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修复了部分的protocol因为XDL更新导致的问题
但是pumptransfer，add，dissolve，separate还没修，后续还需要写virtual固体加料器
This commit is contained in:
KCFeng425
@@ -1,61 +1,110 @@
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from typing import List, Dict, Any
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from typing import List, Dict, Any, Optional
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import networkx as nx
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import logging
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from .pump_protocol import generate_pump_protocol
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logger = logging.getLogger(__name__)
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def debug_print(message):
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"""调试输出"""
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print(f"[EVAPORATE] {message}", flush=True)
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logger.info(f"[EVAPORATE] {message}")
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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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"""获取容器中的液体体积"""
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debug_print(f"检查容器 '{vessel}' 的液体体积...")
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if vessel not in G.nodes():
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debug_print(f"容器 '{vessel}' 不存在")
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return 0.0
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vessel_data = G.nodes[vessel].get('data', {})
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debug_print(f"容器数据: {vessel_data}")
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# 检查多种体积字段
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volume_keys = ['total_volume', 'volume', 'liquid_volume', 'current_volume']
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for key in volume_keys:
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if key in vessel_data:
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try:
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volume = float(vessel_data[key])
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debug_print(f"从 '{key}' 读取到体积: {volume}mL")
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return volume
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except (ValueError, TypeError):
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continue
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# 检查liquid数组
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liquids = vessel_data.get('liquid', [])
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if isinstance(liquids, list):
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total_volume = 0.0
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for liquid in liquids:
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if isinstance(liquid, dict):
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for vol_key in ['liquid_volume', 'volume', 'amount']:
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if vol_key in liquid:
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try:
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vol = float(liquid[vol_key])
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total_volume += vol
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debug_print(f"从液体数据 '{vol_key}' 读取: {vol}mL")
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except (ValueError, TypeError):
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continue
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if total_volume > 0:
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return total_volume
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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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debug_print(f"未检测到液体体积，返回 0.0")
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return 0.0
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def find_rotavap_device(G: nx.DiGraph) -> str:
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def find_rotavap_device(G: nx.DiGraph) -> Optional[str]:
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"""查找旋转蒸发仪设备"""
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rotavap_nodes = [node for node in G.nodes()
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if (G.nodes[node].get('class') or '') == 'virtual_rotavap']
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debug_print("查找旋转蒸发仪设备...")
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if rotavap_nodes:
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return rotavap_nodes[0]
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# 查找各种可能的旋转蒸发仪设备
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possible_devices = []
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for node in G.nodes():
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node_data = G.nodes[node]
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node_class = node_data.get('class', '')
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if any(keyword in node_class.lower() for keyword in ['rotavap', 'evaporator']):
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possible_devices.append(node)
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debug_print(f"找到旋转蒸发仪设备: {node}")
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raise ValueError("系统中未找到旋转蒸发仪设备")
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if possible_devices:
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return possible_devices[0]
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debug_print("未找到旋转蒸发仪设备")
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return None
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def find_solvent_recovery_vessel(G: nx.DiGraph) -> str:
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"""查找溶剂回收容器"""
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possible_names = [
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"flask_distillate",
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"bottle_distillate",
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"vessel_distillate",
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"distillate",
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"solvent_recovery",
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"flask_solvent_recovery",
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"collection_flask"
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def find_rotavap_vessel(G: nx.DiGraph) -> Optional[str]:
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"""查找旋转蒸发仪样品容器"""
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debug_print("查找旋转蒸发仪样品容器...")
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possible_vessels = [
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"rotavap", "rotavap_flask", "flask_rotavap",
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"evaporation_flask", "evaporator", "rotary_evaporator"
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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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for vessel in possible_vessels:
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if vessel in G.nodes():
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debug_print(f"找到旋转蒸发仪样品容器: {vessel}")
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return vessel
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# 如果找不到专门的回收容器，使用废液容器
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waste_names = ["waste_workup", "flask_waste", "bottle_waste", "waste"]
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for vessel_name in waste_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"未找到溶剂回收容器。尝试了以下名称: {possible_names + waste_names}")
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debug_print("未找到旋转蒸发仪样品容器")
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return None
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def find_recovery_vessel(G: nx.DiGraph) -> Optional[str]:
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"""查找溶剂回收容器"""
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debug_print("查找溶剂回收容器...")
