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https://github.com/dptech-corp/Uni-Lab-OS.git
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修复了很多protocol，亲测能跑
This commit is contained in:
KCFeng425
@@ -1,288 +1,381 @@
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import networkx as nx
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from typing import List, Dict, Any
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def generate_add_protocol(
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G: nx.DiGraph,
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vessel: str,
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reagent: str,
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volume: float,
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mass: float,
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amount: str,
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time: float,
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stir: bool,
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stir_speed: float,
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viscous: bool,
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purpose: str
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) -> List[Dict[str, Any]]:
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"""
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生成添加试剂的协议序列
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流程：
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1. 找到包含目标试剂的试剂瓶
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2. 配置八通阀门到试剂瓶位置
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3. 使用注射器泵吸取试剂
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4. 配置八通阀门到反应器位置
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5. 使用注射器泵推送试剂到反应器
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6. 如果需要，启动搅拌
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"""
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action_sequence = []
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# 验证目标容器存在
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if vessel not in G.nodes():
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raise ValueError(f"目标容器 {vessel} 不存在")
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# 如果指定了体积，执行液体转移
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if volume > 0:
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# 1. 查找注射器泵 (transfer pump)
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transfer_pump_nodes = [node for node in G.nodes()
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if G.nodes[node].get('class') == 'virtual_transfer_pump']
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if not transfer_pump_nodes:
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raise ValueError("没有找到可用的注射器泵 (virtual_transfer_pump)")
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transfer_pump_id = transfer_pump_nodes[0]
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# 2. 查找八通阀门
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multiway_valve_nodes = [node for node in G.nodes()
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if G.nodes[node].get('class') == 'virtual_multiway_valve']
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if not multiway_valve_nodes:
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raise ValueError("没有找到可用的八通阀门 (virtual_multiway_valve)")
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valve_id = multiway_valve_nodes[0]
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# 3. 查找包含指定试剂的试剂瓶
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reagent_vessel = None
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available_flasks = [node for node in G.nodes()
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if node.startswith('flask_')
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and G.nodes[node].get('type') == 'container']
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# 简化：使用第一个可用的试剂瓶，实际应该根据试剂名称匹配
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if available_flasks:
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reagent_vessel = available_flasks[0]
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else:
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raise ValueError("没有找到可用的试剂容器")
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# 4. 获取试剂瓶和反应器对应的阀门位置
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# 这需要根据实际连接图来确定，这里假设：
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reagent_valve_position = 1 # 试剂瓶连接到阀门位置1
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reactor_valve_position = 2 # 反应器连接到阀门位置2
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# 5. 执行添加操作序列
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# 5.1 设置阀门到试剂瓶位置
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action_sequence.append({
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"device_id": valve_id,
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"action_name": "set_position",
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"action_kwargs": {
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"position": reagent_valve_position
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}
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})
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# 5.2 使用注射器泵从试剂瓶吸取液体
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action_sequence.append({
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"device_id": transfer_pump_id,
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"action_name": "transfer",
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"action_kwargs": {
