from __future__ import annotations import asyncio import time import traceback from collections import Counter from typing import List, Sequence, Optional, Literal, Union, Iterator, Dict, Any, Callable, Set, cast from pylabrobot.liquid_handling import LiquidHandler, LiquidHandlerBackend, LiquidHandlerChatterboxBackend, Strictness from unilabos.devices.liquid_handling.rviz_backend import UniLiquidHandlerRvizBackend from unilabos.devices.liquid_handling.laiyu.backend.laiyu_v_backend import UniLiquidHandlerLaiyuBackend from pylabrobot.liquid_handling.liquid_handler import TipPresenceProbingMethod from pylabrobot.liquid_handling.standard import GripDirection from pylabrobot.resources import ( Resource, TipRack, Container, Coordinate, Well, Deck, TipSpot, Plate, ResourceStack, ResourceHolder, Lid, Trash, Tip, ) from unilabos.ros.nodes.base_device_node import BaseROS2DeviceNode class LiquidHandlerMiddleware(LiquidHandler): def __init__(self, backend: LiquidHandlerBackend, deck: Deck, simulator: bool = False, channel_num: int = 8, total_height: float = 310, **kwargs): self._simulator = simulator self.channel_num = channel_num joint_config = kwargs.get("joint_config", None) if simulator: self._simulate_backend = UniLiquidHandlerRvizBackend(channel_num,total_height, joint_config=joint_config, lh_device_id = deck.name) self._simulate_handler = LiquidHandlerAbstract(self._simulate_backend, deck, False) if hasattr(backend, "total_height"): backend.total_height = total_height super().__init__(backend, deck) async def setup(self, **backend_kwargs): if self._simulator: return await self._simulate_handler.setup(**backend_kwargs) return await super().setup(**backend_kwargs) def serialize_state(self) -> Dict[str, Any]: if self._simulator: self._simulate_handler.serialize_state() return super().serialize_state() def load_state(self, state: Dict[str, Any]): if self._simulator: self._simulate_handler.load_state(state) super().load_state(state) def update_head_state(self, state: Dict[int, Optional[Tip]]): if self._simulator: self._simulate_handler.update_head_state(state) super().update_head_state(state) def clear_head_state(self): if self._simulator: self._simulate_handler.clear_head_state() super().clear_head_state() def _run_async_in_thread(self, func, *args, **kwargs): super()._run_async_in_thread(func, *args, **kwargs) def _send_assigned_resource_to_backend(self, resource: Resource): if self._simulator: self._simulate_handler._send_assigned_resource_to_backend(resource) super()._send_assigned_resource_to_backend(resource) def _send_unassigned_resource_to_backend(self, resource: Resource): if self._simulator: self._simulate_handler._send_unassigned_resource_to_backend(resource) super()._send_unassigned_resource_to_backend(resource) def summary(self): if self._simulator: self._simulate_handler.summary() super().summary() def _assert_positions_unique(self, positions: List[str]): super()._assert_positions_unique(positions) def _assert_resources_exist(self, resources: Sequence[Resource]): super()._assert_resources_exist(resources) def _check_args( self, method: Callable, backend_kwargs: Dict[str, Any], default: Set[str], strictness: Strictness ) -> Set[str]: return super()._check_args(method, backend_kwargs, default, strictness) def _make_sure_channels_exist(self, channels: List[int]): super()._make_sure_channels_exist(channels) def _format_param(self, value: Any) -> Any: return super()._format_param(value) def _log_command(self, name: str, **kwargs) -> None: super()._log_command(name, **kwargs) async def pick_up_tips( self, tip_spots: List[TipSpot], use_channels: Optional[List[int]] = None, offsets: Optional[List[Coordinate]] = None, **backend_kwargs, ): if self._simulator: return await self._simulate_handler.pick_up_tips(tip_spots, use_channels, offsets, **backend_kwargs) return await super().pick_up_tips(tip_spots, use_channels, offsets, **backend_kwargs) async def drop_tips( self, tip_spots: Sequence[Union[TipSpot, Trash]], use_channels: Optional[List[int]] = None, offsets: Optional[List[Coordinate]] = None, allow_nonzero_volume: bool = False, **backend_kwargs, ): if self._simulator: return await self._simulate_handler.drop_tips( tip_spots, use_channels, offsets, allow_nonzero_volume, **backend_kwargs ) return await super().drop_tips(tip_spots, use_channels, offsets, allow_nonzero_volume, **backend_kwargs) async def return_tips( self, use_channels: Optional[list[int]] = None, allow_nonzero_volume: bool = False, **backend_kwargs ): if self._simulator: return await self._simulate_handler.return_tips(use_channels, allow_nonzero_volume, **backend_kwargs) return await super().return_tips(use_channels, allow_nonzero_volume, **backend_kwargs) async def discard_tips( self, use_channels: Optional[List[int]] = None, allow_nonzero_volume: bool = True, offsets: Optional[List[Coordinate]] = None, **backend_kwargs, ): if