from __future__ import annotations import traceback from typing import List, Sequence, Optional, Literal, Union, Iterator import asyncio import time from pylabrobot.liquid_handling import LiquidHandler from pylabrobot.resources import Resource, TipRack, Container, Coordinate, Well class LiquidHandlerAbstract(LiquidHandler): """Extended LiquidHandler with additional operations.""" # --------------------------------------------------------------- # REMOVE LIQUID -------------------------------------------------- # --------------------------------------------------------------- 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.""" trash = self.deck.get_trash_area() try: if is_96_well: pass # This mode is not verified else: if len(vols) != len(sources): raise ValueError("Length of `vols` must match `sources`.") for src, vol in zip(sources, vols): await self.move_to(src, dis_to_top=top[0] if top else 0) tip = next(self.current_tip) await self.pick_up_tips(tip) await self.aspirate( resources=[src], vols=[vol], use_channels=use_channels, # only aspirate96 used, default to None 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, ) await self.custom_delay(seconds=delays[0] if delays else 0) await self.dispense( resources=waste_liquid, vols=[vol], use_channels=use_channels, flow_rates=[flow_rates[1]] if flow_rates else None, offsets=[offsets[1]] if offsets else None, liquid_height=[liquid_height[1]] if liquid_height else None, blow_out_air_volume=blow_out_air_volume[1] if blow_out_air_volume else None, spread=spread, ) await self.discard_tips() # For now, each of tips is discarded after use except Exception as e: raise RuntimeError(f"Liquid removal 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: tip = [] for _ in range(len(use_channels)): tip.extend(next(self.current_tip)) await self.pick_up_tips(tip) for _ in range(len(targets)): 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: tip = [] for _ in range(len(use_channels)): tip.extend(next(self.current_tip)) await self.pick_up_tips(tip) # 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 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 :i + 16] if flow_rates else [None] * 8 current_asp_offset = offsets[i:i + 8] if offsets else [None] * 8 current_dis_offset = offsets[i+8 :i + 16] 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 :i + 16] 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 :i + 16] 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) 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[List[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. """ 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: tip = [] for _ in range(len(use_channels)): tip.extend(next(self.current_tip)) await self.pick_up_tips(tip) for _ in range(len(targets)): 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: tip = [] for _ in range(len(use_channels)): tip.extend(next(self.current_tip)) await self.pick_up_tips(tip) # 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 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 :i + 16] 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 :i + 16] 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 :i + 16] 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) 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 asyncio.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.""" 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)