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"from_vessel": reagent_vessel,
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"to_vessel": transfer_pump_id, # 吸入到注射器
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"volume": volume,
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"amount": amount,
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"time": time / 2, # 吸取时间为总时间的一半
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"viscous": viscous,
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"rinsing_solvent": "",
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"rinsing_volume": 0.0,
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"rinsing_repeats": 0,
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"solid": False
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}
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})
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# 5.3 设置阀门到反应器位置
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action_sequence.append({
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"device_id": valve_id,
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"action_name": "set_position",
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"action_kwargs": {
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"position": reactor_valve_position
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}
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})
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# 5.4 使用注射器泵将液体推送到反应器
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action_sequence.append({
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"device_id": transfer_pump_id,
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"action_name": "transfer",
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"action_kwargs": {
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"from_vessel": transfer_pump_id, # 从注射器推出
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"to_vessel": vessel,
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"volume": volume,
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"amount": amount,
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"time": time / 2, # 推送时间为总时间的一半
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"viscous": viscous,
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"rinsing_solvent": "",
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"rinsing_volume": 0.0,
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"rinsing_repeats": 0,
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"solid": False
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}
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})
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# 6. 如果需要搅拌，启动搅拌器
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if stir:
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stirrer_nodes = [node for node in G.nodes()
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if G.nodes[node].get('class') == 'virtual_stirrer']
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if stirrer_nodes:
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stirrer_id = stirrer_nodes[0]
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action_sequence.append({
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"device_id": stirrer_id,
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"action_name": "start_stir",
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"action_kwargs": {
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"vessel": vessel,
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"stir_speed": stir_speed,
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"purpose": f"添加 {reagent} 后搅拌混合"
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}
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})
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else:
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print("警告：需要搅拌但未找到搅拌设备")
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return action_sequence
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import networkx as nx
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from typing import List, Dict, Any
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from .pump_protocol import generate_pump_protocol_with_rinsing
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def find_valve_position_for_vessel(G: nx.DiGraph, valve_id: str, vessel_id: str) -> int:
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def find_reagent_vessel(G: nx.DiGraph, reagent: str) -> str:
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"""
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根据连接图找到容器对应的阀门位置
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根据试剂名称查找对应的试剂瓶
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Args:
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G: 网络图
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valve_id: 阀门设备ID
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vessel_id: 容器ID
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reagent: 试剂名称
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Returns:
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int: 阀门位置编号 (1-8)
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str: 试剂瓶的vessel ID
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Raises:
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ValueError: 如果找不到对应的试剂瓶
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"""
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# 查找阀门到容器的连接
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edges = G.edges(data=True)
