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Device Visualization & Mock Devices (#44) [37-biomek-i5i7 (#40), Device visualization (#39), Add Mock Device for Organic Synthesis\添加有机合成的虚拟仪器和Protocol (#43)]

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* add biomek.py demo implementation

* 更新LiquidHandlerBiomek类，添加资源创建功能，优化协议创建方法，修复部分代码格式问题，更新YAML配置以支持新功能。

* Test

* fix biomek success type

* Convert LH action to biomek.

* Update biomek.py

* 注册表上报handle和schema (param input)

* 修复biomek缺少的字段

* delete 's'

* Remove warnings

* Update biomek.py

* Biomek test

* Update biomek.py

* 新增transfer_biomek的msg

* New transfer_biomek

* Updated transfer_biomek

* 更新transfer_biomek的msg

* 更新transfer_biomek的msg

* 支持Biomek创建

* new action

* fix key name typo

* New parameter for biomek to run.

* Refine

* Update

* new actions

* new actions

* 1

* registry

* fix biomek startup
add action handles

* fix handles not as default entry

* biomek_test.py

biomek_test.py是最新的版本，运行它会生成complete_biomek_protocol.json

* Update biomek.py

* biomek_test.py

* fix liquid_handler.biomek handles

* host node新增resource add时间统计
create_resource新增handle
bump version to 0.9.2

* 修正物料上传时间
改用biomek_test
增加ResultInfoEncoder
支持返回结果上传

* 正确发送return_info结果

* 同步执行状态信息

* 取消raiseValueError提示

* Update biomek_test.py

* 0608 DONE

* 同步了Biomek.py 现在应可用

* biomek switch back to non-test

* temp disable initialize resource

* 37-biomek-i5i7 (#40)

* add biomek.py demo implementation

* 更新LiquidHandlerBiomek类，添加资源创建功能，优化协议创建方法，修复部分代码格式问题，更新YAML配置以支持新功能。

* Test

* fix biomek success type

* Convert LH action to biomek.

* Update biomek.py

* 注册表上报handle和schema (param input)

* 修复biomek缺少的字段

* delete 's'

* Remove warnings

* Update biomek.py

* Biomek test

* Update biomek.py

* 新增transfer_biomek的msg

* New transfer_biomek

* Updated transfer_biomek

* 更新transfer_biomek的msg

* 更新transfer_biomek的msg

* 支持Biomek创建

* new action

* fix key name typo

* New parameter for biomek to run.

* Refine

* Update

* new actions

* new actions

* 1

* registry

* fix biomek startup
add action handles

* fix handles not as default entry

* biomek_test.py

biomek_test.py是最新的版本，运行它会生成complete_biomek_protocol.json

* Update biomek.py

* biomek_test.py

* fix liquid_handler.biomek handles

* host node新增resource add时间统计
create_resource新增handle
bump version to 0.9.2

* 修正物料上传时间
改用biomek_test
增加ResultInfoEncoder
支持返回结果上传

* 正确发送return_info结果

* 同步执行状态信息

* 取消raiseValueError提示

* Update biomek_test.py

* 0608 DONE

* 同步了Biomek.py 现在应可用

* biomek switch back to non-test

* temp disable initialize resource

* Refine biomek

* Refine copy issue

* Refine

---------

Co-authored-by: Junhan Chang <changjh@pku.edu.cn>
Co-authored-by: Guangxin Zhang <guangxin.zhang.bio@gmail.com>
Co-authored-by: qxw138 <qxw@stu.pku.edu.cn>

* Device visualization (#39)

* Update README and MQTTClient for installation instructions and code improvements

* feat: 支持local_config启动
add: 增加对crt path的说明，为传入config.py的相对路径
move: web component

* add: registry description

* add 3d visualization

* 完成在main中启动设备可视化

完成在main中启动设备可视化，并输出物料ID：mesh的对应关系resource_model

添加物料模型管理类，遍历物料与resource_model，完成TF数据收集

* 完成TF发布

* 修改模型方向，在yaml中添加变换属性

* 添加物料tf变化时，发送topic到前端

另外修改了物料初始化的方法，防止在tf还未发布时提前建立物料模型与发布话题

* 添加关节发布节点与物料可视化节点进入unilab

* 使用json启动plr与3D模型仿真

* feat: node_info_update srv
fix: OTDeck cant create

* close #12
feat: slave node registry

* feat: show machine name
fix: host node registry not uploaded

* feat: add hplc registry

* feat: add hplc registry

* fix: hplc status typo

* fix: devices/

* 完成启动OT并联动rviz

* add 3d visualization

* 完成在main中启动设备可视化

完成在main中启动设备可视化，并输出物料ID：mesh的对应关系resource_model

添加物料模型管理类，遍历物料与resource_model，完成TF数据收集

* 完成TF发布

* 修改模型方向，在yaml中添加变换属性

* 添加物料tf变化时，发送topic到前端

另外修改了物料初始化的方法，防止在tf还未发布时提前建立物料模型与发布话题

* 添加关节发布节点与物料可视化节点进入unilab

* 使用json启动plr与3D模型仿真

* 完成启动OT并联动rviz

* fix: device.class possible null

* fix: HPLC additions with online service

* fix: slave mode spin not working

* fix: slave mode spin not working

* 修复rviz位置问题,

修复rviz位置问题,
在无tf变动时减缓发送频率
在backend中添加物料跟随方法

* feat: 多ProtocolNode 允许子设备ID相同
feat: 上报发现的ActionClient
feat: Host重启动，通过discover机制要求slaveNode重新注册，实现信息及时上报

* feat: 支持env设置config

* fix: running logic

* fix: running logic

* fix: missing ot

* 在main中直接初始化republisher和物料的mesh节点

* 将joint_republisher和resource_mesh_manager添加进 main_slave_run.py中

* Device visualization (#14)

* add 3d visualization

* 完成在main中启动设备可视化

完成在main中启动设备可视化，并输出物料ID：mesh的对应关系resource_model

添加物料模型管理类，遍历物料与resource_model，完成TF数据收集

* 完成TF发布

* 修改模型方向，在yaml中添加变换属性

* 添加物料tf变化时，发送topic到前端

另外修改了物料初始化的方法，防止在tf还未发布时提前建立物料模型与发布话题

* 添加关节发布节点与物料可视化节点进入unilab

* 使用json启动plr与3D模型仿真

* 完成启动OT并联动rviz

* add 3d visualization

* 完成在main中启动设备可视化

完成在main中启动设备可视化，并输出物料ID：mesh的对应关系resource_model

添加物料模型管理类，遍历物料与resource_model，完成TF数据收集

* 完成TF发布

* 修改模型方向，在yaml中添加变换属性

* 添加物料tf变化时，发送topic到前端

另外修改了物料初始化的方法，防止在tf还未发布时提前建立物料模型与发布话题

* 添加关节发布节点与物料可视化节点进入unilab

* 使用json启动plr与3D模型仿真

* 完成启动OT并联动rviz

* 修复rviz位置问题,

修复rviz位置问题,
在无tf变动时减缓发送频率
在backend中添加物料跟随方法

* fix: running logic

* fix: running logic

* fix: missing ot

* 在main中直接初始化republisher和物料的mesh节点

* 将joint_republisher和resource_mesh_manager添加进 main_slave_run.py中

---------

Co-authored-by: zhangshixiang <@zhangshixiang>
Co-authored-by: wznln <18435084+Xuwznln@users.noreply.github.com>

* fix: missing hostname in devices_names
fix: upload_file for model file

* fix: missing paho-mqtt package
bump version to 0.9.0

* fix startup
add ResourceCreateFromOuter.action

* fix type hint

* update actions

* update actions

* host node add_resource_from_outer
fix cmake list

* pass device config to device class

* add: bind_parent_ids to resource create action
fix: message convert string

* fix: host node should not be re_discovered

* feat: resource tracker support dict

* feat: add more necessary params

* feat: fix boolean null in registry action data

* feat: add outer resource

* 编写mesh添加action

* feat: append resource

* add action

* feat: vis 2d for plr

* fix

* fix: browser on rviz

* fix: cloud bridge error fallback to local

* fix: salve auto run rviz

* 初始化两个plate

* Device visualization (#22)

* add 3d visualization

* 完成在main中启动设备可视化

完成在main中启动设备可视化，并输出物料ID：mesh的对应关系resource_model

添加物料模型管理类，遍历物料与resource_model，完成TF数据收集

* 完成TF发布

* 修改模型方向，在yaml中添加变换属性

* 添加物料tf变化时，发送topic到前端

另外修改了物料初始化的方法，防止在tf还未发布时提前建立物料模型与发布话题

* 添加关节发布节点与物料可视化节点进入unilab

* 使用json启动plr与3D模型仿真

* 完成启动OT并联动rviz

* add 3d visualization

* 完成在main中启动设备可视化

完成在main中启动设备可视化，并输出物料ID：mesh的对应关系resource_model

添加物料模型管理类，遍历物料与resource_model，完成TF数据收集

* 完成TF发布

* 修改模型方向，在yaml中添加变换属性

* 添加物料tf变化时，发送topic到前端

另外修改了物料初始化的方法，防止在tf还未发布时提前建立物料模型与发布话题

* 添加关节发布节点与物料可视化节点进入unilab

* 使用json启动plr与3D模型仿真

* 完成启动OT并联动rviz

* 修复rviz位置问题,

修复rviz位置问题,
在无tf变动时减缓发送频率
在backend中添加物料跟随方法

* fix: running logic

* fix: running logic

* fix: missing ot

* 在main中直接初始化republisher和物料的mesh节点

* 将joint_republisher和resource_mesh_manager添加进 main_slave_run.py中

* 编写mesh添加action

* add action

* fix

* fix: browser on rviz

* fix: cloud bridge error fallback to local

* fix: salve auto run rviz

* 初始化两个plate

---------

Co-authored-by: zhangshixiang <@zhangshixiang>
Co-authored-by: wznln <18435084+Xuwznln@users.noreply.github.com>

* fix: multi channel

* fix: aspirate

* fix: aspirate

* fix: aspirate

* fix: aspirate

* 提交

* fix: jobadd

* fix: jobadd

* fix: msg converter

* tijiao

* add resource creat easy action

* identify debug msg

* mq client id

* 提取lh的joint发布

* unify liquid_handler definition

* 修改物料跟随与物料添加逻辑

修改物料跟随与物料添加逻辑
将joint_publisher类移出lh的backends，但仍需要对lh的backends进行一些改写

* Revert "修改物料跟随与物料添加逻辑"

This reverts commit 498c997ad7.

* Reapply "修改物料跟随与物料添加逻辑"

This reverts commit 3a60d2ae81.

* Revert "Merge remote-tracking branch 'upstream/dev' into device_visualization"

This reverts commit fa727220af, reversing
changes made to 498c997ad7.

* 修改物料放下时的方法，如果选择

修改物料放下时的方法，
如果选择drop_trash，则删除物料显示
如果选择drop，则让其解除连接

* add biomek.py demo implementation

* 更新LiquidHandlerBiomek类，添加资源创建功能，优化协议创建方法，修复部分代码格式问题，更新YAML配置以支持新功能。

* Test

* fix biomek success type

* Convert LH action to biomek.

* Update biomek.py

* 注册表上报handle和schema (param input)

* 修复biomek缺少的字段

* delete 's'

* Remove warnings

* Update biomek.py

* Biomek test

* Update biomek.py

* 新增transfer_biomek的msg

* New transfer_biomek

* Updated transfer_biomek

* 更新transfer_biomek的msg

* 更新transfer_biomek的msg

* 支持Biomek创建

* new action

* fix key name typo

* New parameter for biomek to run.

