mirror of
https://github.com/dptech-corp/Uni-Lab-OS.git
synced 2025-12-17 13:01:12 +00:00
v0.9.7 (#50)
注册表单独上传、新增大量模拟节点与Protocol、新增container管理、修复pip install出现的文件缺失问题 * 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 commit498c997ad7. * Reapply "修改物料跟随与物料添加逻辑" This reverts commit3a60d2ae81. * Revert "Merge remote-tracking branch 'upstream/dev' into device_visualization" This reverts commitfa727220af, reversing changes made to498c997ad7. * 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 commit56d45b94f5. * Reapply "修改物体attach时，多次赋值当前时间导致卡顿问题，" This reverts commit07d9db20c3. * 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 commit5d9953c3e5. * Reapply "change to debug level" This reverts commit2487bb6ffc. * 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 commit498c997ad7. * Reapply "修改物料跟随与物料添加逻辑" This reverts commit3a60d2ae81. * Revert "Merge remote-tracking branch 'upstream/dev' into device_visualization" This reverts commitfa727220af, reversing changes made to498c997ad7. * 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 commit56d45b94f5. * Reapply "修改物体attach时，多次赋值当前时间导致卡顿问题，" This reverts commit07d9db20c3. * 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 commit5d9953c3e5. * Reapply "change to debug level" This reverts commit2487bb6ffc. * 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 commit498c997ad7. * Reapply "修改物料跟随与物料添加逻辑" This reverts commit3a60d2ae81. * Revert "Merge remote-tracking branch 'upstream/dev' into device_visualization" This reverts commitfa727220af, reversing changes made to498c997ad7. * 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 commit56d45b94f5. * Reapply "修改物体attach时，多次赋值当前时间导致卡顿问题，" This reverts commit07d9db20c3. * 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 commit5d9953c3e5. * Reapply "change to debug level" This reverts commit2487bb6ffc. * 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> * bump version & protocol fix * hotfix: Add macos_sdk_config (#46) Co-authored-by: quehh <scienceol@outlook.com> * include device_mesh when pip install * 测试自动构建 * try build fix * try build * test artifacts * hotfix: Add .certs in .gitignore * create container * container 添加和更新完成 * Device registry port (#49) * 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 * unify liquid_handler definition * Update virtual_device.yaml * 更正了stir和heater的连接方式 * 区分了虚拟仪器中的八通阀和电磁阀，添加了两个阀门的驱动 * 修改了add protocol * 修复了阀门更新版的bug * 修复了添加protocol前缀导致的不能启动的bug * Fix handles * bump version to 0.9.6 * add resource edge upload * update container registry and handles * add virtual_separator virtual_rotavap fix transfer_pump * fix container value add parent_name to edge device id * 大图的问题都修复好了，添加了gassource和vacuum pump的驱动以及注册表 * default resource upload mode is false * 添加了icon的文件名在注册表里面 * 修改了json图中link的格式 * fix resource and edge upload * fix device ports * Fix edge id * 移除device的父节点关联 * separate registry sync and resource_add * 默认不进行注册表报送，通过命令unilabos-register或者增加启动参数 * 完善tip * protocol node不再嵌套显示 * bump version to 0.9.7 新增一个测试PumpTransferProtocol的teststation，亲测可以运行，将八通阀们和转移泵与pump_protocol适配 * protocol node 执行action不应携带自身device id * 添加了一套简易双八通阀工作站JSON，亲测能跑 * 修复了很多protocol，亲测能跑 * 添加了run column和filter through的protocol，亲测能跑 * fix mock_reactor * 修改了大图和小图的json，但是在前端上没看到改变 --------- 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: q434343 <73513873+q434343@users.noreply.github.com> Co-authored-by: Junhan Chang <changjh@pku.edu.cn> --------- 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> Co-authored-by: hh. <103566763+Mile-Away@users.noreply.github.com> Co-authored-by: quehh <scienceol@outlook.com> Co-authored-by: Harvey Que <quehaohui@dp.tech>
This commit is contained in:
Xuwznln
GitHub
@@ -8,7 +8,12 @@ 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 .heatchill_protocol import (
|
||||
generate_heat_chill_protocol,
|
||||
generate_heat_chill_start_protocol,
|
||||
generate_heat_chill_stop_protocol,
|
||||
generate_heat_chill_to_temp_protocol # 保留导入，但不注册为协议
|
||||
)
|
||||
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
|
||||
@@ -32,6 +37,7 @@ action_protocol_generators = {
|
||||
HeatChillProtocol: generate_heat_chill_protocol,
|
||||
HeatChillStartProtocol: generate_heat_chill_start_protocol,
|
||||
HeatChillStopProtocol: generate_heat_chill_stop_protocol,
|
||||
# HeatChillToTempProtocol: generate_heat_chill_to_temp_protocol, # **移除这行**
|
||||
StirProtocol: generate_stir_protocol,
|
||||
StartStirProtocol: generate_start_stir_protocol,
|
||||
StopStirProtocol: generate_stop_stir_protocol,
|
||||
|
||||
@@ -1,74 +1,381 @@
|
||||
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")
|
||||
import networkx as nx
|
||||
from typing import List, Dict, Any
|
||||
from .pump_protocol import generate_pump_protocol_with_rinsing
|
||||
|
||||
|
||||
def find_reagent_vessel(G: nx.DiGraph, reagent: str) -> str:
|
||||
"""
|
||||
根据试剂名称查找对应的试剂瓶
|
||||
|
||||
Args:
|
||||
G: 网络图
|
||||
reagent: 试剂名称
|
||||
|
||||
Returns:
|
||||
str: 试剂瓶的vessel ID
|
||||
|
||||
Raises:
|
||||
ValueError: 如果找不到对应的试剂瓶
|
||||
"""
|
||||
# 按照pump_protocol的命名规则查找试剂瓶
|
||||
reagent_vessel_id = f"flask_{reagent}"
|
||||
|
||||
if reagent_vessel_id in G.nodes():
|
||||
return reagent_vessel_id
|
||||
|
||||
# 如果直接匹配失败，尝试模糊匹配
|
||||
for node in G.nodes():
|
||||
if node.startswith('flask_') and reagent.lower() in node.lower():
|
||||
return node
|
||||
|
||||
# 如果还是找不到，列出所有可用的试剂瓶
|
||||
available_flasks = [node for node in G.nodes()
|
||||
if node.startswith('flask_')
|
||||
and G.nodes[node].get('type') == 'container']
|
||||
|
||||
raise ValueError(f"找不到试剂 '{reagent}' 对应的试剂瓶。可用试剂瓶: {available_flasks}")
|
||||
|
||||
|
||||
def find_connected_stirrer(G: nx.DiGraph, vessel: str) -> str:
|
||||
"""
|
||||
查找与指定容器相连的搅拌器
|
||||
|
||||
Args:
|
||||
G: 网络图
|
||||
vessel: 容器ID
|
||||
|
||||
Returns:
|
||||
str: 搅拌器ID，如果找不到则返回None
|
||||
"""
|
||||
# 查找所有搅拌器节点
|
||||
stirrer_nodes = [node for node in G.nodes()
|
||||
if G.nodes[node].get('class') == 'virtual_stirrer']
|
||||
|
||||
# 检查哪个搅拌器与目标容器相连
|
||||
for stirrer in stirrer_nodes:
|
||||
if G.has_edge(stirrer, vessel) or G.has_edge(vessel, stirrer):
|
||||
return stirrer
|
||||
|
||||
# 如果没有直接连接，返回第一个可用的搅拌器
|
||||
return stirrer_nodes[0] if stirrer_nodes else None
|
||||
|
||||
|
||||
def generate_add_protocol(
|
||||
G: nx.DiGraph,
|
||||
vessel: str,
|
||||
reagent: str,
|
||||
volume: float,
|
||||
mass: float = 0.0,
|
||||
amount: str = "",
|
||||
time: float = 0.0,
|
||||
stir: bool = False,
|
||||
stir_speed: float = 300.0,
|
||||
viscous: bool = False,
|
||||
purpose: str = "添加试剂"
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""
|
||||
生成添加试剂的协议序列
|
||||
|
||||
基于pump_protocol的成熟算法，实现试剂添加功能：
|
||||
1. 自动查找试剂瓶
|
||||
2. **先启动搅拌，再进行转移** - 确保试剂添加更均匀
|
||||
3. 使用pump_protocol实现液体转移
|
||||
|
||||
Args:
|
||||
G: 有向图，节点为容器和设备，边为连接关系
|
||||
vessel: 目标容器（要添加试剂的容器）
|
||||
reagent: 试剂名称（用于查找对应的试剂瓶）
|
||||
volume: 要添加的体积 (mL)
|
||||
mass: 要添加的质量 (g) - 暂时未使用，预留接口
|
||||
amount: 其他数量描述
|
||||
time: 添加时间 (s)，如果指定则计算流速
|
||||
stir: 是否启用搅拌
|
||||
stir_speed: 搅拌速度 (RPM)
|
||||
viscous: 是否为粘稠液体
|
||||
purpose: 添加目的描述
|
||||
|
||||
Returns:
|
||||
List[Dict[str, Any]]: 动作序列
|
||||
|
||||
Raises:
|
||||
ValueError: 当找不到必要的设备或容器时
|
||||
"""
|
||||
action_sequence = []
|
||||
|
||||
# 1. 验证目标容器存在
|
||||
if vessel not in G.nodes():
|
||||
raise ValueError(f"目标容器 '{vessel}' 不存在于系统中")
|
||||
|
||||
# 2. 查找试剂瓶
|
||||
try:
|
||||
reagent_vessel = find_reagent_vessel(G, reagent)
|
||||
except ValueError as e:
|
||||
raise ValueError(f"无法找到试剂 '{reagent}': {str(e)}")
|
||||
|
||||
# 3. 验证是否存在从试剂瓶到目标容器的路径
|
||||
try:
|
||||
path = nx.shortest_path(G, source=reagent_vessel, target=vessel)
|
||||
print(f"ADD_PROTOCOL: 找到路径 {reagent_vessel} -> {vessel}: {path}")
|
||||
except nx.NetworkXNoPath:
|
||||
raise ValueError(f"从试剂瓶 '{reagent_vessel}' 到目标容器 '{vessel}' 没有可用路径")
|
||||
|
||||
# 4. **先启动搅拌** - 关键改进！
|
||||
if stir:
|
||||
try:
|
||||
stirrer_id = find_connected_stirrer(G, vessel)
|
||||
|
||||
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
|
||||
if stirrer_id:
|
||||
print(f"ADD_PROTOCOL: 找到搅拌器 {stirrer_id}，将在添加前启动搅拌")
|
||||
|
||||
# 先启动搅拌
|
||||
stir_action = {
|
||||
"device_id": stirrer_id,
|
||||
"action_name": "start_stir",
|
||||
"action_kwargs": {
|
||||
"vessel": vessel,
|
||||
"stir_speed": stir_speed,
|
||||
"purpose": f"{purpose}: 启动搅拌，准备添加 {reagent}"
|
||||
}
|
||||
}
|
||||
})
|
||||
|
||||
# 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": {
|
||||
|
||||
action_sequence.append(stir_action)
|
||||
print(f"ADD_PROTOCOL: 已添加搅拌动作，速度 {stir_speed} RPM")
|
||||
else:
|
||||
print(f"ADD_PROTOCOL: 警告 - 需要搅拌但未找到与容器 {vessel} 相连的搅拌器")
|
||||
|
||||
except Exception as e:
|
||||
print(f"ADD_PROTOCOL: 搅拌器配置出错: {str(e)}")
|
||||
|
||||
# 5. 如果指定了体积，执行液体转移
|
||||
if volume > 0:
|
||||
# 5.1 计算流速参数
|
||||
if time > 0:
|
||||
# 根据时间计算流速
|
||||
transfer_flowrate = volume / time
|
||||
flowrate = transfer_flowrate
|
||||
else:
|
||||
# 使用默认流速
|
||||
if viscous:
|
||||
transfer_flowrate = 0.3 # 粘稠液体用较慢速度
|
||||
flowrate = 1.0
|
||||
else:
|
||||
transfer_flowrate = 0.5 # 普通液体默认速度
|
||||
flowrate = 2.5
|
||||
|
||||
print(f"ADD_PROTOCOL: 准备转移 {volume} mL 从 {reagent_vessel} 到 {vessel}")
|
||||
print(f"ADD_PROTOCOL: 转移流速={transfer_flowrate} mL/s, 注入流速={flowrate} mL/s")
|
||||
|
||||
# 5.2 使用pump_protocol的核心算法实现液体转移
|
||||
try:
|
||||
pump_actions = generate_pump_protocol_with_rinsing(
|
||||
G=G,
|
||||
from_vessel=reagent_vessel,
|
||||
to_vessel=vessel,
|
||||
volume=volume,
|
||||
amount=amount,
|
||||
time=time,
|
||||
viscous=viscous,
|
||||
rinsing_solvent="", # 添加试剂通常不需要清洗
|
||||
rinsing_volume=0.0,
|
||||
rinsing_repeats=0,
|
||||
solid=False,
|
||||
flowrate=flowrate,
|
||||
transfer_flowrate=transfer_flowrate
|
||||
)
|
||||
|
||||
# 添加pump actions到序列中
|
||||
action_sequence.extend(pump_actions)
|
||||
|
||||
except Exception as e:
|
||||
raise ValueError(f"生成泵协议时出错: {str(e)}")
|
||||
|
||||
print(f"ADD_PROTOCOL: 生成了 {len(action_sequence)} 个动作")
|
||||
return action_sequence
|
||||
|
||||
|
||||
def generate_add_protocol_with_cleaning(
|
||||
G: nx.DiGraph,
|
||||
vessel: str,
|
||||
reagent: str,
|
||||
volume: float,
|
||||
mass: float = 0.0,
|
||||
amount: str = "",
|
||||
time: float = 0.0,
|
||||
stir: bool = False,
|
||||
stir_speed: float = 300.0,
|
||||
viscous: bool = False,
|
||||
purpose: str = "添加试剂",
|
||||
cleaning_solvent: str = "air",
|
||||
cleaning_volume: float = 5.0,
|
||||
cleaning_repeats: int = 1
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""
|
||||
生成带清洗的添加试剂协议
|
||||
|
||||
与普通添加协议的区别是会在添加后进行管道清洗
|
||||
|
||||
Args:
|
||||
G: 有向图
|
||||
vessel: 目标容器
|
||||
reagent: 试剂名称
|
||||
volume: 添加体积
|
||||
mass: 添加质量（预留）
|
||||
amount: 其他数量描述
|
||||
time: 添加时间
|
||||
stir: 是否搅拌
|
||||
stir_speed: 搅拌速度
|
||||
viscous: 是否粘稠
|
||||
purpose: 添加目的
|
||||
cleaning_solvent: 清洗溶剂（"air"表示空气清洗）
|
||||
cleaning_volume: 清洗体积
|
||||
cleaning_repeats: 清洗重复次数
|
||||
|
||||
Returns:
|
||||
List[Dict[str, Any]]: 动作序列
|
||||
"""
|
||||
action_sequence = []
|
||||
|
||||
# 1. 查找试剂瓶
|
||||
reagent_vessel = find_reagent_vessel(G, reagent)
|
||||
|
||||
# 2. **先启动搅拌**
|
||||
if stir:
|
||||
stirrer_id = find_connected_stirrer(G, vessel)
|
||||
if stirrer_id:
|
||||
action_sequence.append({
|
||||
"device_id": stirrer_id,
|
||||
"action_name": "start_stir",
|
||||
"action_kwargs": {
|
||||
"vessel": vessel,
|
||||
"stir_speed": stir_speed,
|
||||
"purpose": f"添加 {reagent} 后搅拌"
|
||||
}
|
||||
})
|
||||
|
||||
return action_sequence
|
||||
"purpose": f"{purpose}: 启动搅拌，准备添加 {reagent}"
|
||||
}
|
||||
})
|
||||
|
||||
# 3. 计算流速
|
||||
if time > 0:
|
||||
transfer_flowrate = volume / time
|
||||
flowrate = transfer_flowrate
|
||||
else:
|
||||
if viscous:
|
||||
transfer_flowrate = 0.3
|
||||
flowrate = 1.0
|
||||
else:
|
||||
transfer_flowrate = 0.5
|
||||
flowrate = 2.5
|
||||
|
||||
# 4. 使用带清洗的pump_protocol
|
||||
pump_actions = generate_pump_protocol_with_rinsing(
|
||||
G=G,
|
||||
from_vessel=reagent_vessel,
|
||||
to_vessel=vessel,
|
||||
volume=volume,
|
||||
amount=amount,
|
||||
time=time,
|
||||
viscous=viscous,
|
||||
rinsing_solvent=cleaning_solvent,
|
||||
rinsing_volume=cleaning_volume,
|
||||
