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21afdb62bc
* 添加了5个缺失的protocol，验证了可以运行 * bump version to 0.9.8 * 修复新增的Action的字段缺失 --------- Co-authored-by: Xuwznln <18435084+Xuwznln@users.noreply.github.com>
411 lines
14 KiB
Python
411 lines
14 KiB
Python
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_acid_base_vessel(G: nx.DiGraph, reagent: str) -> str:
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"""
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查找酸碱试剂容器，支持多种匹配模式
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Args:
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G: 网络图
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reagent: 试剂名称（如 "hydrochloric acid", "sodium hydroxide"）
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Returns:
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str: 试剂容器ID
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"""
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print(f"ADJUST_PH: 正在查找试剂 '{reagent}' 的容器...")
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# 常见酸碱试剂的别名映射
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reagent_aliases = {
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"hydrochloric acid": ["HCl", "hydrochloric_acid", "hcl", "muriatic_acid"],
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"sodium hydroxide": ["NaOH", "sodium_hydroxide", "naoh", "caustic_soda"],
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"sulfuric acid": ["H2SO4", "sulfuric_acid", "h2so4"],
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"nitric acid": ["HNO3", "nitric_acid", "hno3"],
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"acetic acid": ["CH3COOH", "acetic_acid", "glacial_acetic_acid"],
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"ammonia": ["NH3", "ammonium_hydroxide", "nh3"],
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"potassium hydroxide": ["KOH", "potassium_hydroxide", "koh"]
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}
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# 构建搜索名称列表
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search_names = [reagent.lower()]
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# 添加别名
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for base_name, aliases in reagent_aliases.items():
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if reagent.lower() in base_name.lower() or base_name.lower() in reagent.lower():
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search_names.extend([alias.lower() for alias in aliases])
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# 构建可能的容器名称
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possible_names = []
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for name in search_names:
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name_clean = name.replace(" ", "_").replace("-", "_")
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possible_names.extend([
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f"flask_{name_clean}",
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f"bottle_{name_clean}",
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f"reagent_{name_clean}",
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f"acid_{name_clean}" if "acid" in name else f"base_{name_clean}",
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f"{name_clean}_bottle",
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f"{name_clean}_flask",
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name_clean
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])
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# 第一步：通过容器名称匹配
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for vessel_name in possible_names:
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if vessel_name in G.nodes():
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print(f"ADJUST_PH: 通过名称匹配找到容器: {vessel_name}")
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return vessel_name
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# 第二步：通过模糊匹配
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for node_id in G.nodes():
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if G.nodes[node_id].get('type') == 'container':
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node_name = G.nodes[node_id].get('name', '').lower()
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# 检查是否包含任何搜索名称
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for search_name in search_names:
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if search_name in node_id.lower() or search_name in node_name:
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print(f"ADJUST_PH: 通过模糊匹配找到容器: {node_id}")
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return node_id
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# 第三步：通过液体类型匹配
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for node_id in G.nodes():
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if G.nodes[node_id].get('type') == 'container':
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vessel_data = G.nodes[node_id].get('data', {})
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liquids = vessel_data.get('liquid', [])
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for liquid in liquids:
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if isinstance(liquid, dict):
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liquid_type = (liquid.get('liquid_type') or liquid.get('name', '')).lower()
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reagent_name = vessel_data.get('reagent_name', '').lower()
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for search_name in search_names:
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if search_name in liquid_type or search_name in reagent_name:
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print(f"ADJUST_PH: 通过液体类型匹配找到容器: {node_id}")
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return node_id
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# 列出可用容器帮助调试
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available_containers = []
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for node_id in G.nodes():
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if G.nodes[node_id].get('type') == 'container':
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vessel_data = G.nodes[node_id].get('data', {})
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liquids = vessel_data.get('liquid', [])
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liquid_types = [liquid.get('liquid_type', '') or liquid.get('name', '')
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for liquid in liquids if isinstance(liquid, dict)]
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available_containers.append({
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'id': node_id,
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'name': G.nodes[node_id].get('name', ''),
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'liquids': liquid_types,
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'reagent_name': vessel_data.get('reagent_name', '')
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})
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print(f"ADJUST_PH: 可用容器列表:")
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for container in available_containers:
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print(f" - {container['id']}: {container['name']}")
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print(f" 液体: {container['liquids']}")
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print(f" 试剂: {container['reagent_name']}")
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raise ValueError(f"找不到试剂 '{reagent}' 对应的容器。尝试了: {possible_names}")
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def find_connected_stirrer(G: nx.DiGraph, vessel: str) -> str:
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"""查找与容器相连的搅拌器"""
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stirrer_nodes = [node for node in G.nodes()
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if (G.nodes[node].get('class') or '') == 'virtual_stirrer']
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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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return stirrer_nodes[0] if stirrer_nodes else None
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def calculate_reagent_volume(target_ph_value: float, reagent: str, vessel_volume: float = 100.0) -> float: # 改为 target_ph_value
