import numpy as np import networkx as nx def generate_pump_protocol( G: nx.DiGraph, from_vessel: str, to_vessel: str, volume: float, flowrate: float = 500.0, transfer_flowrate: float = 0, ) -> list[dict]: """ 生成泵操作的动作序列。 :param G: 有向图, 节点为容器和注射泵, 边为流体管道, A→B边的属性为管道接A端的阀门位置 :param from_vessel: 容器A :param to_vessel: 容器B :param volume: 转移的体积 :param flowrate: 最终注入容器B时的流速 :param transfer_flowrate: 泵骨架中转移流速（若不指定，默认与注入流速相同） :return: 泵操作的动作序列 """ # 生成泵操作的动作序列 pump_action_sequence = [] nodes = G.nodes(data=True) # 从from_vessel到to_vessel的最短路径 shortest_path = nx.shortest_path(G, source=from_vessel, target=to_vessel) print(shortest_path) pump_backbone = shortest_path if not from_vessel.startswith("pump"): pump_backbone = pump_backbone[1:] if not to_vessel.startswith("pump"): pump_backbone = pump_backbone[:-1] if transfer_flowrate == 0: transfer_flowrate = flowrate min_transfer_volume = min([nodes[pump]["max_volume"] for pump in pump_backbone]) repeats = int(np.ceil(volume / min_transfer_volume)) if repeats > 1 and (from_vessel.startswith("pump") or to_vessel.startswith("pump")): raise ValueError("Cannot transfer volume larger than min_transfer_volume between two pumps.") volume_left = volume # 生成泵操作的动作序列 for i in range(repeats): # 单泵依次执行阀指令、活塞指令，将液体吸入与之相连的第一台泵 if not from_vessel.startswith("pump"): pump_action_sequence.extend([ { "device_id": pump_backbone[0], "action_name": "set_valve_position", "action_kwargs": { "command": G.get_edge_data(pump_backbone[0], from_vessel)["port"][pump_backbone[0]] } }, { "device_id": pump_backbone[0], "action_name": "set_position", "action_kwargs": { "position": float(min(volume_left, min_transfer_volume)), "max_velocity": transfer_flowrate } } ]) pump_action_sequence.append({"action_name": "wait", "action_kwargs": {"time": 5}}) for pumpA, pumpB in zip(pump_backbone[:-1], pump_backbone[1:]): # 相邻两泵同时切换阀门至连通位置 pump_action_sequence.append([ { "device_id": pumpA, "action_name": "set_valve_position", "action_kwargs": { "command": G.get_edge_data(pumpA, pumpB)["port"][pumpA] } }, { "device_id": pumpB, "action_name": "set_valve_position", "action_kwargs": { "command": G.get_edge_data(pumpB, pumpA)["port"][pumpB], } } ]) # 相邻两泵液体转移：泵A排出液体，泵B吸入液体 pump_action_sequence.append([ { "device_id": pumpA, "action_name": "set_position", "action_kwargs": { "position": 0.0, "max_velocity": transfer_flowrate } }, { "device_id": pumpB, "action_name": "set_position", "action_kwargs": { "position": float(min(volume_left, min_transfer_volume)), "max_velocity": transfer_flowrate } } ]) pump_action_sequence.append({"action_name": "wait", "action_kwargs": {"time": 5}}) if not to_vessel.startswith("pump"): # 单泵依次执行阀指令、活塞指令，将最后一台泵液体缓慢加入容器B pump_action_sequence.extend([ { "device_id": pump_backbone[-1], "action_name": "set_valve_position", "action_kwargs": { "command": G.get_edge_data(pump_backbone[-1], to_vessel)["port"][pump_backbone[-1]] } }, { "device_id": pump_backbone[-1], "action_name": "set_position", "action_kwargs": { "position": 0.0, "max_velocity": flowrate } } ]) pump_action_sequence.append({"action_name": "wait", "action_kwargs": {"time": 5}}) volume_left -= min_transfer_volume return pump_action_sequence # Pump protocol compilation def generate_pump_protocol_with_rinsing( G: nx.DiGraph, from_vessel: str, to_vessel: str, volume: float, amount: str = "", time: float = 0, viscous: bool = False, rinsing_solvent: str = "air", rinsing_volume: float = 5000.0, rinsing_repeats: int = 2, solid: bool = False, flowrate: float = 2500.0, transfer_flowrate: float = 500.0, ) -> list[dict]: """ Generates a pump protocol for transferring a specified volume between vessels, including rinsing steps with a chosen solvent. This function constructs a sequence of pump actions based on the provided parameters and the shortest path in a directed graph. Args: G (nx.DiGraph): The directed graph representing the vessels and connections. 