protocol完整修复版本& bump version to 0.9.10

This commit is contained in:
KCFeng425
2025-07-10 16:48:09 +08:00
parent d82ccd5cf1
commit 7b93332bf5
25 changed files with 3760 additions and 1843 deletions

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@@ -1,230 +1,448 @@
import numpy as np
import networkx as nx
import re
import logging
from typing import List, Dict, Any, Union
from .pump_protocol import generate_pump_protocol_with_rinsing
logger = logging.getLogger(__name__)
def debug_print(message):
"""调试输出"""
print(f"[SEPARATE] {message}", flush=True)
logger.info(f"[SEPARATE] {message}")
def parse_volume_input(volume_input: Union[str, float]) -> float:
"""
解析体积输入,支持带单位的字符串
Args:
volume_input: 体积输入(如 "200 mL", "?", 50.0
Returns:
float: 体积(毫升)
"""
if isinstance(volume_input, (int, float)):
return float(volume_input)
if not volume_input or not str(volume_input).strip():
return 0.0
volume_str = str(volume_input).lower().strip()
debug_print(f"解析体积输入: '{volume_str}'")
# 处理未知体积
if volume_str in ['?', 'unknown', 'tbd', 'to be determined']:
default_volume = 100.0 # 默认100mL
debug_print(f"检测到未知体积,使用默认值: {default_volume}mL")
return default_volume
# 移除空格并提取数字和单位
volume_clean = re.sub(r'\s+', '', volume_str)
# 匹配数字和单位的正则表达式
match = re.match(r'([0-9]*\.?[0-9]+)\s*(ml|l|μl|ul|microliter|milliliter|liter)?', volume_clean)
if not match:
debug_print(f"⚠️ 无法解析体积: '{volume_str}'使用默认值100mL")
return 100.0
value = float(match.group(1))
unit = match.group(2) or 'ml' # 默认单位为毫升
# 转换为毫升
if unit in ['l', 'liter']:
volume = value * 1000.0 # L -> mL
elif unit in ['μl', 'ul', 'microliter']:
volume = value / 1000.0 # μL -> mL
else: # ml, milliliter 或默认
volume = value # 已经是mL
debug_print(f"体积转换: {value}{unit}{volume}mL")
return volume
def find_solvent_vessel(G: nx.DiGraph, solvent: str) -> str:
"""查找溶剂容器"""
if not solvent or not solvent.strip():
return ""
debug_print(f"查找溶剂 '{solvent}' 的容器...")
# 🔧 方法1直接搜索 data.reagent_name 和 config.reagent
for node in G.nodes():
node_data = G.nodes[node].get('data', {})
node_type = G.nodes[node].get('type', '')
config_data = G.nodes[node].get('config', {})
# 只搜索容器类型的节点
if node_type == 'container':
reagent_name = node_data.get('reagent_name', '').lower()
config_reagent = config_data.get('reagent', '').lower()
# 精确匹配
if reagent_name == solvent.lower() or config_reagent == solvent.lower():
debug_print(f"✅ 通过reagent字段找到容器: {node}")
return node
# 模糊匹配
if (solvent.lower() in reagent_name and reagent_name) or \
(solvent.lower() in config_reagent and config_reagent):
debug_print(f"✅ 通过reagent字段模糊匹配到容器: {node}")
return node
# 🔧 方法2常见的容器命名规则
solvent_clean = solvent.lower().replace(' ', '_').replace('-', '_')
possible_names = [
f"flask_{solvent_clean}",
f"bottle_{solvent_clean}",
f"vessel_{solvent_clean}",
f"{solvent_clean}_flask",
f"{solvent_clean}_bottle",
f"solvent_{solvent_clean}",
f"reagent_{solvent_clean}",
f"reagent_bottle_{solvent_clean}"
]
for name in possible_names:
if name in G.nodes():
node_type = G.nodes[name].get('type', '')
if node_type == 'container':
debug_print(f"✅ 通过命名规则找到容器: {name}")
return name
# 🔧 方法3使用第一个试剂瓶作为备选
for node_id in G.nodes():
node_data = G.nodes[node_id]
if (node_data.get('type') == 'container' and
('reagent' in node_id.lower() or 'bottle' in node_id.lower())):
debug_print(f"⚠️ 未找到专用容器,使用备选容器: {node_id}")
return node_id
debug_print(f"⚠️ 未找到溶剂 '{solvent}' 的容器")
return ""
def find_separator_device(G: nx.DiGraph, vessel: str) -> str:
"""查找分离器设备"""
debug_print(f"查找容器 '{vessel}' 对应的分离器设备...")