* Refine

* Update

* new actions

* new actions

* 1

* registry

* fix biomek startup
add action handles

* fix handles not as default entry

* unilab添加moveit启动

1,整合所有moveit节点到一个move_group中，并整合所有的controller依次激活
2,添加pymoveit2的节点，使用json可直接启动
3,修改机械臂规划方式，添加约束，让冗余关节不会进行过多移动

* biomek_test.py

biomek_test.py是最新的版本，运行它会生成complete_biomek_protocol.json

* Update biomek.py

* biomek_test.py

* fix liquid_handler.biomek handles

* 修改物体attach时，多次赋值当前时间导致卡顿问题，

* Revert "修改物体attach时，多次赋值当前时间导致卡顿问题，"

This reverts commit 56d45b94f5.

* Reapply "修改物体attach时，多次赋值当前时间导致卡顿问题，"

This reverts commit 07d9db20c3.

* 添加缺少物料："plate_well_G12",

* host node新增resource add时间统计
create_resource新增handle
bump version to 0.9.2

* 修正物料上传时间
改用biomek_test
增加ResultInfoEncoder
支持返回结果上传

* 正确发送return_info结果

* 同步执行状态信息

* 取消raiseValueError提示

* Update biomek_test.py

* 0608 DONE

* 同步了Biomek.py 现在应可用

* biomek switch back to non-test

* temp disable initialize resource

* add

* fix tip resource data

* liquid states

* change to debug level

* Revert "change to debug level"

This reverts commit 5d9953c3e5.

* Reapply "change to debug level"

This reverts commit 2487bb6ffc.

* fix tip resource data

* add full device

* add moveit yaml

* 修复moveit
增加post_init阶段，给予ros_node反向

* remove necessary node

* fix moveit action client

* remove necessary imports

* Update moveit_interface.py

* fix handler_key uppercase

* json add liquids

* fix setup

* add

* change to "sources" and "targets" for lh

* bump version

* remove parent's parent link

---------

Co-authored-by: Harvey Que <Q-Query@outlook.com>
Co-authored-by: wznln <18435084+Xuwznln@users.noreply.github.com>
Co-authored-by: zhangshixiang <@zhangshixiang>
Co-authored-by: Junhan Chang <changjh@pku.edu.cn>
Co-authored-by: Guangxin Zhang <guangxin.zhang.bio@gmail.com>
Co-authored-by: qxw138 <qxw@stu.pku.edu.cn>

* Device visualization (#41)

* Update README and MQTTClient for installation instructions and code improvements

* feat: 支持local_config启动
add: 增加对crt path的说明，为传入config.py的相对路径
move: web component

* add: registry description

* add 3d visualization

* 完成在main中启动设备可视化

完成在main中启动设备可视化，并输出物料ID：mesh的对应关系resource_model

添加物料模型管理类，遍历物料与resource_model，完成TF数据收集

* 完成TF发布

* 修改模型方向，在yaml中添加变换属性

* 添加物料tf变化时，发送topic到前端

另外修改了物料初始化的方法，防止在tf还未发布时提前建立物料模型与发布话题

* 添加关节发布节点与物料可视化节点进入unilab

* 使用json启动plr与3D模型仿真

* feat: node_info_update srv
fix: OTDeck cant create

* close #12
feat: slave node registry

* feat: show machine name
fix: host node registry not uploaded

* feat: add hplc registry

* feat: add hplc registry

* fix: hplc status typo

* fix: devices/

* 完成启动OT并联动rviz

* add 3d visualization

* 完成在main中启动设备可视化

完成在main中启动设备可视化，并输出物料ID：mesh的对应关系resource_model

添加物料模型管理类，遍历物料与resource_model，完成TF数据收集

* 完成TF发布

* 修改模型方向，在yaml中添加变换属性

* 添加物料tf变化时，发送topic到前端

另外修改了物料初始化的方法，防止在tf还未发布时提前建立物料模型与发布话题

* 添加关节发布节点与物料可视化节点进入unilab

* 使用json启动plr与3D模型仿真

* 完成启动OT并联动rviz

* fix: device.class possible null

* fix: HPLC additions with online service

* fix: slave mode spin not working

* fix: slave mode spin not working

* 修复rviz位置问题,

修复rviz位置问题,
在无tf变动时减缓发送频率
在backend中添加物料跟随方法

* feat: 多ProtocolNode 允许子设备ID相同
feat: 上报发现的ActionClient
feat: Host重启动，通过discover机制要求slaveNode重新注册，实现信息及时上报

* feat: 支持env设置config

* fix: running logic

* fix: running logic

* fix: missing ot

* 在main中直接初始化republisher和物料的mesh节点

* 将joint_republisher和resource_mesh_manager添加进 main_slave_run.py中

* Device visualization (#14)

* add 3d visualization

* 完成在main中启动设备可视化

完成在main中启动设备可视化，并输出物料ID：mesh的对应关系resource_model

添加物料模型管理类，遍历物料与resource_model，完成TF数据收集

* 完成TF发布

* 修改模型方向，在yaml中添加变换属性

* 添加物料tf变化时，发送topic到前端

另外修改了物料初始化的方法，防止在tf还未发布时提前建立物料模型与发布话题

* 添加关节发布节点与物料可视化节点进入unilab

* 使用json启动plr与3D模型仿真

* 完成启动OT并联动rviz

* add 3d visualization

* 完成在main中启动设备可视化

完成在main中启动设备可视化，并输出物料ID：mesh的对应关系resource_model

添加物料模型管理类，遍历物料与resource_model，完成TF数据收集

* 完成TF发布

* 修改模型方向，在yaml中添加变换属性

* 添加物料tf变化时，发送topic到前端

另外修改了物料初始化的方法，防止在tf还未发布时提前建立物料模型与发布话题

* 添加关节发布节点与物料可视化节点进入unilab

* 使用json启动plr与3D模型仿真

* 完成启动OT并联动rviz

* 修复rviz位置问题,

修复rviz位置问题,
在无tf变动时减缓发送频率
在backend中添加物料跟随方法

* fix: running logic

* fix: running logic

* fix: missing ot

* 在main中直接初始化republisher和物料的mesh节点

* 将joint_republisher和resource_mesh_manager添加进 main_slave_run.py中

---------

Co-authored-by: zhangshixiang <@zhangshixiang>
Co-authored-by: wznln <18435084+Xuwznln@users.noreply.github.com>

* fix: missing hostname in devices_names
fix: upload_file for model file

* fix: missing paho-mqtt package
bump version to 0.9.0

* fix startup
add ResourceCreateFromOuter.action

* fix type hint

* update actions

* update actions

* host node add_resource_from_outer
fix cmake list

* pass device config to device class

* add: bind_parent_ids to resource create action
fix: message convert string

* fix: host node should not be re_discovered

* feat: resource tracker support dict

* feat: add more necessary params

* feat: fix boolean null in registry action data

* feat: add outer resource

* 编写mesh添加action

* feat: append resource

* add action

* feat: vis 2d for plr

* fix

* fix: browser on rviz

* fix: cloud bridge error fallback to local

* fix: salve auto run rviz

* 初始化两个plate

* Device visualization (#22)

* add 3d visualization

* 完成在main中启动设备可视化

完成在main中启动设备可视化，并输出物料ID：mesh的对应关系resource_model

添加物料模型管理类，遍历物料与resource_model，完成TF数据收集

* 完成TF发布

* 修改模型方向，在yaml中添加变换属性

* 添加物料tf变化时，发送topic到前端

另外修改了物料初始化的方法，防止在tf还未发布时提前建立物料模型与发布话题

* 添加关节发布节点与物料可视化节点进入unilab

* 使用json启动plr与3D模型仿真

* 完成启动OT并联动rviz

* add 3d visualization

* 完成在main中启动设备可视化

完成在main中启动设备可视化，并输出物料ID：mesh的对应关系resource_model

添加物料模型管理类，遍历物料与resource_model，完成TF数据收集

* 完成TF发布

* 修改模型方向，在yaml中添加变换属性

* 添加物料tf变化时，发送topic到前端

另外修改了物料初始化的方法，防止在tf还未发布时提前建立物料模型与发布话题

* 添加关节发布节点与物料可视化节点进入unilab

* 使用json启动plr与3D模型仿真

* 完成启动OT并联动rviz

* 修复rviz位置问题,

修复rviz位置问题,
在无tf变动时减缓发送频率
在backend中添加物料跟随方法

* fix: running logic

* fix: running logic

* fix: missing ot

* 在main中直接初始化republisher和物料的mesh节点

* 将joint_republisher和resource_mesh_manager添加进 main_slave_run.py中

* 编写mesh添加action

* add action

* fix

* fix: browser on rviz

* fix: cloud bridge error fallback to local

* fix: salve auto run rviz

* 初始化两个plate

---------

Co-authored-by: zhangshixiang <@zhangshixiang>
Co-authored-by: wznln <18435084+Xuwznln@users.noreply.github.com>

* fix: multi channel

* fix: aspirate

* fix: aspirate

* fix: aspirate

* fix: aspirate

* 提交

* fix: jobadd

* fix: jobadd

* fix: msg converter

* tijiao

* add resource creat easy action

* identify debug msg

* mq client id

* 提取lh的joint发布

* unify liquid_handler definition

* 修改物料跟随与物料添加逻辑

修改物料跟随与物料添加逻辑
将joint_publisher类移出lh的backends，但仍需要对lh的backends进行一些改写

* Revert "修改物料跟随与物料添加逻辑"

This reverts commit 498c997ad7.

* Reapply "修改物料跟随与物料添加逻辑"

This reverts commit 3a60d2ae81.

* Revert "Merge remote-tracking branch 'upstream/dev' into device_visualization"

This reverts commit fa727220af, reversing
changes made to 498c997ad7.

* 修改物料放下时的方法，如果选择

修改物料放下时的方法，
如果选择drop_trash，则删除物料显示
如果选择drop，则让其解除连接

* add biomek.py demo implementation

* 更新LiquidHandlerBiomek类，添加资源创建功能，优化协议创建方法，修复部分代码格式问题，更新YAML配置以支持新功能。

* Test

* fix biomek success type

* Convert LH action to biomek.

* Update biomek.py

* 注册表上报handle和schema (param input)

* 修复biomek缺少的字段

* delete 's'

* Remove warnings

* Update biomek.py

* Biomek test

* Update biomek.py

* 新增transfer_biomek的msg

* New transfer_biomek

* Updated transfer_biomek

* 更新transfer_biomek的msg

* 更新transfer_biomek的msg

* 支持Biomek创建

* new action

* fix key name typo

* New parameter for biomek to run.

* Refine

* Update

* new actions

* new actions

* 1

* registry

* fix biomek startup
add action handles

* fix handles not as default entry

* unilab添加moveit启动

1,整合所有moveit节点到一个move_group中，并整合所有的controller依次激活
2,添加pymoveit2的节点，使用json可直接启动
3,修改机械臂规划方式，添加约束，让冗余关节不会进行过多移动

* biomek_test.py

biomek_test.py是最新的版本，运行它会生成complete_biomek_protocol.json

* Update biomek.py

* biomek_test.py

* fix liquid_handler.biomek handles

* 修改物体attach时，多次赋值当前时间导致卡顿问题，

* Revert "修改物体attach时，多次赋值当前时间导致卡顿问题，"

This reverts commit 56d45b94f5.

* Reapply "修改物体attach时，多次赋值当前时间导致卡顿问题，"

This reverts commit 07d9db20c3.