有向图, 节点为容器和注射泵, 边为流体管道, A→B边的属性为管道接A端的阀门位置 from_vessel (str): The name of the vessel to transfer from. to_vessel (str): The name of the vessel to transfer to. volume (float): The volume to transfer. amount (str, optional): Additional amount specification (default is ""). time (float, optional): Time over which to perform the transfer (default is 0). viscous (bool, optional): Indicates if the fluid is viscous (default is False). rinsing_solvent (str, optional): The solvent to use for rinsing (default is "air"). rinsing_volume (float, optional): The volume of rinsing solvent to use (default is 5000.0). rinsing_repeats (int, optional): The number of times to repeat rinsing (default is 2). solid (bool, optional): Indicates if the transfer involves a solid (default is False). flowrate (float, optional): The flow rate for the transfer (default is 2500.0). 最终注入容器B时的流速 transfer_flowrate (float, optional): The flow rate for the transfer action (default is 500.0). 泵骨架中转移流速（若不指定，默认与注入流速相同） Returns: list[dict]: A sequence of pump actions to be executed for the transfer and rinsing process. 泵操作的动作序列. Raises: AssertionError: If the number of rinsing solvents does not match the number of rinsing repeats. Examples: pump_protocol = generate_pump_protocol_with_rinsing(G, "vessel_A", "vessel_B", 100.0, rinsing_solvent="water") """ air_vessel = "flask_air" waste_vessel = f"waste_workup" shortest_path = nx.shortest_path(G, source=from_vessel, target=to_vessel) pump_backbone = shortest_path[1: -1] nodes = G.nodes(data=True) min_transfer_volume = float(min([nodes[pump]["max_volume"] for pump in pump_backbone])) if time != 0: flowrate = transfer_flowrate = volume / time pump_action_sequence = generate_pump_protocol(G, from_vessel, to_vessel, float(volume), flowrate, transfer_flowrate) if rinsing_solvent != "air": if "," in rinsing_solvent: rinsing_solvents = rinsing_solvent.split(",") assert len(rinsing_solvents) == rinsing_repeats, "Number of rinsing solvents must match number of rinsing repeats." else: rinsing_solvents = [rinsing_solvent] * rinsing_repeats for rinsing_solvent in rinsing_solvents: solvent_vessel = f"flask_{rinsing_solvent}" # 清洗泵 pump_action_sequence.extend( generate_pump_protocol(G, solvent_vessel, pump_backbone[0], min_transfer_volume, flowrate, transfer_flowrate) + generate_pump_protocol(G, pump_backbone[0], pump_backbone[-1], min_transfer_volume, flowrate, transfer_flowrate) + generate_pump_protocol(G, pump_backbone[-1], waste_vessel, min_transfer_volume, flowrate, transfer_flowrate) ) # 如果转移的是溶液，第一种冲洗溶剂请选用溶液的溶剂，稀释泵内、转移管道内的溶液。后续冲洗溶剂不需要此操作。 if rinsing_solvent == rinsing_solvents[0]: pump_action_sequence.extend(generate_pump_protocol(G, solvent_vessel, from_vessel, rinsing_volume, flowrate, transfer_flowrate)) pump_action_sequence.extend(generate_pump_protocol(G, solvent_vessel, to_vessel, rinsing_volume, flowrate, transfer_flowrate)) pump_action_sequence.extend(generate_pump_protocol(G, air_vessel, solvent_vessel, rinsing_volume, flowrate, transfer_flowrate)) pump_action_sequence.extend(generate_pump_protocol(G, air_vessel, waste_vessel, rinsing_volume, flowrate, transfer_flowrate)) pump_action_sequence.extend(generate_pump_protocol(G, air_vessel, from_vessel, rinsing_volume, flowrate, transfer_flowrate) * 2) pump_action_sequence.extend(generate_pump_protocol(G, air_vessel, to_vessel, rinsing_volume, flowrate, transfer_flowrate) * 2) return pump_action_sequence # End Protocols