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# 按照pump_protocol的命名规则查找试剂瓶
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reagent_vessel_id = f"flask_{reagent}"
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for source, target, data in edges:
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if source == valve_id and target == vessel_id:
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# 从连接数据中提取端口信息
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port_info = data.get('port', {})
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valve_port = port_info.get(valve_id, '')
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# 解析端口名称获取位置编号
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if valve_port.startswith('multiway-valve-port-'):
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position = valve_port.split('-')[-1]
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return int(position)
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if reagent_vessel_id in G.nodes():
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return reagent_vessel_id
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# 默认返回位置1
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return 1
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# 如果直接匹配失败，尝试模糊匹配
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for node in G.nodes():
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if node.startswith('flask_') and reagent.lower() in node.lower():
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return node
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# 如果还是找不到，列出所有可用的试剂瓶
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available_flasks = [node for node in G.nodes()
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if node.startswith('flask_')
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and G.nodes[node].get('type') == 'container']
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raise ValueError(f"找不到试剂 '{reagent}' 对应的试剂瓶。可用试剂瓶: {available_flasks}")
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def generate_add_with_autodiscovery(
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G: nx.DiGraph,
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vessel: str,
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reagent: str,
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volume: float,
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**kwargs
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def find_connected_stirrer(G: nx.DiGraph, vessel: str) -> str:
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"""
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查找与指定容器相连的搅拌器
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Args:
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G: 网络图
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vessel: 容器ID
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Returns:
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str: 搅拌器ID，如果找不到则返回None
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"""
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# 查找所有搅拌器节点
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stirrer_nodes = [node for node in G.nodes()
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if G.nodes[node].get('class') == 'virtual_stirrer']
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# 检查哪个搅拌器与目标容器相连
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for stirrer in stirrer_nodes:
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if G.has_edge(stirrer, vessel) or G.has_edge(vessel, stirrer):
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return stirrer
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# 如果没有直接连接，返回第一个可用的搅拌器
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return stirrer_nodes[0] if stirrer_nodes else None
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def generate_add_protocol(
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G: nx.DiGraph,
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vessel: str,
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reagent: str,
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volume: float,
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mass: float = 0.0,
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amount: str = "",
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time: float = 0.0,
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stir: bool = False,
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stir_speed: float = 300.0,
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viscous: bool = False,
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purpose: str = "添加试剂"
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) -> List[Dict[str, Any]]:
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"""
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智能添加协议生成器 - 自动发现设备连接关系
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生成添加试剂的协议序列
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基于pump_protocol的成熟算法，实现试剂添加功能：
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1. 自动查找试剂瓶
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2. **先启动搅拌，再进行转移** - 确保试剂添加更均匀
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3. 使用pump_protocol实现液体转移
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Args:
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G: 有向图，节点为容器和设备，边为连接关系
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vessel: 目标容器（要添加试剂的容器）
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reagent: 试剂名称（用于查找对应的试剂瓶）
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volume: 要添加的体积 (mL)