* 添加缺少物料："plate_well_G12",

* host node新增resource add时间统计
create_resource新增handle
bump version to 0.9.2

* 修正物料上传时间
改用biomek_test
增加ResultInfoEncoder
支持返回结果上传

* 正确发送return_info结果

* 同步执行状态信息

* 取消raiseValueError提示

* Update biomek_test.py

* 0608 DONE

* 同步了Biomek.py 现在应可用

* biomek switch back to non-test

* temp disable initialize resource

* add

* fix tip resource data

* liquid states

* change to debug level

* Revert "change to debug level"

This reverts commit 5d9953c3e5.

* Reapply "change to debug level"

This reverts commit 2487bb6ffc.

* fix tip resource data

* add full device

* add moveit yaml

* 修复moveit
增加post_init阶段，给予ros_node反向

* remove necessary node

* fix moveit action client

* remove necessary imports

* Update moveit_interface.py

* fix handler_key uppercase

* json add liquids

* fix setup

* add

* change to "sources" and "targets" for lh

* bump version

* remove parent's parent link

* change arm's name

* change name

---------

Co-authored-by: Harvey Que <Q-Query@outlook.com>
Co-authored-by: zhangshixiang <@zhangshixiang>
Co-authored-by: q434343 <73513873+q434343@users.noreply.github.com>
Co-authored-by: Junhan Chang <changjh@pku.edu.cn>
Co-authored-by: Guangxin Zhang <guangxin.zhang.bio@gmail.com>
Co-authored-by: qxw138 <qxw@stu.pku.edu.cn>

* fix move it

* fix move it

* create_resource

* bump ver
modify slot type

* 增加modbus支持
调整protocol node以更好支持多种类型的read和write

* 调整protocol node以更好支持多种类型的read和write

* 补充日志

* Device visualization (#42)

* Update README and MQTTClient for installation instructions and code improvements

* feat: 支持local_config启动
add: 增加对crt path的说明，为传入config.py的相对路径
move: web component

* add: registry description

* add 3d visualization

* 完成在main中启动设备可视化

完成在main中启动设备可视化，并输出物料ID：mesh的对应关系resource_model

添加物料模型管理类，遍历物料与resource_model，完成TF数据收集

* 完成TF发布

* 修改模型方向，在yaml中添加变换属性

* 添加物料tf变化时，发送topic到前端

另外修改了物料初始化的方法，防止在tf还未发布时提前建立物料模型与发布话题

* 添加关节发布节点与物料可视化节点进入unilab

* 使用json启动plr与3D模型仿真

* feat: node_info_update srv
fix: OTDeck cant create

* close #12
feat: slave node registry

* feat: show machine name
fix: host node registry not uploaded

* feat: add hplc registry

* feat: add hplc registry

* fix: hplc status typo

* fix: devices/

* 完成启动OT并联动rviz

* add 3d visualization

* 完成在main中启动设备可视化

完成在main中启动设备可视化，并输出物料ID：mesh的对应关系resource_model

添加物料模型管理类，遍历物料与resource_model，完成TF数据收集

* 完成TF发布

* 修改模型方向，在yaml中添加变换属性

* 添加物料tf变化时，发送topic到前端

另外修改了物料初始化的方法，防止在tf还未发布时提前建立物料模型与发布话题

* 添加关节发布节点与物料可视化节点进入unilab

* 使用json启动plr与3D模型仿真

* 完成启动OT并联动rviz

* fix: device.class possible null

* fix: HPLC additions with online service

* fix: slave mode spin not working

* fix: slave mode spin not working

* 修复rviz位置问题,

修复rviz位置问题,
在无tf变动时减缓发送频率
在backend中添加物料跟随方法

* feat: 多ProtocolNode 允许子设备ID相同
feat: 上报发现的ActionClient
feat: Host重启动，通过discover机制要求slaveNode重新注册，实现信息及时上报

* feat: 支持env设置config

* fix: running logic

* fix: running logic

* fix: missing ot

* 在main中直接初始化republisher和物料的mesh节点

* 将joint_republisher和resource_mesh_manager添加进 main_slave_run.py中

* Device visualization (#14)

* add 3d visualization

* 完成在main中启动设备可视化

完成在main中启动设备可视化，并输出物料ID：mesh的对应关系resource_model

添加物料模型管理类，遍历物料与resource_model，完成TF数据收集

* 完成TF发布

* 修改模型方向，在yaml中添加变换属性

* 添加物料tf变化时，发送topic到前端

另外修改了物料初始化的方法，防止在tf还未发布时提前建立物料模型与发布话题

* 添加关节发布节点与物料可视化节点进入unilab

* 使用json启动plr与3D模型仿真

* 完成启动OT并联动rviz

* add 3d visualization

* 完成在main中启动设备可视化

完成在main中启动设备可视化，并输出物料ID：mesh的对应关系resource_model

添加物料模型管理类，遍历物料与resource_model，完成TF数据收集

* 完成TF发布

* 修改模型方向，在yaml中添加变换属性

* 添加物料tf变化时，发送topic到前端

另外修改了物料初始化的方法，防止在tf还未发布时提前建立物料模型与发布话题

* 添加关节发布节点与物料可视化节点进入unilab

* 使用json启动plr与3D模型仿真

* 完成启动OT并联动rviz

* 修复rviz位置问题,

修复rviz位置问题,
在无tf变动时减缓发送频率
在backend中添加物料跟随方法

* fix: running logic

* fix: running logic

* fix: missing ot

* 在main中直接初始化republisher和物料的mesh节点

* 将joint_republisher和resource_mesh_manager添加进 main_slave_run.py中

---------

Co-authored-by: zhangshixiang <@zhangshixiang>
Co-authored-by: wznln <18435084+Xuwznln@users.noreply.github.com>

* fix: missing hostname in devices_names
fix: upload_file for model file

* fix: missing paho-mqtt package
bump version to 0.9.0

* fix startup
add ResourceCreateFromOuter.action

* fix type hint

* update actions

* update actions

* host node add_resource_from_outer
fix cmake list

* pass device config to device class

* add: bind_parent_ids to resource create action
fix: message convert string

* fix: host node should not be re_discovered

* feat: resource tracker support dict

* feat: add more necessary params

* feat: fix boolean null in registry action data

* feat: add outer resource

* 编写mesh添加action

* feat: append resource

* add action

* feat: vis 2d for plr

* fix

* fix: browser on rviz

* fix: cloud bridge error fallback to local

* fix: salve auto run rviz

* 初始化两个plate

* Device visualization (#22)

* add 3d visualization

* 完成在main中启动设备可视化

完成在main中启动设备可视化，并输出物料ID：mesh的对应关系resource_model

添加物料模型管理类，遍历物料与resource_model，完成TF数据收集

* 完成TF发布

* 修改模型方向，在yaml中添加变换属性

* 添加物料tf变化时，发送topic到前端

另外修改了物料初始化的方法，防止在tf还未发布时提前建立物料模型与发布话题

* 添加关节发布节点与物料可视化节点进入unilab

* 使用json启动plr与3D模型仿真

* 完成启动OT并联动rviz

* add 3d visualization

* 完成在main中启动设备可视化

完成在main中启动设备可视化，并输出物料ID：mesh的对应关系resource_model

添加物料模型管理类，遍历物料与resource_model，完成TF数据收集

* 完成TF发布

* 修改模型方向，在yaml中添加变换属性

* 添加物料tf变化时，发送topic到前端

另外修改了物料初始化的方法，防止在tf还未发布时提前建立物料模型与发布话题

* 添加关节发布节点与物料可视化节点进入unilab

* 使用json启动plr与3D模型仿真

* 完成启动OT并联动rviz

* 修复rviz位置问题,

修复rviz位置问题,
在无tf变动时减缓发送频率
在backend中添加物料跟随方法

* fix: running logic

* fix: running logic

* fix: missing ot

* 在main中直接初始化republisher和物料的mesh节点

* 将joint_republisher和resource_mesh_manager添加进 main_slave_run.py中

* 编写mesh添加action

* add action

* fix

* fix: browser on rviz

* fix: cloud bridge error fallback to local

* fix: salve auto run rviz

* 初始化两个plate

---------

Co-authored-by: zhangshixiang <@zhangshixiang>
Co-authored-by: wznln <18435084+Xuwznln@users.noreply.github.com>

* fix: multi channel

* fix: aspirate

* fix: aspirate

* fix: aspirate

* fix: aspirate

* 提交

* fix: jobadd

* fix: jobadd

* fix: msg converter

* tijiao

* add resource creat easy action

* identify debug msg

* mq client id

* 提取lh的joint发布

* unify liquid_handler definition

* 修改物料跟随与物料添加逻辑

修改物料跟随与物料添加逻辑
将joint_publisher类移出lh的backends，但仍需要对lh的backends进行一些改写

* Revert "修改物料跟随与物料添加逻辑"

This reverts commit 498c997ad7.

* Reapply "修改物料跟随与物料添加逻辑"

This reverts commit 3a60d2ae81.

* Revert "Merge remote-tracking branch 'upstream/dev' into device_visualization"

This reverts commit fa727220af, reversing
changes made to 498c997ad7.

* 修改物料放下时的方法，如果选择

修改物料放下时的方法，
如果选择drop_trash，则删除物料显示
如果选择drop，则让其解除连接

* unilab添加moveit启动

1,整合所有moveit节点到一个move_group中，并整合所有的controller依次激活
2,添加pymoveit2的节点，使用json可直接启动
3,修改机械臂规划方式，添加约束，让冗余关节不会进行过多移动

* 修改物体attach时，多次赋值当前时间导致卡顿问题，

* Revert "修改物体attach时，多次赋值当前时间导致卡顿问题，"

This reverts commit 56d45b94f5.

* Reapply "修改物体attach时，多次赋值当前时间导致卡顿问题，"

This reverts commit 07d9db20c3.

* 添加缺少物料："plate_well_G12",

* add

* fix tip resource data

* liquid states

* change to debug level

* Revert "change to debug level"

This reverts commit 5d9953c3e5.

* Reapply "change to debug level"

This reverts commit 2487bb6ffc.