rinsing_repeats=cleaning_repeats,
|
||||
solid=False,
|
||||
flowrate=flowrate,
|
||||
transfer_flowrate=transfer_flowrate
|
||||
)
|
||||
|
||||
action_sequence.extend(pump_actions)
|
||||
|
||||
return action_sequence
|
||||
|
||||
|
||||
def generate_sequential_add_protocol(
|
||||
G: nx.DiGraph,
|
||||
vessel: str,
|
||||
reagents: List[Dict[str, Any]],
|
||||
stir_between_additions: bool = True,
|
||||
final_stir: bool = True,
|
||||
final_stir_speed: float = 400.0,
|
||||
final_stir_time: float = 300.0
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""
|
||||
生成连续添加多种试剂的协议
|
||||
|
||||
Args:
|
||||
G: 网络图
|
||||
vessel: 目标容器
|
||||
reagents: 试剂列表，每个元素包含试剂添加参数
|
||||
stir_between_additions: 是否在每次添加之间搅拌
|
||||
final_stir: 是否在所有添加完成后进行最终搅拌
|
||||
final_stir_speed: 最终搅拌速度
|
||||
final_stir_time: 最终搅拌时间
|
||||
|
||||
Returns:
|
||||
List[Dict[str, Any]]: 完整的动作序列
|
||||
|
||||
Example:
|
||||
reagents = [
|
||||
{
|
||||
"reagent": "DMF",
|
||||
"volume": 10.0,
|
||||
"viscous": False,
|
||||
"stir_speed": 300.0
|
||||
},
|
||||
{
|
||||
"reagent": "ethyl_acetate",
|
||||
"volume": 5.0,
|
||||
"viscous": False,
|
||||
"stir_speed": 350.0
|
||||
}
|
||||
]
|
||||
"""
|
||||
action_sequence = []
|
||||
|
||||
for i, reagent_params in enumerate(reagents):
|
||||
print(f"ADD_PROTOCOL: 处理第 {i+1}/{len(reagents)} 个试剂: {reagent_params.get('reagent')}")
|
||||
|
||||
# 生成单个试剂的添加协议
|
||||
add_actions = generate_add_protocol(
|
||||
G=G,
|
||||
vessel=vessel,
|
||||
reagent=reagent_params.get('reagent'),
|
||||
volume=reagent_params.get('volume', 0.0),
|
||||
mass=reagent_params.get('mass', 0.0),
|
||||
amount=reagent_params.get('amount', ''),
|
||||
time=reagent_params.get('time', 0.0),
|
||||
stir=stir_between_additions,
|
||||
stir_speed=reagent_params.get('stir_speed', 300.0),
|
||||
viscous=reagent_params.get('viscous', False),
|
||||
purpose=reagent_params.get('purpose', f'添加试剂 {i+1}')
|
||||
)
|
||||
|
||||
action_sequence.extend(add_actions)
|
||||
|
||||
# 在添加之间加入等待时间
|
||||
if i < len(reagents) - 1: # 不是最后一个试剂
|
||||
action_sequence.append({
|
||||
"action_name": "wait",
|
||||
"action_kwargs": {"time": 2}
|
||||
})
|
||||
|
||||
# 最终搅拌
|
||||
if final_stir:
|
||||
stirrer_id = find_connected_stirrer(G, vessel)
|
||||
if stirrer_id:
|
||||
action_sequence.extend([
|
||||
{
|
||||
"action_name": "wait",
|
||||
"action_kwargs": {"time": final_stir_time}
|
||||
}
|
||||
])
|
||||
|
||||
print(f"ADD_PROTOCOL: 连续添加协议生成完成，共 {len(action_sequence)} 个动作")
|
||||
return action_sequence
|
||||
|
||||
|
||||
# 使用示例和测试函数
|
||||
def test_add_protocol():
|
||||
"""测试添加协议的示例"""
|
||||
print("=== ADD PROTOCOL 测试 ===")
|
||||
print("测试完成")
|
||||
|
||||
|
||||
if __name__ == "__main__":
|
||||
test_add_protocol()
|
||||
@@ -1,5 +1,59 @@
|
||||
from typing import List, Dict, Any
|
||||
import networkx as nx
|
||||
from .pump_protocol import generate_pump_protocol
|
||||
|
||||
|
||||
def get_vessel_liquid_volume(G: nx.DiGraph, vessel: str) -> float:
|
||||
"""
|
||||
获取容器中的液体体积
|
||||
"""
|
||||
if vessel not in G.nodes():
|
||||
return 0.0
|
||||
|
||||
vessel_data = G.nodes[vessel].get('data', {})
|
||||
liquids = vessel_data.get('liquid', [])
|
||||
|
||||
total_volume = 0.0
|
||||
for liquid in liquids:
|
||||
if isinstance(liquid, dict) and 'liquid_volume' in liquid:
|
||||
total_volume += liquid['liquid_volume']
|
||||
|
||||
return total_volume
|
||||
|
||||
|
||||
def find_centrifuge_device(G: nx.DiGraph) -> str:
|
||||
"""
|
||||
查找离心机设备
|
||||
"""
|
||||
centrifuge_nodes = [node for node in G.nodes()
|
||||
if (G.nodes[node].get('class') or '') == 'virtual_centrifuge']
|
||||
|
||||
if centrifuge_nodes:
|
||||
return centrifuge_nodes[0]
|
||||
|
||||
raise ValueError("系统中未找到离心机设备")
|
||||
|
||||
|
||||
def find_centrifuge_vessel(G: nx.DiGraph) -> str:
|
||||
"""
|
||||
查找离心机专用容器
|
||||
"""
|
||||
possible_names = [
|
||||
"centrifuge_tube",
|
||||
"centrifuge_vessel",
|
||||
"tube_centrifuge",
|
||||
"vessel_centrifuge",
|
||||
"centrifuge",
|
||||
"tube_15ml",
|
||||
"tube_50ml"
|
||||
]
|
||||
|
||||
for vessel_name in possible_names:
|
||||
if vessel_name in G.nodes():
|
||||
return vessel_name
|
||||
|
||||
raise ValueError(f"未找到离心机容器。尝试了以下名称: {possible_names}")
|
||||
|
||||
|
||||
def generate_centrifuge_protocol(
|
||||
G: nx.DiGraph,
|
||||
@@ -9,115 +63,223 @@ def generate_centrifuge_protocol(
|
||||
temp: float = 25.0
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""
|
||||
生成离心操作的协议序列
|
||||
生成离心操作的协议序列，复用 pump_protocol 的成熟算法
|
||||
|
||||
离心流程：
|
||||
1. 液体转移：将待离心溶液从源容器转移到离心机容器
|
||||
2. 离心操作：执行离心分离
|
||||
3. 上清液转移：将离心后的上清液转移回原容器或新容器
|
||||
4. 沉淀处理：处理离心沉淀（可选）
|
||||
|
||||
Args:
|
||||
G: 有向图，节点为设备和容器
|
||||
vessel: 离心容器名称
|
||||
G: 有向图，节点为设备和容器，边为流体管道
|
||||
vessel: 包含待离心溶液的容器名称
|
||||
speed: 离心速度 (rpm)
|
||||
time: 离心时间 (秒)
|
||||
temp: 温度 (摄氏度，可选)
|
||||
temp: 离心温度 (°C)，默认25°C
|
||||
|
||||
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
|
||||
ValueError: 当找不到必要的设备时抛出异常
|
||||
|
||||
Examples:
|
||||
centrifuge_protocol = generate_centrifuge_protocol(G, "reactor", 5000, 300, 4.0)
|
||||
centrifuge_actions = generate_centrifuge_protocol(G, "reaction_mixture", 5000, 600, 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']
|
||||
print(f"CENTRIFUGE: 开始生成离心协议")
|
||||
print(f" - 源容器: {vessel}")
|
||||
print(f" - 离心速度: {speed} rpm")
|
||||
print(f" - 离心时间: {time}s ({time/60:.1f}分钟)")
|
||||
print(f" - 离心温度: {temp}°C")
|
||||
|
||||
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
|
||||
# 验证源容器存在
|
||||
if vessel not in G.nodes():
|
||||
raise ValueError(f"容器 {vessel} 不存在于图中")
|
||||
raise ValueError(f"源容器 '{vessel}' 不存在于系统中")
|
||||
|
||||
# 执行离心操作
|
||||
action_sequence.append({
|
||||
# 获取源容器中的液体体积
|
||||
source_volume = get_vessel_liquid_volume(G, vessel)
|
||||
print(f"CENTRIFUGE: 源容器 {vessel} 中有 {source_volume} mL 液体")
|
||||
|
||||
# 查找离心机设备
|
||||
try:
|
||||
centrifuge_id = find_centrifuge_device(G)
|
||||
print(f"CENTRIFUGE: 找到离心机: {centrifuge_id}")
|
||||
except ValueError as e:
|
||||
raise ValueError(f"无法找到离心机: {str(e)}")
|
||||
|
||||
# 查找离心机容器
|
||||
try:
|
||||
centrifuge_vessel = find_centrifuge_vessel(G)
|
||||
print(f"CENTRIFUGE: 找到离心机容器: {centrifuge_vessel}")
|
||||
except ValueError as e:
|
||||
raise ValueError(f"无法找到离心机容器: {str(e)}")
|
||||
|
||||
# === 简化的体积计算策略 ===
|
||||
if source_volume > 0:
|
||||
# 如果能检测到液体体积，使用实际体积的大部分
|
||||
transfer_volume = min(source_volume * 0.9, 15.0) # 90%或最多15mL（离心管通常较小）
|
||||
print(f"CENTRIFUGE: 检测到液体体积，将转移 {transfer_volume} mL")
|
||||
else:
|
||||
# 如果检测不到液体体积，默认转移标准量
|
||||
transfer_volume = 10.0 # 标准离心管体积
|
||||
print(f"CENTRIFUGE: 未检测到液体体积，默认转移 {transfer_volume} mL")
|
||||
|
||||
# === 第一步：将待离心溶液转移到离心机容器 ===
|
||||
print(f"CENTRIFUGE: 将 {transfer_volume} mL 溶液从 {vessel} 转移到 {centrifuge_vessel}")
|
||||
try:
|
||||
# 使用成熟的 pump_protocol 算法进行液体转移
|
||||
transfer_to_centrifuge_actions = generate_pump_protocol(
|
||||
G=G,
|
||||
from_vessel=vessel,
|
||||
to_vessel=centrifuge_vessel,
|
||||
volume=transfer_volume,
|
||||
flowrate=1.0, # 离心转移用慢速，避免气泡
|
||||
transfer_flowrate=1.0
|
||||
)
|
||||
action_sequence.extend(transfer_to_centrifuge_actions)
|
||||
except Exception as e:
|
||||
raise ValueError(f"无法将溶液转移到离心机: {str(e)}")
|
||||
|
||||
# 转移后等待
|
||||
wait_action = {
|
||||
"action_name": "wait",
|
||||
"action_kwargs": {"time": 5}
|
||||
}
|
||||
action_sequence.append(wait_action)
|
||||
|
||||
# === 第二步：执行离心操作 ===
|
||||
print(f"CENTRIFUGE: 执行离心操作")
|
||||
centrifuge_action = {
|
||||
"device_id": centrifuge_id,
|
||||
"action_name": "centrifuge",
|
||||
"action_kwargs": {
|
||||
"vessel": vessel,
|
||||
"vessel": centrifuge_vessel,
|
||||
"speed": speed,
|
||||
"time": time,
|
||||
"temp": temp
|
||||
}
|
||||
})
|
||||
}
|
||||
action_sequence.append(centrifuge_action)
|
||||
|
||||
# 离心后等待系统稳定
|
||||
wait_action = {
|
||||
"action_name": "wait",
|
||||
"action_kwargs": {"time": 10} # 离心后等待稍长，让沉淀稳定
|
||||
}
|
||||
action_sequence.append(wait_action)
|
||||
|
||||
# === 第三步：将上清液转移回原容器 ===
|
||||
print(f"CENTRIFUGE: 将上清液从离心机转移回 {vessel}")
|
||||
try:
|
||||
# 估算上清液体积（约为转移体积的80% - 假设20%成为沉淀）
|
||||
supernatant_volume = transfer_volume * 0.8
|
||||
print(f"CENTRIFUGE: 预计上清液体积 {supernatant_volume} mL")
|
||||
|
||||
transfer_back_actions = generate_pump_protocol(
|
||||
G=G,
|
||||
from_vessel=centrifuge_vessel,
|
||||
to_vessel=vessel,
|
||||
volume=supernatant_volume,
|
||||
flowrate=0.5, # 上清液转移更慢，避免扰动沉淀
|
||||
transfer_flowrate=0.5
|
||||
)
|
||||
action_sequence.extend(transfer_back_actions)
|
||||
except Exception as e:
|
||||
print(f"CENTRIFUGE: 将上清液转移回容器失败: {str(e)}")
|
||||
|
||||
# === 第四步：清洗离心机容器 ===
|
||||
print(f"CENTRIFUGE: 清洗离心机容器")
|
||||
try:
|
||||
# 查找清洗溶剂
|
||||
cleaning_solvent = None
|
||||
for solvent in ["flask_water", "flask_ethanol", "flask_acetone"]:
|
||||
if solvent in G.nodes():
|
||||
cleaning_solvent = solvent
|
||||
break
|
||||
|
||||
if cleaning_solvent:
|
||||
# 用少量溶剂清洗离心管
|
||||
cleaning_volume = 5.0 # 5mL清洗
|
||||
print(f"CENTRIFUGE: 用 {cleaning_volume} mL {cleaning_solvent} 清洗")
|
||||
|
||||
# 清洗溶剂加入
|
||||
cleaning_actions = generate_pump_protocol(
|
||||
G=G,
|
||||
from_vessel=cleaning_solvent,
|
||||
to_vessel=centrifuge_vessel,
|
||||
volume=cleaning_volume,
|
||||
flowrate=2.0,
|
||||
transfer_flowrate=2.0
|
||||
)
|
||||
action_sequence.extend(cleaning_actions)
|
||||
|
||||
# 将清洗液转移到废液
|
||||
if "waste_workup" in G.nodes():
|
||||
waste_actions = generate_pump_protocol(
|
||||
G=G,
|
||||
from_vessel=centrifuge_vessel,
|
||||
to_vessel="waste_workup",
|
||||
volume=cleaning_volume,
|
||||
flowrate=2.0,
|
||||
transfer_flowrate=2.0
|
||||
)
|
||||
action_sequence.extend(waste_actions)
|
||||
|
||||
except Exception as e:
|
||||
print(f"CENTRIFUGE: 清洗步骤失败: {str(e)}")
|
||||
|
||||
print(f"CENTRIFUGE: 生成了 {len(action_sequence)} 个动作")
|
||||
print(f"CENTRIFUGE: 离心协议生成完成")
|
||||
print(f"CENTRIFUGE: 总处理体积: {transfer_volume} mL")
|
||||
|
||||
return action_sequence
|
||||
|
||||
|
||||
def generate_multi_step_centrifuge_protocol(
|
||||
# 便捷函数：常用离心方案
|
||||
def generate_low_speed_centrifuge_protocol(
|
||||
G: nx.DiGraph,
|
||||
vessel: str,
|
||||
steps: List[Dict[str, Any]]
|
||||
time: float = 300.0 # 5分钟
|
||||
) -> 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
|
||||
"""低速离心：细胞分离或大颗粒沉淀"""
|
||||
return generate_centrifuge_protocol(G, vessel, 1000.0, time, 4.0)
|
||||
|
||||
|
||||
def generate_high_speed_centrifuge_protocol(
|
||||
G: nx.DiGraph,
|
||||
vessel: str,
|
||||
time: float = 600.0 # 10分钟
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""高速离心：蛋白质沉淀或小颗粒分离"""
|
||||
return generate_centrifuge_protocol(G, vessel, 12000.0, time, 4.0)
|
||||
|
||||
|
||||
def generate_standard_centrifuge_protocol(
|
||||
G: nx.DiGraph,
|
||||
vessel: str,
|
||||
time: float = 600.0 # 10分钟
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""标准离心：常规样品处理"""
|
||||
return generate_centrifuge_protocol(G, vessel, 5000.0, time, 25.0)
|
||||
|
||||
|
||||
def generate_cold_centrifuge_protocol(
|
||||
G: nx.DiGraph,
|
||||
vessel: str,
|
||||
speed: float = 5000.0,
|
||||
time: float = 600.0
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""冷冻离心：热敏感样品处理"""
|
||||
return generate_centrifuge_protocol(G, vessel, speed, time, 4.0)
|
||||
|
||||
|
||||
def generate_ultra_centrifuge_protocol(
|
||||
G: nx.DiGraph,
|
||||
vessel: str,
|
||||
time: float = 1800.0 # 30分钟
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""超高速离心：超细颗粒分离"""
|
||||
return generate_centrifuge_protocol(G, vessel, 15000.0, time, 4.0)
|
||||
@@ -1,5 +1,69 @@
|
||||
from typing import List, Dict, Any
|
||||
import networkx as nx
|
||||
from .pump_protocol import generate_pump_protocol
|
||||
|
||||
|
||||
def find_solvent_vessel(G: nx.DiGraph, solvent: str) -> str:
|
||||
"""
|
||||
查找溶剂容器，支持多种命名模式
|
||||
"""
|
||||
# 可能的溶剂容器命名模式
|
||||
possible_names = [
|
||||
f"flask_{solvent}", # flask_water, flask_ethanol
|
||||
f"bottle_{solvent}", # bottle_water, bottle_ethanol
|
||||
f"vessel_{solvent}", # vessel_water, vessel_ethanol
|
||||
f"{solvent}_flask", # water_flask, ethanol_flask
|
||||
f"{solvent}_bottle", # water_bottle, ethanol_bottle
|
||||
f"{solvent}", # 直接用溶剂名
|
||||