# 方法1查找连接到容器的分离器设备
for node in G.nodes():
node_class = G.nodes[node].get('class', '').lower()
if 'separator' in node_class:
# 检查是否连接到目标容器
if G.has_edge(node, vessel) or G.has_edge(vessel, node):
debug_print(f"✅ 找到连接的分离器: {node}")
return node
# 方法2根据命名规则查找
possible_names = [
f"{vessel}_controller",
f"{vessel}_separator",
vessel, # 容器本身可能就是分离器
"separator_1",
"virtual_separator"
]
for name in possible_names:
if name in G.nodes():
node_class = G.nodes[name].get('class', '').lower()
if 'separator' in node_class:
debug_print(f"✅ 通过命名规则找到分离器: {name}")
return name
# 方法3查找第一个分离器设备
for node in G.nodes():
node_class = G.nodes[node].get('class', '').lower()
if 'separator' in node_class:
debug_print(f"⚠️ 使用第一个分离器设备: {node}")
return node
debug_print(f"⚠️ 未找到分离器设备")
return ""
def generate_separate_protocol(
G: nx.DiGraph,
purpose: str, # 'wash' or 'extract'. 'wash' means that product phase will not be the added solvent phase, 'extract' means product phase will be the added solvent phase. If no solvent is added just use 'extract'.
product_phase: str, # 'top' or 'bottom'. Phase that product will be in.
from_vessel: str, #Contents of from_vessel are transferred to separation_vessel and separation is performed.
separation_vessel: str, # Vessel in which separation of phases will be carried out.
to_vessel: str, # Vessel to send product phase to.
waste_phase_to_vessel: str, # Optional. Vessel to send waste phase to.
solvent: str, # Optional. Solvent to add to separation vessel after contents of from_vessel has been transferred to create two phases.
solvent_volume: float = 50, # Optional. Volume of solvent to add (mL).
through: str = "", # Optional. Solid chemical to send product phase through on way to to_vessel, e.g. 'celite'.
repeats: int = 1, # Optional. Number of separations to perform.
stir_time: float = 30, # Optional. Time stir for after adding solvent, before separation of phases.
stir_speed: float = 300, # Optional. Speed to stir at after adding solvent, before separation of phases.
settling_time: float = 300 # Optional. Time
) -> list[dict]:
G: nx.DiGraph,
# 🔧 基础参数支持XDL的vessel参数
vessel: str = "", # XDL: 分离容器
purpose: str = "separate", # 分离目的
product_phase: str = "top", # 产物相
# 🔧 可选的详细参数
from_vessel: str = "", # 源容器通常在separate前已经transfer了
separation_vessel: str = "", # 分离容器与vessel同义
to_vessel: str = "", # 目标容器(可选)
waste_phase_to_vessel: str = "", # 废相目标容器
product_vessel: str = "", # XDL: 产物容器与to_vessel同义
waste_vessel: str = "", # XDL: 废液容器与waste_phase_to_vessel同义
# 🔧 溶剂相关参数
solvent: str = "", # 溶剂名称
solvent_volume: Union[str, float] = 0.0, # 溶剂体积
volume: Union[str, float] = 0.0, # XDL: 体积与solvent_volume同义
# 🔧 操作参数
through: str = "", # 通过材料
repeats: int = 1, # 重复次数
stir_time: float = 30.0, # 搅拌时间(秒)
stir_speed: float = 300.0, # 搅拌速度
settling_time: float = 300.0, # 沉降时间(秒)
**kwargs
) -> List[Dict[str, Any]]:
"""
Generate a protocol to clean a vessel with a solvent.
生成分离操作的协议序列 - 修复版
:param G: Directed graph. Nodes are containers and pumps, edges are fluidic connections.
:param vessel: Vessel to clean.
:param solvent: Solvent to clean vessel with.
:param volume: Volume of solvent to clean vessel with.
:param temp: Temperature to heat vessel to while cleaning.
:param repeats: Number of cleaning cycles to perform.
:return: List of actions to clean vessel.
