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https://github.com/dptech-corp/Uni-Lab-OS.git
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Create 5 new protocols & bump version 0.9.8 (#59)
* 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>
This commit is contained in:
Kongchang Feng
GitHub
@@ -49,7 +49,7 @@ conda env update --file unilabos-[YOUR_OS].yml -n environment_name
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# Currently, you need to install the `unilabos_msgs` package
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# You can download the system-specific package from the Release page
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conda install ros-humble-unilabos-msgs-0.9.7-xxxxx.tar.bz2
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conda install ros-humble-unilabos-msgs-0.9.8-xxxxx.tar.bz2
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# Install PyLabRobot and other prerequisites
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git clone https://github.com/PyLabRobot/pylabrobot plr_repo
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@@ -49,7 +49,7 @@ conda env update --file unilabos-[YOUR_OS].yml -n 环境名
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# 现阶段，需要安装 `unilabos_msgs` 包
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# 可以前往 Release 页面下载系统对应的包进行安装
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conda install ros-humble-unilabos-msgs-0.9.7-xxxxx.tar.bz2
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conda install ros-humble-unilabos-msgs-0.9.8-xxxxx.tar.bz2
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# 安装PyLabRobot等前置
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git clone https://github.com/PyLabRobot/pylabrobot plr_repo
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@@ -1,6 +1,6 @@
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package:
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name: ros-humble-unilabos-msgs
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version: 0.9.7
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version: 0.9.8
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source:
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path: ../../unilabos_msgs
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folder: ros-humble-unilabos-msgs/src/work
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@@ -1,6 +1,6 @@
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package:
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name: unilabos
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version: "0.9.7"
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version: "0.9.8"
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source:
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path: ../..
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2
setup.py
2
setup.py
@@ -4,7 +4,7 @@ package_name = 'unilabos'
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setup(
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name=package_name,
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version='0.9.7',
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version='0.9.8',
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packages=find_packages(),
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include_package_data=True,
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install_requires=['setuptools'],
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@@ -23,6 +23,7 @@
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HeatChillProtocol: generate_heat_chill_protocol, (√)
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HeatChillStartProtocol: generate_heat_chill_start_protocol, (√)
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HeatChillStopProtocol: generate_heat_chill_stop_protocol, (√)
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HeatChillToTempProtocol:
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StirProtocol: generate_stir_protocol, (√)
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StartStirProtocol: generate_start_stir_protocol, (√)
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StopStirProtocol: generate_stop_stir_protocol, (√)
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@@ -30,7 +31,13 @@
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CleanVesselProtocol: generate_clean_vessel_protocol, (√)
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DissolveProtocol: generate_dissolve_protocol, (√)
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FilterThroughProtocol: generate_filter_through_protocol, (√)
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RunColumnProtocol: generate_run_column_protocol, (×)
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WashSolidProtocol: generate_wash_solid_protocol, (×)
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RunColumnProtocol: generate_run_column_protocol, (√)<RunColumn Rf="?" column="column" from_vessel="rotavap" ratio="5:95" solvent1="methanol" solvent2="chloroform" to_vessel="rotavap"/>
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上下文体积搜索
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上下文体积搜索
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3. 还没创建的protocol
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ResetHandling 写完了 <ResetHandling solvent="methanol"/>
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Dry 写完了 <Dry compound="product" vessel="filter"/>
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AdjustPH 写完了 <AdjustPH pH="8.0" reagent="hydrochloric acid" vessel="main_reactor"/>
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Recrystallize 写完了 <Recrystallize ratio="?" solvent1="dichloromethane" solvent2="methanol" vessel="filter" volume="?"/>
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TakeSample <TakeSample id="a" vessel="rotavap"/>
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Hydrogenate <Hydrogenate temp="45 °C" time="?" vessel="main_reactor"/>
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@@ -23,8 +23,10 @@
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"waste_bottle_2",
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"solenoid_valve_1",
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"solenoid_valve_2",
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"solenoid_valve_3",
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"vacuum_pump_1",
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"gas_source_1",
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"h2_gas_source",
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"filter_1",
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"column_1",
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"separator_1",
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@@ -60,7 +62,12 @@
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"HeatChillStartProtocol",
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"HeatChillStopProtocol",
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"EvacuateAndRefillProtocol",
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"PumpTransferProtocol"
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"PumpTransferProtocol",
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"AdjustPHProtocol",
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"ResetHandlingProtocol",
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"DryProtocol",
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"HydrogenateProtocol",
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"RecrystallizeProtocol"
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]
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},
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"data": {}
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@@ -461,6 +468,28 @@
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"is_open": false
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}
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},
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{
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"id": "solenoid_valve_3",
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"name": "氢气电磁阀",
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"children": [],
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"parent": "OrganicSynthesisStation",
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"type": "device",
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"class": "virtual_solenoid_valve",
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"position": {
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"x": 450,
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"y": 400,
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"z": 0
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},
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"config": {
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"voltage": 12.0,
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"response_time": 0.1,
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"gas_compatible": true
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},
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"data": {
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"valve_state": "Closed",
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"is_open": false
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}
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},
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{
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"id": "vacuum_pump_1",
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"name": "真空泵",
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@@ -500,6 +529,29 @@
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"max_pressure": 5.0
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}
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},
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{
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"id": "h2_gas_source",
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"name": "氢气气源",
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"children": [],
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"parent": "OrganicSynthesisStation",
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"type": "device",
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"class": "virtual_gas_source",
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"position": {
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"x": 500,
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"y": 350,
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"z": 0
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},
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"config": {
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"max_pressure": 10.0,
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"gas_type": "hydrogen"
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},
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"data": {
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"gas_type": "hydrogen",
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"max_pressure": 10.0,
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"current_pressure": 0.0,
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"status": "OFF"
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}
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},
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{
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"id": "filter_1",
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"name": "过滤器",
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@@ -874,14 +926,14 @@
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}
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},
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{
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"id": "link_filter_filtrate_to_collection1",
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"source": "filter_1",
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"target": "collection_bottle_1",
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"type": "transport",
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"port": {
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"filter_1": "filtrateout",
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"collection_bottle_1": "top"
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}
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"id": "link_filter_filtrate_to_collection1",
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"source": "filter_1",
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"target": "collection_bottle_1",
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"type": "transport",
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"port": {
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"filter_1": "filtrateout",
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"collection_bottle_1": "top"
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}
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},
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{
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"id": "link_filter_retentate_to_waste1",
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@@ -892,6 +944,26 @@
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"filter_1": "retentateout",
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"waste_bottle_1": "top"
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}
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},
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{
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"id": "link_h2_gas_to_valve3",
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"source": "h2_gas_source",
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"target": "solenoid_valve_3",
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"type": "fluid",
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"port": {
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"h2_gas_source": "gassource",
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"solenoid_valve_3": "in"
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}
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},
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{
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"id": "link_valve3_to_reactor",
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"source": "solenoid_valve_3",
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"target": "main_reactor",
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"type": "fluid",
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"port": {
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"solenoid_valve_3": "out",
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"main_reactor": "top"
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}
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}
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]
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}
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@@ -21,16 +21,23 @@ from .dissolve_protocol import generate_dissolve_protocol
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from .filter_through_protocol import generate_filter_through_protocol
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from .run_column_protocol import generate_run_column_protocol
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from .wash_solid_protocol import generate_wash_solid_protocol
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from .adjustph_protocol import generate_adjust_ph_protocol
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from .reset_handling_protocol import generate_reset_handling_protocol
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from .dry_protocol import generate_dry_protocol
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from .recrystallize_protocol import generate_recrystallize_protocol
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from .hydrogenate_protocol import generate_hydrogenate_protocol
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# Define a dictionary of protocol generators.