* fix tip resource data

* add full device

* add moveit yaml

* 修复moveit
增加post_init阶段，给予ros_node反向

* remove necessary node

* fix moveit action client

* remove necessary imports

* Update moveit_interface.py

* fix handler_key uppercase

* json add liquids

* fix setup

* add

* change to "sources" and "targets" for lh

* bump version

* remove parent's parent link

* change arm's name

* change name

* fix ik error

---------

Co-authored-by: Harvey Que <Q-Query@outlook.com>
Co-authored-by: zhangshixiang <@zhangshixiang>
Co-authored-by: q434343 <73513873+q434343@users.noreply.github.com>
Co-authored-by: Junhan Chang <changjh@pku.edu.cn>

* Add Mock Device for Organic Synthesis\添加有机合成的虚拟仪器和Protocol (#43)

* Add Device MockChiller

Add device MockChiller

* Add Device MockFilter

* Add Device MockPump

* Add Device MockRotavap

* Add Device MockSeparator

* Add Device MockStirrer

* Add Device MockHeater

* Add Device MockVacuum

* Add Device MockSolenoidValve

* Add Device Mock \_init_.py

* 规范模拟设备代码与注册表信息

* 更改Mock大写文件夹名

* 删除大写目录

* Edited Mock device json

* Match mock device with action

* Edit mock device yaml

* Add new action

* Add Virtual Device, Action, YAML, Protocol for Organic Syn

* 单独分类测试的protocol文件夹

* 更名Action

---------

Co-authored-by: Xuwznln <18435084+Xuwznln@users.noreply.github.com>

---------

Co-authored-by: Junhan Chang <changjh@pku.edu.cn>
Co-authored-by: Guangxin Zhang <guangxin.zhang.bio@gmail.com>
Co-authored-by: qxw138 <qxw@stu.pku.edu.cn>
Co-authored-by: q434343 <73513873+q434343@users.noreply.github.com>
Co-authored-by: Harvey Que <Q-Query@outlook.com>
Co-authored-by: Kongchang Feng <2100011801@stu.pku.edu.cn>
This commit is contained in:
Xuwznln
2025-06-12 21:01:04 +08:00
committed by GitHub
parent 3470a1cb69
commit aa1c67de29
264 changed files with 48914 additions and 2955 deletions
Download Patch File Download Diff File Expand all files Collapse all files

27
unilabos/compile/__init__.py
View File

@@ -5,6 +5,17 @@ from .separate_protocol import generate_separate_protocol
from .evaporate_protocol import generate_evaporate_protocol
from .evacuateandrefill_protocol import generate_evacuateandrefill_protocol
from .agv_transfer_protocol import generate_agv_transfer_protocol
from .add_protocol import generate_add_protocol
from .centrifuge_protocol import generate_centrifuge_protocol
from .filter_protocol import generate_filter_protocol
from .heatchill_protocol import generate_heat_chill_protocol, generate_heat_chill_start_protocol, generate_heat_chill_stop_protocol
from .stir_protocol import generate_stir_protocol, generate_start_stir_protocol, generate_stop_stir_protocol
from .transfer_protocol import generate_transfer_protocol
from .clean_vessel_protocol import generate_clean_vessel_protocol
from .dissolve_protocol import generate_dissolve_protocol
from .filter_through_protocol import generate_filter_through_protocol
from .run_column_protocol import generate_run_column_protocol
from .wash_solid_protocol import generate_wash_solid_protocol
# Define a dictionary of protocol generators.
@@ -15,5 +26,19 @@ action_protocol_generators = {
EvaporateProtocol: generate_evaporate_protocol,
EvacuateAndRefillProtocol: generate_evacuateandrefill_protocol,
AGVTransferProtocol: generate_agv_transfer_protocol,
CentrifugeProtocol: generate_centrifuge_protocol,
AddProtocol: generate_add_protocol,
FilterProtocol: generate_filter_protocol,
HeatChillProtocol: generate_heat_chill_protocol,
HeatChillStartProtocol: generate_heat_chill_start_protocol,
HeatChillStopProtocol: generate_heat_chill_stop_protocol,
StirProtocol: generate_stir_protocol,
StartStirProtocol: generate_start_stir_protocol,
StopStirProtocol: generate_stop_stir_protocol,
TransferProtocol: generate_transfer_protocol,
CleanVesselProtocol: generate_clean_vessel_protocol,
DissolveProtocol: generate_dissolve_protocol,
FilterThroughProtocol: generate_filter_through_protocol,
RunColumnProtocol: generate_run_column_protocol,
WashSolidProtocol: generate_wash_solid_protocol,
}
# End Protocols

74
unilabos/compile/add_protocol.py Normal file
View File

@@ -0,0 +1,74 @@
import networkx as nx
from typing import List, Dict, Any
def generate_add_protocol(
G: nx.DiGraph,
vessel: str,
reagent: str,
volume: float,
mass: float,
amount: str,
time: float,
stir: bool,
stir_speed: float,
viscous: bool,
purpose: str
) -> List[Dict[str, Any]]:
"""
生成添加试剂的协议序列 - 严格按照 Add.action
"""
action_sequence = []
# 如果指定了体积，执行液体转移
if volume > 0:
# 查找可用的试剂瓶
available_flasks = [node for node in G.nodes()
if node.startswith('flask_')
and G.nodes[node].get('type') == 'container']
if not available_flasks:
raise ValueError("没有找到可用的试剂容器")
reagent_vessel = available_flasks[0]
# 查找泵设备
pump_nodes = [node for node in G.nodes()
if G.nodes[node].get('class') == 'virtual_pump']
if pump_nodes:
pump_id = pump_nodes[0]
action_sequence.append({
"device_id": pump_id,
"action_name": "transfer",
"action_kwargs": {
"from_vessel": reagent_vessel,
"to_vessel": vessel,
"volume": volume,
"amount": amount,
"time": time,
"viscous": viscous,
"rinsing_solvent": "",
"rinsing_volume": 0.0,
"rinsing_repeats": 0,
"solid": False
}
})
# 如果需要搅拌，使用 StartStir 而不是 Stir
if stir:
stirrer_nodes = [node for node in G.nodes()
if G.nodes[node].get('class') == 'virtual_stirrer']
if stirrer_nodes:
stirrer_id = stirrer_nodes[0]
action_sequence.append({
"device_id": stirrer_id,
"action_name": "start_stir", # 使用 start_stir 而不是 stir
"action_kwargs": {
"vessel": vessel,
"stir_speed": stir_speed,
"purpose": f"添加 {reagent} 后搅拌"
}
})
return action_sequence

123
unilabos/compile/centrifuge_protocol.py Normal file
View File

@@ -0,0 +1,123 @@
from typing import List, Dict, Any
import networkx as nx
def generate_centrifuge_protocol(
G: nx.DiGraph,
vessel: str,
speed: float,
time: float,
temp: float = 25.0
) -> List[Dict[str, Any]]:
"""
生成离心操作的协议序列
Args:
G: 有向图，节点为设备和容器
vessel: 离心容器名称
speed: 离心速度 (rpm)
time: 离心时间 (秒)
temp: 温度 (摄氏度，可选)
Returns:
List[Dict[str, Any]]: 离心操作的动作序列
Raises:
ValueError: 当找不到离心机设备时抛出异常
Examples:
centrifuge_protocol = generate_centrifuge_protocol(G, "reactor", 5000, 300, 4.0)
"""
action_sequence = []
# 查找离心机设备
centrifuge_nodes = [node for node in G.nodes()
if G.nodes[node].get('class') == 'virtual_centrifuge']
if not centrifuge_nodes:
raise ValueError("没有找到可用的离心机设备")
# 使用第一个可用的离心机
centrifuge_id = centrifuge_nodes[0]
# 验证容器是否存在
if vessel not in G.nodes():
raise ValueError(f"容器 {vessel} 不存在于图中")
# 执行离心操作
action_sequence.append({
"device_id": centrifuge_id,
"action_name": "centrifuge",
"action_kwargs": {
"vessel": vessel,
"speed": speed,
"time": time,
"temp": temp
}
})
return action_sequence
def generate_multi_step_centrifuge_protocol(
G: nx.DiGraph,
vessel: str,
steps: List[Dict[str, Any]]
) -> List[Dict[str, Any]]:
"""
生成多步骤离心操作的协议序列
Args:
G: 有向图，节点为设备和容器
vessel: 离心容器名称
steps: 离心步骤列表，每个步骤包含 speed, time, temp 参数
Returns:
List[Dict[str, Any]]: 多步骤离心操作的动作序列
Examples:
steps = [
{"speed": 1000, "time": 60, "temp": 4.0}, # 低速预离心
{"speed": 12000, "time": 600, "temp": 4.0} # 高速离心
]
protocol = generate_multi_step_centrifuge_protocol(G, "reactor", steps)
"""
action_sequence = []
# 查找离心机设备
centrifuge_nodes = [node for node in G.nodes()
if G.nodes[node].get('class') == 'virtual_centrifuge']
if not centrifuge_nodes:
raise ValueError("没有找到可用的离心机设备")
centrifuge_id = centrifuge_nodes[0]
# 验证容器是否存在
if vessel not in G.nodes():
raise ValueError(f"容器 {vessel} 不存在于图中")
# 执行每个离心步骤
for i, step in enumerate(steps):
speed = step.get('speed', 5000)
time = step.get('time', 300)
temp = step.get('temp', 25.0)
action_sequence.append({
"device_id": centrifuge_id,
"action_name": "centrifuge",
"action_kwargs": {
"vessel": vessel,
"speed": speed,
"time": time,
"temp": temp
}
})
# 步骤间等待时间（除了最后一步）
if i < len(steps) - 1:
action_sequence.append({
"action_name": "wait",
"action_kwargs": {"time": 3}
})
return action_sequence

126
unilabos/compile/clean_vessel_protocol.py Normal file
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from typing import List, Dict, Any
import networkx as nx
def generate_clean_vessel_protocol(
G: nx.DiGraph,
vessel: str,
solvent: str,
volume: float,
temp: float,
repeats: int = 1
) -> List[Dict[str, Any]]:
"""
生成容器清洗操作的协议序列，使用transfer操作实现清洗
Args:
G: 有向图，节点为设备和容器
vessel: 要清洗的容器名称
solvent: 用于清洗容器的溶剂名称
volume: 清洗溶剂的体积
temp: 清洗时的温度
repeats: 清洗操作的重复次数，默认为 1
Returns:
List[Dict[str, Any]]: 容器清洗操作的动作序列
Raises:
ValueError: 当找不到必要的设备时抛出异常
Examples:
clean_vessel_protocol = generate_clean_vessel_protocol(G, "reactor", "water", 50.0, 25.0, 2)
"""
action_sequence = []
# 查找虚拟转移泵设备进行清洗操作
pump_nodes = [node for node in G.nodes()
if G.nodes[node].get('class') == 'virtual_transfer_pump']
if not pump_nodes:
raise ValueError("没有找到可用的转移泵设备进行容器清洗")
pump_id = pump_nodes[0]
# 验证容器是否存在
if vessel not in G.nodes():
raise ValueError(f"容器 {vessel} 不存在于图中")
# 查找溶剂容器
solvent_vessel = f"flask_{solvent}"
if solvent_vessel not in G.nodes():
raise ValueError(f"溶剂容器 {solvent_vessel} 不存在于图中")
# 查找废液容器
waste_vessel = "flask_waste"
if waste_vessel not in G.nodes():
raise ValueError(f"废液容器 {waste_vessel} 不存在于图中")
# 查找加热设备（如果需要加热）
heatchill_nodes = [node for node in G.nodes()
if G.nodes[node].get('class') == 'virtual_heatchill']
heatchill_id = heatchill_nodes[0] if heatchill_nodes else None
# 执行清洗操作序列
for repeat in range(repeats):
# 1. 如果需要加热，先设置温度
if temp > 25.0 and heatchill_id:
action_sequence.append({
"device_id": heatchill_id,
"action_name": "heat_chill_start",
"action_kwargs": {
"vessel": vessel,
"temp": temp,
"purpose": "cleaning"
}
})
# 2. 使用transfer操作：从溶剂容器转移清洗溶剂到目标容器
action_sequence.append({
"device_id": pump_id,
"action_name": "transfer",
"action_kwargs": {
"from_vessel": solvent_vessel,
"to_vessel": vessel,
"volume": volume,
"amount": f"cleaning with {solvent} - cycle {repeat + 1}",
"time": 0.0,
"viscous": False,
"rinsing_solvent": "",
"rinsing_volume": 0.0,
"rinsing_repeats": 0,
"solid": False
}
})
# 3. 等待清洗作用时间（可选，可以添加wait操作）
# 这里省略wait操作，直接进行下一步
# 4. 将清洗后的溶剂转移到废液容器
action_sequence.append({
"device_id": pump_id,
"action_name": "transfer",
"action_kwargs": {
"from_vessel": vessel,
"to_vessel": waste_vessel,
"volume": volume,
"amount": f"waste from cleaning {vessel} - cycle {repeat + 1}",
"time": 0.0,
"viscous": False,
"rinsing_solvent": "",
"rinsing_volume": 0.0,
"rinsing_repeats": 0,
"solid": False
}
})
# 5. 如果加热了，停止加热
if temp > 25.0 and heatchill_id:
action_sequence.append({
"device_id": heatchill_id,
"action_name": "heat_chill_stop",
"action_kwargs": {
"vessel": vessel
}
})
return action_sequence

