mirror of
https://github.com/dptech-corp/Uni-Lab-OS.git
synced 2025-12-17 21:11:12 +00:00
323 lines
11 KiB
Python
323 lines
11 KiB
Python
"""
|
|
自动化液体处理工作站物料类定义 - 简化版
|
|
Automated Liquid Handling Station Resource Classes - Simplified Version
|
|
"""
|
|
|
|
from __future__ import annotations
|
|
|
|
from typing import Dict, Optional
|
|
|
|
from pylabrobot.resources.coordinate import Coordinate
|
|
from pylabrobot.resources.container import Container
|
|
from pylabrobot.resources.resource_holder import ResourceHolder
|
|
from pylabrobot.resources import Resource as ResourcePLR
|
|
|
|
|
|
class Bottle(Container):
|
|
"""瓶子类 - 简化版，不追踪瓶盖"""
|
|
|
|
def __init__(
|
|
self,
|
|
name: str,
|
|
diameter: float,
|
|
height: float,
|
|
max_volume: float,
|
|
size_x: float = 0.0,
|
|
size_y: float = 0.0,
|
|
size_z: float = 0.0,
|
|
barcode: Optional[str] = "",
|
|
category: str = "container",
|
|
model: Optional[str] = None,
|
|
):
|
|
super().__init__(
|
|
name=name,
|
|
size_x=diameter,
|
|
size_y=diameter,
|
|
size_z=height,
|
|
max_volume=max_volume,
|
|
category=category,
|
|
model=model,
|
|
)
|
|
self.diameter = diameter
|
|
self.height = height
|
|
self.barcode = barcode
|
|
|
|
def serialize(self) -> dict:
|
|
return {
|
|
**super().serialize(),
|
|
"diameter": self.diameter,
|
|
"height": self.height,
|
|
"barcode": self.barcode,
|
|
}
|
|
|
|
|
|
from string import ascii_uppercase as LETTERS
|
|
from typing import Dict, List, Optional, Type, TypeVar, Union, Sequence, Tuple
|
|
|
|
import pylabrobot
|
|
from pylabrobot.resources.resource_holder import ResourceHolder
|
|
|
|
T = TypeVar("T", bound=ResourceHolder)
|
|
|
|
S = TypeVar("S", bound=ResourceHolder)
|
|
|
|
|
|
class ItemizedCarrier(ResourcePLR):
|
|
"""Base class for all carriers."""
|
|
|
|
def __init__(
|
|
self,
|
|
name: str,
|
|
size_x: float,
|
|
size_y: float,
|
|
size_z: float,
|
|
sites: Optional[Dict[Union[int, str], Optional[ResourcePLR]]] = None,
|
|
category: Optional[str] = "carrier",
|
|
model: Optional[str] = None,
|
|
):
|
|
super().__init__(
|
|
name=name,
|
|
size_x=size_x,
|
|
size_y=size_y,
|
|
size_z=size_z,
|
|
category=category,
|
|
model=model,
|
|
)
|
|
sites = sites or {}
|
|
self.sites: List[Optional[ResourcePLR]] = list(sites.values())
|
|
self._ordering = sites
|
|
self.num_items = len(self.sites)
|
|
self.child_locations: Dict[str, Coordinate] = {}
|
|
for spot, resource in sites.items():
|
|
if resource is not None and getattr(resource, "location", None) is None:
|
|
raise ValueError(f"resource {resource} has no location")
|
|
if resource is not None:
|
|
self.child_locations[spot] = resource.location
|
|
else:
|
|
self.child_locations[spot] = Coordinate.zero()
|
|
|
|
@property
|
|
def capacity(self):
|
|
"""The number of sites on this carrier."""
|
|
return len(self.sites)
|
|
|
|
def __len__(self) -> int:
|
|
"""Return the number of sites on this carrier."""