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possible_vessels = [
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"flask_distillate", "distillate", "solvent_recovery",
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"rotavap_condenser", "condenser", "waste_workup", "waste"
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]
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for vessel in possible_vessels:
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if vessel in G.nodes():
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debug_print(f"找到回收容器: {vessel}")
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return vessel
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debug_print("未找到回收容器")
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return None
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def generate_evaporate_protocol(
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G: nx.DiGraph,
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@@ -63,264 +112,276 @@ def generate_evaporate_protocol(
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pressure: float = 0.1,
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temp: float = 60.0,
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time: float = 1800.0,
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stir_speed: float = 100.0
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stir_speed: float = 100.0,
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solvent: str = "",
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**kwargs # 接受任意额外参数，增强兼容性
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) -> List[Dict[str, Any]]:
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"""
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生成蒸发操作的协议序列
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蒸发流程：
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1. 液体转移：将待蒸发溶液从源容器转移到旋转蒸发仪
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2. 蒸发操作：执行旋转蒸发
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3. (可选) 溶剂回收：将冷凝的溶剂转移到回收容器
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4. 残留物转移：将浓缩物从旋转蒸发仪转移回原容器或新容器
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生成蒸发操作的协议序列 - 增强兼容性版本
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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: 包含待蒸发溶液的容器名称
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pressure: 蒸发时的真空度 (bar)，默认0.1 bar
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temp: 蒸发时的加热温度 (°C)，默认60°C
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time: 蒸发时间 (秒)，默认1800秒(30分钟)
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stir_speed: 旋转速度 (RPM)，默认100 RPM
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G: 设备图
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vessel: 蒸发容器名称（必需）
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pressure: 真空度 (bar)，默认0.1
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temp: 加热温度 (°C)，默认60
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time: 蒸发时间 (秒)，默认1800
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stir_speed: 旋转速度 (RPM)，默认100
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solvent: 溶剂名称（可选，用于参数优化）
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**kwargs: 其他参数（兼容性）
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Returns:
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List[Dict[str, Any]]: 蒸发操作的动作序列
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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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evaporate_actions = generate_evaporate_protocol(G, "reaction_mixture", 0.05, 80.0, 3600.0)
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List[Dict[str, Any]]: 动作序列
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"""
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debug_print("=" * 50)
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debug_print("开始生成蒸发协议")
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debug_print(f"输入参数:")
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debug_print(f" - vessel: {vessel}")
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debug_print(f" - pressure: {pressure} bar")
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debug_print(f" - temp: {temp}°C")
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debug_print(f" - time: {time}s ({time/60:.1f}分钟)")
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debug_print(f" - stir_speed: {stir_speed} RPM")
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debug_print(f" - solvent: '{solvent}'")
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debug_print(f" - 其他参数: {kwargs}")
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debug_print("=" * 50)
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action_sequence = []
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print(f"EVAPORATE: 开始生成蒸发协议")
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print(f" - 源容器: {vessel}")
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print(f" - 真空度: {pressure} bar")
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print(f" - 温度: {temp}°C")
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print(f" - 时间: {time}s ({time/60:.1f}分钟)")
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print(f" - 旋转速度: {stir_speed} RPM")
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# === 参数验证和修正 ===
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debug_print("步骤1: 参数验证和修正...")
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# 验证必需参数
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if not vessel:
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raise ValueError("vessel 参数不能为空")
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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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raise ValueError(f"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"EVAPORATE: 源容器 {vessel} 中有 {source_volume} mL 液体")
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# 修正参数范围
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if pressure <= 0 or pressure > 1.0:
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debug_print(f"真空度 {pressure} bar 超出范围，修正为 0.1 bar")
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pressure = 0.1
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# 查找旋转蒸发仪
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try:
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rotavap_id = find_rotavap_device(G)
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print(f"EVAPORATE: 找到旋转蒸发仪: {rotavap_id}")
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except ValueError as e:
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raise ValueError(f"无法找到旋转蒸发仪: {str(e)}")
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if temp < 10.0 or temp > 200.0:
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debug_print(f"温度 {temp}°C 超出范围，修正为 60°C")
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temp = 60.0
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if time <= 0:
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debug_print(f"时间 {time}s 无效，修正为 1800s")
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time = 1800.0
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if stir_speed < 10.0 or stir_speed > 300.0:
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debug_print(f"旋转速度 {stir_speed} RPM 超出范围，修正为 100 RPM")
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stir_speed = 100.0
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# 根据溶剂优化参数
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if solvent:
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debug_print(f"根据溶剂 '{solvent}' 优化参数...")