162
unilabos/compile/dissolve_protocol.py Normal file
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@@ -0,0 +1,162 @@
from typing import List, Dict, Any
import networkx as nx
def generate_dissolve_protocol(
G: nx.DiGraph,
vessel: str,
solvent: str,
volume: float,
amount: str = "",
temp: float = 25.0,
time: float = 0.0,
stir_speed: float = 0.0
) -> List[Dict[str, Any]]:
"""
生成溶解操作的协议序列
Args:
G: 有向图，节点为设备和容器
vessel: 装有要溶解物质的容器名称
solvent: 用于溶解物质的溶剂名称
volume: 溶剂的体积，可选参数
amount: 要溶解物质的量，可选参数
temp: 溶解时的温度，可选参数
time: 溶解的时间，可选参数
stir_speed: 搅拌速度，可选参数
Returns:
List[Dict[str, Any]]: 溶解操作的动作序列
Raises:
ValueError: 当找不到必要的设备时抛出异常
Examples:
dissolve_protocol = generate_dissolve_protocol(G, "reactor", "water", 100.0, "NaCl 5g", 60.0, 300.0, 500.0)
"""
action_sequence = []
# 验证容器是否存在
if vessel not in G.nodes():
raise ValueError(f"容器 {vessel} 不存在于图中")
# 查找溶剂容器
solvent_vessel = f"flask_{solvent}"
if solvent_vessel not in G.nodes():
# 如果没有找到特定溶剂容器，查找可用的源容器
available_vessels = [node for node in G.nodes()
if node.startswith('flask_') and
G.nodes[node].get('type') == 'container']
if available_vessels:
solvent_vessel = available_vessels[0]
else:
raise ValueError(f"没有找到溶剂容器 {solvent}")
# 查找转移泵设备
pump_nodes = [node for node in G.nodes()
if G.nodes[node].get('class') == 'virtual_transfer_pump']
if not pump_nodes:
raise ValueError("没有找到可用的转移泵设备")
pump_id = pump_nodes[0]
# 查找加热设备（如果需要加热）
heatchill_nodes = [node for node in G.nodes()
if G.nodes[node].get('class') == 'virtual_heatchill']
heatchill_id = heatchill_nodes[0] if heatchill_nodes else None
# 查找搅拌设备（如果需要搅拌）
stirrer_nodes = [node for node in G.nodes()
if G.nodes[node].get('class') == 'virtual_stirrer']
stirrer_id = stirrer_nodes[0] if stirrer_nodes else None
# 步骤1：如果需要加热，先设置温度
if temp > 25.0 and heatchill_id:
action_sequence.append({
"device_id": heatchill_id,
"action_name": "heat_chill_start",
"action_kwargs": {
"vessel": vessel,
"temp": temp,
"purpose": "dissolution"
}
})
# 步骤2：添加溶剂到容器中
if volume > 0:
action_sequence.append({
"device_id": pump_id,
"action_name": "transfer",
"action_kwargs": {
"from_vessel": solvent_vessel,
"to_vessel": vessel,
"volume": volume,
"amount": f"solvent {solvent} for dissolving {amount}",
"time": 0.0,
"viscous": False,
"rinsing_solvent": "",
"rinsing_volume": 0.0,
"rinsing_repeats": 0,
"solid": False
}
})
# 步骤3：如果需要搅拌，开始搅拌
if stir_speed > 0 and stirrer_id:
action_sequence.append({
"device_id": stirrer_id,
"action_name": "start_stir",
"action_kwargs": {
"vessel": vessel,
"stir_speed": stir_speed,
"purpose": f"dissolving {amount} in {solvent}"
}
})
# 步骤4：如果指定了溶解时间，等待溶解完成
if time > 0:
# 这里可以添加等待操作，或者使用搅拌操作来模拟溶解时间
if stirrer_id and stir_speed > 0:
# 停止之前的搅拌，使用定时搅拌
action_sequence.append({
"device_id": stirrer_id,
"action_name": "stop_stir",
"action_kwargs": {
"vessel": vessel
}
})
# 开始定时搅拌
action_sequence.append({
"device_id": stirrer_id,
"action_name": "stir",
"action_kwargs": {
"stir_time": time,
"stir_speed": stir_speed,
"settling_time": 10.0 # 搅拌后静置10秒
}
})
# 步骤5：如果加热了，停止加热
if temp > 25.0 and heatchill_id:
action_sequence.append({
"device_id": heatchill_id,
"action_name": "heat_chill_stop",
"action_kwargs": {
"vessel": vessel
}
})
# 步骤6：如果还在搅拌，停止搅拌（除非已经用定时搅拌）
if stir_speed > 0 and stirrer_id and time == 0:
action_sequence.append({
"device_id": stirrer_id,
"action_name": "stop_stir",
"action_kwargs": {
"vessel": vessel
}
})
return action_sequence

10
unilabos/compile/evacuateandrefill_protocol.py
View File

@@ -69,14 +69,14 @@ def generate_evacuateandrefill_protocol(
"device_id": vacuum_backbone["pump"],
"action_name": "set_status",
"action_kwargs": {
"command": "ON"
"string": "ON"
}
},
{
"device_id": vacuum_backbone["gas"],
"action_name": "set_status",
"action_kwargs": {
"command": "OFF"
"string": "OFF"
}
}
])
@@ -106,14 +106,14 @@ def generate_evacuateandrefill_protocol(
"device_id": vacuum_backbone["pump"],
"action_name": "set_status",
"action_kwargs": {
"command": "OFF"
"string": "OFF"
}
},
{
"device_id": vacuum_backbone["gas"],
"action_name": "set_status",
"action_kwargs": {
"command": "ON"
"string": "ON"
}
}
])
@@ -125,7 +125,7 @@ def generate_evacuateandrefill_protocol(
"device_id": vacuum_backbone["gas"],
"action_name": "set_status",
"action_kwargs": {
"command": "OFF"
"string": "OFF"
}
}
)

70
unilabos/compile/filter_protocol.py Normal file
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from typing import List, Dict, Any
import networkx as nx
def generate_filter_protocol(
G: nx.DiGraph,
vessel: str,
filtrate_vessel: str = "",
stir: bool = False,
stir_speed: float = 300.0,
temp: float = 25.0,
continue_heatchill: bool = False,
volume: float = 0.0
) -> List[Dict[str, Any]]:
"""
生成过滤操作的协议序列
Args:
G: 有向图，节点为设备和容器
vessel: 过滤容器
filtrate_vessel: 滤液容器（可选）
stir: 是否搅拌
stir_speed: 搅拌速度（可选）
temp: 温度（可选，摄氏度）
continue_heatchill: 是否继续加热冷却
volume: 过滤体积（可选）
Returns:
List[Dict[str, Any]]: 过滤操作的动作序列
Raises:
ValueError: 当找不到过滤设备时抛出异常
Examples:
filter_protocol = generate_filter_protocol(G, "reactor", "filtrate_vessel", stir=True, volume=100.0)
"""
action_sequence = []
# 查找过滤设备
filter_nodes = [node for node in G.nodes()
if G.nodes[node].get('class') == 'virtual_filter']
if not filter_nodes:
raise ValueError("没有找到可用的过滤设备")
# 使用第一个可用的过滤器
filter_id = filter_nodes[0]
# 验证容器是否存在
if vessel not in G.nodes():
raise ValueError(f"过滤容器 {vessel} 不存在于图中")
if filtrate_vessel and filtrate_vessel not in G.nodes():
raise ValueError(f"滤液容器 {filtrate_vessel} 不存在于图中")
# 执行过滤操作
action_sequence.append({
"device_id": filter_id,
"action_name": "filter_sample",
"action_kwargs": {
"vessel": vessel,
"filtrate_vessel": filtrate_vessel,
"stir": stir,
"stir_speed": stir_speed,
"temp": temp,
"continue_heatchill": continue_heatchill,
"volume": volume
}
})
return action_sequence

150
unilabos/compile/filter_through_protocol.py Normal file
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from typing import List, Dict, Any
import networkx as nx
def generate_filter_through_protocol(
G: nx.DiGraph,
from_vessel: str,
to_vessel: str,
filter_through: str,
eluting_solvent: str = "",
eluting_volume: float = 0.0,
eluting_repeats: int = 0,
residence_time: float = 0.0
) -> List[Dict[str, Any]]:
"""
生成通过过滤介质过滤的协议序列
Args:
G: 有向图，节点为设备和容器
from_vessel: 源容器的名称，即物质起始所在的容器
to_vessel: 目标容器的名称，物质过滤后要到达的容器
filter_through: 过滤时所通过的介质，如滤纸、柱子等
eluting_solvent: 洗脱溶剂的名称，可选参数
eluting_volume: 洗脱溶剂的体积，可选参数
eluting_repeats: 洗脱操作的重复次数，默认为 0
residence_time: 物质在过滤介质中的停留时间，可选参数
Returns:
List[Dict[str, Any]]: 过滤操作的动作序列
Raises:
ValueError: 当找不到必要的设备时抛出异常
Examples:
filter_through_protocol = generate_filter_through_protocol(
G, "reactor", "collection_flask", "celite", "ethanol", 50.0, 2, 60.0
)
"""
action_sequence = []
# 验证容器是否存在
if from_vessel not in G.nodes():
raise ValueError(f"源容器 {from_vessel} 不存在于图中")
if to_vessel not in G.nodes():
raise ValueError(f"目标容器 {to_vessel} 不存在于图中")
# 查找转移泵设备（用于液体转移）
pump_nodes = [node for node in G.nodes()
if G.nodes[node].get('class') == 'virtual_transfer_pump']
if not pump_nodes:
raise ValueError("没有找到可用的转移泵设备")
pump_id = pump_nodes[0]
# 查找过滤设备（可选，如果有专门的过滤设备）
filter_nodes = [node for node in G.nodes()
if G.nodes[node].get('class') == 'virtual_filter']
filter_id = filter_nodes[0] if filter_nodes else None
# 查找洗脱溶剂容器（如果需要洗脱）
eluting_vessel = None
if eluting_solvent and eluting_volume > 0:
eluting_vessel = f"flask_{eluting_solvent}"
if eluting_vessel not in G.nodes():
# 查找可用的溶剂容器
available_vessels = [node for node in G.nodes()
if node.startswith('flask_') and
G.nodes[node].get('type') == 'container']
if available_vessels:
eluting_vessel = available_vessels[0]
else:
raise ValueError(f"没有找到洗脱溶剂容器 {eluting_solvent}")
# 步骤1：将样品从源容器转移到过滤装置（模拟通过过滤介质）
# 这里我们将过滤过程分解为多个转移步骤来模拟通过介质的过程
# 首先转移样品（模拟样品通过过滤介质）
action_sequence.append({
"device_id": pump_id,
"action_name": "transfer",
"action_kwargs": {
"from_vessel": from_vessel,
"to_vessel": to_vessel,
"volume": 0.0, # 转移所有液体，体积由系统确定
"amount": f"通过 {filter_through} 过滤",
"time": residence_time if residence_time > 0 else 0.0,
"viscous": False,
"rinsing_solvent": "",
"rinsing_volume": 0.0,
"rinsing_repeats": 0,
"solid": True # 通过过滤介质可能涉及固体分离
}
})
# 步骤2：如果有专门的过滤设备，使用过滤设备处理
if filter_id:
action_sequence.append({
"device_id": filter_id,
"action_name": "filter_sample",
"action_kwargs": {
"vessel": to_vessel,
"filtrate_vessel": to_vessel,
"stir": False,
"stir_speed": 0.0,
"temp": 25.0,
"continue_heatchill": False,
"volume": 0.0
}
})
# 步骤3：洗脱操作（如果指定了洗脱溶剂和重复次数）
if eluting_solvent and eluting_volume > 0 and eluting_repeats > 0 and eluting_vessel:
for repeat in range(eluting_repeats):
# 添加洗脱溶剂
action_sequence.append({
"device_id": pump_id,
"action_name": "transfer",
"action_kwargs": {
"from_vessel": eluting_vessel,
"to_vessel": to_vessel,
"volume": eluting_volume,
"amount": f"洗脱溶剂 {eluting_solvent} - 第 {repeat + 1} 次",
"time": 0.0,
"viscous": False,
"rinsing_solvent": "",
"rinsing_volume": 0.0,
"rinsing_repeats": 0,
"solid": False
}
})
# 如果有过滤设备，再次过滤洗脱液
if filter_id:
action_sequence.append({
"device_id": filter_id,
"action_name": "filter_sample",
"action_kwargs": {
"vessel": to_vessel,
"filtrate_vessel": to_vessel,
"stir": False,
"stir_speed": 0.0,
"temp": 25.0,
"continue_heatchill": False,
"volume": eluting_volume
}
})
return action_sequence