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action_protocol_generators = {
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AddProtocol: generate_add_protocol,
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AGVTransferProtocol: generate_agv_transfer_protocol,
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AdjustPHProtocol: generate_adjust_ph_protocol,
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CentrifugeProtocol: generate_centrifuge_protocol,
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CleanProtocol: generate_clean_protocol,
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CleanVesselProtocol: generate_clean_vessel_protocol,
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DissolveProtocol: generate_dissolve_protocol,
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DryProtocol: generate_dry_protocol,
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EvacuateAndRefillProtocol: generate_evacuateandrefill_protocol,
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EvaporateProtocol: generate_evaporate_protocol,
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FilterProtocol: generate_filter_protocol,
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@@ -38,7 +45,10 @@ action_protocol_generators = {
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HeatChillProtocol: generate_heat_chill_protocol,
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HeatChillStartProtocol: generate_heat_chill_start_protocol,
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HeatChillStopProtocol: generate_heat_chill_stop_protocol,
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HydrogenateProtocol: generate_hydrogenate_protocol,
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PumpTransferProtocol: generate_pump_protocol_with_rinsing,
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RecrystallizeProtocol: generate_recrystallize_protocol,
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ResetHandlingProtocol: generate_reset_handling_protocol,
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RunColumnProtocol: generate_run_column_protocol,
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SeparateProtocol: generate_separate_protocol,
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StartStirProtocol: generate_start_stir_protocol,
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411
unilabos/compile/adjustph_protocol.py
Normal file
411
unilabos/compile/adjustph_protocol.py
Normal file
@@ -0,0 +1,411 @@
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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_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:
|
||||
List[Dict[str, Any]]: 动作序列
|
||||
"""
|
||||
action_sequence = []
|
||||
|
||||
# 从kwargs中获取可选参数，如果没有则使用默认值
|
||||
volume = kwargs.get('volume', 0.0) # 自动估算体积
|
||||
stir = kwargs.get('stir', True) # 默认搅拌
|
||||
stir_speed = kwargs.get('stir_speed', 300.0) # 默认搅拌速度
|
||||
stir_time = kwargs.get('stir_time', 60.0) # 默认搅拌时间
|
||||
settling_time = kwargs.get('settling_time', 30.0) # 默认平衡时间
|
||||
|
||||
print(f"ADJUST_PH: 开始生成pH调节协议")
|
||||
print(f" - 目标容器: {vessel}")
|
||||
print(f" - 目标pH: {ph_value}") # 改为 ph_value
|
||||
print(f" - 试剂: {reagent}")
|
||||
print(f" - 使用默认参数: 体积=自动估算, 搅拌=True, 搅拌速度=300RPM")
|
||||
|
||||
# 1. 验证目标容器存在
|
||||
if vessel not in G.nodes():
|
||||
raise ValueError(f"目标容器 '{vessel}' 不存在于系统中")
|
||||
|
||||
# 2. 查找酸碱试剂容器
|
||||
try:
|
||||
reagent_vessel = find_acid_base_vessel(G, reagent)
|
||||
print(f"ADJUST_PH: 找到试剂容器: {reagent_vessel}")
|
||||
except ValueError as e:
|
||||
raise ValueError(f"无法找到试剂 '{reagent}': {str(e)}")
|
||||
|
||||
# 3. 如果未指定体积，自动估算
|
||||
if volume <= 0:
|
||||
# 获取目标容器的体积信息
|
||||
vessel_data = G.nodes[vessel].get('data', {})
|
||||
vessel_volume = vessel_data.get('max_volume', 100.0) # 默认100mL
|
||||
|
||||
estimated_volume = calculate_reagent_volume(ph_value, reagent, vessel_volume) # 改为 ph_value
|
||||
volume = estimated_volume
|
||||
print(f"ADJUST_PH: 自动估算试剂体积: {volume:.2f} mL")
|
||||
|
||||
# 4. 验证路径存在
|
||||
try:
|
||||
path = nx.shortest_path(G, source=reagent_vessel, target=vessel)
|
||||
print(f"ADJUST_PH: 找到路径: {' → '.join(path)}")
|
||||
except nx.NetworkXNoPath:
|
||||
raise ValueError(f"从试剂容器 '{reagent_vessel}' 到目标容器 '{vessel}' 没有可用路径")
|
||||
|
||||
# 5. 先启动搅拌（如果需要）
|
||||
stirrer_id = None
|
||||
if stir:
|
||||
try:
|
||||
stirrer_id = find_connected_stirrer(G, vessel)
|
||||
|
||||
if stirrer_id:
|
||||
print(f"ADJUST_PH: 找到搅拌器 {stirrer_id}，启动搅拌")
|
||||
action_sequence.append({
|
||||
"device_id": stirrer_id,
|
||||
"action_name": "start_stir",
|
||||
"action_kwargs": {
|
||||
"vessel": vessel,
|
||||
"stir_speed": stir_speed,
|
||||
"purpose": f"pH调节: 启动搅拌，准备添加 {reagent}"
|
||||
}
|
||||
})
|
||||
|
||||
# 等待搅拌稳定
|
||||
action_sequence.append({
|
||||
"action_name": "wait",
|
||||
"action_kwargs": {"time": 5}
|
||||
})
|
||||
else:
|
||||
print(f"ADJUST_PH: 警告 - 未找到搅拌器，继续执行")
|
||||
|
||||
except Exception as e:
|
||||
print(f"ADJUST_PH: 搅拌器配置出错: {str(e)}")
|
||||
|
||||
# 6. 缓慢添加试剂 - 使用pump_protocol
|
||||
print(f"ADJUST_PH: 开始添加试剂 {volume:.2f} mL")
|
||||
|
||||
# 计算添加时间（pH调节需要缓慢添加）
|
||||
addition_time = max(30.0, volume * 2.0) # 至少30秒，每mL需要2秒
|
||||
|
||||
try:
|
||||
pump_actions = generate_pump_protocol_with_rinsing(
|
||||
G=G,
|
||||
from_vessel=reagent_vessel,
|
||||
to_vessel=vessel,
|
||||
volume=volume,
|
||||
amount="",
|
||||
time=addition_time,
|
||||
viscous=False,
|
||||
rinsing_solvent="", # pH调节不需要清洗
|
||||
rinsing_volume=0.0,
|
||||
rinsing_repeats=0,
|
||||
solid=False,
|
||||
flowrate=0.5 # 缓慢注入
|
||||
)
|
||||
|
||||
action_sequence.extend(pump_actions)
|
||||
|
||||
except Exception as e:
|
||||
raise ValueError(f"生成泵协议时出错: {str(e)}")
|
||||
|
||||
# 7. 持续搅拌以混合和平衡
|
||||
if stir and stirrer_id:
|
||||
print(f"ADJUST_PH: 持续搅拌 {stir_time} 秒以混合试剂")
|
||||
action_sequence.append({
|
||||
"device_id": stirrer_id,
|
||||
"action_name": "stir",
|
||||
"action_kwargs": {
|
||||
"stir_time": stir_time,
|
||||
"stir_speed": stir_speed,
|
||||
"settling_time": settling_time,
|
||||
"purpose": f"pH调节: 混合试剂，目标pH={ph_value}" # 改为 ph_value
|
||||
}
|
||||
})
|
||||
|
||||
# 8. 等待反应平衡
|
||||
action_sequence.append({
|
||||
"action_name": "wait",
|
||||
"action_kwargs": {
|
||||
"time": settling_time,
|
||||