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"""
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估算需要的试剂体积来调节pH
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Args:
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target_ph_value: 目标pH值 # 改为 target_ph_value
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reagent: 试剂名称
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vessel_volume: 容器体积 (mL)
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Returns:
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float: 估算的试剂体积 (mL)
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"""
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# 简化的pH调节体积估算（实际应用中需要更精确的计算）
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if "acid" in reagent.lower() or "hcl" in reagent.lower():
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# 酸性试剂：pH越低需要的体积越大
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if target_ph_value < 3: # 改为 target_ph_value
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return vessel_volume * 0.05 # 5%
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elif target_ph_value < 5: # 改为 target_ph_value
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return vessel_volume * 0.02 # 2%
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else:
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return vessel_volume * 0.01 # 1%
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elif "hydroxide" in reagent.lower() or "naoh" in reagent.lower():
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# 碱性试剂：pH越高需要的体积越大
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if target_ph_value > 11: # 改为 target_ph_value
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return vessel_volume * 0.05 # 5%
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elif target_ph_value > 9: # 改为 target_ph_value
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return vessel_volume * 0.02 # 2%
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else:
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return vessel_volume * 0.01 # 1%
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else:
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# 未知试剂，使用默认值
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return vessel_volume * 0.01
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def generate_adjust_ph_protocol(
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G: nx.DiGraph,
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vessel: str,
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ph_value: float, # 改为 ph_value
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reagent: str,
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**kwargs
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) -> List[Dict[str, Any]]:
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"""
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生成调节pH的协议序列
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Args:
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G: 有向图，节点为容器和设备
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vessel: 目标容器（需要调节pH的容器）
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ph_value: 目标pH值（从XDL传入） # 改为 ph_value
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reagent: 酸碱试剂名称（从XDL传入）
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**kwargs: 其他可选参数，使用默认值
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Returns:
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List[Dict[str, Any]]: 动作序列
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"""
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action_sequence = []
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# 从kwargs中获取可选参数，如果没有则使用默认值
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volume = kwargs.get('volume', 0.0) # 自动估算体积
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stir = kwargs.get('stir', True) # 默认搅拌
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stir_speed = kwargs.get('stir_speed', 300.0) # 默认搅拌速度
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stir_time = kwargs.get('stir_time', 60.0) # 默认搅拌时间
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settling_time = kwargs.get('settling_time', 30.0) # 默认平衡时间
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print(f"ADJUST_PH: 开始生成pH调节协议")
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print(f" - 目标容器: {vessel}")
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print(f" - 目标pH: {ph_value}") # 改为 ph_value
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print(f" - 试剂: {reagent}")
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print(f" - 使用默认参数: 体积=自动估算, 搅拌=True, 搅拌速度=300RPM")
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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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# 2. 查找酸碱试剂容器
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try:
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reagent_vessel = find_acid_base_vessel(G, reagent)
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print(f"ADJUST_PH: 找到试剂容器: {reagent_vessel}")
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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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# 3. 如果未指定体积，自动估算
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if volume <= 0:
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# 获取目标容器的体积信息
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vessel_data = G.nodes[vessel].get('data', {})
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vessel_volume = vessel_data.get('max_volume', 100.0) # 默认100mL
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estimated_volume = calculate_reagent_volume(ph_value, reagent, vessel_volume) # 改为 ph_value
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volume = estimated_volume
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print(f"ADJUST_PH: 自动估算试剂体积: {volume:.2f} mL")
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# 4. 验证路径存在
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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"ADJUST_PH: 找到路径: {' → '.join(path)}")
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except nx.NetworkXNoPath:
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raise ValueError(f"从试剂容器 '{reagent_vessel}' 到目标容器 '{vessel}' 没有可用路径")
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# 5. 先启动搅拌（如果需要）
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stirrer_id = None
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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"ADJUST_PH: 找到搅拌器 {stirrer_id}，启动搅拌")
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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"pH调节: 启动搅拌，准备添加 {reagent}"
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}
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})
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# 等待搅拌稳定
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action_sequence.append({
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"action_name": "wait",
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"action_kwargs": {"time": 5}
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})
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else:
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print(f"ADJUST_PH: 警告 - 未找到搅拌器，继续执行")
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except Exception as e:
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print(f"ADJUST_PH: 搅拌器配置出错: {str(e)}")
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# 6. 缓慢添加试剂 - 使用pump_protocol
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print(f"ADJUST_PH: 开始添加试剂 {volume:.2f} mL")
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# 计算添加时间（pH调节需要缓慢添加）
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addition_time = max(30.0, volume * 2.0) # 至少30秒，每mL需要2秒
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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="",
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time=addition_time,
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viscous=False,
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rinsing_solvent="", # pH调节不需要清洗
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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=0.5 # 缓慢注入