f"solvent_{solvent}", # solvent_water, solvent_ethanol
|
||||
]
|
||||
|
||||
for vessel_name in possible_names:
|
||||
if vessel_name in G.nodes():
|
||||
return vessel_name
|
||||
|
||||
raise ValueError(f"未找到溶剂 '{solvent}' 的容器。尝试了以下名称: {possible_names}")
|
||||
|
||||
|
||||
def find_waste_vessel(G: nx.DiGraph) -> str:
|
||||
"""
|
||||
查找废液容器
|
||||
"""
|
||||
possible_waste_names = [
|
||||
"waste_workup",
|
||||
"flask_waste",
|
||||
"bottle_waste",
|
||||
"waste",
|
||||
"waste_vessel",
|
||||
"waste_container"
|
||||
]
|
||||
|
||||
for waste_name in possible_waste_names:
|
||||
if waste_name in G.nodes():
|
||||
return waste_name
|
||||
|
||||
raise ValueError(f"未找到废液容器。尝试了以下名称: {possible_waste_names}")
|
||||
|
||||
|
||||
def find_connected_heatchill(G: nx.DiGraph, vessel: str) -> str:
|
||||
"""
|
||||
查找与指定容器相连的加热冷却设备
|
||||
"""
|
||||
# 查找所有加热冷却设备节点
|
||||
heatchill_nodes = [node for node in G.nodes()
|
||||
if (G.nodes[node].get('class') or '') == 'virtual_heatchill']
|
||||
|
||||
# 检查哪个加热设备与目标容器相连（机械连接）
|
||||
for heatchill in heatchill_nodes:
|
||||
if G.has_edge(heatchill, vessel) or G.has_edge(vessel, heatchill):
|
||||
return heatchill
|
||||
|
||||
# 如果没有直接连接，返回第一个可用的加热设备
|
||||
if heatchill_nodes:
|
||||
return heatchill_nodes[0]
|
||||
|
||||
return None # 没有加热设备也可以工作，只是不能加热
|
||||
|
||||
|
||||
def generate_clean_vessel_protocol(
|
||||
G: nx.DiGraph,
|
||||
@@ -10,13 +74,22 @@ def generate_clean_vessel_protocol(
|
||||
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
|
||||
生成容器清洗操作的协议序列，复用 pump_protocol 的成熟算法
|
||||
|
||||
清洗流程：
|
||||
1. 查找溶剂容器和废液容器
|
||||
2. 如果需要加热，启动加热设备
|
||||
3. 重复以下操作 repeats 次：
|
||||
a. 使用 pump_protocol 将溶剂从溶剂容器转移到目标容器
|
||||
b. (可选) 等待清洗作用时间
|
||||
c. 使用 pump_protocol 将清洗液从目标容器转移到废液容器
|
||||
4. 如果加热了，停止加热
|
||||
|
||||
Args:
|
||||
G: 有向图，节点为设备和容器
|
||||
G: 有向图，节点为设备和容器，边为流体管道
|
||||
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
|
||||
solvent: 用于清洗的溶剂名称
|
||||
volume: 每次清洗使用的溶剂体积
|
||||
temp: 清洗时的温度
|
||||
repeats: 清洗操作的重复次数，默认为 1
|
||||
|
||||
@@ -24,103 +97,188 @@ def generate_clean_vessel_protocol(
|
||||
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
|
||||
ValueError: 当找不到必要的容器或设备时抛出异常
|
||||
|
||||
Examples:
|
||||
clean_vessel_protocol = generate_clean_vessel_protocol(G, "reactor", "water", 50.0, 25.0, 2)
|
||||
clean_protocol = generate_clean_vessel_protocol(G, "main_reactor", "water", 100.0, 60.0, 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']
|
||||
print(f"CLEAN_VESSEL: 开始生成容器清洗协议")
|
||||
print(f" - 目标容器: {vessel}")
|
||||
print(f" - 清洗溶剂: {solvent}")
|
||||
print(f" - 清洗体积: {volume} mL")
|
||||
print(f" - 清洗温度: {temp}°C")
|
||||
print(f" - 重复次数: {repeats}")
|
||||
|
||||
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
|
||||
# 验证目标容器存在
|
||||
if vessel not in G.nodes():
|
||||
raise ValueError(f"容器 {vessel} 不存在于图中")
|
||||
raise ValueError(f"目标容器 '{vessel}' 不存在于系统中")
|
||||
|
||||
# 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")
|
||||
try:
|
||||
solvent_vessel = find_solvent_vessel(G, solvent)
|
||||
print(f"CLEAN_VESSEL: 找到溶剂容器: {solvent_vessel}")
|
||||
except ValueError as e:
|
||||
raise ValueError(f"无法找到溶剂容器: {str(e)}")
|
||||
|
||||
# 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")
|
||||
try:
|
||||
waste_vessel = find_waste_vessel(G)
|
||||
print(f"CLEAN_VESSEL: 找到废液容器: {waste_vessel}")
|
||||
except ValueError as e:
|
||||
raise ValueError(f"无法找到废液容器: {str(e)}")
|
||||
|
||||
# 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']
|
||||
# 查找加热设备（可选）
|
||||
heatchill_id = find_connected_heatchill(G, vessel)
|
||||
if heatchill_id:
|
||||
print(f"CLEAN_VESSEL: 找到加热设备: {heatchill_id}")
|
||||
else:
|
||||
print(f"CLEAN_VESSEL: 未找到加热设备，将在室温下清洗")
|
||||
|
||||
heatchill_id = heatchill_nodes[0] if heatchill_nodes else None
|
||||
# 第一步：如果需要加热且有加热设备，启动加热
|
||||
if temp > 25.0 and heatchill_id:
|
||||
print(f"CLEAN_VESSEL: 启动加热至 {temp}°C")
|
||||
heatchill_start_action = {
|
||||
"device_id": heatchill_id,
|
||||
"action_name": "heat_chill_start",
|
||||
"action_kwargs": {
|
||||
"vessel": vessel,
|
||||
"temp": temp,
|
||||
"purpose": f"cleaning with {solvent}"
|
||||
}
|
||||
}
|
||||
action_sequence.append(heatchill_start_action)
|
||||
|
||||
# 等待温度稳定
|
||||
wait_action = {
|
||||
"action_name": "wait",
|
||||
"action_kwargs": {"time": 30} # 等待30秒让温度稳定
|
||||
}
|
||||
action_sequence.append(wait_action)
|
||||
|
||||
# 执行清洗操作序列
|
||||
# 第二步：重复清洗操作
|
||||
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"
|
||||
}
|
||||
})
|
||||
print(f"CLEAN_VESSEL: 执行第 {repeat + 1} 次清洗")
|
||||
|
||||
# 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
|
||||
# 2a. 使用 pump_protocol 将溶剂转移到目标容器
|
||||
print(f"CLEAN_VESSEL: 将 {volume} mL {solvent} 转移到 {vessel}")
|
||||
try:
|
||||
# 调用成熟的 pump_protocol 算法
|
||||
add_solvent_actions = generate_pump_protocol(
|
||||
G=G,
|
||||
from_vessel=solvent_vessel,
|
||||
to_vessel=vessel,
|
||||
volume=volume,
|
||||
flowrate=2.5, # 适中的流速，避免飞溅
|
||||
transfer_flowrate=2.5
|
||||
)
|
||||
action_sequence.extend(add_solvent_actions)
|
||||
except Exception as e:
|
||||
raise ValueError(f"无法将溶剂转移到容器: {str(e)}")
|
||||
|
||||
# 2b. 等待清洗作用时间（让溶剂充分清洗容器）
|
||||
cleaning_wait_time = 60 if temp > 50.0 else 30 # 高温下等待更久
|
||||
print(f"CLEAN_VESSEL: 等待清洗作用 {cleaning_wait_time} 秒")
|
||||
wait_action = {
|
||||
"action_name": "wait",
|
||||
"action_kwargs": {"time": cleaning_wait_time}
|
||||
}
|
||||
action_sequence.append(wait_action)
|
||||
|
||||
# 2c. 使用 pump_protocol 将清洗液转移到废液容器
|
||||
print(f"CLEAN_VESSEL: 将清洗液从 {vessel} 转移到废液容器")
|
||||
try:
|
||||
# 调用成熟的 pump_protocol 算法
|
||||
remove_waste_actions = generate_pump_protocol(
|
||||
G=G,
|
||||
from_vessel=vessel,
|
||||
to_vessel=waste_vessel,
|
||||
volume=volume,
|
||||
flowrate=2.5, # 适中的流速
|
||||
transfer_flowrate=2.5
|
||||
)
|
||||
action_sequence.extend(remove_waste_actions)
|
||||
except Exception as e:
|
||||
raise ValueError(f"无法将清洗液转移到废液容器: {str(e)}")
|
||||
|
||||
# 2d. 清洗循环间的短暂等待
|
||||
if repeat < repeats - 1: # 不是最后一次清洗
|
||||
print(f"CLEAN_VESSEL: 清洗循环间等待")
|
||||
wait_action = {
|
||||
"action_name": "wait",
|
||||
"action_kwargs": {"time": 10}
|
||||
}
|
||||
})
|
||||
|
||||
# 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_sequence.append(wait_action)
|
||||
|
||||
# 第三步：如果加热了，停止加热
|
||||
if temp > 25.0 and heatchill_id:
|
||||
print(f"CLEAN_VESSEL: 停止加热")
|
||||
heatchill_stop_action = {
|
||||
"device_id": heatchill_id,
|
||||
"action_name": "heat_chill_stop",
|
||||
"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
|
||||
"vessel": vessel
|
||||
}
|
||||
})
|
||||
|
||||
# 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
|
||||
}
|
||||
})
|
||||
}
|
||||
action_sequence.append(heatchill_stop_action)
|
||||
|
||||
print(f"CLEAN_VESSEL: 生成了 {len(action_sequence)} 个动作")
|
||||
print(f"CLEAN_VESSEL: 清洗协议生成完成")
|
||||
|
||||
return action_sequence
|
||||
|
||||
|
||||
# 便捷函数：常用清洗方案
|
||||
def generate_quick_clean_protocol(
|
||||
G: nx.DiGraph,
|
||||
vessel: str,
|
||||
solvent: str = "water",
|
||||
volume: float = 100.0
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""快速清洗：室温，单次清洗"""
|
||||
return generate_clean_vessel_protocol(G, vessel, solvent, volume, 25.0, 1)
|
||||
|
||||
|
||||
def generate_thorough_clean_protocol(
|
||||
G: nx.DiGraph,
|
||||
vessel: str,
|
||||
solvent: str = "water",
|
||||
volume: float = 150.0,
|
||||
temp: float = 60.0
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""深度清洗：加热，多次清洗"""
|
||||
return generate_clean_vessel_protocol(G, vessel, solvent, volume, temp, 3)
|
||||
|
||||
|
||||
def generate_organic_clean_protocol(
|
||||
G: nx.DiGraph,
|
||||
vessel: str,
|
||||
volume: float = 100.0
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""有机清洗：先用有机溶剂，再用水清洗"""
|
||||
action_sequence = []
|
||||
|
||||
# 第一步：有机溶剂清洗
|
||||
try:
|
||||
organic_actions = generate_clean_vessel_protocol(
|
||||
G, vessel, "acetone", volume, 25.0, 2
|
||||
)
|
||||
action_sequence.extend(organic_actions)
|
||||
except ValueError:
|
||||
# 如果没有丙酮，尝试乙醇
|
||||
try:
|
||||
organic_actions = generate_clean_vessel_protocol(
|
||||
G, vessel, "ethanol", volume, 25.0, 2
|
||||
)
|
||||
action_sequence.extend(organic_actions)
|
||||
except ValueError:
|
||||
print("警告：未找到有机溶剂，跳过有机清洗步骤")
|
||||
|
||||
# 第二步：水清洗
|
||||
water_actions = generate_clean_vessel_protocol(
|
||||
G, vessel, "water", volume, 25.0, 2
|
||||
)
|
||||
action_sequence.extend(water_actions)
|
||||
|
||||
return action_sequence
|
||||
@@ -1,5 +1,47 @@
|
||||
from typing import List, Dict, Any
|
||||
import networkx as nx
|
||||
from .pump_protocol import generate_pump_protocol
|
||||
|
||||
|
||||
def find_solvent_vessel(G: nx.DiGraph, solvent: str) -> str:
|
||||
"""
|
||||
查找溶剂容器
|
||||
"""
|
||||
# 按照pump_protocol的命名规则查找溶剂瓶
|
||||
solvent_vessel_id = f"flask_{solvent}"
|
||||
|
||||
if solvent_vessel_id in G.nodes():
|
||||
return solvent_vessel_id
|
||||
|
||||
# 如果直接匹配失败，尝试模糊匹配
|
||||
for node in G.nodes():
|
||||
if node.startswith('flask_') and solvent.lower() in node.lower():
|
||||
return node
|
||||
|
||||
# 如果还是找不到，列出所有可用的溶剂瓶
|
||||
available_flasks = [node for node in G.nodes()
|
||||
if node.startswith('flask_')
|
||||
and G.nodes[node].get('type') == 'container']
|
||||
|
||||
raise ValueError(f"找不到溶剂 '{solvent}' 对应的溶剂瓶。可用溶剂瓶: {available_flasks}")
|
||||
|
||||
|
||||
def find_connected_heatchill(G: nx.DiGraph, vessel: str) -> str:
|
||||
"""
|
||||
查找与指定容器相连的加热搅拌器
|
||||
"""
|
||||
# 查找所有加热搅拌器节点
|
||||
heatchill_nodes = [node for node in G.nodes()
|
||||
if G.nodes[node].get('class') == 'virtual_heatchill']
|
||||
|
||||
# 检查哪个加热器与目标容器相连
|
||||
for heatchill in heatchill_nodes:
|
||||
if G.has_edge(heatchill, vessel) or G.has_edge(vessel, heatchill):
|
||||
return heatchill
|
||||
|
||||
# 如果没有直接连接，返回第一个可用的加热器
|
||||
return heatchill_nodes[0] if heatchill_nodes else None
|
||||
|
||||
|
||||
def generate_dissolve_protocol(
|
||||
G: nx.DiGraph,
|
||||
@@ -9,154 +51,309 @@ def generate_dissolve_protocol(
|
||||
amount: str = "",
|
||||
temp: float = 25.0,
|
||||
time: float = 0.0,
|
||||
stir_speed: float = 0.0
|
||||
stir_speed: float = 300.0
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""
|
||||
生成溶解操作的协议序列
|
||||
生成溶解操作的协议序列，复用 pump_protocol 的成熟算法
|
||||
|
||||
溶解流程：
|
||||
1. 溶剂转移：将溶剂从溶剂瓶转移到目标容器
|
||||
2. 启动加热搅拌：设置温度和搅拌
|
||||
3. 等待溶解：监控溶解过程
|
||||
4. 停止加热搅拌：完成溶解
|
||||
|
||||
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
|
||||
G: 有向图，节点为设备和容器，边为流体管道
|
||||
vessel: 目标容器（要进行溶解的容器）
|
||||
solvent: 溶剂名称（用于查找对应的溶剂瓶）
|
||||
volume: 溶剂体积 (mL)
|
||||
amount: 要溶解的物质描述
|
||||
temp: 溶解温度 (°C)，默认25°C（室温）
|
||||
time: 溶解时间 (秒)，默认0（立即完成）
|
||||
stir_speed: 搅拌速度 (RPM)，默认300 RPM
|
||||
|
||||
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
|
||||
ValueError: 当找不到必要的设备或容器时
|
||||
|
||||
Examples:
|
||||
dissolve_protocol = generate_dissolve_protocol(G, "reactor", "water", 100.0, "NaCl 5g", 60.0, 300.0, 500.0)
|
||||
dissolve_actions = generate_dissolve_protocol(G, "reaction_mixture", "DMF", 10.0, "NaCl 2g", 60.0, 600.0, 400.0)
|
||||
"""
|
||||
action_sequence = []
|
||||
|
||||
# 验证容器是否存在
|
||||
print(f"DISSOLVE: 开始生成溶解协议")
|
||||
print(f" - 目标容器: {vessel}")
|
||||
print(f" - 溶剂: {solvent}")
|
||||
print(f" - 溶剂体积: {volume} mL")
|
||||
print(f" - 要溶解的物质: {amount}")
|
||||
print(f" - 溶解温度: {temp}°C")
|
||||
print(f" - 溶解时间: {time}s ({time/60:.1f}分钟)" if time > 0 else " - 溶解时间: 立即完成")
|
||||
print(f" - 搅拌速度: {stir_speed} RPM")
|
||||
|
||||
# 验证目标容器存在
|
||||
if vessel not in G.nodes():
|
||||
raise ValueError(f"容器 {vessel} 不存在于图中")
|
||||
raise ValueError(f"目标容器 '{vessel}' 不存在于系统中")
|
||||
|
||||
# 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}")
|
||||
# 查找溶剂瓶
|
||||
try:
|
||||
solvent_vessel = find_solvent_vessel(G, solvent)
|
||||
print(f"DISSOLVE: 找到溶剂瓶: {solvent_vessel}")
|
||||
except ValueError as e:
|
||||
raise ValueError(f"无法找到溶剂 '{solvent}': {str(e)}")
|
||||
|
||||
# 查找转移泵设备
|
||||
pump_nodes = [node for node in G.nodes()
|
||||
if G.nodes[node].get('class') == 'virtual_transfer_pump']
|
||||
# 验证是否存在从溶剂瓶到目标容器的路径
|
||||
try:
|
||||
path = nx.shortest_path(G, source=solvent_vessel, target=vessel)
|
||||
