from typing import List, Dict, Any import networkx as nx from .pump_protocol import generate_pump_protocol def get_vessel_liquid_volume(G: nx.DiGraph, vessel: str) -> float: """ 获取容器中的液体体积 """ if vessel not in G.nodes(): return 0.0 vessel_data = G.nodes[vessel].get('data', {}) liquids = vessel_data.get('liquid', []) total_volume = 0.0 for liquid in liquids: if isinstance(liquid, dict) and 'liquid_volume' in liquid: total_volume += liquid['liquid_volume'] return total_volume def find_centrifuge_device(G: nx.DiGraph) -> str: """ 查找离心机设备 """ centrifuge_nodes = [node for node in G.nodes() if (G.nodes[node].get('class') or '') == 'virtual_centrifuge'] if centrifuge_nodes: return centrifuge_nodes[0] raise ValueError("系统中未找到离心机设备") def find_centrifuge_vessel(G: nx.DiGraph) -> str: """ 查找离心机专用容器 """ possible_names = [ "centrifuge_tube", "centrifuge_vessel", "tube_centrifuge", "vessel_centrifuge", "centrifuge", "tube_15ml", "tube_50ml" ] for vessel_name in possible_names: if vessel_name in G.nodes(): return vessel_name raise ValueError(f"未找到离心机容器。尝试了以下名称: {possible_names}") def generate_centrifuge_protocol( G: nx.DiGraph, vessel: str, speed: float, time: float, temp: float = 25.0 ) -> List[Dict[str, Any]]: """ 生成离心操作的协议序列，复用 pump_protocol 的成熟算法 离心流程： 1. 液体转移：将待离心溶液从源容器转移到离心机容器 2. 离心操作：执行离心分离 3. 上清液转移：将离心后的上清液转移回原容器或新容器 4. 沉淀处理：处理离心沉淀（可选） Args: G: 有向图，节点为设备和容器，边为流体管道 vessel: 包含待离心溶液的容器名称 speed: 离心速度 (rpm) time: 离心时间 (秒) temp: 离心温度 (°C)，默认25°C Returns: List[Dict[str, Any]]: 离心操作的动作序列 Raises: ValueError: 当找不到必要的设备时抛出异常 Examples: centrifuge_actions = generate_centrifuge_protocol(G, "reaction_mixture", 5000, 600, 4.0) """ action_sequence = [] print(f"CENTRIFUGE: 开始生成离心协议") print(f" - 源容器: {vessel}") print(f" - 离心速度: {speed} rpm") print(f" - 离心时间: {time}s ({time/60:.1f}分钟)") print(f" - 离心温度: {temp}°C") # 验证源容器存在 if vessel not in G.nodes(): raise ValueError(f"源容器 '{vessel}' 不存在于系统中") # 获取源容器中的液体体积 source_volume = get_vessel_liquid_volume(G, vessel) print(f"CENTRIFUGE: 源容器 {vessel} 中有 {source_volume} mL 液体") # 查找离心机设备 try: centrifuge_id = find_centrifuge_device(G) print(f"CENTRIFUGE: 找到离心机: {centrifuge_id}") except ValueError as e: raise ValueError(f"无法找到离心机: {str(e)}") # 查找离心机容器 try: centrifuge_vessel = find_centrifuge_vessel(G) print(f"CENTRIFUGE: 找到离心机容器: {centrifuge_vessel}") except ValueError as e: raise ValueError(f"无法找到离心机容器: {str(e)}") # === 简化的体积计算策略 === if source_volume > 0: # 如果能检测到液体体积，使用实际体积的大部分 transfer_volume = min(source_volume * 0.9, 15.0) # 90%或最多15mL（离心管通常较小） print(f"CENTRIFUGE: 检测到液体体积，将转移 {transfer_volume} mL") else: # 如果检测不到液体体积，默认转移标准量 transfer_volume = 10.0 # 标准离心管体积 print(f"CENTRIFUGE: 未检测到液体体积，默认转移 {transfer_volume} mL") # === 第一步：将待离心溶液转移到离心机容器 === print(f"CENTRIFUGE: 将 {transfer_volume} mL 溶液从 {vessel} 转移到 {centrifuge_vessel}") try: # 使用成熟的 pump_protocol 算法进行液体转移 transfer_to_centrifuge_actions = generate_pump_protocol( G=G, from_vessel=vessel, to_vessel=centrifuge_vessel, volume=transfer_volume, flowrate=1.0, # 离心转移用慢速，避免气泡 transfer_flowrate=1.0 ) action_sequence.extend(transfer_to_centrifuge_actions) except Exception as e: raise ValueError(f"无法将溶液转移到离心机: {str(e)}") # 