not offsets or (isinstance(offsets, list) and len(offsets) != len(use_channels)): offsets = [Coordinate.zero()] * len(use_channels) if self._simulator: return await self._simulate_handler.discard_tips(use_channels, allow_nonzero_volume, offsets, **backend_kwargs) return await super().discard_tips(use_channels, allow_nonzero_volume, offsets, **backend_kwargs) def _check_containers(self, resources: Sequence[Resource]): super()._check_containers(resources) async def aspirate( self, resources: Sequence[Container], vols: List[float], use_channels: Optional[List[int]] = None, flow_rates: Optional[List[Optional[float]]] = None, offsets: Optional[List[Coordinate]] = None, liquid_height: Optional[List[Optional[float]]] = None, blow_out_air_volume: Optional[List[Optional[float]]] = None, spread: Literal["wide", "tight", "custom"] = "wide", **backend_kwargs, ): if self._simulator: return await self._simulate_handler.aspirate( resources, vols, use_channels, flow_rates, offsets, liquid_height, blow_out_air_volume, spread, **backend_kwargs, ) return await super().aspirate( resources, vols, use_channels, flow_rates, offsets, liquid_height, blow_out_air_volume, spread, **backend_kwargs, ) async def dispense( self, resources: Sequence[Container], vols: List[float], use_channels: Optional[List[int]] = None, flow_rates: Optional[List[Optional[float]]] = None, offsets: Optional[List[Coordinate]] = None, liquid_height: Optional[List[Optional[float]]] = None, blow_out_air_volume: Optional[List[Optional[float]]] = None, spread: Literal["wide", "tight", "custom"] = "wide", **backend_kwargs, ): if self._simulator: return await self._simulate_handler.dispense( resources, vols, use_channels, flow_rates, offsets, liquid_height, blow_out_air_volume, spread, **backend_kwargs, ) return await super().dispense( resources, vols, use_channels, flow_rates, offsets, liquid_height, blow_out_air_volume, **backend_kwargs, ) async def transfer( self, source: Well, targets: List[Well], source_vol: Optional[float] = None, ratios: Optional[List[float]] = None, target_vols: Optional[List[float]] = None, aspiration_flow_rate: Optional[float] = None, dispense_flow_rates: Optional[List[Optional[float]]] = None, **backend_kwargs, ): if self._simulator: return await self._simulate_handler.transfer( source, targets, source_vol, ratios, target_vols, aspiration_flow_rate, dispense_flow_rates, **backend_kwargs, ) return await super().transfer( source, targets, source_vol, ratios, target_vols, aspiration_flow_rate, dispense_flow_rates, **backend_kwargs, ) def use_channels(self, channels: List[int]): if self._simulator: self._simulate_handler.use_channels(channels) return super().use_channels(channels) async def pick_up_tips96(self, tip_rack: TipRack, offset: Coordinate = Coordinate.zero(), **backend_kwargs): if self._simulator: return await self._simulate_handler.pick_up_tips96(tip_rack, offset, **backend_kwargs) return await super().pick_up_tips96(tip_rack, offset, **backend_kwargs) async def drop_tips96( self, resource: Union[TipRack, Trash], offset: Coordinate = Coordinate.zero(), allow_nonzero_volume: bool = False, **backend_kwargs, ): if self._simulator: return await self._simulate_handler.drop_tips96(resource, offset, allow_nonzero_volume, **backend_kwargs) return await super().drop_tips96(resource, offset, allow_nonzero_volume, **backend_kwargs) def _get_96_head_origin_tip_rack(self) -> Optional[TipRack]: return super()._get_96_head_origin_tip_rack() async def return_tips96(self, allow_nonzero_volume: bool = False, **backend_kwargs): if self._simulator: return await self._simulate_handler.return_tips96(allow_nonzero_volume, **backend_kwargs) return await super().return_tips96(allow_nonzero_volume, **backend_kwargs) async def discard_tips96(self, allow_nonzero_volume: bool = True, **backend_kwargs): if self._simulator: return await self._simulate_handler.discard_tips96(allow_nonzero_volume, **backend_kwargs) return await super().discard_tips96(allow_nonzero_volume, **backend_kwargs) async def aspirate96( self, resource: Union[Plate, Container, List[Well]], volume: float, offset: Coordinate = Coordinate.zero(), flow_rate: Optional[float] = None, blow_out_air_volume: Optional[float] = None, **backend_kwargs, ): if self._simulator: return await self._simulate_handler.aspirate96( resource, volume, offset, flow_rate, blow_out_air_volume, **backend_kwargs ) return await super().aspirate96(resource, volume, offset, flow_rate, blow_out_air_volume, **backend_kwargs) async def dispense96( self, resource: Union[Plate, Container, List[Well]], volume: float, offset: Coordinate = Coordinate.zero(), flow_rate: Optional[float] = None, blow_out_air_volume: Optional[float] = None, **backend_kwargs, ): if self._simulator: return await self._simulate_handler.dispense96( resource, volume, offset, flow_rate, blow_out_air_volume, **backend_kwargs ) return await super().dispense96(resource, volume, offset, flow_rate, blow_out_air_volume, **backend_kwargs) async def stamp( self, source: Plate, target: Plate, volume: float, aspiration_flow_rate: Optional[float] = None, dispense_flow_rate: Optional[float] = None, ): if self._simulator: return await self._simulate_handler.stamp(source, target, volume, aspiration_flow_rate, dispense_flow_rate) return await super().stamp(source, target, volume, aspiration_flow_rate, dispense_flow_rate) async def pick_up_resource( self, resource: Resource, offset: Coordinate = Coordinate.zero(), pickup_distance_from_top: float = 0, direction: GripDirection = GripDirection.FRONT, **backend_kwargs, ): if self._simulator: return await self._simulate_handler.pick_up_resource( resource, offset, pickup_distance_from_top, direction, **backend_kwargs ) return await super().pick_up_resource(resource, offset, pickup_distance_from_top, direction, **backend_kwargs) async def move_picked_up_resource( self, to: Coordinate, offset: Coordinate = Coordinate.zero(), direction: Optional[GripDirection] = None, **backend_kwargs, ): if self._simulator: return await self._simulate_handler.move_picked_up_resource(to, offset, direction, **backend_kwargs) return await super().move_picked_up_resource(to, offset, direction, **backend_kwargs) async def drop_resource( self, destination: Union[ResourceStack, ResourceHolder, Resource, Coordinate], offset: Coordinate = Coordinate.zero(), direction: GripDirection = GripDirection.FRONT, **backend_kwargs, ): if self._simulator: return await self._simulate_handler.drop_resource(destination, offset, direction, **backend_kwargs) return await super().drop_resource(destination, offset, direction, **backend_kwargs) async def move_resource( self, resource: Resource, to: Union[ResourceStack, ResourceHolder, Resource, Coordinate], intermediate_locations: Optional[List[Coordinate]] = None, pickup_offset: Coordinate = Coordinate.zero(), destination_offset: Coordinate = Coordinate.zero(), pickup_distance_from_top: float = 0, pickup_direction: GripDirection = GripDirection.FRONT, drop_direction: GripDirection = GripDirection.FRONT, **backend_kwargs, ): if self._simulator: return await self._simulate_handler.move_resource( resource, to, intermediate_locations, pickup_offset, destination_offset, pickup_distance_from_top, pickup_direction, drop_direction, **backend_kwargs, ) return await super().move_resource( resource, to, intermediate_locations, pickup_offset, destination_offset, pickup_distance_from_top, pickup_direction, drop_direction, **backend_kwargs, ) async def move_lid( self, lid: Lid, to: Union[Plate, ResourceStack, Coordinate], intermediate_locations: Optional[List[Coordinate]] = None, pickup_offset: Coordinate = Coordinate.zero(), destination_offset: Coordinate = Coordinate.zero(), pickup_direction: GripDirection = GripDirection.FRONT, drop_direction: GripDirection = GripDirection.FRONT, pickup_distance_from_top: float = 5.7 - 3.33, **backend_kwargs, ): if self._simulator: return await self._simulate_handler.move_lid( lid, to, intermediate_locations, pickup_offset, destination_offset, pickup_direction, drop_direction, pickup_distance_from_top, **backend_kwargs, ) return await super().move_lid( lid, to, intermediate_locations, pickup_offset, destination_offset, pickup_direction, drop_direction, pickup_distance_from_top, **backend_kwargs, ) async def move_plate( self, plate: Plate, to: Union[ResourceStack, ResourceHolder, Resource, Coordinate], intermediate_locations: Optional[List[Coordinate]] = None, pickup_offset: Coordinate = Coordinate.zero(), destination_offset: Coordinate = Coordinate.zero(), drop_direction: GripDirection = GripDirection.FRONT, pickup_direction: GripDirection = GripDirection.FRONT, pickup_distance_from_top: float = 13.2 - 3.33, **backend_kwargs, ): if self._simulator: return await self._simulate_handler.move_plate( plate, to, intermediate_locations, pickup_offset, destination_offset, drop_direction, pickup_direction, pickup_distance_from_top, **backend_kwargs, ) return await super().move_plate( plate, to, intermediate_locations, pickup_offset, destination_offset, drop_direction, pickup_direction, pickup_distance_from_top, **backend_kwargs, ) def serialize(self): if self._simulator: self._simulate_handler.serialize() return super().serialize() @classmethod def deserialize(cls, data: dict, allow_marshal: bool = False) -> LiquidHandler: return super().deserialize(data, allow_marshal) @classmethod def load(cls, path: str) -> LiquidHandler: return super().load(path) async def prepare_for_manual_channel_operation(self, channel: int): if self._simulator: return await self._simulate_handler.prepare_for_manual_channel_operation(channel) return await super().prepare_for_manual_channel_operation(channel) async def move_channel_x(self, channel: int, x: float): if self._simulator: return await self._simulate_handler.move_channel_x(channel, x) return await super().move_channel_x(channel, x) async def move_channel_y(self, channel: int, y: float): if self._simulator: return await self._simulate_handler.move_channel_y(channel, y) return await super().move_channel_y(channel, y) async def move_channel_z(self, channel: int, z: float): if self._simulator: return await self._simulate_handler.move_channel_z(channel, z) return await super().move_channel_z(channel, z) def assign_child_resource(self, resource: Resource, location: Optional[Coordinate], reassign: bool = True): if self._simulator: self._simulate_handler.assign_child_resource(resource, location, reassign) pass async def probe_tip_presence_via_pickup( self, tip_spots: List[TipSpot], use_channels: Optional[List[int]] = None ) -> Dict[str, bool]: if self._simulator: return await self._simulate_handler.probe_tip_presence_via_pickup(tip_spots, use_channels) return await super().probe_tip_presence_via_pickup(tip_spots, use_channels) async def probe_tip_inventory( self, tip_spots: List[TipSpot], probing_fn: Optional[TipPresenceProbingMethod] = None, use_channels: Optional[List[int]] = None, ) -> Dict[str, bool]: if self._simulator: return await self._simulate_handler.probe_tip_inventory(tip_spots, probing_fn, use_channels) return await super().probe_tip_inventory(tip_spots, probing_fn, use_channels) async def consolidate_tip_inventory(self, tip_racks: List[TipRack], use_channels: Optional[List[int]] = None): if self._simulator: return await self._simulate_handler.consolidate_tip_inventory(tip_racks, use_channels) return await super().consolidate_tip_inventory(tip_racks, use_channels) class LiquidHandlerAbstract(LiquidHandlerMiddleware): """Extended LiquidHandler with additional operations.""" support_touch_tip = True _ros_node: BaseROS2DeviceNode def __init__(self, backend: LiquidHandlerBackend, deck: Deck, simulator: bool=False, channel_num:int = 8,total_height: float = 310,**backend_kwargs): """Initialize a LiquidHandler. Args: backend: Backend to use. deck: Deck to use. """ backend_type = None if isinstance(backend, dict) and "type" in backend: backend_dict = backend.copy() type_str = backend_dict.pop("type") try: # Try to get class from string using globals (current module), or fallback to pylabrobot or unilabos namespaces backend_cls = None if type_str in globals(): backend_cls = globals()[type_str] else: # Try resolving dotted notation, e.g. "xxx.yyy.ClassName" components = type_str.split(".") mod = None if len(components) > 1: module_name = ".".join(components[:-1]) try: import importlib mod = importlib.import_module(module_name) except ImportError: mod = None if mod is not None: backend_cls = getattr(mod, components[-1], None) if backend_cls is None: # Try pylabrobot style import (if available) try: import pylabrobot backend_cls = getattr(pylabrobot, type_str, None) except Exception: backend_cls = None if backend_cls is not None and isinstance(backend_cls, type): backend_type = backend_cls(**backend_dict) # pass the rest of dict as kwargs except Exception as exc: raise RuntimeError(f"Failed to convert backend type '{type_str}' to class: {exc}") else: backend_type = backend self._simulator = simulator self.group_info = dict() super().__init__(backend_type, deck, simulator, channel_num,total_height,**backend_kwargs) def post_init(self, ros_node: BaseROS2DeviceNode): self._ros_node = ros_node @classmethod def set_liquid(cls, wells: list[Well], liquid_names: list[str], volumes: list[float]): """Set the liquid in a well.""" for well, liquid_name, volume in zip(wells, liquid_names, volumes): well.set_liquids([(liquid_name, volume)]) # type: ignore # --------------------------------------------------------------- # REMOVE LIQUID -------------------------------------------------- # --------------------------------------------------------------- def set_group(self, group_name: str, wells: List[Well], volumes: List[float]): if self.channel_num == 8 and len(wells) != 8: raise RuntimeError(f"Expected 8 wells, got {len(wells)}") self.group_info[group_name] = wells self.set_liquid(wells, [group_name] * len(wells), volumes) async def transfer_group(self, source_group_name: str, target_group_name: str, unit_volume: float): source_wells = self.group_info.get(source_group_name, []) target_wells = self.group_info.get(target_group_name, []) rack_info = dict() for child in self.deck.children: if issubclass(child.