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solvent_lower = solvent.lower()
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if any(s in solvent_lower for s in ['water', 'aqueous', 'h2o']):
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temp = max(temp, 80.0)
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pressure = max(pressure, 0.2)
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debug_print("水系溶剂：提高温度和真空度")
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elif any(s in solvent_lower for s in ['ethanol', 'methanol', 'acetone']):
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temp = min(temp, 50.0)
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pressure = min(pressure, 0.05)
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debug_print("易挥发溶剂：降低温度和真空度")
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elif any(s in solvent_lower for s in ['dmso', 'dmi', 'toluene']):
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temp = max(temp, 100.0)
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pressure = min(pressure, 0.01)
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debug_print("高沸点溶剂：提高温度，降低真空度")
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debug_print(f"最终参数: pressure={pressure}, temp={temp}, time={time}, stir_speed={stir_speed}")
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# === 查找设备 ===
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debug_print("步骤2: 查找设备...")
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# 查找旋转蒸发仪设备
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rotavap_device = find_rotavap_device(G)
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if not rotavap_device:
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debug_print("未找到旋转蒸发仪设备，使用通用设备")
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rotavap_device = "rotavap_1" # 默认设备ID
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# 查找旋转蒸发仪样品容器
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rotavap_vessel = None
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possible_rotavap_vessels = ["rotavap_flask", "rotavap", "flask_rotavap", "evaporation_flask"]
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for rv in possible_rotavap_vessels:
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if rv in G.nodes():
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rotavap_vessel = rv
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break
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rotavap_vessel = find_rotavap_vessel(G)
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if not rotavap_vessel:
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raise ValueError(f"未找到旋转蒸发仪样品容器。尝试了: {possible_rotavap_vessels}")
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debug_print("未找到旋转蒸发仪样品容器，使用默认容器")
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rotavap_vessel = "rotavap" # 默认容器
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print(f"EVAPORATE: 找到旋转蒸发仪样品容器: {rotavap_vessel}")
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# 查找回收容器
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recovery_vessel = find_recovery_vessel(G)
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# 查找溶剂回收容器
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try:
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distillate_vessel = find_solvent_recovery_vessel(G)
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print(f"EVAPORATE: 找到溶剂回收容器: {distillate_vessel}")
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except ValueError as e:
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print(f"EVAPORATE: 警告 - {str(e)}")
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distillate_vessel = None
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debug_print(f"设备配置:")
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debug_print(f" - 旋转蒸发仪设备: {rotavap_device}")
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debug_print(f" - 样品容器: {rotavap_vessel}")
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debug_print(f" - 回收容器: {recovery_vessel}")
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# === 体积计算 ===
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debug_print("步骤3: 体积计算...")
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source_volume = get_vessel_liquid_volume(G, vessel)
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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, 250.0) # 90%或最多250mL
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print(f"EVAPORATE: 检测到液体体积，将转移 {transfer_volume} mL")
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debug_print(f"检测到液体体积 {source_volume}mL，转移 {transfer_volume}mL")
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else:
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# 如果检测不到液体体积，默认转移一整瓶 250mL
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transfer_volume = 250.0
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print(f"EVAPORATE: 未检测到液体体积，默认转移整瓶 {transfer_volume} mL")
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transfer_volume = 50.0 # 默认小体积，更安全
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debug_print(f"未检测到液体体积，使用默认转移体积 {transfer_volume}mL")
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# === 第一步：将待蒸发溶液转移到旋转蒸发仪 ===
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print(f"EVAPORATE: 将 {transfer_volume} mL 溶液从 {vessel} 转移到 {rotavap_vessel}")
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try:
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transfer_to_rotavap_actions = generate_pump_protocol(
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G=G,
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from_vessel=vessel,
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to_vessel=rotavap_vessel,
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volume=transfer_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(transfer_to_rotavap_actions)
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except Exception as e:
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raise ValueError(f"无法将溶液转移到旋转蒸发仪: {str(e)}")
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# === 生成动作序列 ===
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debug_print("步骤4: 生成动作序列...")