转移后等待 wait_action = { "action_name": "wait", "action_kwargs": {"time": 5} } action_sequence.append(wait_action) # === 第二步：执行离心操作 === print(f"CENTRIFUGE: 执行离心操作") centrifuge_action = { "device_id": centrifuge_id, "action_name": "centrifuge", "action_kwargs": { "vessel": {"id": centrifuge_vessel}, "speed": speed, "time": time, "temp": temp } } action_sequence.append(centrifuge_action) # 离心后等待系统稳定 wait_action = { "action_name": "wait", "action_kwargs": {"time": 10} # 离心后等待稍长，让沉淀稳定 } action_sequence.append(wait_action) # === 第三步：将上清液转移回原容器 === print(f"CENTRIFUGE: 将上清液从离心机转移回 {vessel}") try: # 估算上清液体积（约为转移体积的80% - 假设20%成为沉淀） supernatant_volume = transfer_volume * 0.8 print(f"CENTRIFUGE: 预计上清液体积 {supernatant_volume} mL") transfer_back_actions = generate_pump_protocol( G=G, from_vessel=centrifuge_vessel, to_vessel=vessel, volume=supernatant_volume, flowrate=0.5, # 上清液转移更慢，避免扰动沉淀 transfer_flowrate=0.5 ) action_sequence.extend(transfer_back_actions) except Exception as e: print(f"CENTRIFUGE: 将上清液转移回容器失败: {str(e)}") # === 第四步：清洗离心机容器 === print(f"CENTRIFUGE: 清洗离心机容器") try: # 查找清洗溶剂 cleaning_solvent = None for solvent in ["flask_water", "flask_ethanol", "flask_acetone"]: if solvent in G.nodes(): cleaning_solvent = solvent break if cleaning_solvent: # 用少量溶剂清洗离心管 cleaning_volume = 5.0 # 5mL清洗 print(f"CENTRIFUGE: 用 {cleaning_volume} mL {cleaning_solvent} 清洗") # 清洗溶剂加入 cleaning_actions = generate_pump_protocol( G=G, from_vessel=cleaning_solvent, to_vessel=centrifuge_vessel, volume=cleaning_volume, flowrate=2.0, transfer_flowrate=2.0 ) action_sequence.extend(cleaning_actions) # 将清洗液转移到废液 if "waste_workup" in G.nodes(): waste_actions = generate_pump_protocol( G=G, from_vessel=centrifuge_vessel, to_vessel="waste_workup", volume=cleaning_volume, flowrate=2.0, transfer_flowrate=2.0 ) action_sequence.extend(waste_actions) except Exception as e: print(f"CENTRIFUGE: 清洗步骤失败: {str(e)}") print(f"CENTRIFUGE: 生成了 {len(action_sequence)} 个动作") print(f"CENTRIFUGE: 离心协议生成完成") print(f"CENTRIFUGE: 总处理体积: {transfer_volume} mL") return action_sequence # 便捷函数：常用离心方案 def generate_low_speed_centrifuge_protocol( G: nx.DiGraph, vessel: str, time: float = 300.0 # 5分钟 ) -> List[Dict[str, Any]]: """低速离心：细胞分离或大颗粒沉淀""" return generate_centrifuge_protocol(G, vessel, 1000.0, time, 4.0) def generate_high_speed_centrifuge_protocol( G: nx.DiGraph, vessel: str, time: float = 600.0 # 10分钟 ) -> List[Dict[str, Any]]: """高速离心：蛋白质沉淀或小颗粒分离""" return generate_centrifuge_protocol(G, vessel, 12000.0, time, 4.0) def generate_standard_centrifuge_protocol( G: nx.DiGraph, vessel: str, time: float = 600.0 # 10分钟 ) -> List[Dict[str, Any]]: """标准离心：常规样品处理""" return generate_centrifuge_protocol(G, vessel, 5000.0, time, 25.0) def generate_cold_centrifuge_protocol( G: nx.DiGraph, vessel: str, speed: float = 5000.0, time: float = 600.0 ) -> List[Dict[str, Any]]: """冷冻离心：热敏感样品处理""" return generate_centrifuge_protocol(G, vessel, speed, time, 4.0) def generate_ultra_centrifuge_protocol( G: nx.DiGraph, vessel: str, time: float = 1800.0 # 30分钟 ) -> List[Dict[str, Any]]: """超高速离心：超细颗粒分离""" return generate_centrifuge_protocol(G, vessel, 15000.0, time, 4.0)