"description": f"等待pH平衡到目标值 {ph_value}" # 改为 ph_value
|
||||
}
|
||||
})
|
||||
|
||||
print(f"ADJUST_PH: 协议生成完成，共 {len(action_sequence)} 个动作")
|
||||
print(f"ADJUST_PH: 预计总时间: {addition_time + stir_time + settling_time:.0f} 秒")
|
||||
|
||||
return action_sequence
|
||||
|
||||
|
||||
def generate_adjust_ph_protocol_stepwise(
|
||||
G: nx.DiGraph,
|
||||
vessel: str,
|
||||
ph_value: float,
|
||||
reagent: str,
|
||||
max_volume: float = 10.0,
|
||||
steps: int = 3
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""
|
||||
分步调节pH的协议（更安全，避免过度调节）
|
||||
|
||||
Args:
|
||||
G: 网络图
|
||||
vessel: 目标容器
|
||||
pH: 目标pH值
|
||||
reagent: 酸碱试剂
|
||||
max_volume: 最大试剂体积
|
||||
steps: 分步数量
|
||||
|
||||
Returns:
|
||||
List[Dict[str, Any]]: 动作序列
|
||||
"""
|
||||
action_sequence = []
|
||||
|
||||
print(f"ADJUST_PH: 开始分步pH调节（{steps}步）")
|
||||
|
||||
# 每步添加的体积
|
||||
step_volume = max_volume / steps
|
||||
|
||||
for i in range(steps):
|
||||
print(f"ADJUST_PH: 第 {i+1}/{steps} 步，添加 {step_volume} mL")
|
||||
|
||||
# 生成单步协议
|
||||
step_actions = generate_adjust_ph_protocol(
|
||||
G=G,
|
||||
vessel=vessel,
|
||||
ph_value=ph_value,
|
||||
reagent=reagent,
|
||||
volume=step_volume,
|
||||
stir=True,
|
||||
stir_speed=300.0,
|
||||
stir_time=30.0,
|
||||
settling_time=20.0
|
||||
)
|
||||
|
||||
action_sequence.extend(step_actions)
|
||||
|
||||
# 步骤间等待
|
||||
if i < steps - 1:
|
||||
action_sequence.append({
|
||||
"action_name": "wait",
|
||||
"action_kwargs": {
|
||||
"time": 30,
|
||||
"description": f"pH调节第{i+1}步完成，等待下一步"
|
||||
}
|
||||
})
|
||||
|
||||
print(f"ADJUST_PH: 分步pH调节完成")
|
||||
return action_sequence
|
||||
|
||||
|
||||
# 便捷函数：常用pH调节
|
||||
def generate_acidify_protocol(
|
||||
G: nx.DiGraph,
|
||||
vessel: str,
|
||||
target_ph: float = 2.0,
|
||||
acid: str = "hydrochloric acid"
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""酸化协议"""
|
||||
return generate_adjust_ph_protocol(
|
||||
G, vessel, target_ph, acid, 0.0, True, 300.0, 120.0, 60.0
|
||||
)
|
||||
|
||||
|
||||
def generate_basify_protocol(
|
||||
G: nx.DiGraph,
|
||||
vessel: str,
|
||||
target_ph: float = 12.0,
|
||||
base: str = "sodium hydroxide"
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""碱化协议"""
|
||||
return generate_adjust_ph_protocol(
|
||||
G, vessel, target_ph, base, 0.0, True, 300.0, 120.0, 60.0
|
||||
)
|
||||
|
||||
|
||||
def generate_neutralize_protocol(
|
||||
G: nx.DiGraph,
|
||||
vessel: str,
|
||||
reagent: str = "sodium hydroxide"
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""中和协议（pH=7）"""
|
||||
return generate_adjust_ph_protocol(
|
||||
G, vessel, 7.0, reagent, 0.0, True, 350.0, 180.0, 90.0
|
||||
)
|
||||
|
||||
|
||||
# 测试函数
|
||||
def test_adjust_ph_protocol():
|
||||
"""测试pH调节协议"""
|
||||
print("=== ADJUST PH PROTOCOL 测试 ===")
|
||||
print("测试完成")
|
||||
|
||||
|
||||
if __name__ == "__main__":
|
||||
test_adjust_ph_protocol()
|
||||
165
unilabos/compile/dry_protocol.py
Normal file
165
unilabos/compile/dry_protocol.py
Normal file
@@ -0,0 +1,165 @@
|
||||
import networkx as nx
|
||||
from typing import List, Dict, Any
|
||||
|
||||
|
||||
def find_connected_heater(G: nx.DiGraph, vessel: str) -> str:
|
||||
"""
|
||||
查找与容器相连的加热器
|
||||
|
||||
Args:
|
||||
G: 网络图
|
||||
vessel: 容器名称
|
||||
|
||||
Returns:
|
||||
str: 加热器ID，如果没有则返回None
|
||||
"""
|
||||
print(f"DRY: 正在查找与容器 '{vessel}' 相连的加热器...")
|
||||
|
||||
# 查找所有加热器节点
|
||||
heater_nodes = [node for node in G.nodes()
|
||||
if ('heater' in node.lower() or
|
||||
'heat' in node.lower() or
|
||||
G.nodes[node].get('class') == 'virtual_heatchill' or
|
||||
G.nodes[node].get('type') == 'heater')]
|
||||
|
||||
print(f"DRY: 找到的加热器节点: {heater_nodes}")
|
||||
|
||||
# 检查是否有加热器与目标容器相连
|
||||
for heater in heater_nodes:
|
||||
if G.has_edge(heater, vessel) or G.has_edge(vessel, heater):
|
||||
print(f"DRY: 找到与容器 '{vessel}' 相连的加热器: {heater}")
|
||||
return heater
|
||||
|
||||
# 如果没有直接连接，查找距离最近的加热器
|
||||
for heater in heater_nodes:
|
||||
try:
|
||||
path = nx.shortest_path(G, source=heater, target=vessel)
|
||||
if len(path) <= 3: # 最多2个中间节点
|
||||
print(f"DRY: 找到距离较近的加热器: {heater}, 路径: {' → '.join(path)}")
|
||||
return heater
|
||||
except nx.NetworkXNoPath:
|
||||
continue
|
||||
|
||||
print(f"DRY: 未找到与容器 '{vessel}' 相连的加热器")
|
||||
return None
|
||||
|
||||
|
||||
def generate_dry_protocol(
|
||||
G: nx.DiGraph,
|
||||
compound: str,
|
||||
vessel: str,
|
||||
**kwargs # 接收其他可能的参数但不使用
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""
|
||||
生成干燥协议序列
|
||||
|
||||
Args:
|
||||
G: 有向图，节点为容器和设备
|
||||
compound: 化合物名称（从XDL传入）
|
||||
vessel: 目标容器（从XDL传入）
|
||||
**kwargs: 其他可选参数，但不使用
|
||||
|
||||
Returns:
|
||||
List[Dict[str, Any]]: 动作序列
|
||||
"""
|
||||
action_sequence = []
|
||||
|
||||
# 默认参数
|
||||
dry_temp = 60.0 # 默认干燥温度 60°C
|
||||
dry_time = 3600.0 # 默认干燥时间 1小时（3600秒）
|
||||
|
||||
print(f"DRY: 开始生成干燥协议")
|
||||
print(f" - 化合物: {compound}")
|
||||
print(f" - 容器: {vessel}")
|
||||
print(f" - 干燥温度: {dry_temp}°C")
|
||||
print(f" - 干燥时间: {dry_time/60:.0f} 分钟")
|
||||
|
||||
# 1. 验证目标容器存在
|
||||
if vessel not in G.nodes():
|
||||
print(f"DRY: 警告 - 容器 '{vessel}' 不存在于系统中，跳过干燥")
|
||||
return action_sequence
|
||||
|
||||
# 2. 查找相连的加热器
|
||||
heater_id = find_connected_heater(G, vessel)
|
||||
|
||||
if heater_id is None:
|
||||
print(f"DRY: 警告 - 未找到与容器 '{vessel}' 相连的加热器，跳过干燥")
|
||||
# 添加一个等待动作，表示干燥过程（模拟）
|
||||
action_sequence.append({
|
||||
"action_name": "wait",
|
||||
"action_kwargs": {
|
||||
"time": 60.0, # 等待1分钟
|
||||
"description": f"模拟干燥 {compound} (无加热器可用)"
|
||||
}
|
||||
})
|
||||
return action_sequence
|
||||
|
||||
# 3. 启动加热器进行干燥
|
||||
print(f"DRY: 启动加热器 {heater_id} 进行干燥")
|
||||
|
||||
# 3.1 启动加热
|
||||
action_sequence.append({
|
||||
"device_id": heater_id,
|
||||
"action_name": "heat_chill_start",
|
||||
"action_kwargs": {
|
||||
"vessel": vessel,
|
||||
"temp": dry_temp,
|
||||
"purpose": f"干燥 {compound}"
|
||||
}
|
||||
})
|
||||
|
||||
# 3.2 等待温度稳定
|
||||
action_sequence.append({
|
||||
"action_name": "wait",
|
||||
"action_kwargs": {
|
||||
"time": 60.0,
|
||||
"description": f"等待温度稳定到 {dry_temp}°C"
|
||||
}
|
||||
})
|
||||
|
||||
# 3.3 保持干燥温度
|
||||
action_sequence.append({
|
||||
"device_id": heater_id,
|
||||
"action_name": "heat_chill",
|
||||
"action_kwargs": {
|
||||
"vessel": vessel,
|
||||
"temp": dry_temp,
|
||||
"time": dry_time,
|
||||