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# 转移后等待
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wait_action = {
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# 动作1: 转移溶液到旋转蒸发仪
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if vessel != rotavap_vessel:
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debug_print(f"转移 {transfer_volume}mL 从 {vessel} 到 {rotavap_vessel}")
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try:
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transfer_actions = generate_pump_protocol(
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G=G,
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from_vessel=vessel,
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to_vessel=rotavap_vessel,
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volume=transfer_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(transfer_actions)
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debug_print(f"添加了 {len(transfer_actions)} 个转移动作")
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except Exception as e:
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debug_print(f"转移失败: {str(e)}")
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# 继续执行，不中断整个流程
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# 等待稳定
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action_sequence.append({
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"action_name": "wait",
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"action_kwargs": {"time": 10}
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}
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action_sequence.append(wait_action)
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})
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# === 第二步：执行旋转蒸发 ===
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print(f"EVAPORATE: 执行旋转蒸发操作")
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# 动作2: 执行蒸发
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debug_print(f"执行蒸发: {rotavap_device}")
|
||||
evaporate_action = {
|
||||
"device_id": rotavap_id,
|
||||
"device_id": rotavap_device,
|
||||
"action_name": "evaporate",
|
||||
"action_kwargs": {
|
||||
"vessel": rotavap_vessel,
|
||||
"pressure": pressure,
|
||||
"temp": temp,
|
||||
"time": time,
|
||||
"stir_speed": stir_speed
|
||||
"stir_speed": stir_speed,
|
||||
"solvent": solvent
|
||||
}
|
||||
}
|
||||
action_sequence.append(evaporate_action)
|
||||
|
||||
# 蒸发后等待系统稳定
|
||||
wait_action = {
|
||||
# 蒸发后等待
|
||||
action_sequence.append({
|
||||
"action_name": "wait",
|
||||
"action_kwargs": {"time": 30}
|
||||
}
|
||||
action_sequence.append(wait_action)
|
||||
})
|
||||
|
||||
# === 第三步：溶剂回收（如果有回收容器）===
|
||||
if distillate_vessel:
|
||||
print(f"EVAPORATE: 回收冷凝溶剂到 {distillate_vessel}")
|
||||
# 动作3: 回收溶剂（如果有回收容器）
|
||||
if recovery_vessel:
|
||||
debug_print(f"回收溶剂到 {recovery_vessel}")
|
||||
try:
|
||||
condenser_vessel = "rotavap_condenser"
|
||||
if condenser_vessel in G.nodes():
|
||||