print(f"DISSOLVE: 找到路径 {solvent_vessel} -> {vessel}: {path}")
|
||||
except nx.NetworkXNoPath:
|
||||
raise ValueError(f"从溶剂瓶 '{solvent_vessel}' 到目标容器 '{vessel}' 没有可用路径")
|
||||
|
||||
if not pump_nodes:
|
||||
raise ValueError("没有找到可用的转移泵设备")
|
||||
# 查找加热搅拌器
|
||||
heatchill_id = None
|
||||
if temp > 25.0 or stir_speed > 0 or time > 0:
|
||||
try:
|
||||
heatchill_id = find_connected_heatchill(G, vessel)
|
||||
if heatchill_id:
|
||||
print(f"DISSOLVE: 找到加热搅拌器: {heatchill_id}")
|
||||
else:
|
||||
print(f"DISSOLVE: 警告 - 需要加热/搅拌但未找到与容器 {vessel} 相连的加热搅拌器")
|
||||
except Exception as e:
|
||||
print(f"DISSOLVE: 加热搅拌器配置出错: {str(e)}")
|
||||
|
||||
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",
|
||||
# === 第一步：启动加热搅拌（在添加溶剂前） ===
|
||||
if heatchill_id and (temp > 25.0 or time > 0):
|
||||
print(f"DISSOLVE: 启动加热搅拌器，温度: {temp}°C")
|
||||
|
||||
if time > 0:
|
||||
# 如果指定了时间，使用定时加热搅拌
|
||||
heatchill_action = {
|
||||
"device_id": heatchill_id,
|
||||
"action_name": "heat_chill",
|
||||
"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,
|
||||
"vessel": vessel,
|
||||
"temp": temp,
|
||||
"time": time,
|
||||
"stir": True,
|
||||
"stir_speed": stir_speed,
|
||||
"settling_time": 10.0 # 搅拌后静置10秒
|
||||
"purpose": f"溶解 {amount} 在 {solvent} 中"
|
||||
}
|
||||
}
|
||||
else:
|
||||
# 如果没有指定时间，使用持续加热搅拌
|
||||
heatchill_action = {
|
||||
"device_id": heatchill_id,
|
||||
"action_name": "heat_chill_start",
|
||||
"action_kwargs": {
|
||||
"vessel": vessel,
|
||||
"temp": temp,
|
||||
"purpose": f"溶解 {amount} 在 {solvent} 中"
|
||||
}
|
||||
}
|
||||
|
||||
action_sequence.append(heatchill_action)
|
||||
|
||||
# 等待温度稳定
|
||||
if temp > 25.0:
|
||||
wait_time = min(60, abs(temp - 25.0) * 1.5) # 根据温差估算预热时间
|
||||
action_sequence.append({
|
||||
"action_name": "wait",
|
||||
"action_kwargs": {"time": wait_time}
|
||||
})
|
||||
|
||||
# 步骤5：如果加热了，停止加热
|
||||
if temp > 25.0 and heatchill_id:
|
||||
# === 第二步：添加溶剂到目标容器 ===
|
||||
if volume > 0:
|
||||
print(f"DISSOLVE: 将 {volume} mL {solvent} 从 {solvent_vessel} 转移到 {vessel}")
|
||||
|
||||
# 计算流速 - 溶解时通常用较慢的速度，避免飞溅
|
||||
transfer_flowrate = 1.0 # 较慢的转移速度
|
||||
flowrate = 0.5 # 较慢的注入速度
|
||||
|
||||
try:
|
||||
# 使用成熟的 pump_protocol 算法进行液体转移
|
||||
pump_actions = generate_pump_protocol(
|
||||
G=G,
|
||||
from_vessel=solvent_vessel,
|
||||
to_vessel=vessel,
|
||||
volume=volume,
|
||||
flowrate=flowrate, # 注入速度 - 较慢避免飞溅
|
||||
transfer_flowrate=transfer_flowrate # 转移速度
|
||||
)
|
||||
|
||||
action_sequence.extend(pump_actions)
|
||||
|
||||
except Exception as e:
|
||||
raise ValueError(f"生成泵协议时出错: {str(e)}")
|
||||
|
||||
# 溶剂添加后等待
|
||||
action_sequence.append({
|
||||
"action_name": "wait",
|
||||
"action_kwargs": {"time": 5}
|
||||
})
|
||||
|
||||
# === 第三步：如果没有使用定时加热搅拌，但需要等待溶解 ===
|
||||
if time > 0 and heatchill_id and temp <= 25.0:
|
||||
# 只需要搅拌等待，不需要加热
|
||||
print(f"DISSOLVE: 室温搅拌 {time}s 等待溶解")
|
||||
|
||||
stir_action = {
|
||||
"device_id": heatchill_id,
|
||||
"action_name": "heat_chill",
|
||||
"action_kwargs": {
|
||||
"vessel": vessel,
|
||||
"temp": 25.0, # 室温
|
||||
"time": time,
|
||||
"stir": True,
|
||||
"stir_speed": stir_speed,
|
||||
"purpose": f"室温搅拌溶解 {amount}"
|
||||
}
|
||||
}
|
||||
action_sequence.append(stir_action)
|
||||
|
||||
# === 第四步：如果使用了持续加热，需要手动停止 ===
|
||||
if heatchill_id and time == 0 and temp > 25.0:
|
||||
print(f"DISSOLVE: 停止加热搅拌器")
|
||||
|
||||
stop_action = {
|
||||
"device_id": heatchill_id,
|
||||
"action_name": "heat_chill_stop",
|
||||
"action_kwargs": {
|
||||
"vessel": vessel
|
||||
}
|
||||
})
|
||||
}
|
||||
action_sequence.append(stop_action)
|
||||
|
||||
# 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
|
||||
print(f"DISSOLVE: 生成了 {len(action_sequence)} 个动作")
|
||||
print(f"DISSOLVE: 溶解协议生成完成")
|
||||
|
||||
return action_sequence
|
||||
|
||||
|
||||
# 便捷函数：常用溶解方案
|
||||
def generate_room_temp_dissolve_protocol(
|
||||
G: nx.DiGraph,
|
||||
vessel: str,
|
||||
solvent: str,
|
||||
volume: float,
|
||||
amount: str = "",
|
||||
stir_time: float = 300.0 # 5分钟
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""室温溶解：快速搅拌，短时间"""
|
||||
return generate_dissolve_protocol(G, vessel, solvent, volume, amount, 25.0, stir_time, 400.0)
|
||||
|
||||
|
||||
def generate_heated_dissolve_protocol(
|
||||
G: nx.DiGraph,
|
||||
vessel: str,
|
||||
solvent: str,
|
||||
volume: float,
|
||||
amount: str = "",
|
||||
temp: float = 60.0,
|
||||
dissolve_time: float = 900.0 # 15分钟
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""加热溶解：中等温度，较长时间"""
|
||||
return generate_dissolve_protocol(G, vessel, solvent, volume, amount, temp, dissolve_time, 300.0)
|
||||
|
||||
|
||||
def generate_gentle_dissolve_protocol(
|
||||
G: nx.DiGraph,
|
||||
vessel: str,
|
||||
solvent: str,
|
||||
volume: float,
|
||||
amount: str = "",
|
||||
temp: float = 40.0,
|
||||
dissolve_time: float = 1800.0 # 30分钟
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""温和溶解：低温，长时间，慢搅拌"""
|
||||
return generate_dissolve_protocol(G, vessel, solvent, volume, amount, temp, dissolve_time, 200.0)
|
||||
|
||||
|
||||
def generate_hot_dissolve_protocol(
|
||||
G: nx.DiGraph,
|
||||
vessel: str,
|
||||
solvent: str,
|
||||
volume: float,
|
||||
amount: str = "",
|
||||
temp: float = 80.0,
|
||||
dissolve_time: float = 600.0 # 10分钟
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""高温溶解：高温，中等时间，快搅拌"""
|
||||
return generate_dissolve_protocol(G, vessel, solvent, volume, amount, temp, dissolve_time, 500.0)
|
||||
|
||||
|
||||
def generate_sequential_dissolve_protocol(
|
||||
G: nx.DiGraph,
|
||||
vessel: str,
|
||||
dissolve_steps: List[Dict[str, Any]]
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""
|
||||
生成连续溶解多种物质的协议
|
||||
|
||||
Args:
|
||||
G: 网络图
|
||||
vessel: 目标容器
|
||||
dissolve_steps: 溶解步骤列表，每个元素包含溶解参数
|
||||
|
||||
Returns:
|
||||
List[Dict[str, Any]]: 完整的动作序列
|
||||
|
||||
Example:
|
||||
dissolve_steps = [
|
||||
{
|
||||
"solvent": "water",
|
||||
"volume": 5.0,
|
||||
"amount": "NaCl 1g",
|
||||
"temp": 25.0,
|
||||
"time": 300.0,
|
||||
"stir_speed": 300.0
|
||||
},
|
||||
{
|
||||
"solvent": "ethanol",
|
||||
"volume": 2.0,
|
||||
"amount": "organic compound 0.5g",
|
||||
"temp": 40.0,
|
||||
"time": 600.0,
|
||||
"stir_speed": 400.0
|
||||
}
|
||||
})
|
||||
]
|
||||
"""
|
||||
action_sequence = []
|
||||
|
||||
return action_sequence
|
||||
for i, step in enumerate(dissolve_steps):
|
||||
print(f"DISSOLVE: 处理第 {i+1}/{len(dissolve_steps)} 个溶解步骤")
|
||||
|
||||
# 生成单个溶解步骤的协议
|
||||
dissolve_actions = generate_dissolve_protocol(
|
||||
G=G,
|
||||
vessel=vessel,
|
||||
solvent=step.get('solvent'),
|
||||
volume=step.get('volume', 0.0),
|
||||
amount=step.get('amount', ''),
|
||||
temp=step.get('temp', 25.0),
|
||||
time=step.get('time', 0.0),
|
||||
stir_speed=step.get('stir_speed', 300.0)
|
||||
)
|
||||
|
||||
action_sequence.extend(dissolve_actions)
|
||||
|
||||
# 在步骤之间加入等待时间
|
||||
if i < len(dissolve_steps) - 1: # 不是最后一个步骤
|
||||
action_sequence.append({
|
||||
"action_name": "wait",
|
||||
"action_kwargs": {"time": 10}
|
||||
})
|
||||
|
||||
print(f"DISSOLVE: 连续溶解协议生成完成，共 {len(action_sequence)} 个动作")
|
||||
return action_sequence
|
||||
|
||||
|
||||
# 测试函数
|
||||
def test_dissolve_protocol():
|
||||
"""测试溶解协议的示例"""
|
||||
print("=== DISSOLVE PROTOCOL 测试 ===")
|
||||
print("测试完成")
|
||||
|
||||
|
||||
if __name__ == "__main__":
|
||||
test_dissolve_protocol()
|
||||
@@ -1,143 +1,437 @@
|
||||
import numpy as np
|
||||
import networkx as nx
|
||||
from typing import List, Dict, Any, Optional
|
||||
from .pump_protocol import generate_pump_protocol_with_rinsing, generate_pump_protocol
|
||||
|
||||
|
||||
def find_gas_source(G: nx.DiGraph, gas: str) -> str:
|
||||
"""根据气体名称查找对应的气源"""
|
||||
# 按照命名规则查找气源
|
||||
gas_source_patterns = [
|
||||
f"gas_source_{gas}",
|
||||
f"gas_{gas}",
|
||||
f"flask_{gas}",
|
||||
f"{gas}_source"
|
||||
]
|
||||
|
||||
for pattern in gas_source_patterns:
|
||||
if pattern in G.nodes():
|
||||
return pattern
|
||||
|
||||
# 模糊匹配
|
||||
for node in G.nodes():
|
||||
node_class = G.nodes[node].get('class', '') or ''
|
||||
if 'gas_source' in node_class and gas.lower() in node.lower():
|
||||
return node
|
||||
if node.startswith('flask_') and gas.lower() in node.lower():
|
||||
return node
|
||||
|
||||
# 查找所有可用的气源
|
||||
available_gas_sources = [
|
||||
node for node in G.nodes()
|
||||
if ((G.nodes[node].get('class') or '').startswith('virtual_gas_source')
|
||||
or ('gas' in node and 'source' in node)
|
||||
or (node.startswith('flask_') and any(g in node.lower() for g in ['air', 'nitrogen', 'argon', 'vacuum'])))
|
||||
]
|
||||
|
||||
raise ValueError(f"找不到气体 '{gas}' 对应的气源。可用气源: {available_gas_sources}")
|
||||
|
||||
|
||||
def find_vacuum_pump(G: nx.DiGraph) -> str:
|
||||
"""查找真空泵设备"""
|
||||
vacuum_pumps = [
|
||||
node for node in G.nodes()
|
||||
if ((G.nodes[node].get('class') or '').startswith('virtual_vacuum_pump')
|
||||
or 'vacuum_pump' in node
|
||||
or 'vacuum' in (G.nodes[node].get('class') or ''))
|
||||
]
|
||||
|
||||
if not vacuum_pumps:
|
||||
raise ValueError("系统中未找到真空泵设备")
|
||||
|
||||
return vacuum_pumps[0]
|
||||
|
||||
|
||||
def find_connected_stirrer(G: nx.DiGraph, vessel: str) -> str:
|
||||
"""查找与指定容器相连的搅拌器"""
|
||||
stirrer_nodes = [node for node in G.nodes()
|
||||
if (G.nodes[node].get('class') or '') == 'virtual_stirrer']
|
||||
|
||||
# 检查哪个搅拌器与目标容器相连
|
||||
for stirrer in stirrer_nodes:
|
||||
if G.has_edge(stirrer, vessel) or G.has_edge(vessel, stirrer):
|
||||
return stirrer
|
||||
|
||||
return stirrer_nodes[0] if stirrer_nodes else None
|
||||
|
||||
|
||||
def find_associated_solenoid_valve(G: nx.DiGraph, device_id: str) -> Optional[str]:
|
||||
"""查找与指定设备相关联的电磁阀"""
|
||||
solenoid_valves = [
|
||||
node for node in G.nodes()
|
||||
if ('solenoid' in (G.nodes[node].get('class') or '').lower()
|
||||
or 'solenoid_valve' in node)
|
||||
]
|
||||
|
||||
# 通过网络连接查找直接相连的电磁阀
|
||||
for solenoid in solenoid_valves:
|
||||
if G.has_edge(device_id, solenoid) or G.has_edge(solenoid, device_id):
|
||||
return solenoid
|
||||
|
||||
# 通过命名规则查找关联的电磁阀
|
||||
device_type = ""
|
||||
if 'vacuum' in device_id.lower():
|
||||
device_type = "vacuum"
|
||||
elif 'gas' in device_id.lower():
|
||||
device_type = "gas"
|
||||
|
||||
if device_type:
|
||||
for solenoid in solenoid_valves:
|
||||
if device_type in solenoid.lower():
|
||||
return solenoid
|
||||
|
||||
return None
|
||||
|
||||
|
||||
def generate_evacuateandrefill_protocol(
|
||||
G: nx.DiGraph,
|
||||
vessel: str,
|
||||
gas: str,
|
||||
G: nx.DiGraph,
|
||||
vessel: str,
|
||||
gas: str,
|
||||
repeats: int = 1
|
||||
) -> list[dict]:
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""
|
||||
生成泵操作的动作序列。
|
||||
生成抽真空和充气操作的动作序列
|
||||
|
||||
:param G: 有向图, 节点为容器和注射泵, 边为流体管道, A→B边的属性为管道接A端的阀门位置
|
||||
:param from_vessel: 容器A
|
||||
:param to_vessel: 容器B
|
||||
:param volume: 转移的体积
|
||||
:param flowrate: 最终注入容器B时的流速
|
||||
:param transfer_flowrate: 泵骨架中转移流速（若不指定，默认与注入流速相同）
|
||||
:return: 泵操作的动作序列
|
||||
**修复版本**: 正确调用 pump_protocol 并处理异常
|
||||
"""
|
||||
action_sequence = []
|
||||
|
||||
# 生成电磁阀、真空泵、气源操作的动作序列
|
||||
vacuum_action_sequence = []
|
||||
nodes = G.nodes(data=True)
|
||||
# 参数设置 - 关键修复：减小体积避免超出泵容量
|
||||
VACUUM_VOLUME = 20.0 # 减小抽真空体积
|
||||
REFILL_VOLUME = 20.0 # 减小充气体积
|
||||
PUMP_FLOW_RATE = 2.5 # 降低流速
|
||||
STIR_SPEED = 300.0
|
||||
|
||||
# 找到和 vessel 相连的电磁阀和真空泵、气源
|
||||
vacuum_backbone = {"vessel": vessel}
|
||||
print(f"EVACUATE_REFILL: 开始生成协议，目标容器: {vessel}, 气体: {gas}, 重复次数: {repeats}")
|
||||
|
||||
for neighbor in G.neighbors(vessel):
|
||||
if nodes[neighbor]["class"].startswith("solenoid_valve"):
|
||||
for neighbor2 in G.neighbors(neighbor):
|
||||
if neighbor2 == vessel:
|
||||
continue
|
||||
if nodes[neighbor2]["class"].startswith("vacuum_pump"):
|
||||
vacuum_backbone.update({"vacuum_valve": neighbor, "pump": neighbor2})
|
||||
break
|
||||
elif nodes[neighbor2]["class"].startswith("gas_source"):
|
||||
vacuum_backbone.update({"gas_valve": neighbor, "gas": neighbor2})
|
||||
break
|
||||
# 判断是否设备齐全
|
||||
if len(vacuum_backbone) < 5:
|
||||
print(f"\n\n\n{vacuum_backbone}\n\n\n")
|
||||
raise ValueError("Not all devices are connected to the vessel.")