__class__, TipRack): rack: TipRack = cast(TipRack, child) if "plate" not in rack.name.lower(): for tip in rack.get_all_tips(): if unit_volume > tip.maximal_volume: break else: rack_info[rack.name] = (rack, tip.maximal_volume - unit_volume) if len(rack_info) == 0: raise ValueError(f"No tip rack can support volume {unit_volume}.") rack_info = sorted(rack_info.items(), key=lambda x: x[1][1]) for child in self.deck.children: if child.name == rack_info[0][0]: target_rack = child target_rack = cast(TipRack, target_rack) available_tips = {} for (idx, tipSpot) in enumerate(target_rack.get_all_items()): if tipSpot.has_tip(): available_tips[idx] = tipSpot continue # 一般移动液体有两种方式，一对多和多对多 print("channel_num", self.channel_num) if self.channel_num == 8: tip_prefix = list(available_tips.values())[0].name.split('_')[0] colnum_list = [int(tip.name.split('_')[-1][1:]) for tip in available_tips.values()] available_cols = [colnum for colnum, count in dict(Counter(colnum_list)).items() if count == 8] available_cols.sort() available_tips_dict = {tip.name: tip for tip in available_tips.values()} tips_to_use = [available_tips_dict[f"{tip_prefix}_{chr(65 + i)}{available_cols[0]}"] for i in range(8)] print("tips_to_use", tips_to_use) await self.pick_up_tips(tips_to_use, use_channels=list(range(0, 8))) print("source_wells", source_wells) await self.aspirate(source_wells, [unit_volume] * 8, use_channels=list(range(0, 8))) print("target_wells", target_wells) await self.dispense(target_wells, [unit_volume] * 8, use_channels=list(range(0, 8))) await self.discard_tips(use_channels=list(range(0, 8))) elif self.channel_num == 1: for num_well in range(len(target_wells)): tip_to_use = available_tips[list(available_tips.keys())[num_well]] print("tip_to_use", tip_to_use) await self.pick_up_tips([tip_to_use], use_channels=[0]) print("source_wells", source_wells) print("target_wells", target_wells) if len(source_wells) == 1: await self.aspirate([source_wells[0]], [unit_volume], use_channels=[0]) else: await self.aspirate([source_wells[num_well]], [unit_volume], use_channels=[0]) await self.dispense([target_wells[num_well]], [unit_volume], use_channels=[0]) await self.discard_tips(use_channels=[0]) else: raise ValueError(f"Unsupported channel number {self.channel_num}.") async def create_protocol( self, protocol_name: str, protocol_description: str, protocol_version: str, protocol_author: str, protocol_date: str, protocol_type: str, none_keys: List[str] = [], ): """Create a new protocol with the given metadata.""" pass async def remove_liquid( self, vols: List[float], sources: Sequence[Container], waste_liquid: Optional[Container] = None, *, use_channels: Optional[List[int]] = None, flow_rates: Optional[List[Optional[float]]] = None, offsets: Optional[List[Coordinate]] = None, liquid_height: Optional[List[Optional[float]]] = None, blow_out_air_volume: Optional[List[Optional[float]]] = None, spread: Optional[Literal["wide", "tight", "custom"]] = "wide", delays: Optional[List[int]] = None, is_96_well: Optional[bool] = False, top: Optional[List[float]] = None, none_keys: List[str] = [], ): """A complete *remove* (aspirate → waste) operation.""" try: if is_96_well: pass # This mode is not verified. else: # 首先应该对任务分组，然后每次1个/8个进行操作处理 if len(use_channels) == 1 and self.backend.num_channels == 1: for _ in range(len(sources)): tip = [] for __ in range(len(use_channels)): tip.extend(next(self.current_tip)) await self.pick_up_tips(tip) await self.aspirate( resources=[sources[_]], vols=[vols[_]], use_channels=use_channels, flow_rates=[flow_rates[0]] if flow_rates else None, offsets=[offsets[0]] if offsets else None, liquid_height=[liquid_height[0]] if liquid_height else None, blow_out_air_volume=[blow_out_air_volume[0]] if blow_out_air_volume else None, spread=spread, ) if delays is not None: await self.custom_delay(seconds=delays[0]) await self.dispense( resources=[waste_liquid], vols=[vols[_]], use_channels=use_channels, flow_rates=[flow_rates[1]] if flow_rates else None, offsets=[offsets[1]] if offsets else None, blow_out_air_volume=[blow_out_air_volume[1]] if blow_out_air_volume else None, liquid_height=[liquid_height[1]] if liquid_height else None, spread=spread, ) await self.discard_tips() elif len(use_channels) == 8 and self.backend.num_channels == 8: # 对于8个的情况，需要判断此时任务是不是能被8通道移液站来成功处理 if len(sources) % 8 != 0: raise ValueError(f"Length of `sources` {len(sources)} must be a multiple of 8 for 8-channel mode.") # 8个8个来取任务序列 for i in range(0, len(sources), 8): tip = [] for _ in range(len(use_channels)): tip.extend(next(self.current_tip)) await self.pick_up_tips(tip) current_targets = waste_liquid[i:i + 8] current_reagent_sources = sources[i:i + 8] current_asp_vols = vols[i:i + 8] current_dis_vols = vols[i:i + 8] current_asp_flow_rates = flow_rates[i:i + 8] if flow_rates else [None] * 8 current_dis_flow_rates = flow_rates[-i*8-8:len(flow_rates)-i*8] if flow_rates else [None] * 8 current_asp_offset = offsets[i:i + 8] if offsets else [None] * 8 current_dis_offset = offsets[-i*8-8:len(offsets)-i*8] if offsets else [None] * 8 current_asp_liquid_height = liquid_height[i:i + 8] if liquid_height else [None] * 8 current_dis_liquid_height = liquid_height[-i*8-8:len(liquid_height)-i*8] if