"purpose": f"干燥 {compound}，保持温度 {dry_temp}°C"
|
||||
}
|
||||
})
|
||||
|
||||
# 3.4 停止加热
|
||||
action_sequence.append({
|
||||
"device_id": heater_id,
|
||||
"action_name": "heat_chill_stop",
|
||||
"action_kwargs": {
|
||||
"vessel": vessel,
|
||||
"purpose": f"干燥完成，停止加热"
|
||||
}
|
||||
})
|
||||
|
||||
# 3.5 等待冷却
|
||||
action_sequence.append({
|
||||
"action_name": "wait",
|
||||
"action_kwargs": {
|
||||
"time": 300.0, # 等待5分钟冷却
|
||||
"description": f"等待 {compound} 冷却"
|
||||
}
|
||||
})
|
||||
|
||||
print(f"DRY: 协议生成完成，共 {len(action_sequence)} 个动作")
|
||||
print(f"DRY: 预计总时间: {(dry_time + 360)/60:.0f} 分钟")
|
||||
|
||||
return action_sequence
|
||||
|
||||
|
||||
# 测试函数
|
||||
def test_dry_protocol():
|
||||
"""测试干燥协议"""
|
||||
print("=== DRY PROTOCOL 测试 ===")
|
||||
print("测试完成")
|
||||
|
||||
|
||||
if __name__ == "__main__":
|
||||
test_dry_protocol()
|
||||
366
unilabos/compile/hydrogenate_protocol.py
Normal file
366
unilabos/compile/hydrogenate_protocol.py
Normal file
@@ -0,0 +1,366 @@
|
||||
import networkx as nx
|
||||
from typing import List, Dict, Any, Optional
|
||||
|
||||
|
||||
def parse_temperature(temp_str: str) -> float:
|
||||
"""
|
||||
解析温度字符串，支持多种格式
|
||||
|
||||
Args:
|
||||
temp_str: 温度字符串（如 "45 °C", "45°C", "45"）
|
||||
|
||||
Returns:
|
||||
float: 温度值（摄氏度）
|
||||
"""
|
||||
try:
|
||||
# 移除常见的温度单位和符号
|
||||
temp_clean = temp_str.replace("°C", "").replace("°", "").replace("C", "").strip()
|
||||
return float(temp_clean)
|
||||
except ValueError:
|
||||
print(f"HYDROGENATE: 无法解析温度 '{temp_str}'，使用默认温度 25°C")
|
||||
return 25.0
|
||||
|
||||
|
||||
def parse_time(time_str: str) -> float:
|
||||
"""
|
||||
解析时间字符串，支持多种格式
|
||||
|
||||
Args:
|
||||
time_str: 时间字符串（如 "2 h", "120 min", "7200 s"）
|
||||
|
||||
Returns:
|
||||
float: 时间值（秒）
|
||||
"""
|
||||
try:
|
||||
time_clean = time_str.lower().strip()
|
||||
|
||||
# 处理小时
|
||||
if "h" in time_clean:
|
||||
hours = float(time_clean.replace("h", "").strip())
|
||||
return hours * 3600.0
|
||||
|
||||
# 处理分钟
|
||||
if "min" in time_clean:
|
||||
minutes = float(time_clean.replace("min", "").strip())
|
||||
return minutes * 60.0
|
||||
|
||||
# 处理秒
|
||||
if "s" in time_clean:
|
||||
seconds = float(time_clean.replace("s", "").strip())
|
||||
return seconds
|
||||
|
||||
# 默认按小时处理
|
||||
return float(time_clean) * 3600.0
|
||||
|
||||
except ValueError:
|
||||
print(f"HYDROGENATE: 无法解析时间 '{time_str}'，使用默认时间 2小时")
|
||||
return 7200.0 # 2小时
|
||||
|
||||
|
||||
def find_associated_solenoid_valve(G: nx.DiGraph, device_id: str) -> Optional[str]:
|
||||
"""查找与指定设备相关联的电磁阀"""
|
||||
solenoid_valves = [
|
||||
node for node in G.nodes()
|
||||
if ('solenoid' in (G.nodes[node].get('class') or '').lower()
|
||||
or 'solenoid_valve' in node)
|
||||
]
|
||||
|
||||
# 通过网络连接查找直接相连的电磁阀
|
||||
for solenoid in solenoid_valves:
|
||||
if G.has_edge(device_id, solenoid) or G.has_edge(solenoid, device_id):
|
||||
return solenoid
|
||||
|
||||
# 通过命名规则查找关联的电磁阀
|
||||
device_type = ""
|
||||
if 'gas' in device_id.lower():
|
||||
device_type = "gas"
|
||||
elif 'h2' in device_id.lower() or 'hydrogen' in device_id.lower():
|
||||
device_type = "gas"
|
||||
|
||||
if device_type:
|
||||
for solenoid in solenoid_valves:
|
||||
if device_type in solenoid.lower():
|
||||
return solenoid
|
||||
|
||||
return None
|
||||
|
||||
|
||||
def find_connected_device(G: nx.DiGraph, vessel: str, device_type: str) -> str:
|
||||
"""
|
||||
查找与容器相连的指定类型设备
|
||||
|
||||
Args:
|
||||
G: 网络图
|
||||
vessel: 容器名称
|
||||
device_type: 设备类型 ('heater', 'stirrer', 'gas_source')
|
||||
|
||||
Returns:
|
||||
str: 设备ID，如果没有则返回None
|
||||
"""
|
||||
print(f"HYDROGENATE: 正在查找与容器 '{vessel}' 相连的 {device_type}...")
|
||||
|
||||
# 根据设备类型定义搜索关键词
|
||||
if device_type == 'heater':
|
||||
keywords = ['heater', 'heat', 'heatchill']
|
||||
device_class = 'virtual_heatchill'
|
||||
elif device_type == 'stirrer':
|
||||
keywords = ['stirrer', 'stir']
|
||||
device_class = 'virtual_stirrer'
|
||||
elif device_type == 'gas_source':
|
||||
keywords = ['gas', 'h2', 'hydrogen']
|
||||
device_class = 'virtual_gas_source'
|
||||
else:
|
||||
return None
|
||||
|
||||
# 查找设备节点
|
||||
device_nodes = []
|
||||
for node in G.nodes():
|
||||
node_data = G.nodes[node]
|
||||
node_name = node.lower()
|
||||
node_class = node_data.get('class', '').lower()
|
||||
|
||||
# 通过名称匹配
|
||||
if any(keyword in node_name for keyword in keywords):
|
||||
device_nodes.append(node)
|
||||
# 通过类型匹配
|
||||
elif device_class in node_class:
|
||||
device_nodes.append(node)
|
||||
|
||||
print(f"HYDROGENATE: 找到的{device_type}节点: {device_nodes}")
|
||||
|
||||
# 检查是否有设备与目标容器相连
|
||||
for device in device_nodes:
|
||||
if G.has_edge(device, vessel) or G.has_edge(vessel, device):
|
||||
print(f"HYDROGENATE: 找到与容器 '{vessel}' 相连的{device_type}: {device}")
|
||||
return device
|
||||
|
||||
# 如果没有直接连接，查找距离最近的设备
|
||||
for device in device_nodes:
|
||||
try:
|
||||
path = nx.shortest_path(G, source=device, target=vessel)
|
||||
if len(path) <= 3: # 最多2个中间节点
|
||||
print(f"HYDROGENATE: 找到距离较近的{device_type}: {device}")
|
||||
return device
|
||||
except nx.NetworkXNoPath:
|
||||
continue
|
||||
|
||||
print(f"HYDROGENATE: 未找到与容器 '{vessel}' 相连的{device_type}")
|
||||
return None
|
||||
|
||||
|
||||
def generate_hydrogenate_protocol(
|
||||
G: nx.DiGraph,
|
||||
temp: str,
|
||||
time: str,
|
||||
vessel: str,
|
||||
**kwargs # 接收其他可能的参数但不使用
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""
|
||||
生成氢化反应协议序列
|
||||
|
||||
Args:
|
||||
G: 有向图，节点为容器和设备
|
||||
temp: 反应温度（如 "45 °C"）
|
||||
time: 反应时间（如 "2 h"）
|
||||
vessel: 反应容器
|
||||
**kwargs: 其他可选参数，但不使用
|
||||
|
||||
Returns:
|
||||
List[Dict[str, Any]]: 动作序列
|
||||
"""
|
||||
action_sequence = []
|
||||
|
||||
# 解析参数
|
||||
temperature = parse_temperature(temp)
|
||||
reaction_time = parse_time(time)
|
||||
|
||||
print(f"HYDROGENATE: 开始生成氢化反应协议")
|
||||
print(f" - 反应温度: {temperature}°C")
|
||||
print(f" - 反应时间: {reaction_time/3600:.1f} 小时")
|
||||
print(f" - 反应容器: {vessel}")
|
||||
|
||||
# 1. 验证目标容器存在
|
||||
if vessel not in G.nodes():
|
||||
print(f"HYDROGENATE: 警告 - 容器 '{vessel}' 不存在于系统中，跳过氢化反应")
|
||||
return action_sequence
|
||||
|
||||
# 2. 查找相连的设备
|
||||
heater_id = find_connected_device(G, vessel, 'heater')
|
||||
stirrer_id = find_connected_device(G, vessel, 'stirrer')
|
||||
gas_source_id = find_connected_device(G, vessel, 'gas_source')