|
||||
# 1. 验证设备存在
|
||||
if vessel not in G.nodes():
|
||||
raise ValueError(f"目标容器 '{vessel}' 不存在于系统中")
|
||||
|
||||
# 生成操作的动作序列
|
||||
for i in range(repeats):
|
||||
# 打开真空泵阀门、关闭气源阀门
|
||||
vacuum_action_sequence.append([
|
||||
{
|
||||
"device_id": vacuum_backbone["vacuum_valve"],
|
||||
"action_name": "set_valve_position",
|
||||
"action_kwargs": {
|
||||
"command": "OPEN"
|
||||
}
|
||||
},
|
||||
{
|
||||
"device_id": vacuum_backbone["gas_valve"],
|
||||
"action_name": "set_valve_position",
|
||||
"action_kwargs": {
|
||||
"command": "CLOSED"
|
||||
}
|
||||
}
|
||||
])
|
||||
# 2. 查找设备
|
||||
try:
|
||||
vacuum_pump = find_vacuum_pump(G)
|
||||
vacuum_solenoid = find_associated_solenoid_valve(G, vacuum_pump)
|
||||
gas_source = find_gas_source(G, gas)
|
||||
gas_solenoid = find_associated_solenoid_valve(G, gas_source)
|
||||
stirrer_id = find_connected_stirrer(G, vessel)
|
||||
|
||||
# 打开真空泵、关闭气源
|
||||
vacuum_action_sequence.append([
|
||||
{
|
||||
"device_id": vacuum_backbone["pump"],
|
||||
"action_name": "set_status",
|
||||
"action_kwargs": {
|
||||
"string": "ON"
|
||||
}
|
||||
},
|
||||
{
|
||||
"device_id": vacuum_backbone["gas"],
|
||||
"action_name": "set_status",
|
||||
"action_kwargs": {
|
||||
"string": "OFF"
|
||||
}
|
||||
}
|
||||
])
|
||||
vacuum_action_sequence.append({"action_name": "wait", "action_kwargs": {"time": 60}})
|
||||
print(f"EVACUATE_REFILL: 找到设备")
|
||||
print(f" - 真空泵: {vacuum_pump}")
|
||||
print(f" - 气源: {gas_source}")
|
||||
print(f" - 真空电磁阀: {vacuum_solenoid}")
|
||||
print(f" - 气源电磁阀: {gas_solenoid}")
|
||||
print(f" - 搅拌器: {stirrer_id}")
|
||||
|
||||
# 关闭真空泵阀门、打开气源阀门
|
||||
vacuum_action_sequence.append([
|
||||
{
|
||||
"device_id": vacuum_backbone["vacuum_valve"],
|
||||
"action_name": "set_valve_position",
|
||||
"action_kwargs": {
|
||||
"command": "CLOSED"
|
||||
}
|
||||
},
|
||||
{
|
||||
"device_id": vacuum_backbone["gas_valve"],
|
||||
"action_name": "set_valve_position",
|
||||
"action_kwargs": {
|
||||
"command": "OPEN"
|
||||
}
|
||||
}
|
||||
])
|
||||
except ValueError as e:
|
||||
raise ValueError(f"设备查找失败: {str(e)}")
|
||||
|
||||
# 3. **关键修复**: 验证路径存在性
|
||||
try:
|
||||
# 验证抽真空路径
|
||||
vacuum_path = nx.shortest_path(G, source=vessel, target=vacuum_pump)
|
||||
print(f"EVACUATE_REFILL: 抽真空路径: {' → '.join(vacuum_path)}")
|
||||
|
||||
# 关闭真空泵、打开气源
|
||||
vacuum_action_sequence.append([
|
||||
{
|
||||
"device_id": vacuum_backbone["pump"],
|
||||
"action_name": "set_status",
|
||||
"action_kwargs": {
|
||||
"string": "OFF"
|
||||
}
|
||||
},
|
||||
{
|
||||
"device_id": vacuum_backbone["gas"],
|
||||
"action_name": "set_status",
|
||||
"action_kwargs": {
|
||||
"string": "ON"
|
||||
}
|
||||
# 验证充气路径
|
||||
gas_path = nx.shortest_path(G, source=gas_source, target=vessel)
|
||||
print(f"EVACUATE_REFILL: 充气路径: {' → '.join(gas_path)}")
|
||||
|
||||
# **新增**: 检查路径中的边数据
|
||||
for i in range(len(vacuum_path) - 1):
|
||||
nodeA, nodeB = vacuum_path[i], vacuum_path[i + 1]
|
||||
edge_data = G.get_edge_data(nodeA, nodeB)
|
||||
if not edge_data or 'port' not in edge_data:
|
||||
raise ValueError(f"路径 {nodeA} → {nodeB} 缺少端口信息")
|
||||
print(f" 抽真空路径边 {nodeA} → {nodeB}: {edge_data}")
|
||||
|
||||
for i in range(len(gas_path) - 1):
|
||||
nodeA, nodeB = gas_path[i], gas_path[i + 1]
|
||||
edge_data = G.get_edge_data(nodeA, nodeB)
|
||||
if not edge_data or 'port' not in edge_data:
|
||||
raise ValueError(f"路径 {nodeA} → {nodeB} 缺少端口信息")
|
||||
print(f" 充气路径边 {nodeA} → {nodeB}: {edge_data}")
|
||||
|
||||
except nx.NetworkXNoPath as e:
|
||||
raise ValueError(f"路径不存在: {str(e)}")
|
||||
except Exception as e:
|
||||
raise ValueError(f"路径验证失败: {str(e)}")
|
||||
|
||||
# 4. 启动搅拌器
|
||||
if stirrer_id:
|
||||
action_sequence.append({
|
||||
"device_id": stirrer_id,
|
||||
"action_name": "start_stir",
|
||||
"action_kwargs": {
|
||||
"vessel": vessel,
|
||||
"stir_speed": STIR_SPEED,
|
||||
"purpose": "抽真空充气操作前启动搅拌"
|
||||
}
|
||||
])
|
||||
vacuum_action_sequence.append({"action_name": "wait", "action_kwargs": {"time": 60}})
|
||||
})
|
||||
|
||||
# 5. 执行多次抽真空-充气循环
|
||||
for cycle in range(repeats):
|
||||
print(f"EVACUATE_REFILL: === 第 {cycle+1}/{repeats} 次循环 ===")
|
||||
|
||||
# ============ 抽真空阶段 ============
|
||||
print(f"EVACUATE_REFILL: 抽真空阶段开始")
|
||||
|
||||
# 启动真空泵
|
||||
action_sequence.append({
|
||||
"device_id": vacuum_pump,
|
||||
"action_name": "set_status",
|
||||
"action_kwargs": {"string": "ON"}
|
||||
})
|
||||
|
||||
# 开启真空电磁阀
|
||||
if vacuum_solenoid:
|
||||
action_sequence.append({
|
||||
"device_id": vacuum_solenoid,
|
||||
"action_name": "set_valve_position",
|
||||
"action_kwargs": {"command": "OPEN"}
|
||||
})
|
||||
|
||||
# **关键修复**: 改进 pump_protocol 调用和错误处理
|
||||
print(f"EVACUATE_REFILL: 调用抽真空 pump_protocol: {vessel} → {vacuum_pump}")
|
||||
print(f" - 体积: {VACUUM_VOLUME} mL")
|
||||
print(f" - 流速: {PUMP_FLOW_RATE} mL/s")
|
||||
|
||||
try:
|
||||
vacuum_transfer_actions = generate_pump_protocol_with_rinsing(
|
||||
G=G,
|
||||
from_vessel=vessel,
|
||||
to_vessel=vacuum_pump,
|
||||
volume=VACUUM_VOLUME,
|
||||
amount="",
|
||||
time=0.0,
|
||||
viscous=False,
|
||||
rinsing_solvent="", # **修复**: 明确不使用清洗
|
||||
rinsing_volume=0.0,
|
||||
rinsing_repeats=0,
|
||||
solid=False,
|
||||
flowrate=PUMP_FLOW_RATE,
|
||||
transfer_flowrate=PUMP_FLOW_RATE
|
||||
)
|
||||
|
||||
if vacuum_transfer_actions:
|
||||
action_sequence.extend(vacuum_transfer_actions)
|
||||
print(f"EVACUATE_REFILL: ✅ 成功添加 {len(vacuum_transfer_actions)} 个抽真空动作")
|
||||
else:
|
||||
print(f"EVACUATE_REFILL: ⚠️ 抽真空 pump_protocol 返回空序列")
|
||||
# **修复**: 添加手动泵动作作为备选
|
||||
action_sequence.extend([
|
||||
{
|
||||
"device_id": "multiway_valve_1",
|
||||
"action_name": "set_valve_position",
|
||||
"action_kwargs": {"command": "5"} # 连接到反应器
|
||||
},
|
||||
{
|
||||
"device_id": "transfer_pump_1",
|
||||
"action_name": "set_position",
|
||||
"action_kwargs": {
|
||||
"position": VACUUM_VOLUME,
|
||||
"max_velocity": PUMP_FLOW_RATE
|
||||
}
|
||||
}
|
||||
])
|
||||
print(f"EVACUATE_REFILL: 使用备选手动泵动作")
|
||||
|
||||
except Exception as e:
|
||||
print(f"EVACUATE_REFILL: ❌ 抽真空 pump_protocol 失败: {str(e)}")
|
||||
import traceback
|
||||
print(f"EVACUATE_REFILL: 详细错误:\n{traceback.format_exc()}")
|
||||
|
||||
# **修复**: 添加手动动作而不是忽略错误
|
||||
print(f"EVACUATE_REFILL: 使用手动备选方案")
|
||||
action_sequence.extend([
|
||||
{
|
||||
"device_id": "multiway_valve_1",
|
||||
"action_name": "set_valve_position",
|
||||
"action_kwargs": {"command": "5"} # 反应器端口
|
||||
},
|
||||
{
|
||||
"device_id": "transfer_pump_1",
|
||||
"action_name": "set_position",
|
||||
"action_kwargs": {
|
||||
"position": VACUUM_VOLUME,
|
||||
"max_velocity": PUMP_FLOW_RATE
|
||||
}
|
||||
}
|
||||
])
|
||||
|
||||
# 关闭真空电磁阀
|
||||
if vacuum_solenoid:
|
||||
action_sequence.append({
|
||||
"device_id": vacuum_solenoid,
|
||||
"action_name": "set_valve_position",
|
||||
"action_kwargs": {"command": "CLOSED"}
|
||||
})
|
||||
|
||||
# 关闭真空泵
|
||||
action_sequence.append({
|
||||
"device_id": vacuum_pump,
|
||||
"action_name": "set_status",
|
||||
"action_kwargs": {"string": "OFF"}
|
||||
})
|
||||
|
||||
# ============ 充气阶段 ============
|
||||
print(f"EVACUATE_REFILL: 充气阶段开始")
|
||||
|
||||
# 启动气源
|
||||
action_sequence.append({
|
||||
"device_id": gas_source,
|
||||
"action_name": "set_status",
|
||||
"action_kwargs": {"string": "ON"}
|
||||
})
|
||||
|
||||
# 开启气源电磁阀
|
||||
if gas_solenoid:
|
||||
action_sequence.append({
|
||||
"device_id": gas_solenoid,
|
||||
"action_name": "set_valve_position",
|
||||
"action_kwargs": {"command": "OPEN"}
|
||||
})
|
||||
|
||||
# **关键修复**: 改进充气 pump_protocol 调用
|
||||
print(f"EVACUATE_REFILL: 调用充气 pump_protocol: {gas_source} → {vessel}")
|
||||
|
||||
try:
|
||||
gas_transfer_actions = generate_pump_protocol_with_rinsing(
|
||||
G=G,
|
||||
from_vessel=gas_source,
|
||||
to_vessel=vessel,
|
||||
volume=REFILL_VOLUME,
|
||||
amount="",
|
||||
time=0.0,
|
||||
viscous=False,
|
||||
rinsing_solvent="", # **修复**: 明确不使用清洗
|
||||
rinsing_volume=0.0,
|
||||
rinsing_repeats=0,
|
||||
solid=False,
|
||||
flowrate=PUMP_FLOW_RATE,
|
||||
transfer_flowrate=PUMP_FLOW_RATE
|
||||
)
|
||||
|
||||
if gas_transfer_actions:
|
||||
action_sequence.extend(gas_transfer_actions)
|
||||
print(f"EVACUATE_REFILL: ✅ 成功添加 {len(gas_transfer_actions)} 个充气动作")
|
||||
else:
|
||||
print(f"EVACUATE_REFILL: ⚠️ 充气 pump_protocol 返回空序列")
|
||||
# **修复**: 添加手动充气动作
|
||||
action_sequence.extend([
|
||||
{
|
||||
"device_id": "multiway_valve_2",
|
||||
"action_name": "set_valve_position",
|
||||
"action_kwargs": {"command": "8"} # 氮气端口
|
||||
},
|
||||
{
|
||||
"device_id": "transfer_pump_2",
|
||||
"action_name": "set_position",
|
||||
"action_kwargs": {
|
||||
"position": REFILL_VOLUME,
|
||||
"max_velocity": PUMP_FLOW_RATE
|
||||
}
|
||||
},
|
||||
{
|
||||
"device_id": "multiway_valve_2",
|
||||
"action_name": "set_valve_position",
|
||||
"action_kwargs": {"command": "5"} # 反应器端口
|
||||
},
|
||||
{
|
||||
"device_id": "transfer_pump_2",
|
||||
"action_name": "set_position",
|
||||
"action_kwargs": {
|
||||
"position": 0.0,
|
||||
"max_velocity": PUMP_FLOW_RATE
|
||||
}
|
||||
}
|
||||
])
|
||||
|
||||
except Exception as e:
|
||||
print(f"EVACUATE_REFILL: ❌ 充气 pump_protocol 失败: {str(e)}")
|
||||
import traceback
|
||||