liquid_height else [None] * 8 current_asp_blow_out_air_volume = blow_out_air_volume[i:i + 8] if blow_out_air_volume else [None] * 8 current_dis_blow_out_air_volume = blow_out_air_volume[-i*8-8:len(blow_out_air_volume)-i*8] if blow_out_air_volume else [None] * 8 await self.aspirate( resources=current_reagent_sources, vols=current_asp_vols, use_channels=use_channels, flow_rates=current_asp_flow_rates, offsets=current_asp_offset, liquid_height=current_asp_liquid_height, blow_out_air_volume=current_asp_blow_out_air_volume, spread=spread, ) if delays is not None: await self.custom_delay(seconds=delays[0]) await self.dispense( resources=current_targets, vols=current_dis_vols, use_channels=use_channels, flow_rates=current_dis_flow_rates, offsets=current_dis_offset, liquid_height=current_dis_liquid_height, blow_out_air_volume=current_dis_blow_out_air_volume, spread=spread, ) if delays is not None: await self.custom_delay(seconds=delays[1]) await self.touch_tip(current_targets) await self.discard_tips() except Exception as e: traceback.print_exc() raise RuntimeError(f"Liquid addition failed: {e}") from e # --------------------------------------------------------------- # ADD LIQUID ----------------------------------------------------- # --------------------------------------------------------------- async def add_liquid( self, asp_vols: Union[List[float], float], dis_vols: Union[List[float], float], reagent_sources: Sequence[Container], targets: Sequence[Container], *, use_channels: Optional[List[int]] = None, flow_rates: Optional[List[Optional[float]]] = None, offsets: Optional[List[Coordinate]] = None, liquid_height: Optional[List[Optional[float]]] = None, blow_out_air_volume: Optional[List[Optional[float]]] = None, spread: Optional[Literal["wide", "tight", "custom"]] = "wide", is_96_well: bool = False, delays: Optional[List[int]] = None, mix_time: Optional[int] = None, mix_vol: Optional[int] = None, mix_rate: Optional[int] = None, mix_liquid_height: Optional[float] = None, none_keys: List[str] = [], ): # """A complete *add* (aspirate reagent → dispense into targets) operation.""" # # try: if is_96_well: pass # This mode is not verified. else: if len(asp_vols) != len(targets): raise ValueError(f"Length of `asp_vols` {len(asp_vols)} must match `targets` {len(targets)}.") # 首先应该对任务分组，然后每次1个/8个进行操作处理 if len(use_channels) == 1: for _ in range(len(targets)): tip = [] for x in range(len(use_channels)): tip.extend(next(self.current_tip)) await self.pick_up_tips(tip) await self.aspirate( resources=[reagent_sources[_]], vols=[asp_vols[_]], use_channels=use_channels, flow_rates=[flow_rates[0]] if flow_rates else None, offsets=[offsets[0]] if offsets else None, liquid_height=[liquid_height[0]] if liquid_height else None, blow_out_air_volume=[blow_out_air_volume[0]] if blow_out_air_volume else None, spread=spread, ) if delays is not None: await self.custom_delay(seconds=delays[0]) await self.dispense( resources=[targets[_]], vols=[dis_vols[_]], use_channels=use_channels, flow_rates=[flow_rates[1]] if flow_rates else None, offsets=[offsets[1]] if offsets else None, blow_out_air_volume=[blow_out_air_volume[1]] if blow_out_air_volume else None, liquid_height=[liquid_height[1]] if liquid_height else None, spread=spread, ) if delays is not None: await self.custom_delay(seconds=delays[1]) await self.mix( targets=[targets[_]], mix_time=mix_time, mix_vol=mix_vol, offsets=offsets if offsets else None, height_to_bottom=mix_liquid_height if mix_liquid_height else None, mix_rate=mix_rate if mix_rate else None, ) if delays is not None: await self.custom_delay(seconds=delays[1]) await self.touch_tip(targets[_]) await self.discard_tips() elif len(use_channels) == 8: # 对于8个的情况，需要判断此时任务是不是能被8通道移液站来成功处理 if len(targets) % 8 != 0: raise ValueError(f"Length of `targets` {len(targets)} must be a multiple of 8 for 8-channel mode.") for i in range(0, len(targets), 8): tip = [] for _ in range(len(use_channels)): tip.extend(next(self.current_tip)) await self.pick_up_tips(tip) current_targets = targets[i:i + 8] current_reagent_sources = reagent_sources[i:i + 8] current_asp_vols = asp_vols[i:i + 8] current_dis_vols = dis_vols[i:i + 8] current_asp_flow_rates = flow_rates[i:i + 8] if flow_rates else [None] * 8 current_dis_flow_rates = flow_rates[-i*8-8:len(flow_rates)-i*8] if flow_rates else [None] * 8 current_asp_offset = offsets[i:i + 8] if offsets else [None] * 8 current_dis_offset = offsets[-i*8-8:len(offsets)-i*8] if offsets else [None] * 8 current_asp_liquid_height = liquid_height[i:i + 8] if liquid_height else [None] * 8 current_dis_liquid_height = liquid_height[-i*8-8:len(liquid_height)-i*8] if liquid_height else [None] * 8 current_asp_blow_out_air_volume = blow_out_air_volume[i:i + 8] if blow_out_air_volume else [None] * 8 current_dis_blow_out_air_volume = blow_out_air_volume[-i*8-8:len(blow_out_air_volume)-i*8] if