|
||||
|
||||
# 3. 启动搅拌器
|
||||
if stirrer_id:
|
||||
print(f"HYDROGENATE: 启动搅拌器 {stirrer_id}")
|
||||
action_sequence.append({
|
||||
"device_id": stirrer_id,
|
||||
"action_name": "start_stir",
|
||||
"action_kwargs": {
|
||||
"vessel": vessel,
|
||||
"stir_speed": 300.0,
|
||||
"purpose": "氢化反应: 开始搅拌"
|
||||
}
|
||||
})
|
||||
else:
|
||||
print(f"HYDROGENATE: 警告 - 未找到搅拌器，继续执行")
|
||||
|
||||
# 4. 启动气源（氢气）- 修复版本
|
||||
if gas_source_id:
|
||||
print(f"HYDROGENATE: 启动气源 {gas_source_id} (氢气)")
|
||||
action_sequence.append({
|
||||
"device_id": gas_source_id,
|
||||
"action_name": "set_status", # 修改为 set_status
|
||||
"action_kwargs": {
|
||||
"string": "ON" # 修改参数格式
|
||||
}
|
||||
})
|
||||
|
||||
# 查找相关的电磁阀
|
||||
gas_solenoid = find_associated_solenoid_valve(G, gas_source_id)
|
||||
if gas_solenoid:
|
||||
print(f"HYDROGENATE: 开启气源电磁阀 {gas_solenoid}")
|
||||
action_sequence.append({
|
||||
"device_id": gas_solenoid,
|
||||
"action_name": "set_valve_position",
|
||||
"action_kwargs": {
|
||||
"command": "OPEN"
|
||||
}
|
||||
})
|
||||
else:
|
||||
print(f"HYDROGENATE: 警告 - 未找到气源，继续执行")
|
||||
|
||||
# 5. 等待气体稳定
|
||||
action_sequence.append({
|
||||
"action_name": "wait",
|
||||
"action_kwargs": {
|
||||
"time": 30.0,
|
||||
"description": "等待氢气环境稳定"
|
||||
}
|
||||
})
|
||||
|
||||
# 6. 启动加热器
|
||||
if heater_id:
|
||||
print(f"HYDROGENATE: 启动加热器 {heater_id} 到 {temperature}°C")
|
||||
action_sequence.append({
|
||||
"device_id": heater_id,
|
||||
"action_name": "heat_chill_start",
|
||||
"action_kwargs": {
|
||||
"vessel": vessel,
|
||||
"temp": temperature,
|
||||
"purpose": f"氢化反应: 加热到 {temperature}°C"
|
||||
}
|
||||
})
|
||||
|
||||
# 等待温度稳定
|
||||
action_sequence.append({
|
||||
"action_name": "wait",
|
||||
"action_kwargs": {
|
||||
"time": 120.0,
|
||||
"description": f"等待温度稳定到 {temperature}°C"
|
||||
}
|
||||
})
|
||||
|
||||
# 保持反应温度
|
||||
action_sequence.append({
|
||||
"device_id": heater_id,
|
||||
"action_name": "heat_chill",
|
||||
"action_kwargs": {
|
||||
"vessel": vessel,
|
||||
"temp": temperature,
|
||||
"time": reaction_time,
|
||||
"purpose": f"氢化反应: 保持 {temperature}°C，反应 {reaction_time/3600:.1f} 小时"
|
||||
}
|
||||
})
|
||||
else:
|
||||
print(f"HYDROGENATE: 警告 - 未找到加热器，使用室温反应")
|
||||
# 室温反应，只等待时间
|
||||
action_sequence.append({
|
||||
"action_name": "wait",
|
||||
"action_kwargs": {
|
||||
"time": reaction_time,
|
||||
"description": f"室温氢化反应 {reaction_time/3600:.1f} 小时"
|
||||
}
|
||||
})
|
||||
|
||||
# 7. 停止加热
|
||||
if heater_id:
|
||||
action_sequence.append({
|
||||
"device_id": heater_id,
|
||||
"action_name": "heat_chill_stop",
|
||||
"action_kwargs": {
|
||||
"vessel": vessel,
|
||||
"purpose": "氢化反应完成，停止加热"
|
||||
}
|
||||
})
|
||||
|
||||
# 8. 等待冷却
|
||||
action_sequence.append({
|
||||
"action_name": "wait",
|
||||
"action_kwargs": {
|
||||
"time": 300.0,
|
||||
"description": "等待反应混合物冷却"
|
||||
}
|
||||
})
|
||||
|
||||
# 9. 停止气源 - 修复版本
|
||||
if gas_source_id:
|
||||
# 先关闭电磁阀
|
||||
gas_solenoid = find_associated_solenoid_valve(G, gas_source_id)
|
||||
if gas_solenoid:
|
||||
print(f"HYDROGENATE: 关闭气源电磁阀 {gas_solenoid}")
|
||||
action_sequence.append({
|
||||
"device_id": gas_solenoid,
|
||||
"action_name": "set_valve_position",
|
||||
"action_kwargs": {
|
||||
"command": "CLOSED"
|
||||
}
|
||||
})
|
||||
|
||||
# 再关闭气源
|
||||
action_sequence.append({
|
||||
"device_id": gas_source_id,
|
||||
"action_name": "set_status", # 修改为 set_status
|
||||
"action_kwargs": {
|
||||
"string": "OFF" # 修改参数格式
|
||||
}
|
||||
})
|
||||
|
||||
# 10. 停止搅拌
|
||||
if stirrer_id:
|
||||
action_sequence.append({
|
||||
"device_id": stirrer_id,
|
||||
"action_name": "stop_stir",
|
||||
"action_kwargs": {
|
||||
"vessel": vessel,
|
||||
"purpose": "氢化反应完成，停止搅拌"
|
||||
}
|
||||
})
|
||||
|
||||
print(f"HYDROGENATE: 协议生成完成，共 {len(action_sequence)} 个动作")
|
||||
print(f"HYDROGENATE: 预计总时间: {(reaction_time + 450)/3600:.1f} 小时")
|
||||
|
||||
return action_sequence
|
||||
|
||||
|
||||
# 测试函数
|
||||
def test_hydrogenate_protocol():
|
||||
"""测试氢化反应协议"""
|
||||
print("=== HYDROGENATE PROTOCOL 测试 ===")
|
||||
|
||||
# 测试温度解析
|
||||
test_temps = ["45 °C", "45°C", "45", "25 C", "invalid"]
|
||||
for temp in test_temps:
|
||||
parsed = parse_temperature(temp)
|
||||
print(f"温度 '{temp}' -> {parsed}°C")
|
||||
|
||||
# 测试时间解析
|
||||
test_times = ["2 h", "120 min", "7200 s", "2", "invalid"]
|
||||
for time in test_times:
|
||||
parsed = parse_time(time)
|
||||
print(f"时间 '{time}' -> {parsed/3600:.1f} 小时")
|
||||
|
||||
print("测试完成")
|
||||
|
||||
|
||||
if __name__ == "__main__":
|
||||
test_hydrogenate_protocol()
|
||||
281
unilabos/compile/recrystallize_protocol.py
Normal file
281
unilabos/compile/recrystallize_protocol.py
Normal file
@@ -0,0 +1,281 @@
|
||||
import networkx as nx
|
||||
from typing import List, Dict, Any, Tuple
|
||||
from .pump_protocol import generate_pump_protocol_with_rinsing
|
||||
|
||||
|
||||
def parse_ratio(ratio_str: str) -> Tuple[float, float]:
|
||||
"""
|
||||
解析比例字符串，支持多种格式
|
||||
|
||||
Args:
|
||||
ratio_str: 比例字符串（如 "1:1", "3:7", "50:50"）
|
||||
|
||||
Returns:
|
||||
Tuple[float, float]: 比例元组 (ratio1, ratio2)
|
||||
"""
|
||||
try:
|
||||
# 处理 "1:1", "3:7", "50:50" 等格式
|
||||
if ":" in ratio_str:
|
||||
parts = ratio_str.split(":")
|
||||
if len(parts) == 2:
|
||||
ratio1 = float(parts[0])
|
||||
ratio2 = float(parts[1])
|
||||
return ratio1, ratio2
|
||||
|
||||
# 处理 "1-1", "3-7" 等格式
|
||||
if "-" in ratio_str:
|
||||
parts = ratio_str.split("-")
|
||||
if len(parts) == 2:
|
||||
ratio1 = float(parts[0])
|
||||
ratio2 = float(parts[1])
|
||||
return ratio1, ratio2
|
||||
|
||||
# 处理 "1,1", "3,7" 等格式
|
||||
if "," in ratio_str:
|
||||
parts = ratio_str.split(",")
|
||||
if len(parts) == 2:
|
||||
ratio1 = float(parts[0])
|
||||
ratio2 = float(parts[1])
|
||||
return ratio1, ratio2
|
||||
|
||||
# 默认 1:1
|
||||
print(f"RECRYSTALLIZE: 无法解析比例 '{ratio_str}'，使用默认比例 1:1")
|
||||
return 1.0, 1.0
|
||||
|
||||
except ValueError:
|
||||
print(f"RECRYSTALLIZE: 比例解析错误 '{ratio_str}'，使用默认比例 1:1")
|
||||
return 1.0, 1.0
|
||||
|
||||
|
||||
def find_solvent_vessel(G: nx.DiGraph, solvent: str) -> str:
|
||||
"""
|
||||
查找溶剂容器
|
||||
|
||||
Args:
|
||||
G: 网络图
|
||||
solvent: 溶剂名称
|
||||
|
||||
Returns:
|
||||
str: 溶剂容器ID
|
||||
"""
|
||||
print(f"RECRYSTALLIZE: 正在查找溶剂 '{solvent}' 的容器...")