117
unilabos/compile/heatchill_protocol.py Normal file
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@@ -0,0 +1,117 @@
from typing import List, Dict, Any
import networkx as nx
def generate_heat_chill_protocol(
G: nx.DiGraph,
vessel: str,
temp: float,
time: float,
stir: bool,
stir_speed: float,
purpose: str
) -> List[Dict[str, Any]]:
"""
生成加热/冷却操作的协议序列 - 严格按照 HeatChill.action
"""
action_sequence = []
# 查找加热/冷却设备
heatchill_nodes = [node for node in G.nodes()
if G.nodes[node].get('class') == 'virtual_heatchill']
if not heatchill_nodes:
raise ValueError("没有找到可用的加热/冷却设备")
heatchill_id = heatchill_nodes[0]
if vessel not in G.nodes():
raise ValueError(f"容器 {vessel} 不存在于图中")
action_sequence.append({
"device_id": heatchill_id,
"action_name": "heat_chill",
"action_kwargs": {
"vessel": vessel,
"temp": temp,
"time": time,
"stir": stir,
"stir_speed": stir_speed,
"purpose": purpose
}
})
return action_sequence
def generate_heat_chill_start_protocol(
G: nx.DiGraph,
vessel: str,
temp: float,
purpose: str
) -> List[Dict[str, Any]]:
"""
生成开始加热/冷却操作的协议序列 - 严格按照 HeatChillStart.action
"""
action_sequence = []
heatchill_nodes = [node for node in G.nodes()
if G.nodes[node].get('class') == 'virtual_heatchill']
if not heatchill_nodes:
raise ValueError("没有找到可用的加热/冷却设备")
heatchill_id = heatchill_nodes[0]
if vessel not in G.nodes():
raise ValueError(f"容器 {vessel} 不存在于图中")
action_sequence.append({
"device_id": heatchill_id,
"action_name": "heat_chill_start",
"action_kwargs": {
"vessel": vessel,
"temp": temp,
"purpose": purpose
}
})
return action_sequence
def generate_heat_chill_stop_protocol(
G: nx.DiGraph,
vessel: str
) -> List[Dict[str, Any]]:
"""
生成停止加热/冷却操作的协议序列
Args:
G: 有向图，节点为设备和容器
vessel: 容器名称
Returns:
List[Dict[str, Any]]: 停止加热/冷却操作的动作序列
"""
action_sequence = []
# 查找加热/冷却设备
heatchill_nodes = [node for node in G.nodes()
if G.nodes[node].get('class') == 'virtual_heatchill']
if not heatchill_nodes:
raise ValueError("没有找到可用的加热/冷却设备")
heatchill_id = heatchill_nodes[0]
if vessel not in G.nodes():
raise ValueError(f"容器 {vessel} 不存在于图中")
action_sequence.append({
"device_id": heatchill_id,
"action_name": "heat_chill_stop",
"action_kwargs": {
"vessel": vessel
}
})
return action_sequence