支持XDL参数格式
- vessel: 分离容器(必需)
- purpose: "wash", "extract", "separate"
- product_phase: "top", "bottom"
- product_vessel: 产物收集容器
- waste_vessel: 废液收集容器
- solvent: 溶剂名称
- volume: "200 mL", "?" 或数值
- repeats: 重复次数
分离流程:
1. (可选)添加溶剂到分离容器
2. 搅拌混合
3. 静置分层
4. 收集指定相到目标容器
5. 重复指定次数
"""
# 生成泵操作的动作序列
pump_action_sequence = []
reactor_volume = 500.0
waste_vessel = waste_phase_to_vessel
debug_print("=" * 60)
debug_print("开始生成分离协议 - 修复版")
debug_print(f"原始参数:")
debug_print(f" - vessel: '{vessel}'")
debug_print(f" - purpose: '{purpose}'")
debug_print(f" - product_phase: '{product_phase}'")
debug_print(f" - solvent: '{solvent}'")
debug_print(f" - volume: {volume} (类型: {type(volume)})")
debug_print(f" - repeats: {repeats}")
debug_print(f" - product_vessel: '{product_vessel}'")
debug_print(f" - waste_vessel: '{waste_vessel}'")
debug_print("=" * 60)
# TODO通过物料管理系统找到溶剂的容器
if "," in solvent:
solvents = solvent.split(",")
assert len(solvents) == repeats, "Number of solvents must match number of repeats."
else:
solvents = [solvent] * repeats
action_sequence = []
# TODO: 通过设备连接图找到分离容器的控制器、底部出口
separator_controller = f"{separation_vessel}_controller"
separation_vessel_bottom = f"flask_{separation_vessel}"
# === 参数验证和标准化 ===
debug_print("步骤1: 参数验证和标准化...")
transfer_flowrate = flowrate = 2.5
# 统一容器参数
final_vessel = vessel or separation_vessel
if not final_vessel:
raise ValueError("必须指定分离容器 (vessel 或 separation_vessel)")
if from_vessel != separation_vessel:
pump_action_sequence.append(
{
"device_id": "",
"action_name": "PumpTransferProtocol",
"action_kwargs": {
"from_vessel": from_vessel,
"to_vessel": separation_vessel,
"volume": reactor_volume,
"time": reactor_volume / flowrate,
# "transfer_flowrate": transfer_flowrate,
final_to_vessel = to_vessel or product_vessel
final_waste_vessel = waste_phase_to_vessel or waste_vessel
# 统一体积参数
final_volume = parse_volume_input(volume or solvent_volume)
# 🔧 修复确保repeats至少为1
if repeats <= 0:
repeats = 1
debug_print(f"⚠️ repeats参数 <= 0自动设置为1")
debug_print(f"标准化参数:")
debug_print(f" - 分离容器: '{final_vessel}'")
debug_print(f" - 产物容器: '{final_to_vessel}'")
debug_print(f" - 废液容器: '{final_waste_vessel}'")
debug_print(f" - 溶剂体积: {final_volume}mL")
debug_print(f" - 重复次数: {repeats}")
# 验证必需参数
if not purpose:
purpose = "separate"
if not product_phase:
product_phase = "top"
if purpose not in ["wash", "extract", "separate"]:
debug_print(f"⚠️ 未知的分离目的 '{purpose}',使用默认值 'separate'")
purpose = "separate"
if product_phase not in ["top", "bottom"]:
debug_print(f"⚠️ 未知的产物相 '{product_phase}',使用默认值 'top'")
product_phase = "top"
debug_print("✅ 参数验证通过")
# === 查找设备 ===
debug_print("步骤2: 查找设备...")
# 查找分离器设备
separator_device = find_separator_device(G, final_vessel)
if not separator_device:
debug_print("⚠️ 未找到分离器设备,可能无法执行分离操作")
# 查找溶剂容器(如果需要)
solvent_vessel = ""
if solvent and solvent.strip():
solvent_vessel = find_solvent_vessel(G, solvent)
debug_print(f"设备映射:")
debug_print(f" - 分离器设备: '{separator_device}'")
debug_print(f" - 溶剂容器: '{solvent_vessel}'")
# === 执行分离流程 ===
debug_print("步骤3: 执行分离流程...")