|
||||
|
||||
# 构建可能的容器名称
|
||||
possible_names = [
|
||||
f"flask_{solvent}",
|
||||
f"bottle_{solvent}",
|
||||
f"reagent_{solvent}",
|
||||
f"reagent_bottle_{solvent}",
|
||||
f"{solvent}_flask",
|
||||
f"{solvent}_bottle",
|
||||
f"{solvent}",
|
||||
f"vessel_{solvent}",
|
||||
]
|
||||
|
||||
# 第一步：通过容器名称匹配
|
||||
for vessel_name in possible_names:
|
||||
if vessel_name in G.nodes():
|
||||
print(f"RECRYSTALLIZE: 通过名称匹配找到容器: {vessel_name}")
|
||||
return vessel_name
|
||||
|
||||
# 第二步：通过模糊匹配
|
||||
for node_id in G.nodes():
|
||||
if G.nodes[node_id].get('type') == 'container':
|
||||
node_name = G.nodes[node_id].get('name', '').lower()
|
||||
|
||||
if solvent.lower() in node_id.lower() or solvent.lower() in node_name:
|
||||
print(f"RECRYSTALLIZE: 通过模糊匹配找到容器: {node_id}")
|
||||
return node_id
|
||||
|
||||
# 第三步：通过液体类型匹配
|
||||
for node_id in G.nodes():
|
||||
if G.nodes[node_id].get('type') == 'container':
|
||||
vessel_data = G.nodes[node_id].get('data', {})
|
||||
liquids = vessel_data.get('liquid', [])
|
||||
|
||||
for liquid in liquids:
|
||||
if isinstance(liquid, dict):
|
||||
liquid_type = (liquid.get('liquid_type') or liquid.get('name', '')).lower()
|
||||
reagent_name = vessel_data.get('reagent_name', '').lower()
|
||||
|
||||
if solvent.lower() in liquid_type or solvent.lower() in reagent_name:
|
||||
print(f"RECRYSTALLIZE: 通过液体类型匹配找到容器: {node_id}")
|
||||
return node_id
|
||||
|
||||
raise ValueError(f"找不到溶剂 '{solvent}' 对应的容器")
|
||||
|
||||
|
||||
def generate_recrystallize_protocol(
|
||||
G: nx.DiGraph,
|
||||
ratio: str,
|
||||
solvent1: str,
|
||||
solvent2: str,
|
||||
vessel: str,
|
||||
volume: float,
|
||||
**kwargs # 接收其他可能的参数但不使用
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""
|
||||
生成重结晶协议序列
|
||||
|
||||
Args:
|
||||
G: 有向图，节点为容器和设备
|
||||
ratio: 溶剂比例（如 "1:1", "3:7"）
|
||||
solvent1: 第一种溶剂名称
|
||||
solvent2: 第二种溶剂名称
|
||||
vessel: 目标容器
|
||||
volume: 总体积 (mL)
|
||||
**kwargs: 其他可选参数，但不使用
|
||||
|
||||
Returns:
|
||||
List[Dict[str, Any]]: 动作序列
|
||||
"""
|
||||
action_sequence = []
|
||||
|
||||
print(f"RECRYSTALLIZE: 开始生成重结晶协议")
|
||||
print(f" - 比例: {ratio}")
|
||||
print(f" - 溶剂1: {solvent1}")
|
||||
print(f" - 溶剂2: {solvent2}")
|
||||
print(f" - 容器: {vessel}")
|
||||
print(f" - 总体积: {volume} mL")
|
||||
|
||||
# 1. 验证目标容器存在
|
||||
if vessel not in G.nodes():
|
||||
raise ValueError(f"目标容器 '{vessel}' 不存在于系统中")
|
||||
|
||||
# 2. 解析比例
|
||||
ratio1, ratio2 = parse_ratio(ratio)
|
||||
total_ratio = ratio1 + ratio2
|
||||
|
||||
# 3. 计算各溶剂体积
|
||||
volume1 = volume * (ratio1 / total_ratio)
|
||||
volume2 = volume * (ratio2 / total_ratio)
|
||||
|
||||
print(f"RECRYSTALLIZE: 解析比例: {ratio1}:{ratio2}")
|
||||
print(f"RECRYSTALLIZE: {solvent1} 体积: {volume1:.2f} mL")
|
||||
print(f"RECRYSTALLIZE: {solvent2} 体积: {volume2:.2f} mL")
|
||||
|
||||
# 4. 查找溶剂容器
|
||||
try:
|
||||
solvent1_vessel = find_solvent_vessel(G, solvent1)
|
||||
print(f"RECRYSTALLIZE: 找到溶剂1容器: {solvent1_vessel}")
|
||||
except ValueError as e:
|
||||
raise ValueError(f"无法找到溶剂1 '{solvent1}': {str(e)}")
|
||||
|
||||
try:
|
||||
solvent2_vessel = find_solvent_vessel(G, solvent2)
|
||||
print(f"RECRYSTALLIZE: 找到溶剂2容器: {solvent2_vessel}")
|
||||
except ValueError as e:
|
||||
raise ValueError(f"无法找到溶剂2 '{solvent2}': {str(e)}")
|
||||
|
||||
# 5. 验证路径存在
|
||||
try:
|
||||
path1 = nx.shortest_path(G, source=solvent1_vessel, target=vessel)
|
||||
print(f"RECRYSTALLIZE: 溶剂1路径: {' → '.join(path1)}")
|
||||
except nx.NetworkXNoPath:
|
||||
raise ValueError(f"从溶剂1容器 '{solvent1_vessel}' 到目标容器 '{vessel}' 没有可用路径")
|
||||
|
||||
try:
|
||||
path2 = nx.shortest_path(G, source=solvent2_vessel, target=vessel)
|
||||
print(f"RECRYSTALLIZE: 溶剂2路径: {' → '.join(path2)}")
|
||||
except nx.NetworkXNoPath:
|
||||
raise ValueError(f"从溶剂2容器 '{solvent2_vessel}' 到目标容器 '{vessel}' 没有可用路径")
|
||||
|
||||
# 6. 添加第一种溶剂
|
||||
print(f"RECRYSTALLIZE: 开始添加溶剂1 {volume1:.2f} mL")
|
||||
|
||||
try:
|
||||
pump_actions1 = generate_pump_protocol_with_rinsing(
|
||||
G=G,
|
||||
from_vessel=solvent1_vessel,
|
||||
to_vessel=vessel,
|
||||
volume=volume1,
|
||||
amount="",
|
||||
time=0.0,
|
||||
viscous=False,
|
||||
rinsing_solvent="", # 重结晶不需要清洗
|
||||
rinsing_volume=0.0,
|
||||
rinsing_repeats=0,
|
||||
solid=False,
|
||||
flowrate=2.0, # 正常流速
|
||||
transfer_flowrate=0.5
|
||||
)
|
||||
|
||||
action_sequence.extend(pump_actions1)
|
||||
|
||||
except Exception as e:
|
||||
raise ValueError(f"生成溶剂1泵协议时出错: {str(e)}")
|
||||
|
||||
# 7. 等待溶剂1稳定
|
||||
action_sequence.append({
|
||||
"action_name": "wait",
|
||||
"action_kwargs": {
|
||||
"time": 10.0,
|
||||
"description": f"等待溶剂1 {solvent1} 稳定"
|
||||
}
|
||||
})
|
||||
|
||||
# 8. 添加第二种溶剂
|
||||
print(f"RECRYSTALLIZE: 开始添加溶剂2 {volume2:.2f} mL")
|
||||
|
||||
try:
|
||||
pump_actions2 = generate_pump_protocol_with_rinsing(
|
||||
G=G,
|
||||
from_vessel=solvent2_vessel,
|
||||
to_vessel=vessel,
|
||||
volume=volume2,
|
||||
amount="",
|
||||
time=0.0,
|
||||
viscous=False,
|
||||
rinsing_solvent="", # 重结晶不需要清洗
|
||||
rinsing_volume=0.0,
|
||||
rinsing_repeats=0,
|
||||
solid=False,
|
||||
flowrate=2.0, # 正常流速
|
||||
transfer_flowrate=0.5
|
||||
)
|
||||
|
||||
action_sequence.extend(pump_actions2)
|
||||
|
||||
except Exception as e:
|
||||
raise ValueError(f"生成溶剂2泵协议时出错: {str(e)}")
|
||||
|
||||
# 9. 等待溶剂2稳定
|
||||
action_sequence.append({
|
||||
"action_name": "wait",
|
||||
"action_kwargs": {
|
||||
"time": 10.0,
|
||||
"description": f"等待溶剂2 {solvent2} 稳定"
|
||||
}
|
||||
})
|
||||
|
||||
# 10. 等待重结晶完成
|
||||
action_sequence.append({
|
||||
"action_name": "wait",
|
||||
"action_kwargs": {
|
||||
"time": 600.0, # 等待10分钟进行重结晶
|
||||
"description": f"等待重结晶完成（{solvent1}:{solvent2} = {ratio}）"
|
||||
}
|
||||
})
|
||||
|