blow_out_air_volume else [None] * 8 await self.aspirate( resources=current_reagent_sources, vols=current_asp_vols, use_channels=use_channels, flow_rates=current_asp_flow_rates, offsets=current_asp_offset, liquid_height=current_asp_liquid_height, blow_out_air_volume=current_asp_blow_out_air_volume, spread=spread, ) if delays is not None: await self.custom_delay(seconds=delays[0]) await self.dispense( resources=current_targets, vols=current_dis_vols, use_channels=use_channels, flow_rates=current_dis_flow_rates, offsets=current_dis_offset, liquid_height=current_dis_liquid_height, blow_out_air_volume=current_dis_blow_out_air_volume, spread=spread, ) if delays is not None: await self.custom_delay(seconds=delays[1]) await self.mix( targets=current_targets, mix_time=mix_time, mix_vol=mix_vol, offsets=offsets if offsets else None, height_to_bottom=mix_liquid_height if mix_liquid_height else None, mix_rate=mix_rate if mix_rate else None, ) if delays is not None: await self.custom_delay(seconds=delays[1]) await self.touch_tip(current_targets) await self.discard_tips() # except Exception as e: # traceback.print_exc() # raise RuntimeError(f"Liquid addition failed: {e}") from e # --------------------------------------------------------------- # TRANSFER LIQUID ------------------------------------------------ # --------------------------------------------------------------- async def transfer_liquid( self, sources: Sequence[Container], targets: Sequence[Container], tip_racks: Sequence[TipRack], *, use_channels: Optional[List[int]] = None, asp_vols: Union[List[float], float], dis_vols: Union[List[float], float], asp_flow_rates: Optional[List[Optional[float]]] = None, dis_flow_rates: Optional[List[Optional[float]]] = None, offsets: Optional[List[Coordinate]] = None, touch_tip: bool = False, liquid_height: Optional[List[Optional[float]]] = None, blow_out_air_volume: Optional[List[Optional[float]]] = None, spread: Literal["wide", "tight", "custom"] = "wide", is_96_well: bool = False, mix_stage: Optional[Literal["none", "before", "after", "both"]] = "none", mix_times: Optional[int] = None, mix_vol: Optional[int] = None, mix_rate: Optional[int] = None, mix_liquid_height: Optional[float] = None, delays: Optional[List[int]] = None, none_keys: List[str] = [], ): """Transfer liquid from each *source* well/plate to the corresponding *target*. Parameters ---------- asp_vols, dis_vols Single volume (µL) or list matching the number of transfers. sources, targets Same‑length sequences of containers (wells or plates). In 96‑well mode each must contain exactly one plate. tip_racks One or more TipRacks providing fresh tips. is_96_well Set *True* to use the 96‑channel head. """ if is_96_well: pass # This mode is not verified. else: if len(asp_vols) != len(targets): raise ValueError(f"Length of `asp_vols` {len(asp_vols)} must match `targets` {len(targets)}.") # 首先应该对任务分组，然后每次1个/8个进行操作处理 if len(use_channels) == 1: for _ in range(len(targets)): tip = [] for ___ in range(len(use_channels)): tip.extend(next(self.current_tip)) await self.pick_up_tips(tip) await self.aspirate( resources=[sources[_]], vols=[asp_vols[_]], use_channels=use_channels, flow_rates=[asp_flow_rates[0]] if asp_flow_rates else None, offsets=[offsets[0]] if offsets else None, liquid_height=[liquid_height[0]] if liquid_height else None, blow_out_air_volume=[blow_out_air_volume[0]] if blow_out_air_volume else None, spread=spread, ) if delays is not None: await self.custom_delay(seconds=delays[0]) await self.dispense( resources=[targets[_]], vols=[dis_vols[_]], use_channels=use_channels, flow_rates=[dis_flow_rates[1]] if dis_flow_rates else None, offsets=[offsets[1]] if offsets else None, blow_out_air_volume=[blow_out_air_volume[1]] if blow_out_air_volume else None, liquid_height=[liquid_height[1]] if liquid_height else None, spread=spread, ) if delays is not None: await self.custom_delay(seconds=delays[1]) await self.mix( targets=[targets[_]], mix_time=mix_times, mix_vol=mix_vol, offsets=offsets if offsets else None, height_to_bottom=mix_liquid_height if mix_liquid_height else None, mix_rate=mix_rate if mix_rate else None, ) if delays is not None: await self.custom_delay(seconds=delays[1]) await self.touch_tip(targets[_]) await self.discard_tips() elif len(use_channels) == 8: # 对于8个的情况，需要判断此时任务是不是能被8通道移液站来成功处理 if len(targets) % 8 != 0: raise ValueError(f"Length of `targets` {len(targets)} must be a multiple of 8 for 8-channel mode.") # 8个8个来取任务序列 for i in range(0, len(targets), 8): # 取出8个任务 tip = [] for _ in range(len(use_channels)): tip.extend(next(self.current_tip)) await self.pick_up_tips(tip) current_targets = targets[i:i + 8] current_reagent_sources = sources[i:i + 8] current_asp_vols = asp_vols[i:i + 8] current_dis_vols = dis_vols[i:i + 8] current_asp_flow_rates = asp_flow_rates[i:i + 8] current_asp_offset = offsets[i:i + 8] if