# 估算回收体积（约为转移体积的70% - 大部分溶剂被蒸发回收）
|
||||
recovery_volume = transfer_volume * 0.7
|
||||
print(f"EVAPORATE: 预计回收 {recovery_volume} mL 溶剂")
|
||||
|
||||
recovery_actions = generate_pump_protocol(
|
||||
G=G,
|
||||
from_vessel=condenser_vessel,
|
||||
to_vessel=distillate_vessel,
|
||||
volume=recovery_volume,
|
||||
flowrate=3.0,
|
||||
transfer_flowrate=3.0
|
||||
)
|
||||
action_sequence.extend(recovery_actions)
|
||||
else:
|
||||
print("EVAPORATE: 未找到冷凝器容器，跳过溶剂回收")
|
||||
except Exception as e:
|
||||
print(f"EVAPORATE: 溶剂回收失败: {str(e)}")
|
||||
|
||||
# === 第四步：将浓缩物转移回原容器 ===
|
||||
print(f"EVAPORATE: 将浓缩物从旋转蒸发仪转移回 {vessel}")
|
||||
try:
|
||||
# 估算浓缩物体积（约为转移体积的20% - 大部分溶剂已蒸发）
|
||||
concentrate_volume = transfer_volume * 0.2
|
||||
print(f"EVAPORATE: 预计浓缩物体积 {concentrate_volume} mL")
|
||||
|
||||
transfer_back_actions = generate_pump_protocol(
|
||||
G=G,
|
||||
from_vessel=rotavap_vessel,
|
||||
to_vessel=vessel,
|
||||
volume=concentrate_volume,
|
||||
flowrate=1.0, # 浓缩物可能粘稠，用较慢流速
|
||||
transfer_flowrate=1.0
|
||||
)
|
||||
action_sequence.extend(transfer_back_actions)
|
||||
except Exception as e:
|
||||
print(f"EVAPORATE: 将浓缩物转移回容器失败: {str(e)}")
|
||||
|
||||
# === 第五步：清洗旋转蒸发仪 ===
|
||||
print(f"EVAPORATE: 清洗旋转蒸发仪")
|
||||
try:
|
||||
# 查找清洗溶剂
|
||||
cleaning_solvent = None
|
||||
for solvent in ["flask_ethanol", "flask_acetone", "flask_water"]:
|
||||
if solvent in G.nodes():
|
||||
cleaning_solvent = solvent
|
||||
break
|
||||
|
||||
if cleaning_solvent and distillate_vessel:
|
||||
# 用固定量溶剂清洗（不依赖检测体积）
|
||||
cleaning_volume = 50.0 # 固定50mL清洗
|
||||
print(f"EVAPORATE: 用 {cleaning_volume} mL {cleaning_solvent} 清洗")
|
||||
|
||||
# 清洗溶剂加入
|
||||
cleaning_actions = generate_pump_protocol(
|
||||
recovery_volume = transfer_volume * 0.7 # 估算回收70%
|
||||
recovery_actions = generate_pump_protocol(
|
||||
G=G,
|
||||
from_vessel=cleaning_solvent,
|
||||
to_vessel=rotavap_vessel,
|
||||
volume=cleaning_volume,
|
||||
flowrate=2.0,
|
||||
transfer_flowrate=2.0
|
||||
from_vessel="rotavap_condenser", # 假设的冷凝器
|
||||
to_vessel=recovery_vessel,
|
||||
volume=recovery_volume,
|
||||
flowrate=3.0,
|
||||
transfer_flowrate=3.0
|
||||
)
|
||||
action_sequence.extend(cleaning_actions)
|
||||
|
||||
# 将清洗液转移到废液/回收容器
|
||||
waste_actions = generate_pump_protocol(
|
||||
action_sequence.extend(recovery_actions)
|
||||
debug_print(f"添加了 {len(recovery_actions)} 个回收动作")
|
||||
except Exception as e:
|
||||
debug_print(f"溶剂回收失败: {str(e)}")
|
||||
|
||||
# 动作4: 转移浓缩物回原容器
|
||||
if vessel != rotavap_vessel:
|
||||
debug_print(f"转移浓缩物从 {rotavap_vessel} 到 {vessel}")
|
||||
try:
|
||||
concentrate_volume = transfer_volume * 0.2 # 估算浓缩物20%
|
||||
transfer_back_actions = generate_pump_protocol(
|
||||
G=G,
|
||||
from_vessel=rotavap_vessel,
|
||||
to_vessel=distillate_vessel, # 使用回收容器作为废液
|
||||
volume=cleaning_volume,
|
||||
flowrate=2.0,
|
||||
transfer_flowrate=2.0
|
||||
to_vessel=vessel,
|
||||
volume=concentrate_volume,
|
||||
flowrate=1.0, # 浓缩物可能粘稠
|
||||
transfer_flowrate=1.0
|
||||
)
|
||||