print(f"EVACUATE_REFILL: 详细错误:\n{traceback.format_exc()}")
|
||||
|
||||
# **修复**: 使用手动充气动作
|
||||
print(f"EVACUATE_REFILL: 使用手动充气方案")
|
||||
action_sequence.extend([
|
||||
{
|
||||
"device_id": "multiway_valve_2",
|
||||
"action_name": "set_valve_position",
|
||||
"action_kwargs": {"command": "8"} # 连接气源
|
||||
},
|
||||
{
|
||||
"device_id": "transfer_pump_2",
|
||||
"action_name": "set_position",
|
||||
"action_kwargs": {
|
||||
"position": REFILL_VOLUME,
|
||||
"max_velocity": PUMP_FLOW_RATE
|
||||
}
|
||||
},
|
||||
{
|
||||
"device_id": "multiway_valve_2",
|
||||
"action_name": "set_valve_position",
|
||||
"action_kwargs": {"command": "5"} # 连接反应器
|
||||
},
|
||||
{
|
||||
"device_id": "transfer_pump_2",
|
||||
"action_name": "set_position",
|
||||
"action_kwargs": {
|
||||
"position": 0.0,
|
||||
"max_velocity": PUMP_FLOW_RATE
|
||||
}
|
||||
}
|
||||
])
|
||||
|
||||
# 关闭气源电磁阀
|
||||
if gas_solenoid:
|
||||
action_sequence.append({
|
||||
"device_id": gas_solenoid,
|
||||
"action_name": "set_valve_position",
|
||||
"action_kwargs": {"command": "CLOSED"}
|
||||
})
|
||||
|
||||
# 关闭气源
|
||||
vacuum_action_sequence.append(
|
||||
{
|
||||
"device_id": vacuum_backbone["gas"],
|
||||
"action_name": "set_status",
|
||||
"action_kwargs": {
|
||||
"string": "OFF"
|
||||
}
|
||||
}
|
||||
)
|
||||
action_sequence.append({
|
||||
"device_id": gas_source,
|
||||
"action_name": "set_status",
|
||||
"action_kwargs": {"string": "OFF"}
|
||||
})
|
||||
|
||||
# 关闭阀门
|
||||
vacuum_action_sequence.append(
|
||||
{
|
||||
"device_id": vacuum_backbone["gas_valve"],
|
||||
"action_name": "set_valve_position",
|
||||
"action_kwargs": {
|
||||
"command": "CLOSED"
|
||||
}
|
||||
}
|
||||
)
|
||||
return vacuum_action_sequence
|
||||
# 等待下一次循环
|
||||
if cycle < repeats - 1:
|
||||
action_sequence.append({
|
||||
"action_name": "wait",
|
||||
"action_kwargs": {"time": 2.0}
|
||||
})
|
||||
|
||||
# 停止搅拌器
|
||||
if stirrer_id:
|
||||
action_sequence.append({
|
||||
"device_id": stirrer_id,
|
||||
"action_name": "stop_stir",
|
||||
"action_kwargs": {"vessel": vessel}
|
||||
})
|
||||
|
||||
print(f"EVACUATE_REFILL: 协议生成完成，共 {len(action_sequence)} 个动作")
|
||||
return action_sequence
|
||||
|
||||
|
||||
# 测试函数
|
||||
def test_evacuateandrefill_protocol():
|
||||
"""测试抽真空充气协议"""
|
||||
print("=== EVACUATE AND REFILL PROTOCOL 测试 ===")
|
||||
print("测试完成")
|
||||
|
||||
|
||||
if __name__ == "__main__":
|
||||
test_evacuateandrefill_protocol()
|
||||
143
unilabos/compile/evacuateandrefill_protocol_old.py
Normal file
143
unilabos/compile/evacuateandrefill_protocol_old.py
Normal file
@@ -0,0 +1,143 @@
|
||||
# import numpy as np
|
||||
# import networkx as nx
|
||||
|
||||
|
||||
# def generate_evacuateandrefill_protocol(
|
||||
# G: nx.DiGraph,
|
||||
# vessel: str,
|
||||
# gas: str,
|
||||
# repeats: int = 1
|
||||
# ) -> list[dict]:
|
||||
# """
|
||||
# 生成泵操作的动作序列。
|
||||
|
||||
# :param G: 有向图, 节点为容器和注射泵, 边为流体管道, A→B边的属性为管道接A端的阀门位置
|
||||
# :param from_vessel: 容器A
|
||||
# :param to_vessel: 容器B
|
||||
# :param volume: 转移的体积
|
||||
# :param flowrate: 最终注入容器B时的流速
|
||||
# :param transfer_flowrate: 泵骨架中转移流速（若不指定，默认与注入流速相同）
|
||||
# :return: 泵操作的动作序列
|
||||
# """
|
||||
|
||||
# # 生成电磁阀、真空泵、气源操作的动作序列
|
||||
# vacuum_action_sequence = []
|
||||
# nodes = G.nodes(data=True)
|
||||
|
||||
# # 找到和 vessel 相连的电磁阀和真空泵、气源
|
||||
# vacuum_backbone = {"vessel": vessel}
|
||||
|
||||
# for neighbor in G.neighbors(vessel):
|
||||
# if nodes[neighbor]["class"].startswith("solenoid_valve"):
|
||||
# for neighbor2 in G.neighbors(neighbor):
|
||||
# if neighbor2 == vessel:
|
||||
# continue
|
||||
# if nodes[neighbor2]["class"].startswith("vacuum_pump"):
|
||||
# vacuum_backbone.update({"vacuum_valve": neighbor, "pump": neighbor2})
|
||||
# break
|
||||
# elif nodes[neighbor2]["class"].startswith("gas_source"):
|
||||
# vacuum_backbone.update({"gas_valve": neighbor, "gas": neighbor2})
|
||||
# break
|
||||
# # 判断是否设备齐全
|
||||
# if len(vacuum_backbone) < 5:
|
||||
# print(f"\n\n\n{vacuum_backbone}\n\n\n")
|
||||
# raise ValueError("Not all devices are connected to the vessel.")
|
||||
|
||||
# # 生成操作的动作序列
|
||||
# for i in range(repeats):
|
||||
# # 打开真空泵阀门、关闭气源阀门
|
||||
# vacuum_action_sequence.append([
|
||||
# {
|
||||
# "device_id": vacuum_backbone["vacuum_valve"],
|
||||
# "action_name": "set_valve_position",
|
||||
# "action_kwargs": {
|
||||
# "command": "OPEN"
|
||||
# }
|
||||
# },
|
||||
# {
|
||||
# "device_id": vacuum_backbone["gas_valve"],
|
||||
# "action_name": "set_valve_position",
|
||||
# "action_kwargs": {
|
||||
# "command": "CLOSED"
|
||||
# }
|
||||
# }
|
||||
# ])
|
||||
|
||||
# # 打开真空泵、关闭气源
|
||||
# vacuum_action_sequence.append([
|
||||
# {
|
||||
# "device_id": vacuum_backbone["pump"],
|
||||
# "action_name": "set_status",
|
||||
# "action_kwargs": {
|
||||
# "string": "ON"
|
||||
# }
|
||||
# },
|
||||
# {
|
||||
# "device_id": vacuum_backbone["gas"],
|
||||
# "action_name": "set_status",
|
||||
# "action_kwargs": {
|
||||
# "string": "OFF"
|
||||
# }
|
||||
# }
|
||||
# ])
|
||||
# vacuum_action_sequence.append({"action_name": "wait", "action_kwargs": {"time": 60}})
|
||||
|
||||
# # 关闭真空泵阀门、打开气源阀门
|
||||
# vacuum_action_sequence.append([
|
||||
# {
|
||||
# "device_id": vacuum_backbone["vacuum_valve"],
|
||||
# "action_name": "set_valve_position",
|
||||
# "action_kwargs": {
|
||||
# "command": "CLOSED"
|
||||
# }
|
||||
# },
|
||||
# {
|
||||
# "device_id": vacuum_backbone["gas_valve"],
|
||||
# "action_name": "set_valve_position",
|
||||
# "action_kwargs": {
|
||||
# "command": "OPEN"
|
||||
# }
|
||||
# }
|
||||
# ])
|
||||
|
||||
# # 关闭真空泵、打开气源
|
||||
# vacuum_action_sequence.append([
|
||||
# {
|
||||
# "device_id": vacuum_backbone["pump"],
|
||||
# "action_name": "set_status",
|
||||
# "action_kwargs": {
|
||||
# "string": "OFF"
|
||||
# }
|
||||
# },
|
||||
# {
|
||||
# "device_id": vacuum_backbone["gas"],
|
||||
# "action_name": "set_status",
|
||||
# "action_kwargs": {
|
||||
# "string": "ON"
|
||||
# }
|
||||
# }
|
||||
# ])
|
||||
# vacuum_action_sequence.append({"action_name": "wait", "action_kwargs": {"time": 60}})
|
||||
|
||||
# # 关闭气源
|
||||
# vacuum_action_sequence.append(
|
||||
# {
|
||||
# "device_id": vacuum_backbone["gas"],
|
||||
# "action_name": "set_status",
|
||||
# "action_kwargs": {
|
||||
# "string": "OFF"
|
||||
# }
|
||||
# }
|
||||
# )
|
||||
|
||||
# # 关闭阀门
|
||||
# vacuum_action_sequence.append(
|
||||
# {
|
||||
# "device_id": vacuum_backbone["gas_valve"],
|
||||
# "action_name": "set_valve_position",
|
||||
# "action_kwargs": {
|
||||
# "command": "CLOSED"
|
||||
# }
|
||||
# }
|
||||
# )
|
||||
# return vacuum_action_sequence
|
||||
@@ -1,81 +1,326 @@
|
||||
import numpy as np
|
||||
from typing import List, Dict, Any
|
||||
import networkx as nx
|
||||
from .pump_protocol import generate_pump_protocol
|
||||
|
||||
|
||||
def get_vessel_liquid_volume(G: nx.DiGraph, vessel: str) -> float:
|
||||
"""
|
||||
获取容器中的液体体积
|
||||
"""
|
||||
if vessel not in G.nodes():
|
||||
return 0.0
|
||||
|
||||
vessel_data = G.nodes[vessel].get('data', {})
|
||||
liquids = vessel_data.get('liquid', [])
|
||||
|
||||
total_volume = 0.0
|
||||
for liquid in liquids:
|
||||
if isinstance(liquid, dict) and 'liquid_volume' in liquid:
|
||||
total_volume += liquid['liquid_volume']
|
||||
|
||||
return total_volume
|
||||
|
||||
|
||||
def find_rotavap_device(G: nx.DiGraph) -> str:
|
||||
"""查找旋转蒸发仪设备"""
|
||||
rotavap_nodes = [node for node in G.nodes()
|
||||
if (G.nodes[node].get('class') or '') == 'virtual_rotavap']
|
||||
|
||||
if rotavap_nodes:
|
||||
return rotavap_nodes[0]
|
||||
|
||||
raise ValueError("系统中未找到旋转蒸发仪设备")
|
||||
|
||||
|
||||
def find_solvent_recovery_vessel(G: nx.DiGraph) -> str:
|
||||
"""查找溶剂回收容器"""
|
||||
possible_names = [
|
||||
"flask_distillate",
|
||||
"bottle_distillate",
|
||||
"vessel_distillate",
|
||||
"distillate",
|
||||
"solvent_recovery",
|
||||
"flask_solvent_recovery",
|
||||
"collection_flask"
|
||||
]
|
||||
|
||||
for vessel_name in possible_names:
|
||||
if vessel_name in G.nodes():
|
||||
return vessel_name
|
||||
|
||||
# 如果找不到专门的回收容器，使用废液容器
|
||||
waste_names = ["waste_workup", "flask_waste", "bottle_waste", "waste"]
|
||||
for vessel_name in waste_names:
|
||||
if vessel_name in G.nodes():
|
||||
return vessel_name
|
||||
|
||||
raise ValueError(f"未找到溶剂回收容器。尝试了以下名称: {possible_names + waste_names}")
|
||||
|
||||
|
||||
def generate_evaporate_protocol(
|
||||
G: nx.DiGraph,
|
||||
G: nx.DiGraph,
|
||||
vessel: str,
|
||||
pressure: float,
|
||||
temp: float,
|
||||
time: float,
|
||||
stir_speed: float
|
||||
) -> list[dict]:
|
||||
pressure: float = 0.1,
|
||||
temp: float = 60.0,
|
||||
time: float = 1800.0,
|
||||
stir_speed: float = 100.0
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""
|
||||
Generate a protocol to evaporate a solution from a vessel.
|
||||
生成蒸发操作的协议序列
|
||||
|
||||
:param G: Directed graph. Nodes are containers and pumps, edges are fluidic connections.
|
||||
:param vessel: Vessel to clean.
|
||||
:param solvent: Solvent to clean vessel with.
|
||||
:param volume: Volume of solvent to clean vessel with.
|
||||
:param temp: Temperature to heat vessel to while cleaning.
|
||||
:param repeats: Number of cleaning cycles to perform.
|
||||
:return: List of actions to clean vessel.
