ||
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| @property | ||
| def count(self) -> int: | ||
| return len(self.items) | ||
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| @property | ||
| def items(self) -> List["T"]: | ||
| """ | ||
| Returns a sorted list of items from the collection | ||
| A copy is returned, preventing direct changes to the collection | ||
| """ | ||
| return sorted(self.__items, key = lambda item: item.id) | ||
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| @items.setter | ||
| def items(self, val: Collection): | ||
| if isinstance(val, dict): | ||
| val = list(val.values()) | ||
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| if val is None: | ||
| self.__items = list() | ||
| elif isinstance(val, Collection) and not isinstance(val, str): | ||
| self.__items = val.copy() | ||
| else: | ||
| raise ValueError(f"Items must be supplied as a valid Collection, not {type(val)}") | ||
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| def add(self, id: int) -> "T": | ||
| """ | ||
| Create a new instance of T and append it to the collection | ||
| :param id: a valid Identified ID number | ||
| :returns: a new instance of T | ||
| """ | ||
| item = Identified(id = id) | ||
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| self.append(item) | ||
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| return item | ||
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| def append(self, item: Type[T]): | ||
| """ | ||
| Append an item to the collection | ||
| :param item: the object to append to the collection | ||
| """ | ||
| if not self.exists(item): | ||
| self.__items.append(item) | ||
| else: | ||
| raise ValueError(f"An item with ID #{item.id} already exists") | ||
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| def exists(self, item: Type[T]) -> bool: | ||
| """ | ||
| Check if an item exists in the item collection | ||
| :param item: an instance of T | ||
| :returns: True if an item is found with matching ID | ||
| """ | ||
| return self.id_exists(item.id) | ||
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| def id_exists(self, id: int) -> bool: | ||
| """ | ||
| Check if an item with the specified ID number exists in the item collection | ||
| :param id: a valid Identified id number | ||
| :returns: True if an item is found with matching ID | ||
| """ | ||
| return Identified._Identified__id_exists(self.items, id) | ||
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| def get_item(self, id: int) -> Optional["T"]: | ||
| """ | ||
| Returns an item with the specified ID number from the item collection | ||
| :param id: a valid Identified ID number | ||
| :returns: an item from the collection, if found | ||
| """ | ||
| for item in self.items: | ||
| if item.id == id: | ||
| return item | ||
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| return None | ||
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| def remove(self, id: int): | ||
| """ | ||
| Remove an item from the collection | ||
| :param id: a valid Identified ID number | ||
| """ | ||
| if self.id_exists(id): | ||
| for item in self.items: | ||
| if item.id == id: | ||
| self.__items.remove(item) | ||
| else: | ||
| raise KeyError(f"No item with ID #{id} could be found") | ||
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| class Named: | ||
| """ | ||
| An object with a string identifier | ||
| """ | ||
| def __init__(self, name: str): | ||
| self.name = name | ||
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| @property | ||
| def name(self) -> str: | ||
| return self.__name | ||
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| @name.setter | ||
| def name(self, val: str): | ||
| self.__name = str(val) | ||
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| class Unique(Identified): | ||
| """ | ||
| An object with a auto incremented integer ID number | ||
| """ | ||
| id_count = 0 | ||
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| def __init__(self): | ||
| self._Identified__id = self.id_increment() | ||
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| @Identified.id.setter | ||
| def id(self, val: int): | ||
| """ | ||
| Overrides base method to make id read-only | ||
| """ | ||
| pass | ||
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| def id_increment(self) -> int: | ||
| """ | ||
| Increments the built-in ID counter | ||
| :returns: the auto incremented ID number | ||
| """ | ||
| Unique.id_count += 1 | ||
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| return Unique.id_count | ||
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| class TimeStamped: | ||
| def __init__(self, timestamp: datetime = None): | ||
| if timestamp is None: | ||
| timestamp = datetime.now() | ||
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| self.timestamp = timestamp | ||
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| @property | ||
| def timestamp(self) -> datetime: | ||
| return self.__timestamp | ||
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| @timestamp.setter | ||
| def timestamp(self, val: datetime): | ||
| self.__timestamp = val | ||
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| class TimeStampElapsed(TimeStamped): | ||
| def __init__(self, timestamp: datetime = None, timestamp_initial: datetime = None): | ||
| if timestamp is None: | ||
| timestamp = datetime.now() | ||
| if timestamp_initial is None: | ||
| timestamp_initial = timestamp | ||
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| self._TimeStamped__timestamp = timestamp | ||
| self.timestamp_initial = timestamp_initial | ||
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| @property | ||
| def timestamp_elapsed(self) -> timedelta: | ||
| return self.timestamp - self.timestamp_initial | ||
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| @property | ||
| def timestamp_elapsed_hours(self) -> float: | ||
| return (self.timestamp_elapsed_seconds / 60) / 60 | ||
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| @property | ||
| def timestamp_elapsed_minutes(self) -> int: | ||
| return int(self.timestamp_elapsed_seconds / 60) | ||
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| @property | ||
| def timestamp_elapsed_seconds(self) -> int: | ||
| return self.timestamp_elapsed.total_seconds() | ||
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| @property | ||
| def timestamp_initial(self) -> datetime: | ||
| return self.__timestamp_initial | ||
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| @timestamp_initial.setter | ||
| def timestamp_initial(self, val: datetime): | ||
| self.__timestamp_initial = val |
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