|
|
return len(self.sites)
|
|
|
|
def assign_child_resource(
|
|
self,
|
|
resource: ResourcePLR,
|
|
location: Optional[Coordinate],
|
|
reassign: bool = True,
|
|
spot: Optional[int] = None,
|
|
):
|
|
idx = spot if spot is not None else len(self.sites)
|
|
if not reassign and self.sites[idx] is not None:
|
|
raise ValueError(f"a site with index {idx} already exists")
|
|
super().assign_child_resource(resource, location=location, reassign=reassign)
|
|
self.sites[idx] = resource
|
|
|
|
def assign_resource_to_site(self, resource: ResourcePLR, spot: int):
|
|
if self.sites[spot] is not None and not isinstance(self.sites[spot], ResourceHolder):
|
|
raise ValueError(f"spot {spot} already has a resource, {resource}")
|
|
self.assign_child_resource(resource, location=self.child_locations.get(str(spot)), spot=spot)
|
|
|
|
def unassign_child_resource(self, resource: ResourcePLR):
|
|
found = False
|
|
for spot, res in enumerate(self.sites):
|
|
if res == resource:
|
|
self.sites[spot] = None
|
|
found = True
|
|
break
|
|
if not found:
|
|
raise ValueError(f"Resource {resource} is not assigned to this carrier")
|
|
if hasattr(resource, "unassign"):
|
|
resource.unassign()
|
|
|
|
def __getitem__(
|
|
self,
|
|
identifier: Union[str, int, Sequence[int], Sequence[str], slice, range],
|
|
) -> Union[List[T], T]:
|
|
"""Get the items with the given identifier.
|
|
|
|
This is a convenience method for getting the items with the given identifier. It is equivalent
|
|
to :meth:`get_items`, but adds support for slicing and supports single items in the same
|
|
functional call. Note that the return type will always be a list, even if a single item is
|
|
requested.
|
|
|
|
Examples:
|
|
Getting the items with identifiers "A1" through "E1":
|
|
|
|
>>> items["A1:E1"]
|
|
|
|
[<Item A1>, <Item B1>, <Item C1>, <Item D1>, <Item E1>]
|
|
|
|
Getting the items with identifiers 0 through 4 (note that this is the same as above):
|
|
|
|
>>> items[range(5)]
|
|
|
|
[<Item A1>, <Item B1>, <Item C1>, <Item D1>, <Item E1>]
|
|
|
|
Getting items with a slice (note that this is the same as above):
|
|
|
|
>>> items[0:5]
|
|
|
|
[<Item A1>, <Item B1>, <Item C1>, <Item D1>, <Item E1>]
|
|
|
|
Getting a single item:
|
|
|
|
>>> items[0]
|
|
|
|
[<Item A1>]
|
|
"""
|
|
|
|
if isinstance(identifier, str):
|
|
if ":" in identifier: # multiple # TODO: deprecate this, use `"A1":"E1"` instead (slice)
|
|
return self.get_items(identifier)
|
|
|
|
return self.get_item(identifier) # single
|
|
|
|
if isinstance(identifier, int):
|
|
return self.get_item(identifier)
|
|
|
|
if isinstance(identifier, (slice, range)):
|
|
start, stop = identifier.start, identifier.stop
|
|
if isinstance(identifier.start, str):
|
|
start = list(self._ordering.keys()).index(identifier.start)
|
|
elif identifier.start is None:
|
|
start = 0
|
|
if isinstance(identifier.stop, str):
|
|
stop = list(self._ordering.keys()).index(identifier.stop)
|
|
elif identifier.stop is None:
|
|
stop = self.num_items
|
|
identifier = list(range(start, stop, identifier.step or 1))
|
|
return self.get_items(identifier)
|
|
|
|
if isinstance(identifier, (list, tuple)):
|
|
return self.get_items(identifier)
|
|
|
|
raise TypeError(f"Invalid identifier type: {type(identifier)}")
|
|
|
|
def get_item(self, identifier: Union[str, int, Tuple[int, int]]) -> T:
|
|
"""Get the item with the given identifier.
|
|
|
|
Args:
|
|
identifier: The identifier of the item. Either a string, an integer, or a tuple. If an
|
|
integer, it is the index of the item in the list of items (counted from 0, top to bottom, left
|
|
to right). If a string, it uses transposed MS Excel style notation, e.g. "A1" for the first
|
|
item, "B1" for the item below that, etc. If a tuple, it is (row, column).
|
|
|
|
Raises:
|
|
IndexError: If the identifier is out of range. The range is 0 to self.num_items-1 (inclusive).
|
|
"""
|
|
|
|
if isinstance(identifier, tuple):
|
|
row, column = identifier
|
|
identifier = LETTERS[row] + str(column + 1) # standard transposed-Excel style notation
|
|
if isinstance(identifier, str):
|
|
try:
|
|
identifier = list(self._ordering.keys()).index(identifier)
|
|
except ValueError as e:
|
|
raise IndexError(
|
|
f"Item with identifier '{identifier}' does not exist on " f"resource '{self.name}'."