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mass: 要添加的质量 (g) - 暂时未使用，预留接口
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amount: 其他数量描述
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time: 添加时间 (s)，如果指定则计算流速
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stir: 是否启用搅拌
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stir_speed: 搅拌速度 (RPM)
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viscous: 是否为粘稠液体
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purpose: 添加目的描述
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Returns:
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List[Dict[str, Any]]: 动作序列
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Raises:
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ValueError: 当找不到必要的设备或容器时
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"""
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action_sequence = []
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# 查找必需的设备
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devices = {
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'transfer_pump': None,
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'multiway_valve': None,
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'stirrer': None
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}
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# 1. 验证目标容器存在
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if vessel not in G.nodes():
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raise ValueError(f"目标容器 '{vessel}' 不存在于系统中")
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for node in G.nodes():
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node_class = G.nodes[node].get('class')
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if node_class == 'virtual_transfer_pump':
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devices['transfer_pump'] = node
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elif node_class == 'virtual_multiway_valve':
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devices['multiway_valve'] = node
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elif node_class == 'virtual_stirrer':
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devices['stirrer'] = node
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# 2. 查找试剂瓶
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try:
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reagent_vessel = find_reagent_vessel(G, reagent)
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except ValueError as e:
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raise ValueError(f"无法找到试剂 '{reagent}': {str(e)}")
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# 验证必需设备
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if not devices['transfer_pump']:
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raise ValueError("缺少注射器泵设备")
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if not devices['multiway_valve']:
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raise ValueError("缺少八通阀门设备")
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# 3. 验证是否存在从试剂瓶到目标容器的路径
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try:
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path = nx.shortest_path(G, source=reagent_vessel, target=vessel)
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print(f"ADD_PROTOCOL: 找到路径 {reagent_vessel} -> {vessel}: {path}")
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except nx.NetworkXNoPath:
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raise ValueError(f"从试剂瓶 '{reagent_vessel}' 到目标容器 '{vessel}' 没有可用路径")
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# 查找试剂容器
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reagent_vessels = [node for node in G.nodes()
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if node.startswith('flask_')
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and G.nodes[node].get('type') == 'container']
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# 4. **先启动搅拌** - 关键改进！
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if stir:
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try:
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stirrer_id = find_connected_stirrer(G, vessel)
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if stirrer_id:
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print(f"ADD_PROTOCOL: 找到搅拌器 {stirrer_id}，将在添加前启动搅拌")
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# 先启动搅拌
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stir_action = {
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"device_id": stirrer_id,
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"action_name": "start_stir",
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"action_kwargs": {
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"vessel": vessel,
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"stir_speed": stir_speed,
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"purpose": f"{purpose}: 启动搅拌，准备添加 {reagent}"
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}
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}
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action_sequence.append(stir_action)
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print(f"ADD_PROTOCOL: 已添加搅拌动作，速度 {stir_speed} RPM")
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else:
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print(f"ADD_PROTOCOL: 警告 - 需要搅拌但未找到与容器 {vessel} 相连的搅拌器")
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except Exception as e:
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print(f"ADD_PROTOCOL: 搅拌器配置出错: {str(e)}")