305
unilabos/compile/pump_protocol.py
View File

@@ -24,10 +24,27 @@ def generate_pump_protocol(
# 生成泵操作的动作序列
pump_action_sequence = []
nodes = G.nodes(data=True)
# 从from_vessel到to_vessel的最短路径
shortest_path = nx.shortest_path(G, source=from_vessel, target=to_vessel)
print(shortest_path)
# 检查节点是否存在
if from_vessel not in G.nodes:
print(f"Warning: Source vessel '{from_vessel}' not found in graph. Skipping.")
return []
if to_vessel not in G.nodes:
print(f"Warning: Target vessel '{to_vessel}' not found in graph. Skipping.")
return []
# 检查是否存在路径
try:
shortest_path = nx.shortest_path(G, source=from_vessel, target=to_vessel)
except nx.NetworkXNoPath:
print(f"Warning: No path from '{from_vessel}' to '{to_vessel}'. Skipping.")
return []
except nx.NodeNotFound as e:
print(f"Warning: Node not found: {e}. Skipping.")
return []
print(f"Shortest path: {shortest_path}")
pump_backbone = shortest_path
if not from_vessel.startswith("pump"):
@@ -35,10 +52,34 @@ def generate_pump_protocol(
if not to_vessel.startswith("pump"):
pump_backbone = pump_backbone[:-1]
print(f"Pump backbone: {pump_backbone}")
# 修复：检查pump_backbone是否为空
if not pump_backbone:
print(f"Warning: No pumps found in path from '{from_vessel}' to '{to_vessel}'. Skipping.")
return []
if transfer_flowrate == 0:
transfer_flowrate = flowrate
min_transfer_volume = min([nodes[pump]["max_volume"] for pump in pump_backbone])
# 修复：正确访问节点数据
pump_max_volumes = []
for pump in pump_backbone:
# 直接使用 G.nodes[pump] 来访问节点数据
pump_data = G.nodes[pump] if pump in G.nodes else {}
# 尝试多种可能的键名，并提供默认值
max_vol = pump_data.get('max_volume') or pump_data.get('max_vol') or pump_data.get('volume')
if max_vol is None:
# 如果是设备节点，尝试从config中获取
config = pump_data.get('config', {})
max_vol = config.get('max_volume', 25.0)
pump_max_volumes.append(float(max_vol))
if pump_max_volumes:
min_transfer_volume = min(pump_max_volumes)
else:
min_transfer_volume = 25.0 # 默认值
repeats = int(np.ceil(volume / min_transfer_volume))
if repeats > 1 and (from_vessel.startswith("pump") or to_vessel.startswith("pump")):
raise ValueError("Cannot transfer volume larger than min_transfer_volume between two pumps.")
@@ -48,84 +89,102 @@ def generate_pump_protocol(
# 生成泵操作的动作序列
for i in range(repeats):
# 单泵依次执行阀指令、活塞指令，将液体吸入与之相连的第一台泵
if not from_vessel.startswith("pump"):
pump_action_sequence.extend([
{
"device_id": pump_backbone[0],
"action_name": "set_valve_position",
"action_kwargs": {
"command": G.get_edge_data(pump_backbone[0], from_vessel)["port"][pump_backbone[0]]
if not from_vessel.startswith("pump") and pump_backbone:
# 修复：添加边缘数据检查
edge_data = G.get_edge_data(pump_backbone[0], from_vessel)
if edge_data and "port" in edge_data:
pump_action_sequence.extend([
{
"device_id": pump_backbone[0],
"action_name": "set_valve_position",
"action_kwargs": {
"command": edge_data["port"][pump_backbone[0]]
}
},
{
"device_id": pump_backbone[0],
"action_name": "set_position",
"action_kwargs": {
"position": float(min(volume_left, min_transfer_volume)),
"max_velocity": transfer_flowrate
}
}
},
{
"device_id": pump_backbone[0],
"action_name": "set_position",
"action_kwargs": {
"position": float(min(volume_left, min_transfer_volume)),
"max_velocity": transfer_flowrate
}
}
])
pump_action_sequence.append({"action_name": "wait", "action_kwargs": {"time": 5}})
for pumpA, pumpB in zip(pump_backbone[:-1], pump_backbone[1:]):
# 相邻两泵同时切换阀门至连通位置
pump_action_sequence.append([
{
"device_id": pumpA,
"action_name": "set_valve_position",
"action_kwargs": {
"command": G.get_edge_data(pumpA, pumpB)["port"][pumpA]
}
},
{
"device_id": pumpB,
"action_name": "set_valve_position",
"action_kwargs": {
"command": G.get_edge_data(pumpB, pumpA)["port"][pumpB],
}
}
])
# 相邻两泵液体转移：泵A排出液体，泵B吸入液体
pump_action_sequence.append([
{
"device_id": pumpA,
"action_name": "set_position",
"action_kwargs": {
"position": 0.0,
"max_velocity": transfer_flowrate
}
},
{
"device_id": pumpB,
"action_name": "set_position",
"action_kwargs": {
"position": float(min(volume_left, min_transfer_volume)),
"max_velocity": transfer_flowrate
}
}
])
pump_action_sequence.append({"action_name": "wait", "action_kwargs": {"time": 5}})
])
pump_action_sequence.append({"action_name": "wait", "action_kwargs": {"time": 5}})
else:
print(f"Warning: No edge data found between {pump_backbone[0]} and {from_vessel}")
if not to_vessel.startswith("pump"):
# 修复：检查pump_backbone长度，避免多泵操作时出错
if len(pump_backbone) > 1:
for pumpA, pumpB in zip(pump_backbone[:-1], pump_backbone[1:]):
# 相邻两泵同时切换阀门至连通位置
edge_AB = G.get_edge_data(pumpA, pumpB)
edge_BA = G.get_edge_data(pumpB, pumpA)
if edge_AB and "port" in edge_AB and edge_BA and "port" in edge_BA:
pump_action_sequence.append([
{
"device_id": pumpA,
"action_name": "set_valve_position",
"action_kwargs": {
"command": edge_AB["port"][pumpA]
}
},
{
"device_id": pumpB,
"action_name": "set_valve_position",
"action_kwargs": {
"command": edge_BA["port"][pumpB],
}
}
])
# 相邻两泵液体转移：泵A排出液体，泵B吸入液体
pump_action_sequence.append([
{
"device_id": pumpA,
"action_name": "set_position",
"action_kwargs": {
"position": 0.0,
"max_velocity": transfer_flowrate
}
},
{
"device_id": pumpB,
"action_name": "set_position",
"action_kwargs": {
"position": float(min(volume_left, min_transfer_volume)),
"max_velocity": transfer_flowrate
}
}
])
pump_action_sequence.append({"action_name": "wait", "action_kwargs": {"time": 5}})
else:
print(f"Warning: No edge data found between {pumpA} and {pumpB}")
if not to_vessel.startswith("pump") and pump_backbone:
# 单泵依次执行阀指令、活塞指令，将最后一台泵液体缓慢加入容器B
pump_action_sequence.extend([
{
"device_id": pump_backbone[-1],
"action_name": "set_valve_position",
"action_kwargs": {
"command": G.get_edge_data(pump_backbone[-1], to_vessel)["port"][pump_backbone[-1]]
edge_data = G.get_edge_data(pump_backbone[-1], to_vessel)
if edge_data and "port" in edge_data:
pump_action_sequence.extend([
{
"device_id": pump_backbone[-1],
"action_name": "set_valve_position",
"action_kwargs": {
"command": edge_data["port"][pump_backbone[-1]]
}
},
{
"device_id": pump_backbone[-1],
"action_name": "set_position",
"action_kwargs": {
"position": 0.0,
"max_velocity": flowrate
}
}
},
{
"device_id": pump_backbone[-1],
"action_name": "set_position",
"action_kwargs": {
"position": 0.0,
"max_velocity": flowrate
}
}
])
pump_action_sequence.append({"action_name": "wait", "action_kwargs": {"time": 5}})
])
pump_action_sequence.append({"action_name": "wait", "action_kwargs": {"time": 5}})
else:
print(f"Warning: No edge data found between {pump_backbone[-1]} and {to_vessel}")
volume_left -= min_transfer_volume
return pump_action_sequence
@@ -174,18 +233,52 @@ def generate_pump_protocol_with_rinsing(
Examples:
pump_protocol = generate_pump_protocol_with_rinsing(G, "vessel_A", "vessel_B", 0.1, rinsing_solvent="water")
"""
air_vessel = "flask_air"
waste_vessel = f"waste_workup"
# 修复：使用实际存在的节点名称
air_vessel = "flask_air" # 这个在你的配置中存在
shortest_path = nx.shortest_path(G, source=from_vessel, target=to_vessel)
pump_backbone = shortest_path[1: -1]
nodes = G.nodes(data=True)
min_transfer_volume = float(min([nodes[pump]["max_volume"] for pump in pump_backbone]))
# 寻找合适的废料容器，如果没有找到则使用空的容器作为替代
waste_vessel = None
available_vessels = [node for node in G.nodes if node.startswith("flask_") and node != air_vessel]
if available_vessels:
# 使用第一个可用的容器作为废料容器
waste_vessel = available_vessels[0]
print(f"Using {waste_vessel} as waste vessel")
else:
waste_vessel = "flask_1" # 备用选择
# 修复：添加路径检查
try:
shortest_path = nx.shortest_path(G, source=from_vessel, target=to_vessel)
pump_backbone = shortest_path[1: -1]
except (nx.NetworkXNoPath, nx.NodeNotFound) as e:
print(f"Warning: Cannot find path from {from_vessel} to {to_vessel}: {e}")
return []
# 修复：正确访问节点数据
pump_max_volumes = []
for pump in pump_backbone:
# 直接使用 G.nodes[pump] 来访问节点数据
pump_data = G.nodes[pump] if pump in G.nodes else {}
# 尝试多种可能的键名，并提供默认值
max_vol = pump_data.get('max_volume') or pump_data.get('max_vol') or pump_data.get('volume')
if max_vol is None:
# 如果是设备节点，尝试从config中获取
config = pump_data.get('config', {})
max_vol = config.get('max_volume', 25.0)
pump_max_volumes.append(float(max_vol))
if pump_max_volumes:
min_transfer_volume = float(min(pump_max_volumes))
else:
min_transfer_volume = 25.0 # 默认值
if time != 0:
flowrate = transfer_flowrate = volume / time
pump_action_sequence = generate_pump_protocol(G, from_vessel, to_vessel, float(volume), flowrate, transfer_flowrate)
if rinsing_solvent != "air":
# 修复：只在需要清洗且相关节点存在时才执行清洗步骤
if rinsing_solvent != "air" and pump_backbone:
if "," in rinsing_solvent:
rinsing_solvents = rinsing_solvent.split(",")
assert len(rinsing_solvents) == rinsing_repeats, "Number of rinsing solvents must match number of rinsing repeats."
@@ -194,20 +287,32 @@ def generate_pump_protocol_with_rinsing(
for rinsing_solvent in rinsing_solvents:
solvent_vessel = f"flask_{rinsing_solvent}"
# 清洗泵
pump_action_sequence.extend(
generate_pump_protocol(G, solvent_vessel, pump_backbone[0], min_transfer_volume, flowrate, transfer_flowrate) +
generate_pump_protocol(G, pump_backbone[0], pump_backbone[-1], min_transfer_volume, flowrate, transfer_flowrate) +
generate_pump_protocol(G, pump_backbone[-1], waste_vessel, min_transfer_volume, flowrate, transfer_flowrate)
)
# 如果转移的是溶液，第一种冲洗溶剂请选用溶液的溶剂，稀释泵内、转移管道内的溶液。后续冲洗溶剂不需要此操作。
if rinsing_solvent == rinsing_solvents[0]:
pump_action_sequence.extend(generate_pump_protocol(G, solvent_vessel, from_vessel, rinsing_volume, flowrate, transfer_flowrate))
pump_action_sequence.extend(generate_pump_protocol(G, solvent_vessel, to_vessel, rinsing_volume, flowrate, transfer_flowrate))
pump_action_sequence.extend(generate_pump_protocol(G, air_vessel, solvent_vessel, rinsing_volume, flowrate, transfer_flowrate))
pump_action_sequence.extend(generate_pump_protocol(G, air_vessel, waste_vessel, rinsing_volume, flowrate, transfer_flowrate))
pump_action_sequence.extend(generate_pump_protocol(G, air_vessel, from_vessel, rinsing_volume, flowrate, transfer_flowrate) * 2)
pump_action_sequence.extend(generate_pump_protocol(G, air_vessel, to_vessel, rinsing_volume, flowrate, transfer_flowrate) * 2)
# 检查溶剂容器是否存在
if solvent_vessel not in G.nodes:
print(f"Warning: Solvent vessel '{solvent_vessel}' not found in graph. Skipping rinsing step.")
continue
# 清洗泵 - 只有当所有必需的节点都存在且pump_backbone不为空时才执行
if pump_backbone and len(pump_backbone) > 0 and waste_vessel in G.nodes:
pump_action_sequence.extend(
generate_pump_protocol(G, solvent_vessel, pump_backbone[0], min_transfer_volume, flowrate, transfer_flowrate) +
generate_pump_protocol(G, pump_backbone[0], pump_backbone[-1], min_transfer_volume, flowrate, transfer_flowrate) +
generate_pump_protocol(G, pump_backbone[-1], waste_vessel, min_transfer_volume, flowrate, transfer_flowrate)
)
# 如果转移的是溶液，第一种冲洗溶剂请选用溶液的溶剂，稀释泵内、转移管道内的溶液。后续冲洗溶剂不需要此操作。
if rinsing_solvent == rinsing_solvents[0]:
pump_action_sequence.extend(generate_pump_protocol(G, solvent_vessel, from_vessel, rinsing_volume, flowrate, transfer_flowrate))
pump_action_sequence.extend(generate_pump_protocol(G, solvent_vessel, to_vessel, rinsing_volume, flowrate, transfer_flowrate))
pump_action_sequence.extend(generate_pump_protocol(G, air_vessel, solvent_vessel, rinsing_volume, flowrate, transfer_flowrate))
pump_action_sequence.extend(generate_pump_protocol(G, air_vessel, waste_vessel, rinsing_volume, flowrate, transfer_flowrate))
# 最后的空气清洗 - 只有当节点存在时才执行
if air_vessel in G.nodes:
pump_action_sequence.extend(generate_pump_protocol(G, air_vessel, from_vessel, rinsing_volume, flowrate, transfer_flowrate) * 2)
pump_action_sequence.extend(generate_pump_protocol(G, air_vessel, to_vessel, rinsing_volume, flowrate, transfer_flowrate) * 2)
return pump_action_sequence
# End Protocols

102
unilabos/compile/run_column_protocol.py Normal file
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@@ -0,0 +1,102 @@
from typing import List, Dict, Any
import networkx as nx
def generate_run_column_protocol(
G: nx.DiGraph,
from_vessel: str,
to_vessel: str,
column: str
) -> List[Dict[str, Any]]:
"""
生成柱层析分离的协议序列
Args:
G: 有向图，节点为设备和容器
from_vessel: 源容器的名称，即样品起始所在的容器
to_vessel: 目标容器的名称，分离后的样品要到达的容器
column: 所使用的柱子的名称
Returns:
List[Dict[str, Any]]: 柱层析分离操作的动作序列
Raises:
ValueError: 当找不到必要的设备时抛出异常
Examples:
run_column_protocol = generate_run_column_protocol(G, "reactor", "collection_flask", "silica_column")
"""
action_sequence = []
# 验证容器是否存在
if from_vessel not in G.nodes():
raise ValueError(f"源容器 {from_vessel} 不存在于图中")
if to_vessel not in G.nodes():
raise ValueError(f"目标容器 {to_vessel} 不存在于图中")
# 查找转移泵设备（用于样品转移）
pump_nodes = [node for node in G.nodes()
if G.nodes[node].get('class') == 'virtual_transfer_pump']
if not pump_nodes:
raise ValueError("没有找到可用的转移泵设备")
pump_id = pump_nodes[0]
# 查找柱层析设备
column_nodes = [node for node in G.nodes()
if G.nodes[node].get('class') == 'virtual_column']
if not column_nodes:
raise ValueError("没有找到可用的柱层析设备")
column_id = column_nodes[0]
# 步骤1：将样品从源容器转移到柱子上
action_sequence.append({
"device_id": pump_id,
"action_name": "transfer",
"action_kwargs": {
"from_vessel": from_vessel,
"to_vessel": column_id, # 将样品转移到柱子设备
"volume": 0.0, # 转移所有液体，体积由系统确定
"amount": f"样品上柱 - 使用 {column}",
"time": 0.0,
"viscous": False,
"rinsing_solvent": "",
"rinsing_volume": 0.0,
"rinsing_repeats": 0,
"solid": False
}
})
# 步骤2：运行柱层析分离
action_sequence.append({
"device_id": column_id,
"action_name": "run_column",
"action_kwargs": {
"from_vessel": from_vessel,
"to_vessel": to_vessel,
"column": column
}
})
# 步骤3：将分离后的产物从柱子转移到目标容器
action_sequence.append({
"device_id": pump_id,
"action_name": "transfer",
"action_kwargs": {
"from_vessel": column_id, # 从柱子设备转移
"to_vessel": to_vessel,
"volume": 0.0, # 转移所有液体，体积由系统确定
"amount": f"收集分离产物 - 来自 {column}",
"time": 0.0,
"viscous": False,
"rinsing_solvent": "",
"rinsing_volume": 0.0,
"rinsing_repeats": 0,
"solid": False
}
})
return action_sequence