||||
print(f"RECRYSTALLIZE: 协议生成完成，共 {len(action_sequence)} 个动作")
|
||||
print(f"RECRYSTALLIZE: 预计总时间: {620/60:.1f} 分钟")
|
||||
|
||||
return action_sequence
|
||||
|
||||
|
||||
# 测试函数
|
||||
def test_recrystallize_protocol():
|
||||
"""测试重结晶协议"""
|
||||
print("=== RECRYSTALLIZE PROTOCOL 测试 ===")
|
||||
|
||||
# 测试比例解析
|
||||
test_ratios = ["1:1", "3:7", "50:50", "1-1", "2,8", "invalid"]
|
||||
for ratio in test_ratios:
|
||||
r1, r2 = parse_ratio(ratio)
|
||||
print(f"比例 '{ratio}' -> {r1}:{r2}")
|
||||
|
||||
print("测试完成")
|
||||
|
||||
|
||||
if __name__ == "__main__":
|
||||
test_recrystallize_protocol()
|
||||
180
unilabos/compile/reset_handling_protocol.py
Normal file
180
unilabos/compile/reset_handling_protocol.py
Normal file
@@ -0,0 +1,180 @@
|
||||
import networkx as nx
|
||||
from typing import List, Dict, Any
|
||||
from .pump_protocol import generate_pump_protocol_with_rinsing
|
||||
|
||||
|
||||
def find_solvent_vessel(G: nx.DiGraph, solvent: str) -> str:
|
||||
"""
|
||||
查找溶剂容器，支持多种匹配模式
|
||||
|
||||
Args:
|
||||
G: 网络图
|
||||
solvent: 溶剂名称（如 "methanol", "ethanol", "water"）
|
||||
|
||||
Returns:
|
||||
str: 溶剂容器ID
|
||||
"""
|
||||
print(f"RESET_HANDLING: 正在查找溶剂 '{solvent}' 的容器...")
|
||||
|
||||
# 构建可能的容器名称
|
||||
possible_names = [
|
||||
f"flask_{solvent}", # flask_methanol
|
||||
f"bottle_{solvent}", # bottle_methanol
|
||||
f"reagent_{solvent}", # reagent_methanol
|
||||
f"reagent_bottle_{solvent}", # reagent_bottle_methanol
|
||||
f"{solvent}_flask", # methanol_flask
|
||||
f"{solvent}_bottle", # methanol_bottle
|
||||
f"{solvent}", # methanol
|
||||
f"vessel_{solvent}", # vessel_methanol
|
||||
]
|
||||
|
||||
# 第一步：通过容器名称匹配
|
||||
for vessel_name in possible_names:
|
||||
if vessel_name in G.nodes():
|
||||
print(f"RESET_HANDLING: 通过名称匹配找到容器: {vessel_name}")
|
||||
return vessel_name
|
||||
|
||||
# 第二步：通过模糊匹配
|
||||
for node_id in G.nodes():
|
||||
if G.nodes[node_id].get('type') == 'container':
|
||||
node_name = G.nodes[node_id].get('name', '').lower()
|
||||
|
||||
# 检查是否包含溶剂名称
|
||||
if solvent.lower() in node_id.lower() or solvent.lower() in node_name:
|
||||
print(f"RESET_HANDLING: 通过模糊匹配找到容器: {node_id}")
|
||||
return node_id
|
||||
|
||||
# 第三步：通过液体类型匹配
|
||||
for node_id in G.nodes():
|
||||
if G.nodes[node_id].get('type') == 'container':
|
||||
vessel_data = G.nodes[node_id].get('data', {})
|
||||
liquids = vessel_data.get('liquid', [])
|
||||
|
||||
for liquid in liquids:
|
||||
if isinstance(liquid, dict):
|
||||
liquid_type = (liquid.get('liquid_type') or liquid.get('name', '')).lower()
|
||||
reagent_name = vessel_data.get('reagent_name', '').lower()
|
||||
|
||||
if solvent.lower() in liquid_type or solvent.lower() in reagent_name:
|
||||
print(f"RESET_HANDLING: 通过液体类型匹配找到容器: {node_id}")
|
||||
return node_id
|
||||
|
||||
# 列出可用容器帮助调试
|
||||
available_containers = []
|
||||
for node_id in G.nodes():
|
||||
if G.nodes[node_id].get('type') == 'container':
|
||||
vessel_data = G.nodes[node_id].get('data', {})
|
||||
liquids = vessel_data.get('liquid', [])
|
||||
liquid_types = [liquid.get('liquid_type', '') or liquid.get('name', '')
|
||||
for liquid in liquids if isinstance(liquid, dict)]
|
||||
|
||||
available_containers.append({
|
||||
'id': node_id,
|
||||
'name': G.nodes[node_id].get('name', ''),
|
||||
'liquids': liquid_types,
|
||||
'reagent_name': vessel_data.get('reagent_name', '')
|
||||
})
|
||||
|
||||
print(f"RESET_HANDLING: 可用容器列表:")
|
||||
for container in available_containers:
|
||||
print(f" - {container['id']}: {container['name']}")
|
||||
print(f" 液体: {container['liquids']}")
|
||||
print(f" 试剂: {container['reagent_name']}")
|
||||
|
||||
raise ValueError(f"找不到溶剂 '{solvent}' 对应的容器。尝试了: {possible_names}")
|
||||
|
||||
|
||||
def generate_reset_handling_protocol(
|
||||
G: nx.DiGraph,
|
||||
solvent: str,
|
||||
**kwargs # 接收其他可能的参数但不使用
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""
|
||||
生成重置处理协议序列
|
||||
|
||||
Args:
|
||||
G: 有向图，节点为容器和设备
|
||||
solvent: 溶剂名称（从XDL传入）
|
||||
**kwargs: 其他可选参数，但不使用
|
||||
|
||||
Returns:
|
||||
List[Dict[str, Any]]: 动作序列
|
||||
"""
|
||||
action_sequence = []
|
||||
|
||||
# 固定参数
|
||||
target_vessel = "main_reactor" # 默认目标容器
|
||||
volume = 100.0 # 默认体积 100 mL
|
||||
|
||||
print(f"RESET_HANDLING: 开始生成重置处理协议")
|
||||
print(f" - 溶剂: {solvent}")
|
||||
print(f" - 目标容器: {target_vessel}")
|
||||
print(f" - 体积: {volume} mL")
|
||||
|
||||
# 1. 验证目标容器存在
|
||||
if target_vessel not in G.nodes():
|
||||
raise ValueError(f"目标容器 '{target_vessel}' 不存在于系统中")
|
||||
|
||||
# 2. 查找溶剂容器
|
||||
try:
|
||||
solvent_vessel = find_solvent_vessel(G, solvent)
|
||||
print(f"RESET_HANDLING: 找到溶剂容器: {solvent_vessel}")
|
||||
except ValueError as e:
|
||||
raise ValueError(f"无法找到溶剂 '{solvent}': {str(e)}")
|
||||
|
||||
# 3. 验证路径存在
|
||||
try:
|
||||
path = nx.shortest_path(G, source=solvent_vessel, target=target_vessel)
|
||||
print(f"RESET_HANDLING: 找到路径: {' → '.join(path)}")
|
||||
except nx.NetworkXNoPath:
|
||||
raise ValueError(f"从溶剂容器 '{solvent_vessel}' 到目标容器 '{target_vessel}' 没有可用路径")
|
||||
|
||||
# 4. 使用pump_protocol转移溶剂
|
||||
print(f"RESET_HANDLING: 开始转移溶剂 {volume} mL")
|
||||
|
||||
try:
|
||||
pump_actions = generate_pump_protocol_with_rinsing(
|
||||
G=G,
|
||||
from_vessel=solvent_vessel,
|
||||
to_vessel=target_vessel,
|
||||
volume=volume,
|
||||
amount="",
|
||||
time=0.0,
|
||||
viscous=False,
|
||||
rinsing_solvent="", # 重置处理不需要清洗
|
||||
rinsing_volume=0.0,
|
||||
rinsing_repeats=0,
|
||||
solid=False,
|
||||
flowrate=2.5, # 正常流速
|
||||
transfer_flowrate=0.5 # 正常转移流速
|
||||
)
|
||||
|
||||
action_sequence.extend(pump_actions)
|
||||
|
||||
except Exception as e:
|
||||
raise ValueError(f"生成泵协议时出错: {str(e)}")
|
||||
|
||||
# 5. 等待溶剂稳定
|
||||