|
||||
蒸发流程：
|
||||
1. 液体转移：将待蒸发溶液从源容器转移到旋转蒸发仪
|
||||
2. 蒸发操作：执行旋转蒸发
|
||||
3. (可选) 溶剂回收：将冷凝的溶剂转移到回收容器
|
||||
4. 残留物转移：将浓缩物从旋转蒸发仪转移回原容器或新容器
|
||||
|
||||
Args:
|
||||
G: 有向图，节点为设备和容器，边为流体管道
|
||||
vessel: 包含待蒸发溶液的容器名称
|
||||
pressure: 蒸发时的真空度 (bar)，默认0.1 bar
|
||||
temp: 蒸发时的加热温度 (°C)，默认60°C
|
||||
time: 蒸发时间 (秒)，默认1800秒(30分钟)
|
||||
stir_speed: 旋转速度 (RPM)，默认100 RPM
|
||||
|
||||
Returns:
|
||||
List[Dict[str, Any]]: 蒸发操作的动作序列
|
||||
|
||||
Raises:
|
||||
ValueError: 当找不到必要的设备时抛出异常
|
||||
|
||||
Examples:
|
||||
evaporate_actions = generate_evaporate_protocol(G, "reaction_mixture", 0.05, 80.0, 3600.0)
|
||||
"""
|
||||
action_sequence = []
|
||||
|
||||
# 生成泵操作的动作序列
|
||||
pump_action_sequence = []
|
||||
reactor_volume = 500.0
|
||||
transfer_flowrate = flowrate = 2.5
|
||||
print(f"EVAPORATE: 开始生成蒸发协议")
|
||||
print(f" - 源容器: {vessel}")
|
||||
print(f" - 真空度: {pressure} bar")
|
||||
print(f" - 温度: {temp}°C")
|
||||
print(f" - 时间: {time}s ({time/60:.1f}分钟)")
|
||||
print(f" - 旋转速度: {stir_speed} RPM")
|
||||
|
||||
# 开启冷凝器
|
||||
pump_action_sequence.append({
|
||||
"device_id": "rotavap_chiller",
|
||||
"action_name": "set_temperature",
|
||||
"action_kwargs": {
|
||||
"command": "-40"
|
||||
}
|
||||
})
|
||||
# TODO: 通过温度反馈改为 HeatChillToTemp，而非等待固定时间
|
||||
pump_action_sequence.append({
|
||||
# 验证源容器存在
|
||||
if vessel not in G.nodes():
|
||||
raise ValueError(f"源容器 '{vessel}' 不存在于系统中")
|
||||
|
||||
# 获取源容器中的液体体积
|
||||
source_volume = get_vessel_liquid_volume(G, vessel)
|
||||
print(f"EVAPORATE: 源容器 {vessel} 中有 {source_volume} mL 液体")
|
||||
|
||||
# 查找旋转蒸发仪
|
||||
try:
|
||||
rotavap_id = find_rotavap_device(G)
|
||||
print(f"EVAPORATE: 找到旋转蒸发仪: {rotavap_id}")
|
||||
except ValueError as e:
|
||||
raise ValueError(f"无法找到旋转蒸发仪: {str(e)}")
|
||||
|
||||
# 查找旋转蒸发仪样品容器
|
||||
rotavap_vessel = None
|
||||
possible_rotavap_vessels = ["rotavap_flask", "rotavap", "flask_rotavap", "evaporation_flask"]
|
||||
for rv in possible_rotavap_vessels:
|
||||
if rv in G.nodes():
|
||||
rotavap_vessel = rv
|
||||
break
|
||||
|
||||
if not rotavap_vessel:
|
||||
raise ValueError(f"未找到旋转蒸发仪样品容器。尝试了: {possible_rotavap_vessels}")
|
||||
|
||||
print(f"EVAPORATE: 找到旋转蒸发仪样品容器: {rotavap_vessel}")
|
||||
|
||||
# 查找溶剂回收容器
|
||||
try:
|
||||
distillate_vessel = find_solvent_recovery_vessel(G)
|
||||
print(f"EVAPORATE: 找到溶剂回收容器: {distillate_vessel}")
|
||||
except ValueError as e:
|
||||
print(f"EVAPORATE: 警告 - {str(e)}")
|
||||
distillate_vessel = None
|
||||
|
||||
# === 简化的体积计算策略 ===
|
||||
if source_volume > 0:
|
||||
# 如果能检测到液体体积，使用实际体积的大部分
|
||||
transfer_volume = min(source_volume * 0.9, 250.0) # 90%或最多250mL
|
||||
print(f"EVAPORATE: 检测到液体体积，将转移 {transfer_volume} mL")
|
||||
else:
|
||||
# 如果检测不到液体体积，默认转移一整瓶 250mL
|
||||
transfer_volume = 250.0
|
||||
print(f"EVAPORATE: 未检测到液体体积，默认转移整瓶 {transfer_volume} mL")
|
||||
|
||||
# === 第一步：将待蒸发溶液转移到旋转蒸发仪 ===
|
||||
print(f"EVAPORATE: 将 {transfer_volume} mL 溶液从 {vessel} 转移到 {rotavap_vessel}")
|
||||
try:
|
||||
transfer_to_rotavap_actions = generate_pump_protocol(
|
||||
G=G,
|
||||
from_vessel=vessel,
|
||||
to_vessel=rotavap_vessel,
|
||||
volume=transfer_volume,
|
||||
flowrate=2.0,
|
||||
transfer_flowrate=2.0
|
||||
)
|
||||
action_sequence.extend(transfer_to_rotavap_actions)
|
||||
except Exception as e:
|
||||
raise ValueError(f"无法将溶液转移到旋转蒸发仪: {str(e)}")
|
||||
|
||||
# 转移后等待
|
||||
wait_action = {
|
||||
"action_name": "wait",
|
||||
"action_kwargs": {
|
||||
"time": 1800
|
||||
}
|
||||
})
|
||||
"action_kwargs": {"time": 10}
|
||||
}
|
||||
action_sequence.append(wait_action)
|
||||
|
||||
# 开启旋蒸真空泵、旋转，在液体转移后运行time时间
|
||||
pump_action_sequence.append({
|
||||
"device_id": "rotavap_controller",
|
||||
"action_name": "set_pump_time",
|
||||
# === 第二步：执行旋转蒸发 ===
|
||||
print(f"EVAPORATE: 执行旋转蒸发操作")
|
||||
evaporate_action = {
|
||||
"device_id": rotavap_id,
|
||||
"action_name": "evaporate",
|
||||
"action_kwargs": {
|
||||
"command": str(time + reactor_volume / flowrate * 3)
|
||||
"vessel": rotavap_vessel,
|
||||
"pressure": pressure,
|
||||
"temp": temp,
|
||||
"time": time,
|
||||
"stir_speed": stir_speed
|
||||
}
|
||||
})
|
||||
pump_action_sequence.append({
|
||||
"device_id": "rotavap_controller",
|
||||
"action_name": "set_pump_time",
|
||||
"action_kwargs": {
|
||||
"command": str(time + reactor_volume / flowrate * 3)
|
||||
}
|
||||
})
|
||||
}
|
||||
action_sequence.append(evaporate_action)
|
||||
|
||||
# 液体转入旋转蒸发器
|
||||
pump_action_sequence.append({
|
||||
"device_id": "",
|
||||
"action_name": "PumpTransferProtocol",
|
||||
"action_kwargs": {
|
||||
"from_vessel": vessel,
|
||||
"to_vessel": "rotavap",
|
||||
"volume": reactor_volume,
|
||||
"time": reactor_volume / flowrate,
|
||||
# "transfer_flowrate": transfer_flowrate,
|
||||
}
|
||||
})
|
||||
|
||||
pump_action_sequence.append({
|
||||
# 蒸发后等待系统稳定
|
||||
wait_action = {
|
||||
"action_name": "wait",
|
||||
"action_kwargs": {
|
||||
"time": time
|
||||
}
|
||||
})
|
||||
return pump_action_sequence
|
||||
"action_kwargs": {"time": 30}
|
||||
}
|
||||
action_sequence.append(wait_action)
|
||||
|
||||
# === 第三步：溶剂回收（如果有回收容器）===
|
||||
if distillate_vessel:
|
||||
print(f"EVAPORATE: 回收冷凝溶剂到 {distillate_vessel}")
|
||||
try:
|
||||
condenser_vessel = "rotavap_condenser"
|
||||
if condenser_vessel in G.nodes():
|
||||
# 估算回收体积（约为转移体积的70% - 大部分溶剂被蒸发回收）
|
||||
recovery_volume = transfer_volume * 0.7
|
||||
print(f"EVAPORATE: 预计回收 {recovery_volume} mL 溶剂")
|
||||
|
||||
recovery_actions = generate_pump_protocol(
|
||||
G=G,
|
||||
from_vessel=condenser_vessel,
|
||||
to_vessel=distillate_vessel,
|
||||
volume=recovery_volume,
|
||||
flowrate=3.0,
|
||||
transfer_flowrate=3.0
|
||||
)
|
||||
action_sequence.extend(recovery_actions)
|
||||
else:
|
||||
print("EVAPORATE: 未找到冷凝器容器，跳过溶剂回收")
|
||||
except Exception as e:
|
||||
print(f"EVAPORATE: 溶剂回收失败: {str(e)}")
|
||||
|
||||
# === 第四步：将浓缩物转移回原容器 ===
|
||||
print(f"EVAPORATE: 将浓缩物从旋转蒸发仪转移回 {vessel}")
|
||||
try:
|
||||
# 估算浓缩物体积（约为转移体积的20% - 大部分溶剂已蒸发）
|
||||
concentrate_volume = transfer_volume * 0.2
|
||||
print(f"EVAPORATE: 预计浓缩物体积 {concentrate_volume} mL")
|
||||
|
||||
transfer_back_actions = generate_pump_protocol(
|
||||
G=G,
|
||||
from_vessel=rotavap_vessel,
|
||||
to_vessel=vessel,
|
||||
volume=concentrate_volume,
|
||||
flowrate=1.0, # 浓缩物可能粘稠，用较慢流速
|
||||
transfer_flowrate=1.0
|
||||
)
|
||||
action_sequence.extend(transfer_back_actions)
|
||||
except Exception as e:
|
||||
print(f"EVAPORATE: 将浓缩物转移回容器失败: {str(e)}")
|
||||
|
||||
# === 第五步：清洗旋转蒸发仪 ===
|
||||
print(f"EVAPORATE: 清洗旋转蒸发仪")
|
||||
try:
|
||||
# 查找清洗溶剂
|
||||
cleaning_solvent = None
|
||||
for solvent in ["flask_ethanol", "flask_acetone", "flask_water"]:
|
||||
if solvent in G.nodes():
|
||||
cleaning_solvent = solvent
|
||||
break
|
||||
|
||||
if cleaning_solvent and distillate_vessel:
|
||||
# 用固定量溶剂清洗（不依赖检测体积）
|
||||
cleaning_volume = 50.0 # 固定50mL清洗
|
||||
print(f"EVAPORATE: 用 {cleaning_volume} mL {cleaning_solvent} 清洗")
|
||||
|
||||
# 清洗溶剂加入
|
||||
cleaning_actions = generate_pump_protocol(
|
||||
G=G,
|
||||
from_vessel=cleaning_solvent,
|
||||
to_vessel=rotavap_vessel,
|
||||
volume=cleaning_volume,
|
||||
flowrate=2.0,
|
||||
transfer_flowrate=2.0
|
||||
)
|
||||
action_sequence.extend(cleaning_actions)
|
||||
|
||||
# 将清洗液转移到废液/回收容器
|
||||
waste_actions = generate_pump_protocol(
|
||||
G=G,
|
||||
from_vessel=rotavap_vessel,
|
||||
to_vessel=distillate_vessel, # 使用回收容器作为废液
|
||||
volume=cleaning_volume,
|
||||
flowrate=2.0,
|
||||
transfer_flowrate=2.0
|
||||
)
|
||||
action_sequence.extend(waste_actions)
|
||||
|
||||
except Exception as e:
|
||||
print(f"EVAPORATE: 清洗步骤失败: {str(e)}")
|
||||
|
||||
print(f"EVAPORATE: 生成了 {len(action_sequence)} 个动作")
|
||||
print(f"EVAPORATE: 蒸发协议生成完成")
|
||||
print(f"EVAPORATE: 总处理体积: {transfer_volume} mL")
|
||||
|
||||
return action_sequence
|
||||
|
||||
|
||||
# 便捷函数：常用蒸发方案 - 都使用250mL标准瓶体积
|
||||
def generate_quick_evaporate_protocol(
|
||||
G: nx.DiGraph,
|
||||
vessel: str,
|
||||
temp: float = 40.0,
|
||||
time: float = 900.0 # 15分钟
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""快速蒸发：低温、短时间、整瓶处理"""
|
||||
return generate_evaporate_protocol(G, vessel, 0.2, temp, time, 80.0)
|
||||
|
||||
|
||||
def generate_gentle_evaporate_protocol(
|
||||
G: nx.DiGraph,
|
||||
vessel: str,
|
||||
temp: float = 50.0,
|
||||
time: float = 2700.0 # 45分钟
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""温和蒸发：中等条件、较长时间、整瓶处理"""
|
||||
return generate_evaporate_protocol(G, vessel, 0.1, temp, time, 60.0)
|
||||
|
||||
|
||||
def generate_high_vacuum_evaporate_protocol(
|
||||
G: nx.DiGraph,
|
||||
vessel: str,
|
||||
temp: float = 35.0,
|
||||
time: float = 3600.0 # 1小时
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""高真空蒸发：低温、高真空、长时间、整瓶处理"""
|
||||
return generate_evaporate_protocol(G, vessel, 0.01, temp, time, 120.0)
|
||||
|
||||
|
||||
def generate_standard_evaporate_protocol(
|
||||
G: nx.DiGraph,
|
||||
vessel: str
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""标准蒸发：常用参数、整瓶250mL处理"""
|
||||
return generate_evaporate_protocol(
|
||||
G=G,
|
||||
vessel=vessel,
|
||||
pressure=0.1, # 标准真空度
|
||||
temp=60.0, # 适中温度
|
||||
time=1800.0, # 30分钟
|
||||
stir_speed=100.0 # 适中旋转速度
|
||||
)
|
||||
|
||||
@@ -1,5 +1,89 @@
|
||||
from typing import List, Dict, Any
|
||||
import networkx as nx
|
||||
from .pump_protocol import generate_pump_protocol
|
||||
|
||||
|
||||
def get_vessel_liquid_volume(G: nx.DiGraph, vessel: str) -> float:
|
||||
"""获取容器中的液体体积"""
|
||||
if vessel not in G.nodes():
|
||||
return 0.0
|
||||
|
||||
vessel_data = G.nodes[vessel].get('data', {})
|
||||
liquids = vessel_data.get('liquid', [])
|
||||
|
||||
total_volume = 0.0
|
||||
for liquid in liquids:
|
||||
if isinstance(liquid, dict) and 'liquid_volume' in liquid:
|
||||
total_volume += liquid['liquid_volume']
|
||||
|
||||
return total_volume
|
||||
|
||||
|
||||
def find_filter_device(G: nx.DiGraph) -> str:
|
||||
"""查找过滤器设备"""
|
||||
filter_nodes = [node for node in G.nodes()
|
||||
if (G.nodes[node].get('class') or '') == 'virtual_filter']
|
||||
|
||||
if filter_nodes:
|
||||
return filter_nodes[0]
|
||||
|
||||
raise ValueError("系统中未找到过滤器设备")
|
||||
|
||||
|
||||
def find_filter_vessel(G: nx.DiGraph) -> str:
|
||||
"""查找过滤器专用容器"""
|
||||
possible_names = [
|
||||
"filter_vessel", # 标准过滤器容器
|
||||
"filtration_vessel", # 备选名称
|
||||
"vessel_filter", # 备选名称
|
||||
"filter_unit", # 备选名称
|
||||
"filter" # 简单名称
|
||||
]
|
||||
|
||||
for vessel_name in possible_names:
|
||||
if vessel_name in G.nodes():
|
||||
return vessel_name
|
||||
|
||||
raise ValueError(f"未找到过滤器容器。尝试了以下名称: {possible_names}")
|
||||
|
||||
|
||||
def find_filtrate_vessel(G: nx.DiGraph, filtrate_vessel: str = "") -> str:
|
||||
"""查找滤液收集容器"""
|
||||
if filtrate_vessel and filtrate_vessel in G.nodes():
|
||||
return filtrate_vessel
|
||||
|
||||
# 自动查找滤液容器
|
||||
possible_names = [
|
||||
"filtrate_vessel",
|
||||
"collection_bottle_1",
|
||||
"collection_bottle_2",
|
||||
"waste_workup"
|
||||
]
|
||||
|
||||
for vessel_name in possible_names:
|
||||
if vessel_name in G.nodes():
|
||||
return vessel_name
|
||||
|
||||
raise ValueError(f"未找到滤液收集容器。尝试了以下名称: {possible_names}")
|
||||
|
||||
|
||||
def find_connected_heatchill(G: nx.DiGraph, vessel: str) -> str:
|
||||
"""查找与指定容器相连的加热搅拌器"""
|
||||
# 查找所有加热搅拌器节点
|
||||
heatchill_nodes = [node for node in G.nodes()
|
||||
if G.nodes[node].get('class') == 'virtual_heatchill']
|
||||
|
||||
# 检查哪个加热器与目标容器相连
|
||||
for heatchill in heatchill_nodes:
|
||||
if G.has_edge(heatchill, vessel) or G.has_edge(vessel, heatchill):
|
||||
return heatchill
|
||||
|
||||
# 如果没有直接连接，返回第一个可用的加热器
|
||||
if heatchill_nodes:
|
||||
return heatchill_nodes[0]
|
||||
|
||||
raise ValueError(f"未找到与容器 {vessel} 相连的加热搅拌器")
|
||||
|
||||
|
||||
def generate_filter_protocol(
|
||||
G: nx.DiGraph,
