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