try:
for repeat_idx in range(repeats):
debug_print(f"3.{repeat_idx+1}: 第 {repeat_idx+1}/{repeats} 次分离")
# 步骤3.1: 添加溶剂(如果需要)
if solvent_vessel and final_volume > 0:
debug_print(f"3.{repeat_idx+1}.1: 添加溶剂 {solvent} ({final_volume}mL)")
# 使用pump protocol添加溶剂
pump_actions = generate_pump_protocol_with_rinsing(
G=G,
from_vessel=solvent_vessel,
to_vessel=final_vessel,
volume=final_volume,
amount="",
time=0.0,
viscous=False,
rinsing_solvent="",
rinsing_volume=0.0,
rinsing_repeats=0,
solid=False,
flowrate=2.5,
transfer_flowrate=0.5,
rate_spec="",
event="",
through="",
**kwargs
)
action_sequence.extend(pump_actions)
debug_print(f"✅ 溶剂添加完成,添加了 {len(pump_actions)} 个动作")
# 步骤3.2: 执行分离操作
if separator_device:
debug_print(f"3.{repeat_idx+1}.2: 执行分离操作")
# 调用分离器设备的separate方法
separate_action = {
"device_id": separator_device,
"action_name": "separate",
"action_kwargs": {
"purpose": purpose,
"product_phase": product_phase,
"from_vessel": from_vessel or final_vessel,
"separation_vessel": final_vessel,
"to_vessel": final_to_vessel or final_vessel,
"waste_phase_to_vessel": final_waste_vessel or final_vessel,
"solvent": solvent,
"solvent_volume": final_volume,
"through": through,
"repeats": 1, # 每次调用只做一次分离
"stir_time": stir_time,
"stir_speed": stir_speed,
"settling_time": settling_time
}
}
action_sequence.append(separate_action)
debug_print(f"✅ 分离操作添加完成")
else:
debug_print(f"3.{repeat_idx+1}.2: 无分离器设备,跳过分离操作")
# 添加等待时间模拟分离
action_sequence.append({
"action_name": "wait",
"action_kwargs": {"time": stir_time + settling_time}
})
# 等待间隔(除了最后一次)
if repeat_idx < repeats - 1:
action_sequence.append({
"action_name": "wait",
"action_kwargs": {"time": 5}
})
except Exception as e:
debug_print(f"⚠️ 分离流程执行失败: {str(e)}")
# 添加错误日志
action_sequence.append({
"device_id": "system",
"action_name": "log_message",
"action_kwargs": {
"message": f"分离操作失败: {str(e)}"
}
)
# for i in range(2):
# pump_action_sequence.append(
# {
# "device_id": "",
# "action_name": "CleanProtocol",
# "action_kwargs": {
# "vessel": from_vessel,
# "solvent": "H2O", # Solvent to clean vessel with.
# "volume": solvent_volume, # Optional. Volume of solvent to clean vessel with.
# "temp": 25.0, # Optional. Temperature to heat vessel to while cleaning.
# "repeats": 1
# }
# }
# )
# pump_action_sequence.append(
# {
# "device_id": "",
# "action_name": "CleanProtocol",
# "action_kwargs": {
# "vessel": from_vessel,
# "solvent": "CH2Cl2", # Solvent to clean vessel with.
# "volume": solvent_volume, # Optional. Volume of solvent to clean vessel with.
# "temp": 25.0, # Optional. Temperature to heat vessel to while cleaning.
# "repeats": 1
# }
# }
# )
})
# 生成泵操作的动作序列
for i in range(repeats):
# 找到当次萃取所用溶剂
solvent_thistime = solvents[i]
solvent_vessel = f"flask_{solvent_thistime}"
pump_action_sequence.append(
{
"device_id": "",
"action_name": "PumpTransferProtocol",
"action_kwargs": {
"from_vessel": solvent_vessel,
"to_vessel": separation_vessel,
"volume": solvent_volume,
"time": solvent_volume / flowrate,
# "transfer_flowrate": transfer_flowrate,
}
}
)
pump_action_sequence.extend([
# 搅拌、静置
{
"device_id": separator_controller,
"action_name": "stir",
"action_kwargs": {
"stir_time": stir_time,
"stir_speed": stir_speed,
"settling_time": settling_time
}
},
# 分液(判断电导突跃)
{
"device_id": separator_controller,
"action_name": "valve_open",
"action_kwargs": {
"command": "delta > 0.05"
}
}
])
if product_phase == "bottom":
# 产物转移到目标瓶
pump_action_sequence.append(
{
"device_id": "",
"action_name": "PumpTransferProtocol",
"action_kwargs": {
"from_vessel": separation_vessel_bottom,
"to_vessel": to_vessel,
"volume": 250.0,
"time": 250.0 / flowrate,
# "transfer_flowrate": transfer_flowrate,
}
}
)
# 放出上面那一相60秒后关阀门
pump_action_sequence.append(
