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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

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