action_sequence.append({
|
||||
"action_name": "wait",
|
||||
"action_kwargs": {
|
||||
"time": 10.0,
|
||||
"description": f"等待溶剂 {solvent} 稳定"
|
||||
}
|
||||
})
|
||||
|
||||
print(f"RESET_HANDLING: 协议生成完成，共 {len(action_sequence)} 个动作")
|
||||
print(f"RESET_HANDLING: 已添加 {volume} mL {solvent} 到 {target_vessel}")
|
||||
|
||||
return action_sequence
|
||||
|
||||
|
||||
# 测试函数
|
||||
def test_reset_handling_protocol():
|
||||
"""测试重置处理协议"""
|
||||
print("=== RESET HANDLING PROTOCOL 测试 ===")
|
||||
print("测试完成")
|
||||
|
||||
|
||||
if __name__ == "__main__":
|
||||
test_reset_handling_protocol()
|
||||
@@ -178,6 +178,31 @@ class WashSolidProtocol(BaseModel):
|
||||
time: float = 0.0
|
||||
repeats: int = 1
|
||||
|
||||
class AdjustPHProtocol(BaseModel):
|
||||
vessel: str = Field(..., description="目标容器")
|
||||
ph_value: float = Field(..., description="目标pH值") # 改为 ph_value
|
||||
reagent: str = Field(..., description="酸碱试剂名称")
|
||||
# 移除其他可选参数，使用默认值
|
||||
|
||||
class ResetHandlingProtocol(BaseModel):
|
||||
solvent: str = Field(..., description="溶剂名称")
|
||||
|
||||
class DryProtocol(BaseModel):
|
||||
compound: str = Field(..., description="化合物名称")
|
||||
vessel: str = Field(..., description="目标容器")
|
||||
|
||||
class RecrystallizeProtocol(BaseModel):
|
||||
ratio: str = Field(..., description="溶剂比例（如 '1:1', '3:7'）")
|
||||
solvent1: str = Field(..., description="第一种溶剂名称")
|
||||
solvent2: str = Field(..., description="第二种溶剂名称")
|
||||
vessel: str = Field(..., description="目标容器")
|
||||
volume: float = Field(..., description="总体积 (mL)")
|
||||
|
||||
class HydrogenateProtocol(BaseModel):
|
||||
temp: str = Field(..., description="反应温度（如 '45 °C'）")
|
||||
time: str = Field(..., description="反应时间（如 '2 h'）")
|
||||
vessel: str = Field(..., description="反应容器")
|
||||
|
||||
__all__ = [
|
||||
"Point3D", "PumpTransferProtocol", "CleanProtocol", "SeparateProtocol",
|
||||
"EvaporateProtocol", "EvacuateAndRefillProtocol", "AGVTransferProtocol",
|
||||
@@ -185,6 +210,8 @@ __all__ = [
|
||||
"HeatChillProtocol", "HeatChillStartProtocol", "HeatChillStopProtocol",
|
||||
"StirProtocol", "StartStirProtocol", "StopStirProtocol",
|
||||
"TransferProtocol", "CleanVesselProtocol", "DissolveProtocol",
|
||||
"FilterThroughProtocol", "RunColumnProtocol", "WashSolidProtocol"
|
||||
"FilterThroughProtocol", "RunColumnProtocol", "WashSolidProtocol",
|
||||
"AdjustPHProtocol", "ResetHandlingProtocol", "DryProtocol",
|
||||
"RecrystallizeProtocol", "HydrogenateProtocol"
|
||||
]
|
||||
# End Protocols
|
||||
|
||||
@@ -1,4 +1,4 @@
|
||||
cmake_minimum_required(VERSION 3.5)
|
||||
cmake_minimum_required(VERSION 3.16)
|
||||
project(unilabos_msgs)
|
||||
|
||||
# Default to C99
|
||||
@@ -28,7 +28,11 @@ set(action_files
|
||||
"action/HeatChill.action"
|
||||
"action/HeatChillStart.action"
|
||||
"action/HeatChillStop.action"
|
||||
|
||||
"action/AdjustPH.action"
|
||||
"action/ResetHandling.action"
|
||||
"action/Dry.action"
|
||||
"action/Hydrogenate.action"
|
||||
"action/Recrystallize.action"
|
||||
"action/CleanVessel.action"
|
||||
"action/Dissolve.action"
|
||||
"action/FilterThrough.action"
|
||||
@@ -39,7 +43,6 @@ set(action_files
|
||||
"action/Add.action"
|
||||
"action/Centrifuge.action"
|
||||
"action/Crystallize.action"
|
||||
"action/Dry.action"
|
||||
"action/Purge.action"
|
||||
"action/StartPurge.action"
|
||||
"action/StartStir.action"
|
||||
|
||||
13
unilabos_msgs/action/AdjustPH.action
Normal file
13
unilabos_msgs/action/AdjustPH.action
Normal file
@@ -0,0 +1,13 @@
|
||||
# Request - 与您的 AdjustPHProtocol 类匹配
|
||||
string vessel
|
||||
float64 ph_value
|
||||
string reagent
|
||||
---
|
||||
# Result - 标准结果格式
|
||||
bool success
|
||||
string message
|
||||
string return_info
|
||||
---
|
||||
# Feedback - 标准反馈格式
|
||||
string status
|
||||
float64 progress
|
||||
@@ -1,17 +1,12 @@
|
||||
# Goal - 干燥操作的目标参数
|
||||
string vessel # 干燥容器
|
||||
float64 time # 干燥时间 (可选，秒)
|
||||
float64 pressure # 压力 (可选，Pa)
|
||||
float64 temp # 温度 (可选，摄氏度)
|
||||
bool continue_heatchill # 是否继续加热冷却
|
||||
# Request
|
||||
string compound # 化合物
|
||||
string vessel # 干燥容器
|
||||
---
|
||||
# Result - 操作结果
|
||||
# Result
|
||||
bool success # 操作是否成功
|
||||
string message # 结果消息
|
||||
string return_info
|
||||
---
|
||||
# Feedback - 实时反馈
|
||||
float64 progress # 进度百分比 (0-100)
|
||||
float64 current_temp # 当前温度
|
||||
float64 current_pressure # 当前压力
|
||||
string current_status # 当前状态描述
|
||||
# Feedback
|
||||
string status # 当前状态描述
|
||||
float64 progress # 进度百分比 (0-100)
|
||||
13
unilabos_msgs/action/Hydrogenate.action
Normal file
13
unilabos_msgs/action/Hydrogenate.action
Normal file
@@ -0,0 +1,13 @@
|
||||
# Request
|
||||
string temp
|
||||
string time
|
||||
string vessel
|
||||
---
|
||||
# Result
|
||||
bool success
|
||||
string message
|
||||
string return_info
|
||||
---
|
||||
# Feedback
|
||||
string status
|
||||
float64 progress
|
||||
15
unilabos_msgs/action/Recrystallize.action
Normal file
15
unilabos_msgs/action/Recrystallize.action
Normal file
@@ -0,0 +1,15 @@
|
||||
# Request
|
||||
string ratio
|
||||
string solvent1
|
||||
string solvent2
|
||||
string vessel
|
||||
float64 volume
|
||||
---
|
||||
# Result
|
||||
bool success
|
||||
string message
|
||||
string return_info
|
||||
---
|
||||
# Feedback
|
||||
string status
|
||||
float64 progress
|
||||
11
unilabos_msgs/action/ResetHandling.action
Normal file
11
unilabos_msgs/action/ResetHandling.action
Normal file
@@ -0,0 +1,11 @@
|
||||
# Request
|
||||
string solvent
|
||||
---
|
||||
# Result
|
||||
bool success
|
||||
string message
|
||||
string return_info
|
||||
---
|
||||
# Feedback
|
||||
string status
|
||||
float64 progress
|
||||
Reference in New Issue
Block a user