137
unilabos/compile/stir_protocol.py Normal file
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@@ -0,0 +1,137 @@
from typing import List, Dict, Any
import networkx as nx
def generate_stir_protocol(
G: nx.DiGraph,
stir_time: float,
stir_speed: float,
settling_time: float
) -> List[Dict[str, Any]]:
"""
生成搅拌操作的协议序列
Args:
G: 有向图，节点为设备和容器
stir_time: 搅拌时间 (秒)
stir_speed: 搅拌速度 (rpm)
settling_time: 沉降时间 (秒)
Returns:
List[Dict[str, Any]]: 搅拌操作的动作序列
Raises:
ValueError: 当找不到搅拌设备时抛出异常
Examples:
stir_protocol = generate_stir_protocol(G, 300.0, 500.0, 60.0)
"""
action_sequence = []
# 查找搅拌设备
stirrer_nodes = [node for node in G.nodes()
if G.nodes[node].get('class') == 'virtual_stirrer']
if not stirrer_nodes:
raise ValueError("没有找到可用的搅拌设备")
# 使用第一个可用的搅拌器
stirrer_id = stirrer_nodes[0]
# 执行搅拌操作
action_sequence.append({
"device_id": stirrer_id,
"action_name": "stir",
"action_kwargs": {
"stir_time": stir_time,
"stir_speed": stir_speed,
"settling_time": settling_time
}
})
return action_sequence
def generate_start_stir_protocol(
G: nx.DiGraph,
vessel: str,
stir_speed: float,
purpose: str
) -> List[Dict[str, Any]]:
"""
生成开始搅拌操作的协议序列
Args:
G: 有向图，节点为设备和容器
vessel: 搅拌容器
stir_speed: 搅拌速度 (rpm)
purpose: 搅拌目的
Returns:
List[Dict[str, Any]]: 开始搅拌操作的动作序列
"""
action_sequence = []
# 查找搅拌设备
stirrer_nodes = [node for node in G.nodes()
if G.nodes[node].get('class') == 'virtual_stirrer']
if not stirrer_nodes:
raise ValueError("没有找到可用的搅拌设备")
stirrer_id = stirrer_nodes[0]
# 验证容器是否存在
if vessel not in G.nodes():
raise ValueError(f"容器 {vessel} 不存在于图中")
action_sequence.append({
"device_id": stirrer_id,
"action_name": "start_stir",
"action_kwargs": {
"vessel": vessel,
"stir_speed": stir_speed,
"purpose": purpose
}
})
return action_sequence
def generate_stop_stir_protocol(
G: nx.DiGraph,
vessel: str
) -> List[Dict[str, Any]]:
"""
生成停止搅拌操作的协议序列
Args:
G: 有向图，节点为设备和容器
vessel: 搅拌容器
Returns:
List[Dict[str, Any]]: 停止搅拌操作的动作序列
"""
action_sequence = []
# 查找搅拌设备
stirrer_nodes = [node for node in G.nodes()
if G.nodes[node].get('class') == 'virtual_stirrer']
if not stirrer_nodes:
raise ValueError("没有找到可用的搅拌设备")
stirrer_id = stirrer_nodes[0]
# 验证容器是否存在
if vessel not in G.nodes():
raise ValueError(f"容器 {vessel} 不存在于图中")
action_sequence.append({
"device_id": stirrer_id,
"action_name": "stop_stir",
"action_kwargs": {
"vessel": vessel
}
})
return action_sequence

79
unilabos/compile/transfer_protocol.py Normal file
View File

@@ -0,0 +1,79 @@
from typing import List, Dict, Any
import networkx as nx
def generate_transfer_protocol(
G: nx.DiGraph,
from_vessel: str,
to_vessel: str,
volume: float,
amount: str = "",
time: float = 0,
viscous: bool = False,
rinsing_solvent: str = "",
rinsing_volume: float = 0.0,
rinsing_repeats: int = 0,
solid: bool = False
) -> List[Dict[str, Any]]:
"""
生成液体转移操作的协议序列
Args:
G: 有向图，节点为设备和容器
from_vessel: 源容器
to_vessel: 目标容器
volume: 转移体积 (mL)
amount: 数量描述 (可选)
time: 转移时间 (秒，可选)
viscous: 是否为粘性液体
rinsing_solvent: 冲洗溶剂 (可选)
rinsing_volume: 冲洗体积 (mL，可选)
rinsing_repeats: 冲洗重复次数
solid: 是否涉及固体
Returns:
List[Dict[str, Any]]: 转移操作的动作序列
Raises:
ValueError: 当找不到合适的转移设备时抛出异常
Examples:
transfer_protocol = generate_transfer_protocol(G, "flask_1", "reactor", 10.0)
"""
action_sequence = []
# 查找虚拟转移泵设备用于液体转移 - 修复：应该查找 virtual_transfer_pump
pump_nodes = [node for node in G.nodes()
if G.nodes[node].get('class') == 'virtual_transfer_pump']
if not pump_nodes:
raise ValueError("没有找到可用的转移泵设备进行液体转移")
# 使用第一个可用的泵
pump_id = pump_nodes[0]
# 验证容器是否存在
if from_vessel not in G.nodes():
raise ValueError(f"源容器 {from_vessel} 不存在于图中")
if to_vessel not in G.nodes():
raise ValueError(f"目标容器 {to_vessel} 不存在于图中")
# 执行液体转移操作 - 参数完全匹配Transfer.action
action_sequence.append({
"device_id": pump_id,
"action_name": "transfer",
"action_kwargs": {
"from_vessel": from_vessel,
"to_vessel": to_vessel,
"volume": volume,
"amount": amount,
"time": time,
"viscous": viscous,
"rinsing_solvent": rinsing_solvent,
"rinsing_volume": rinsing_volume,
"rinsing_repeats": rinsing_repeats,
"solid": solid
}
})
return action_sequence

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from typing import List, Dict, Any
import networkx as nx
def generate_wash_solid_protocol(
G: nx.DiGraph,
vessel: str,
solvent: str,
volume: float,
filtrate_vessel: str = "",
temp: float = 25.0,
stir: bool = False,
stir_speed: float = 0.0,
time: float = 0.0,
repeats: int = 1
) -> List[Dict[str, Any]]:
"""
生成固体清洗的协议序列
Args:
G: 有向图，节点为设备和容器
vessel: 装有固体物质的容器名称
solvent: 用于清洗固体的溶剂名称
volume: 清洗溶剂的体积
filtrate_vessel: 滤液要收集到的容器名称，可选参数
temp: 清洗时的温度，可选参数
stir: 是否在清洗过程中搅拌，默认为 False
stir_speed: 搅拌速度，可选参数
time: 清洗的时间，可选参数
repeats: 清洗操作的重复次数，默认为 1
Returns:
List[Dict[str, Any]]: 固体清洗操作的动作序列
Raises:
ValueError: 当找不到必要的设备时抛出异常
Examples:
wash_solid_protocol = generate_wash_solid_protocol(
G, "reactor", "ethanol", 100.0, "waste_flask", 60.0, True, 300.0, 600.0, 3
)
"""
action_sequence = []
# 验证容器是否存在
if vessel not in G.nodes():
raise ValueError(f"固体容器 {vessel} 不存在于图中")
if filtrate_vessel and filtrate_vessel not in G.nodes():
raise ValueError(f"滤液容器 {filtrate_vessel} 不存在于图中")
# 查找转移泵设备（用于添加溶剂和转移滤液）
pump_nodes = [node for node in G.nodes()
if G.nodes[node].get('class') == 'virtual_transfer_pump']
if not pump_nodes:
raise ValueError("没有找到可用的转移泵设备")
pump_id = pump_nodes[0]
# 查找加热设备（如果需要加热）
heatchill_nodes = [node for node in G.nodes()
if G.nodes[node].get('class') == 'virtual_heatchill']
heatchill_id = heatchill_nodes[0] if heatchill_nodes else None
# 查找搅拌设备（如果需要搅拌）
stirrer_nodes = [node for node in G.nodes()
if G.nodes[node].get('class') == 'virtual_stirrer']
stirrer_id = stirrer_nodes[0] if stirrer_nodes else None
# 查找过滤设备（用于分离固体和滤液）
filter_nodes = [node for node in G.nodes()
if G.nodes[node].get('class') == 'virtual_filter']
filter_id = filter_nodes[0] if filter_nodes else None
# 查找溶剂容器
solvent_vessel = f"flask_{solvent}"
if solvent_vessel not in G.nodes():
# 如果没有找到特定溶剂容器，查找可用的源容器
available_vessels = [node for node in G.nodes()
if node.startswith('flask_') and
G.nodes[node].get('type') == 'container']
if available_vessels:
solvent_vessel = available_vessels[0]
else:
raise ValueError(f"没有找到溶剂容器 {solvent}")
# 如果没有指定滤液容器，使用废液容器
if not filtrate_vessel:
waste_vessels = [node for node in G.nodes()
if 'waste' in node.lower() and
G.nodes[node].get('type') == 'container']
filtrate_vessel = waste_vessels[0] if waste_vessels else "waste_flask"
# 重复清洗操作
for repeat in range(repeats):
repeat_num = repeat + 1
# 步骤1：如果需要加热，先设置温度
if temp > 25.0 and heatchill_id:
action_sequence.append({
"device_id": heatchill_id,
"action_name": "heat_chill_start",
"action_kwargs": {
"vessel": vessel,
"temp": temp,
"purpose": f"固体清洗 - 第 {repeat_num} 次"
}
})
# 步骤2：添加清洗溶剂到固体容器
action_sequence.append({
"device_id": pump_id,
"action_name": "transfer",
"action_kwargs": {
"from_vessel": solvent_vessel,
"to_vessel": vessel,
"volume": volume,
"amount": f"清洗溶剂 {solvent} - 第 {repeat_num} 次",
"time": 0.0,
"viscous": False,
"rinsing_solvent": "",
"rinsing_volume": 0.0,
"rinsing_repeats": 0,
"solid": False
}
})
# 步骤3：如果需要搅拌，开始搅拌
if stir and stir_speed > 0 and stirrer_id:
if time > 0:
# 定时搅拌
action_sequence.append({
"device_id": stirrer_id,
"action_name": "stir",
"action_kwargs": {
"stir_time": time,
"stir_speed": stir_speed,
"settling_time": 30.0 # 搅拌后静置30秒
}
})
else:
# 开始搅拌（需要手动停止）
action_sequence.append({
"device_id": stirrer_id,
"action_name": "start_stir",
"action_kwargs": {
"vessel": vessel,
"stir_speed": stir_speed,
"purpose": f"固体清洗搅拌 - 第 {repeat_num} 次"
}
})
# 步骤4：如果指定了清洗时间但没有搅拌，等待清洗时间
if time > 0 and (not stir or stir_speed == 0):
# 这里可以添加等待操作，暂时跳过
pass
# 步骤5：如果有搅拌且没有定时，停止搅拌
if stir and stir_speed > 0 and time == 0 and stirrer_id:
action_sequence.append({
"device_id": stirrer_id,
"action_name": "stop_stir",
"action_kwargs": {
"vessel": vessel
}
})
# 步骤6：过滤分离固体和滤液
if filter_id:
action_sequence.append({
"device_id": filter_id,
"action_name": "filter_sample",
"action_kwargs": {
"vessel": vessel,
"filtrate_vessel": filtrate_vessel,
"stir": False,
"stir_speed": 0.0,
"temp": temp,
"continue_heatchill": temp > 25.0,
"volume": volume
}
})
else:
# 没有专门的过滤设备，使用转移泵模拟过滤过程
# 将滤液转移到滤液容器
action_sequence.append({
"device_id": pump_id,
"action_name": "transfer",
"action_kwargs": {
"from_vessel": vessel,
"to_vessel": filtrate_vessel,
"volume": volume,
"amount": f"转移滤液 - 第 {repeat_num} 次清洗",
"time": 0.0,
"viscous": False,
"rinsing_solvent": "",
"rinsing_volume": 0.0,
"rinsing_repeats": 0,
"solid": False
}
})
# 步骤7：如果加热了，停止加热（在最后一次清洗后）
if temp > 25.0 and heatchill_id and repeat_num == repeats:
action_sequence.append({
"device_id": heatchill_id,
"action_name": "heat_chill_stop",
"action_kwargs": {
"vessel": vessel
}
})
return action_sequence