action_sequence.extend(waste_actions)
|
||||
|
||||
except Exception as e:
|
||||
print(f"EVAPORATE: 清洗步骤失败: {str(e)}")
|
||||
action_sequence.extend(transfer_back_actions)
|
||||
debug_print(f"添加了 {len(transfer_back_actions)} 个转移回收动作")
|
||||
except Exception as e:
|
||||
debug_print(f"浓缩物转移失败: {str(e)}")
|
||||
|
||||
print(f"EVAPORATE: 生成了 {len(action_sequence)} 个动作")
|
||||
print(f"EVAPORATE: 蒸发协议生成完成")
|
||||
print(f"EVAPORATE: 总处理体积: {transfer_volume} mL")
|
||||
# === 总结 ===
|
||||
debug_print("=" * 50)
|
||||
debug_print(f"蒸发协议生成完成")
|
||||
debug_print(f"总动作数: {len(action_sequence)}")
|
||||
debug_print(f"处理体积: {transfer_volume}mL")
|
||||
debug_print(f"蒸发参数: {pressure} bar, {temp}°C, {time}s, {stir_speed} RPM")
|
||||
debug_print("=" * 50)
|
||||
|
||||
return action_sequence
|
||||
|
||||
# === 便捷函数 ===
|
||||
|
||||
# 便捷函数：常用蒸发方案 - 都使用250mL标准瓶体积
|
||||
def generate_quick_evaporate_protocol(
|
||||
G: nx.DiGraph,
|
||||
vessel: str,
|
||||
temp: float = 40.0,
|
||||
time: float = 900.0 # 15分钟
|
||||
**kwargs
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""快速蒸发：低温、短时间、整瓶处理"""
|
||||
return generate_evaporate_protocol(G, vessel, 0.2, temp, time, 80.0)
|
||||
|
||||
"""快速蒸发：低温短时间"""
|
||||
return generate_evaporate_protocol(
|
||||
G, vessel,
|
||||
pressure=0.2,
|
||||
temp=40.0,
|
||||
time=900.0,
|
||||
stir_speed=80.0,
|
||||
**kwargs
|
||||
)
|
||||
|
||||
def generate_gentle_evaporate_protocol(
|
||||
G: nx.DiGraph,
|
||||
vessel: str,
|
||||
temp: float = 50.0,
|
||||
time: float = 2700.0 # 45分钟
|
||||
**kwargs
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""温和蒸发：中等条件、较长时间、整瓶处理"""
|
||||
return generate_evaporate_protocol(G, vessel, 0.1, temp, time, 60.0)
|
||||
|
||||
"""温和蒸发：中等条件"""
|
||||
return generate_evaporate_protocol(
|
||||
G, vessel,
|
||||
pressure=0.1,
|
||||
temp=50.0,
|
||||
time=2700.0,
|
||||
stir_speed=60.0,
|
||||
**kwargs
|
||||
)
|
||||
|
||||
def generate_high_vacuum_evaporate_protocol(
|
||||
G: nx.DiGraph,
|
||||
vessel: str,
|
||||
temp: float = 35.0,
|
||||
time: float = 3600.0 # 1小时
|
||||
**kwargs
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""高真空蒸发：低温、高真空、长时间、整瓶处理"""
|
||||
return generate_evaporate_protocol(G, vessel, 0.01, temp, time, 120.0)
|
||||
|
||||
"""高真空蒸发：低温高真空"""
|
||||
return generate_evaporate_protocol(
|
||||
G, vessel,
|
||||
pressure=0.01,
|
||||
temp=35.0,
|
||||
time=3600.0,
|
||||
stir_speed=120.0,
|
||||
**kwargs
|
||||
)
|
||||
|
||||
def generate_standard_evaporate_protocol(
|
||||
G: nx.DiGraph,
|
||||
vessel: str
|
||||
vessel: str,
|
||||
**kwargs
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""标准蒸发：常用参数、整瓶250mL处理"""
|
||||
"""标准蒸发：常用参数"""
|
||||
return generate_evaporate_protocol(
|
||||
G=G,
|
||||
vessel=vessel,
|
||||
pressure=0.1, # 标准真空度
|
||||
temp=60.0, # 适中温度
|
||||
time=1800.0, # 30分钟
|
||||
stir_speed=100.0 # 适中旋转速度
|
||||
G, vessel,
|
||||
pressure=0.1,
|
||||
temp=60.0,
|
||||
time=1800.0,
|
||||
stir_speed=100.0,
|
||||
**kwargs
|
||||
)
|
||||
|
||||
Reference in New Issue
Block a user