{
"device_id": separator_controller,
"action_name": "valve_open",
"action_kwargs": {
"command": "time > 60"
}
}
)
# 弃去上面那一相进废液
pump_action_sequence.append(
{
"device_id": "",
"action_name": "PumpTransferProtocol",
"action_kwargs": {
"from_vessel": separation_vessel_bottom,
"to_vessel": waste_vessel,
"volume": 250.0,
"time": 250.0 / flowrate,
# "transfer_flowrate": transfer_flowrate,
}
}
)
elif product_phase == "top":
# 弃去下面那一相进废液
pump_action_sequence.append(
{
"device_id": "",
"action_name": "PumpTransferProtocol",
"action_kwargs": {
"from_vessel": separation_vessel_bottom,
"to_vessel": waste_vessel,
"volume": 250.0,
"time": 250.0 / flowrate,
# "transfer_flowrate": transfer_flowrate,
}
}
)
# 放出上面那一相
pump_action_sequence.append(
{
"device_id": separator_controller,
"action_name": "valve_open",
"action_kwargs": {
"command": "time > 60"
}
}
)
# 产物转移到目标瓶
pump_action_sequence.append(
{
"device_id": "",
"action_name": "PumpTransferProtocol",
"action_kwargs": {
"from_vessel": separation_vessel_bottom,
"to_vessel": to_vessel,
"volume": 250.0,
"time": 250.0 / flowrate,
# "transfer_flowrate": transfer_flowrate,
}
}
)
elif product_phase == "organic":
pass
# 如果不是最后一次,从中转瓶转移回分液漏斗
if i < repeats - 1:
pump_action_sequence.append(
{
"device_id": "",
"action_name": "PumpTransferProtocol",
"action_kwargs": {
"from_vessel": to_vessel,
"to_vessel": separation_vessel,
"volume": 250.0,
"time": 250.0 / flowrate,
# "transfer_flowrate": transfer_flowrate,
}
}
)
return pump_action_sequence
# === 最终结果 ===
debug_print("=" * 60)
debug_print(f"✅ 分离协议生成完成")
debug_print(f"📊 总动作数: {len(action_sequence)}")
debug_print(f"📋 处理总结:")
debug_print(f" - 分离容器: {final_vessel}")
debug_print(f" - 分离目的: {purpose}")
debug_print(f" - 产物相: {product_phase}")
debug_print(f" - 重复次数: {repeats}")
if solvent:
debug_print(f" - 溶剂: {solvent} ({final_volume}mL)")
if final_to_vessel:
debug_print(f" - 产物容器: {final_to_vessel}")
if final_waste_vessel:
debug_print(f" - 废液容器: {final_waste_vessel}")
debug_print("=" * 60)
return action_sequence
# === 便捷函数 ===
def separate_phases_only(G: nx.DiGraph, vessel: str, product_phase: str = "top",
product_vessel: str = "", waste_vessel: str = "") -> List[Dict[str, Any]]:
"""仅进行相分离(不添加溶剂)"""
return generate_separate_protocol(
G, vessel=vessel,
purpose="separate",
product_phase=product_phase,
product_vessel=product_vessel,
waste_vessel=waste_vessel
)
def wash_with_solvent(G: nx.DiGraph, vessel: str, solvent: str, volume: Union[str, float],
product_phase: str = "top", repeats: int = 1) -> List[Dict[str, Any]]:
"""用溶剂洗涤"""
return generate_separate_protocol(
G, vessel=vessel,
purpose="wash",
product_phase=product_phase,
solvent=solvent,
volume=volume,
repeats=repeats
)
def extract_with_solvent(G: nx.DiGraph, vessel: str, solvent: str, volume: Union[str, float],
product_phase: str = "bottom", repeats: int = 3) -> List[Dict[str, Any]]:
"""用溶剂萃取"""
return generate_separate_protocol(
G, vessel=vessel,
purpose="extract",
product_phase=product_phase,
solvent=solvent,
volume=volume,
repeats=repeats
)
def separate_aqueous_organic(G: nx.DiGraph, vessel: str, organic_phase: str = "top",
product_vessel: str = "", waste_vessel: str = "") -> List[Dict[str, Any]]:
"""水-有机相分离"""
return generate_separate_protocol(
G, vessel=vessel,
purpose="separate",
product_phase=organic_phase,
product_vessel=product_vessel,
waste_vessel=waste_vessel
)
# 测试函数
def test_separate_protocol():
"""测试分离协议的各种参数解析"""
print("=== SEPARATE PROTOCOL 增强版测试 ===")
# 测试体积解析
volumes = ["200 mL", "?", 100.0, "1 L", "500 μL"]
for vol in volumes:
result = parse_volume_input(vol)
print(f"体积解析: {vol}{result}mL")
print("✅ 测试完成")
if __name__ == "__main__":
test_separate_protocol()