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)
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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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# 7. 持续搅拌以混合和平衡
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if stir and stirrer_id:
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print(f"ADJUST_PH: 持续搅拌 {stir_time} 秒以混合试剂")
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action_sequence.append({
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"device_id": stirrer_id,
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"action_name": "stir",
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"action_kwargs": {
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"stir_time": stir_time,
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"stir_speed": stir_speed,
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"settling_time": settling_time,
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"purpose": f"pH调节: 混合试剂，目标pH={ph_value}" # 改为 ph_value
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}
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})
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# 8. 等待反应平衡
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action_sequence.append({
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"action_name": "wait",
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"action_kwargs": {
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"time": settling_time,
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"description": f"等待pH平衡到目标值 {ph_value}" # 改为 ph_value
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}
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})
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print(f"ADJUST_PH: 协议生成完成，共 {len(action_sequence)} 个动作")
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print(f"ADJUST_PH: 预计总时间: {addition_time + stir_time + settling_time:.0f} 秒")
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return action_sequence
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def generate_adjust_ph_protocol_stepwise(
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G: nx.DiGraph,
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vessel: str,
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ph_value: float,
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reagent: str,
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max_volume: float = 10.0,
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steps: int = 3
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) -> List[Dict[str, Any]]:
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"""
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分步调节pH的协议（更安全，避免过度调节）
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Args:
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G: 网络图
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vessel: 目标容器
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pH: 目标pH值
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reagent: 酸碱试剂
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max_volume: 最大试剂体积
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steps: 分步数量
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Returns:
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List[Dict[str, Any]]: 动作序列
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"""
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action_sequence = []
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print(f"ADJUST_PH: 开始分步pH调节（{steps}步）")
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# 每步添加的体积
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step_volume = max_volume / steps
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for i in range(steps):
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print(f"ADJUST_PH: 第 {i+1}/{steps} 步，添加 {step_volume} mL")
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# 生成单步协议
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step_actions = generate_adjust_ph_protocol(
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G=G,
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vessel=vessel,
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ph_value=ph_value,
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reagent=reagent,
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volume=step_volume,
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stir=True,
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stir_speed=300.0,
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stir_time=30.0,
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settling_time=20.0
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)
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action_sequence.extend(step_actions)
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# 步骤间等待
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if i < steps - 1:
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action_sequence.append({
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"action_name": "wait",
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"action_kwargs": {
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"time": 30,
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"description": f"pH调节第{i+1}步完成，等待下一步"
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}
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})
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print(f"ADJUST_PH: 分步pH调节完成")
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return action_sequence
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# 便捷函数：常用pH调节
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def generate_acidify_protocol(
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G: nx.DiGraph,
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vessel: str,
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target_ph: float = 2.0,
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acid: str = "hydrochloric acid"
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) -> List[Dict[str, Any]]:
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"""酸化协议"""
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return generate_adjust_ph_protocol(
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G, vessel, target_ph, acid, 0.0, True, 300.0, 120.0, 60.0
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)
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def generate_basify_protocol(
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G: nx.DiGraph,
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vessel: str,
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target_ph: float = 12.0,
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base: str = "sodium hydroxide"
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) -> List[Dict[str, Any]]:
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"""碱化协议"""
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return generate_adjust_ph_protocol(
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G, vessel, target_ph, base, 0.0, True, 300.0, 120.0, 60.0
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)
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def generate_neutralize_protocol(
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G: nx.DiGraph,
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vessel: str,
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reagent: str = "sodium hydroxide"
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) -> List[Dict[str, Any]]:
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"""中和协议（pH=7）"""
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return generate_adjust_ph_protocol(
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G, vessel, 7.0, reagent, 0.0, True, 350.0, 180.0, 90.0
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)
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# 测试函数
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def test_adjust_ph_protocol():
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"""测试pH调节协议"""
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print("=== ADJUST PH PROTOCOL 测试 ===")
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print("测试完成")
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if __name__ == "__main__":
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test_adjust_ph_protocol() |