offsets else [None] * 8 current_dis_offset = offsets[-i*8-8:len(offsets)-i*8] if offsets else [None] * 8 current_asp_liquid_height = liquid_height[i:i + 8] if liquid_height else [None] * 8 current_dis_liquid_height = liquid_height[-i*8-8:len(liquid_height)-i*8] if liquid_height else [None] * 8 current_asp_blow_out_air_volume = blow_out_air_volume[i:i + 8] if blow_out_air_volume else [None] * 8 current_dis_blow_out_air_volume = blow_out_air_volume[-i*8-8:len(blow_out_air_volume)-i*8] if blow_out_air_volume else [None] * 8 current_dis_flow_rates = dis_flow_rates[i:i + 8] if dis_flow_rates else [None] * 8 await self.aspirate( resources=current_reagent_sources, vols=current_asp_vols, use_channels=use_channels, flow_rates=current_asp_flow_rates, offsets=current_asp_offset, blow_out_air_volume=current_asp_blow_out_air_volume, liquid_height=current_asp_liquid_height, spread=spread, ) if delays is not None: await self.custom_delay(seconds=delays[0]) await self.dispense( resources=current_targets, vols=current_dis_vols, use_channels=use_channels, flow_rates=current_dis_flow_rates, offsets=current_dis_offset, blow_out_air_volume=current_dis_blow_out_air_volume, liquid_height=current_dis_liquid_height, spread=spread, ) if delays is not None: await self.custom_delay(seconds=delays[1]) await self.mix( targets=current_targets, mix_time=mix_times, mix_vol=mix_vol, offsets=offsets if offsets else None, height_to_bottom=mix_liquid_height if mix_liquid_height else None, mix_rate=mix_rate if mix_rate else None, ) if delays is not None: await self.custom_delay(seconds=delays[1]) await self.touch_tip(current_targets) await self.discard_tips([0,1,2,3,4,5,6,7]) # except Exception as e: # traceback.print_exc() # raise RuntimeError(f"Liquid addition failed: {e}") from e # --------------------------------------------------------------- # Helper utilities # --------------------------------------------------------------- async def custom_delay(self, seconds=0, msg=None): """ seconds: seconds to wait msg: information to be printed """ if seconds != None and seconds > 0: if msg: print(f"Waiting time: {msg}") print(f"Current time: {time.strftime('%H:%M:%S')}") print(f"Time to finish: {time.strftime('%H:%M:%S', time.localtime(time.time() + seconds))}") await self._ros_node.sleep(seconds) if msg: print(f"Done: {msg}") print(f"Current time: {time.strftime('%H:%M:%S')}") async def touch_tip(self, targets: Sequence[Container]): """Touch the tip to the side of the well.""" if not self.support_touch_tip: return await self.aspirate( resources=[targets], vols=[0], use_channels=None, flow_rates=None, offsets=[Coordinate(x=-targets.get_size_x() / 2, y=0, z=0)], liquid_height=None, blow_out_air_volume=None, ) # await self.custom_delay(seconds=1) # In the simulation, we do not need to wait await self.aspirate( resources=[targets], vols=[0], use_channels=None, flow_rates=None, offsets=[Coordinate(x=targets.get_size_x() / 2, y=0, z=0)], liquid_height=None, blow_out_air_volume=None, ) async def mix( self, targets: Sequence[Container], mix_time: int = None, mix_vol: Optional[int] = None, height_to_bottom: Optional[float] = None, offsets: Optional[Coordinate] = None, mix_rate: Optional[float] = None, none_keys: List[str] = [], ): if mix_time is None: # No mixing required return """Mix the liquid in the target wells.""" for _ in range(mix_time): await self.aspirate( resources=[targets], vols=[mix_vol], flow_rates=[mix_rate] if mix_rate else None, offsets=[offsets] if offsets else None, liquid_height=[height_to_bottom] if height_to_bottom else None, ) await self.custom_delay(seconds=1) await self.dispense( resources=[targets], vols=[mix_vol], flow_rates=[mix_rate] if mix_rate else None, offsets=[offsets] if offsets else None, liquid_height=[height_to_bottom] if height_to_bottom else None, ) def iter_tips(self, tip_racks: Sequence[TipRack]) -> Iterator[Resource]: """Yield tips from a list of TipRacks one-by-one until depleted.""" for rack in tip_racks: for tip in rack: yield tip raise RuntimeError("Out of tips!") def set_tiprack(self, tip_racks: Sequence[TipRack]): """Set the tip racks for the liquid handler.""" self.tip_racks = tip_racks tip_iter = self.iter_tips(tip_racks) self.current_tip = tip_iter async def move_to(self, well: Well, dis_to_top: float = 0, channel: int = 0): """ Move a single channel to a specific well with a given z-height. Parameters ---------- well : Well The target well. dis_to_top : float Height in mm to move to relative to the well top. channel : int Pipetting channel to move (default: 0). """ await self.prepare_for_manual_channel_operation(channel=channel) abs_loc = well.get_absolute_location() well_height = well.get_absolute_size_z() await self.move_channel_x(channel, abs_loc.x) await self.move_channel_y(channel, abs_loc.y) await self.move_channel_z(channel, abs_loc.z + well_height + dis_to_top)