|
|
) from e
|
|
|
|
if not 0 <= identifier < self.capacity:
|
|
raise IndexError(
|
|
f"Item with identifier '{identifier}' does not exist on " f"resource '{self.name}'."
|
|
)
|
|
|
|
# Cast child to item type. Children will always be `T`, but the type checker doesn't know that.
|
|
return self.sites[identifier]
|
|
|
|
def get_items(self, identifiers: Union[str, Sequence[int], Sequence[str]]) -> List[T]:
|
|
"""Get the items with the given identifier.
|
|
|
|
Args:
|
|
identifier: Deprecated. Use `identifiers` instead. # TODO(deprecate-ordered-items)
|
|
identifiers: The identifiers of the items. Either a string range or a list of integers. If a
|
|
string, it uses transposed MS Excel style notation. Regions of items can be specified using
|
|
a colon, e.g. "A1:H1" for the first column. If a list of integers, it is the indices of the
|
|
items in the list of items (counted from 0, top to bottom, left to right).
|
|
|
|
Examples:
|
|
Getting the items with identifiers "A1" through "E1":
|
|
|
|
>>> items.get_items("A1:E1")
|
|
|
|
[<Item A1>, <Item B1>, <Item C1>, <Item D1>, <Item E1>]
|
|
|
|
Getting the items with identifiers 0 through 4:
|
|
|
|
>>> items.get_items(range(5))
|
|
|
|
[<Item A1>, <Item B1>, <Item C1>, <Item D1>, <Item E1>]
|
|
"""
|
|
|
|
if isinstance(identifiers, str):
|
|
identifiers = pylabrobot.utils.expand_string_range(identifiers)
|
|
return [self.get_item(i) for i in identifiers]
|
|
|
|
def __setitem__(self, idx: Union[int, str], resource: Optional[ResourcePLR]):
|
|
"""Assign a resource to this carrier."""
|
|
if resource is None: # setting to None
|
|
assigned_resource = self[idx]
|
|
if assigned_resource is not None:
|
|
self.unassign_child_resource(assigned_resource)
|
|
else:
|
|
idx = list(self._ordering.keys()).index(idx) if isinstance(idx, str) else idx
|
|
self.assign_resource_to_site(resource, spot=idx)
|
|
|
|
def __delitem__(self, idx: int):
|
|
"""Unassign a resource from this carrier."""
|
|
assigned_resource = self[idx]
|
|
if assigned_resource is not None:
|
|
self.unassign_child_resource(assigned_resource)
|
|
|
|
def get_resources(self) -> List[ResourcePLR]:
|
|
"""Get all resources assigned to this carrier."""
|
|
return [resource for resource in self.sites.values() if resource is not None]
|
|
|
|
def __eq__(self, other):
|
|
return super().__eq__(other) and self.sites == other.sites
|
|
|
|
def get_free_sites(self) -> List[int]:
|
|
return [spot for spot, resource in self.sites.items() if resource is None]
|
|
|
|
def serialize(self):
|
|
return {
|
|
**super().serialize(),
|
|
"slots": [{
|
|
"label": str(identifier),
|
|
"visible": True if self[identifier] is not None else False,
|
|
"position": {"x": location.x, "y": location.y, "z": location.z},
|
|
"size": {"width": self._size_x, "height": self._size_y, "depth": self._size_z},
|
|
"content_type": ["bottle", "container", "tube", "bottle_carrier", "tip_rack"]
|
|
} for identifier, location in self.child_locations.items()]
|
|
}
|
|
|
|
|
|
class BottleCarrier(ItemizedCarrier):
|
|
"""瓶载架 - 直接继承自 TubeCarrier"""
|
|
|
|
def __init__(
|
|
self,
|
|
name: str,
|
|
size_x: float,
|
|
size_y: float,
|
|
size_z: float,
|
|
sites: Optional[Dict[Union[int, str], ResourceHolder]] = None,
|
|
category: str = "bottle_carrier",
|
|
model: Optional[str] = None,
|
|
):
|
|
super().__init__(
|
|
name=name,
|
|
size_x=size_x,
|
|
size_y=size_y,
|
|
size_z=size_z,
|
|
sites=sites,
|
|
category=category,
|
|
model=model,
|
|
)
|