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if not reagent_vessels:
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raise ValueError("没有找到试剂容器")
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# 5. 如果指定了体积，执行液体转移
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if volume > 0:
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# 5.1 计算流速参数
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if time > 0:
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# 根据时间计算流速
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transfer_flowrate = volume / time
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flowrate = transfer_flowrate
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else:
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# 使用默认流速
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if viscous:
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transfer_flowrate = 0.3 # 粘稠液体用较慢速度
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flowrate = 1.0
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else:
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transfer_flowrate = 0.5 # 普通液体默认速度
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flowrate = 2.5
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print(f"ADD_PROTOCOL: 准备转移 {volume} mL 从 {reagent_vessel} 到 {vessel}")
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print(f"ADD_PROTOCOL: 转移流速={transfer_flowrate} mL/s, 注入流速={flowrate} mL/s")
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# 5.2 使用pump_protocol的核心算法实现液体转移
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try:
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pump_actions = generate_pump_protocol_with_rinsing(
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G=G,
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from_vessel=reagent_vessel,
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to_vessel=vessel,
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volume=volume,
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amount=amount,
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time=time,
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viscous=viscous,
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rinsing_solvent="", # 添加试剂通常不需要清洗
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rinsing_volume=0.0,
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rinsing_repeats=0,
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solid=False,
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flowrate=flowrate,
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transfer_flowrate=transfer_flowrate
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)
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# 添加pump actions到序列中
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action_sequence.extend(pump_actions)
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except Exception as e:
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raise ValueError(f"生成泵协议时出错: {str(e)}")
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# 执行添加流程
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reagent_vessel = reagent_vessels[0]
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reagent_pos = find_valve_position_for_vessel(G, devices['multiway_valve'], reagent_vessel)
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reactor_pos = find_valve_position_for_vessel(G, devices['multiway_valve'], vessel)
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print(f"ADD_PROTOCOL: 生成了 {len(action_sequence)} 个动作")
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return action_sequence
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def generate_add_protocol_with_cleaning(
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G: nx.DiGraph,
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vessel: str,
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reagent: str,
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volume: float,
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mass: float = 0.0,
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amount: str = "",
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time: float = 0.0,
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stir: bool = False,
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stir_speed: float = 300.0,
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viscous: bool = False,
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purpose: str = "添加试剂",
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cleaning_solvent: str = "air",
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cleaning_volume: float = 5.0,
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cleaning_repeats: int = 1
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) -> List[Dict[str, Any]]:
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"""
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生成带清洗的添加试剂协议
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# 生成操作序列
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action_sequence.extend([
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# 切换到试剂瓶
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{
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"device_id": devices['multiway_valve'],
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||||
"action_name": "set_position",
|
||||
"action_kwargs": {"position": reagent_pos}
|
||||
},
|
||||
# 吸取试剂
|
||||
{
|
||||
"device_id": devices['transfer_pump'],
|
||||
"action_name": "transfer",
|
||||
"action_kwargs": {
|
||||
"from_vessel": reagent_vessel,
|
||||
"to_vessel": devices['transfer_pump'],
|
||||
"volume": volume,
|
||||
"amount": kwargs.get('amount', ''),
|
||||
"time": kwargs.get('time', 10.0) / 2,
|
||||
"viscous": kwargs.get('viscous', False),
|
||||
"rinsing_solvent": "",
|
||||
"rinsing_volume": 0.0,
|
||||
"rinsing_repeats": 0,
|
||||
"solid": False
|
||||
与普通添加协议的区别是会在添加后进行管道清洗
|
||||
|
||||
Args:
|
||||
G: 有向图
|
||||
vessel: 目标容器
|
||||
reagent: 试剂名称
|
||||
volume: 添加体积
|
||||
mass: 添加质量（预留）
|
||||
amount: 其他数量描述
|
||||
time: 添加时间
|
||||
stir: 是否搅拌
|
||||
stir_speed: 搅拌速度
|
||||
viscous: 是否粘稠
|
||||
purpose: 添加目的
|
||||
cleaning_solvent: 清洗溶剂（"air"表示空气清洗）
|
||||
cleaning_volume: 清洗体积
|
||||
cleaning_repeats: 清洗重复次数
|
||||
|
||||
Returns:
|
||||
List[Dict[str, Any]]: 动作序列
|
||||
"""
|
||||
action_sequence = []
|
||||
|
||||
# 1. 查找试剂瓶
|
||||
reagent_vessel = find_reagent_vessel(G, reagent)
|
||||
|
||||
# 2. **先启动搅拌**
|
||||
if stir:
|
||||
stirrer_id = find_connected_stirrer(G, vessel)
|
||||
if stirrer_id:
|
||||
action_sequence.append({
|
||||
"device_id": stirrer_id,
|
||||
"action_name": "start_stir",
|
||||
"action_kwargs": {
|
||||
"vessel": vessel,
|
||||
"stir_speed": stir_speed,
|
||||
"purpose": f"{purpose}: 启动搅拌，准备添加 {reagent}"
|
||||
}
|
||||
})
|
||||
|
||||
# 3. 计算流速
|
||||
if time > 0:
|
||||
transfer_flowrate = volume / time
|
||||
flowrate = transfer_flowrate
|
||||
else:
|
||||
if viscous:
|
||||
transfer_flowrate = 0.3
|
||||
flowrate = 1.0
|
||||
else:
|
||||
transfer_flowrate = 0.5
|
||||
flowrate = 2.5
|
||||
|
||||
# 4. 使用带清洗的pump_protocol
|
||||
pump_actions = generate_pump_protocol_with_rinsing(
|
||||
G=G,
|
||||
from_vessel=reagent_vessel,
|
||||
to_vessel=vessel,
|
||||
volume=volume,
|
||||
amount=amount,
|
||||
time=time,
|
||||
viscous=viscous,
|
||||
rinsing_solvent=cleaning_solvent,
|
||||
rinsing_volume=cleaning_volume,
|
||||
rinsing_repeats=cleaning_repeats,
|
||||
solid=False,
|
||||
flowrate=flowrate,
|
||||
transfer_flowrate=transfer_flowrate
|
||||
)
|
||||
|
||||
action_sequence.extend(pump_actions)
|
||||
|
||||
return action_sequence
|
||||
|
||||
|
||||
def generate_sequential_add_protocol(
|
||||
G: nx.DiGraph,
|
||||
vessel: str,
|
||||
reagents: List[Dict[str, Any]],
|
||||
stir_between_additions: bool = True,
|
||||
final_stir: bool = True,
|
||||
final_stir_speed: float = 400.0,
|
||||
final_stir_time: float = 300.0
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""
|
||||
生成连续添加多种试剂的协议
|
||||
|
||||
Args:
|
||||
G: 网络图
|
||||
vessel: 目标容器
|
||||
reagents: 试剂列表，每个元素包含试剂添加参数
|
||||
stir_between_additions: 是否在每次添加之间搅拌
|
||||
final_stir: 是否在所有添加完成后进行最终搅拌
|
||||
final_stir_speed: 最终搅拌速度
|
||||
final_stir_time: 最终搅拌时间
|
||||
|
||||
Returns:
|
||||
List[Dict[str, Any]]: 完整的动作序列
|
||||
|
||||
Example:
|
||||
reagents = [
|
||||
{
|
||||
"reagent": "DMF",
|
||||
"volume": 10.0,
|
||||
"viscous": False,
|
||||
"stir_speed": 300.0
|
||||
},
|
||||
{
|
||||
"reagent": "ethyl_acetate",
|
||||
"volume": 5.0,
|
||||
"viscous": False,
|
||||
"stir_speed": 350.0
|
||||
}
|
||||
},
|
||||
# 切换到反应器
|
||||
{
|
||||
"device_id": devices['multiway_valve'],
|
||||
"action_name": "set_position",
|
||||
"action_kwargs": {"position": reactor_pos}
|
||||
},
|
||||
# 推送到反应器
|
||||
{
|
||||
"device_id": devices['transfer_pump'],
|
||||
"action_name": "transfer",
|
||||
"action_kwargs": {
|
||||
"from_vessel": devices['transfer_pump'],
|
||||
"to_vessel": vessel,
|
||||
"volume": volume,
|
||||
"amount": kwargs.get('amount', ''),
|
||||
"time": kwargs.get('time', 10.0) / 2,
|
||||
"viscous": kwargs.get('viscous', False),
|
||||
"rinsing_solvent": "",
|
||||
"rinsing_volume": 0.0,
|
||||
"rinsing_repeats": 0,
|
||||
"solid": False
|
||||
}
|
||||
}
|
||||
])
|
||||
]
|
||||
"""
|
||||
action_sequence = []
|
||||
|
||||
# 如果需要搅拌
|
||||
if kwargs.get('stir', False) and devices['stirrer']:
|
||||
action_sequence.append({
|
||||
"device_id": devices['stirrer'],
|
||||
"action_name": "start_stir",
|
||||
"action_kwargs": {
|
||||
"vessel": vessel,
|
||||
"stir_speed": kwargs.get('stir_speed', 300.0),
|
||||
"purpose": f"添加 {reagent} 后混合"
|
||||
}
|
||||
})
|
||||
for i, reagent_params in enumerate(reagents):
|
||||
print(f"ADD_PROTOCOL: 处理第 {i+1}/{len(reagents)} 个试剂: {reagent_params.get('reagent')}")
|
||||
|
||||
# 生成单个试剂的添加协议
|
||||
add_actions = generate_add_protocol(
|
||||
G=G,
|
||||
vessel=vessel,
|
||||
reagent=reagent_params.get('reagent'),
|
||||
volume=reagent_params.get('volume', 0.0),
|
||||
mass=reagent_params.get('mass', 0.0),
|
||||
amount=reagent_params.get('amount', ''),
|
||||
time=reagent_params.get('time', 0.0),
|
||||
stir=stir_between_additions,
|
||||
stir_speed=reagent_params.get('stir_speed', 300.0),
|
||||
viscous=reagent_params.get('viscous', False),
|
||||
purpose=reagent_params.get('purpose', f'添加试剂 {i+1}')
|
||||
)
|
||||
|
||||
action_sequence.extend(add_actions)
|
||||
|
||||
# 在添加之间加入等待时间
|
||||
if i < len(reagents) - 1: # 不是最后一个试剂
|
||||
action_sequence.append({
|
||||
"action_name": "wait",
|
||||
"action_kwargs": {"time": 2}
|
||||
})
|
||||
|
||||
return action_sequence
|
||||
# 最终搅拌
|
||||
if final_stir:
|
||||
stirrer_id = find_connected_stirrer(G, vessel)
|
||||
if stirrer_id:
|
||||
action_sequence.extend([
|
||||
{
|
||||
"action_name": "wait",
|
||||
"action_kwargs": {"time": final_stir_time}
|
||||
}
|
||||
])
|
||||
|
||||
print(f"ADD_PROTOCOL: 连续添加协议生成完成，共 {len(action_sequence)} 个动作")
|
||||
return action_sequence
|
||||
|
||||
|
||||
# 使用示例和测试函数
|
||||
def test_add_protocol():
|
||||
"""测试添加协议的示例"""
|
||||
print("=== ADD PROTOCOL 测试 ===")
|
||||
print("测试完成")
|
||||
|
||||
|
||||
if __name__ == "__main__":
|
||||
test_add_protocol()
|
||||
Reference in New Issue
Block a user