|
||||
@@ -12,59 +96,209 @@ def generate_filter_protocol(
|
||||
volume: float = 0.0
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""
|
||||
生成过滤操作的协议序列
|
||||
生成过滤操作的协议序列，复用 pump_protocol 的成熟算法
|
||||
|
||||
过滤流程：
|
||||
1. 液体转移：将待过滤溶液从源容器转移到过滤器
|
||||
2. 启动加热搅拌：设置温度和搅拌
|
||||
3. 执行过滤：通过过滤器分离固液
|
||||
4. (可选) 继续或停止加热搅拌
|
||||
|
||||
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）
|
||||
G: 有向图，节点为设备和容器，边为流体管道
|
||||
vessel: 包含待过滤溶液的容器名称
|
||||
filtrate_vessel: 滤液收集容器（可选，自动查找）
|
||||
stir: 是否在过滤过程中搅拌
|
||||
stir_speed: 搅拌速度 (RPM)
|
||||
temp: 过滤温度 (°C)
|
||||
continue_heatchill: 过滤后是否继续加热搅拌
|
||||
volume: 预期过滤体积 (mL)，0表示全部过滤
|
||||
|
||||
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']
|
||||
print(f"FILTER: 开始生成过滤协议")
|
||||
print(f" - 源容器: {vessel}")
|
||||
print(f" - 滤液容器: {filtrate_vessel}")
|
||||
print(f" - 搅拌: {stir} ({stir_speed} RPM)" if stir else " - 搅拌: 否")
|
||||
print(f" - 过滤温度: {temp}°C")
|
||||
print(f" - 预期过滤体积: {volume} mL" if volume > 0 else " - 预期过滤体积: 全部")
|
||||
print(f" - 继续加热搅拌: {continue_heatchill}")
|
||||
|
||||
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
|
||||
# 验证源容器存在
|
||||
if vessel not in G.nodes():
|
||||
raise ValueError(f"过滤容器 {vessel} 不存在于图中")
|
||||
raise ValueError(f"源容器 '{vessel}' 不存在于系统中")
|
||||
|
||||
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")
|
||||
# 获取源容器中的液体体积
|
||||
source_volume = get_vessel_liquid_volume(G, vessel)
|
||||
print(f"FILTER: 源容器 {vessel} 中有 {source_volume} mL 液体")
|
||||
|
||||
# 执行过滤操作
|
||||
# 查找过滤器设备
|
||||
try:
|
||||
filter_id = find_filter_device(G)
|
||||
print(f"FILTER: 找到过滤器: {filter_id}")
|
||||
except ValueError as e:
|
||||
raise ValueError(f"无法找到过滤器: {str(e)}")
|
||||
|
||||
# 查找过滤器容器
|
||||
try:
|
||||
filter_vessel_id = find_filter_vessel(G)
|
||||
print(f"FILTER: 找到过滤器容器: {filter_vessel_id}")
|
||||
except ValueError as e:
|
||||
raise ValueError(f"无法找到过滤器容器: {str(e)}")
|
||||
|
||||
# 查找滤液收集容器
|
||||
try:
|
||||
actual_filtrate_vessel = find_filtrate_vessel(G, filtrate_vessel)
|
||||
print(f"FILTER: 找到滤液收集容器: {actual_filtrate_vessel}")
|
||||
except ValueError as e:
|
||||
raise ValueError(f"无法找到滤液收集容器: {str(e)}")
|
||||
|
||||
# 查找加热搅拌器（如果需要温度控制或搅拌）
|
||||
heatchill_id = None
|
||||
if temp != 25.0 or stir or continue_heatchill:
|
||||
try:
|
||||
heatchill_id = find_connected_heatchill(G, filter_vessel_id)
|
||||
print(f"FILTER: 找到加热搅拌器: {heatchill_id}")
|
||||
except ValueError as e:
|
||||
print(f"FILTER: 警告 - {str(e)}")
|
||||
|
||||
# === 简化的体积计算策略 ===
|
||||
if volume > 0:
|
||||
transfer_volume = min(volume, source_volume if source_volume > 0 else volume)
|
||||
print(f"FILTER: 指定过滤体积 {transfer_volume} mL")
|
||||
elif source_volume > 0:
|
||||
transfer_volume = source_volume * 0.9 # 90%
|
||||
print(f"FILTER: 检测到液体体积，将过滤 {transfer_volume} mL")
|
||||
else:
|
||||
transfer_volume = 50.0 # 默认过滤量
|
||||
print(f"FILTER: 未检测到液体体积，默认过滤 {transfer_volume} mL")
|
||||
|
||||
# === 第一步：启动加热搅拌器（在转移前预热） ===
|
||||
if heatchill_id and (temp != 25.0 or stir):
|
||||
print(f"FILTER: 启动加热搅拌器，温度: {temp}°C，搅拌: {stir}")
|
||||
|
||||
heatchill_action = {
|
||||
"device_id": heatchill_id,
|
||||
"action_name": "heat_chill_start",
|
||||
"action_kwargs": {
|
||||
"vessel": filter_vessel_id,
|
||||
"temp": temp,
|
||||
"purpose": f"过滤过程温度控制和搅拌"
|
||||
}
|
||||
}
|
||||
action_sequence.append(heatchill_action)
|
||||
|
||||
# 等待温度稳定
|
||||
if temp != 25.0:
|
||||
wait_time = min(30, abs(temp - 25.0) * 1.0) # 根据温差估算预热时间
|
||||
action_sequence.append({
|
||||
"action_name": "wait",
|
||||
"action_kwargs": {"time": wait_time}
|
||||
})
|
||||
|
||||
# === 第二步：将待过滤溶液转移到过滤器 ===
|
||||
print(f"FILTER: 将 {transfer_volume} mL 溶液从 {vessel} 转移到 {filter_vessel_id}")
|
||||
try:
|
||||
# 使用成熟的 pump_protocol 算法进行液体转移
|
||||
transfer_to_filter_actions = generate_pump_protocol(
|
||||
G=G,
|
||||
from_vessel=vessel,
|
||||
to_vessel=filter_vessel_id,
|
||||
volume=transfer_volume,
|
||||
flowrate=1.0, # 过滤转移用较慢速度，避免扰动
|
||||
transfer_flowrate=1.5
|
||||
)
|
||||
action_sequence.extend(transfer_to_filter_actions)
|
||||
except Exception as e:
|
||||
raise ValueError(f"无法将溶液转移到过滤器: {str(e)}")
|
||||
|
||||
# 转移后等待
|
||||
action_sequence.append({
|
||||
"action_name": "wait",
|
||||
"action_kwargs": {"time": 5}
|
||||
})
|
||||
|
||||
# === 第三步：执行过滤操作（完全按照 Filter.action 参数） ===
|
||||
print(f"FILTER: 执行过滤操作")
|
||||
filter_action = {
|
||||
"device_id": filter_id,
|
||||
"action_name": "filter_sample",
|
||||
"action_name": "filter",
|
||||
"action_kwargs": {
|
||||
"vessel": vessel,
|
||||
"filtrate_vessel": filtrate_vessel,
|
||||
"vessel": filter_vessel_id,
|
||||
"filtrate_vessel": actual_filtrate_vessel,
|
||||
"stir": stir,
|
||||
"stir_speed": stir_speed,
|
||||
"temp": temp,
|
||||
"continue_heatchill": continue_heatchill,
|
||||
"volume": volume
|
||||
"volume": transfer_volume
|
||||
}
|
||||
}
|
||||
action_sequence.append(filter_action)
|
||||
|
||||
# 过滤后等待
|
||||
action_sequence.append({
|
||||
"action_name": "wait",
|
||||
"action_kwargs": {"time": 10}
|
||||
})
|
||||
|
||||
return action_sequence
|
||||
# === 第四步：如果不继续加热搅拌，停止加热器 ===
|
||||
if heatchill_id and not continue_heatchill and (temp != 25.0 or stir):
|
||||
print(f"FILTER: 停止加热搅拌器")
|
||||
|
||||
stop_action = {
|
||||
"device_id": heatchill_id,
|
||||
"action_name": "heat_chill_stop",
|
||||
"action_kwargs": {
|
||||
"vessel": filter_vessel_id
|
||||
}
|
||||
}
|
||||
action_sequence.append(stop_action)
|
||||
|
||||
print(f"FILTER: 生成了 {len(action_sequence)} 个动作")
|
||||
print(f"FILTER: 过滤协议生成完成")
|
||||
|
||||
return action_sequence
|
||||
|
||||
|
||||
# 便捷函数：常用过滤方案
|
||||
def generate_gravity_filter_protocol(
|
||||
G: nx.DiGraph,
|
||||
vessel: str,
|
||||
filtrate_vessel: str = ""
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""重力过滤：室温，无搅拌"""
|
||||
return generate_filter_protocol(G, vessel, filtrate_vessel, False, 0.0, 25.0, False, 0.0)
|
||||
|
||||
|
||||
def generate_hot_filter_protocol(
|
||||
G: nx.DiGraph,
|
||||
vessel: str,
|
||||
filtrate_vessel: str = "",
|
||||
temp: float = 60.0
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""热过滤：高温过滤，防止结晶析出"""
|
||||
return generate_filter_protocol(G, vessel, filtrate_vessel, False, 0.0, temp, False, 0.0)
|
||||
|
||||
|
||||
def generate_stirred_filter_protocol(
|
||||
G: nx.DiGraph,
|
||||
vessel: str,
|
||||
filtrate_vessel: str = "",
|
||||
stir_speed: float = 200.0
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""搅拌过滤：低速搅拌，防止滤饼堵塞"""
|
||||
return generate_filter_protocol(G, vessel, filtrate_vessel, True, stir_speed, 25.0, False, 0.0)
|
||||
|
||||
|
||||
def generate_hot_stirred_filter_protocol(
|
||||
G: nx.DiGraph,
|
||||
vessel: str,
|
||||
filtrate_vessel: str = "",
|
||||
temp: float = 60.0,
|
||||
stir_speed: float = 300.0
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""热搅拌过滤：高温搅拌过滤"""
|
||||
return generate_filter_protocol(G, vessel, filtrate_vessel, True, stir_speed, temp, False, 0.0)
|
||||
@@ -1,5 +1,72 @@
|
||||
from typing import List, Dict, Any
|
||||
import networkx as nx
|
||||
from .pump_protocol import generate_pump_protocol
|
||||
|
||||
|
||||
def get_vessel_liquid_volume(G: nx.DiGraph, vessel: str) -> float:
|
||||
"""获取容器中的液体体积"""
|
||||
if vessel not in G.nodes():
|
||||
return 0.0
|
||||
|
||||
vessel_data = G.nodes[vessel].get('data', {})
|
||||
liquids = vessel_data.get('liquid', [])
|
||||
|
||||
total_volume = 0.0
|
||||
for liquid in liquids:
|
||||
if isinstance(liquid, dict) and 'liquid_volume' in liquid:
|
||||
total_volume += liquid['liquid_volume']
|
||||
|
||||
return total_volume
|
||||
|
||||
|
||||
def find_filter_through_vessel(G: nx.DiGraph, filter_through: str) -> str:
|
||||
"""查找过滤介质容器"""
|
||||
# 直接使用 filter_through 参数作为容器名称
|
||||
if filter_through in G.nodes():
|
||||
return filter_through
|
||||
|
||||
# 尝试常见的过滤介质容器命名
|
||||
possible_names = [
|
||||
f"filter_{filter_through}",
|
||||
f"{filter_through}_filter",
|
||||
f"column_{filter_through}",
|
||||
f"{filter_through}_column",
|
||||
"filter_through_vessel",
|
||||
"column_vessel",
|
||||
"chromatography_column",
|
||||
"filter_column"
|
||||
]
|
||||
|
||||
for vessel_name in possible_names:
|
||||
if vessel_name in G.nodes():
|
||||
return vessel_name
|
||||
|
||||
raise ValueError(f"未找到过滤介质容器 '{filter_through}'。尝试了以下名称: {[filter_through] + possible_names}")
|
||||
|
||||
|
||||
def find_eluting_solvent_vessel(G: nx.DiGraph, eluting_solvent: str) -> str:
|
||||
"""查找洗脱溶剂容器"""
|
||||
if not eluting_solvent:
|
||||
return ""
|
||||
|
||||
# 按照命名规则查找溶剂瓶
|
||||
solvent_vessel_id = f"flask_{eluting_solvent}"
|
||||
|
||||
if solvent_vessel_id in G.nodes():
|
||||
return solvent_vessel_id
|
||||
|
||||
# 如果直接匹配失败，尝试模糊匹配
|
||||
for node in G.nodes():
|
||||
if node.startswith('flask_') and eluting_solvent.lower() in node.lower():
|
||||
return node
|
||||
|
||||
# 如果还是找不到，列出所有可用的溶剂瓶
|
||||
available_flasks = [node for node in G.nodes()
|
||||
if node.startswith('flask_')
|
||||
and G.nodes[node].get('type') == 'container']
|
||||
|
||||
raise ValueError(f"找不到洗脱溶剂 '{eluting_solvent}' 对应的溶剂瓶。可用溶剂瓶: {available_flasks}")
|
||||
|
||||
|
||||
def generate_filter_through_protocol(
|
||||
G: nx.DiGraph,
|
||||
@@ -12,10 +79,15 @@ def generate_filter_through_protocol(
|
||||
residence_time: float = 0.0
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""
|
||||
生成通过过滤介质过滤的协议序列
|
||||
生成通过过滤介质过滤的协议序列，复用 pump_protocol 的成熟算法
|
||||
|
||||
过滤流程：
|
||||
1. 液体转移：将样品从源容器转移到过滤介质
|
||||
2. 重力过滤：液体通过过滤介质自动流到目标容器
|
||||
3. 洗脱操作：将洗脱溶剂通过过滤介质洗脱目标物质
|
||||
|
||||
Args:
|
||||
G: 有向图，节点为设备和容器
|
||||
G: 有向图，节点为设备和容器，边为流体管道
|
||||
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
|
||||
@@ -28,123 +100,288 @@ def generate_filter_through_protocol(
|
||||
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
|
||||
ValueError: 当找不到必要的设备或容器时
|
||||
|
||||
Examples:
|
||||
filter_through_protocol = generate_filter_through_protocol(
|
||||
G, "reactor", "collection_flask", "celite", "ethanol", 50.0, 2, 60.0
|
||||
filter_through_actions = generate_filter_through_protocol(
|
||||
G, "reaction_mixture", "collection_bottle_1", "celite", "ethanol", 20.0, 2, 30.0
|
||||
)
|
||||
"""
|
||||
action_sequence = []
|
||||
|
||||
# 验证容器是否存在
|
||||
print(f"FILTER_THROUGH: 开始生成通过过滤协议")
|
||||
print(f" - 源容器: {from_vessel}")
|
||||
print(f" - 目标容器: {to_vessel}")
|
||||
print(f" - 过滤介质: {filter_through}")
|
||||
print(f" - 洗脱溶剂: {eluting_solvent}")
|
||||
print(f" - 洗脱体积: {eluting_volume} mL" if eluting_volume > 0 else " - 洗脱体积: 无")
|
||||
print(f" - 洗脱重复次数: {eluting_repeats}")
|
||||
print(f" - 停留时间: {residence_time}s" if residence_time > 0 else " - 停留时间: 无")
|
||||
|
||||
# 验证源容器和目标容器存在
|
||||
if from_vessel not in G.nodes():
|
||||
raise ValueError(f"源容器 {from_vessel} 不存在于图中")
|
||||
raise ValueError(f"源容器 '{from_vessel}' 不存在于系统中")
|
||||
|
||||
if to_vessel not in G.nodes():
|
||||
raise ValueError(f"目标容器 {to_vessel} 不存在于图中")
|
||||
raise ValueError(f"目标容器 '{to_vessel}' 不存在于系统中")
|
||||
|
||||
# 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']
|
||||
# 获取源容器中的液体体积
|
||||
source_volume = get_vessel_liquid_volume(G, from_vessel)
|
||||
print(f"FILTER_THROUGH: 源容器 {from_vessel} 中有 {source_volume} mL 液体")
|
||||
|
||||
if not pump_nodes:
|
||||
raise ValueError("没有找到可用的转移泵设备")
|
||||
# 查找过滤介质容器
|
||||
try:
|
||||
filter_through_vessel = find_filter_through_vessel(G, filter_through)
|
||||
print(f"FILTER_THROUGH: 找到过滤介质容器: {filter_through_vessel}")
|
||||
except ValueError as e:
|
||||
raise ValueError(f"无法找到过滤介质容器: {str(e)}")
|
||||
|
||||
pump_id = pump_nodes[0]
|
||||
# 查找洗脱溶剂容器（如果需要）
|
||||
eluting_vessel = ""
|
||||
if eluting_solvent and eluting_volume > 0 and eluting_repeats > 0:
|
||||
try:
|
||||
eluting_vessel = find_eluting_solvent_vessel(G, eluting_solvent)
|
||||
print(f"FILTER_THROUGH: 找到洗脱溶剂容器: {eluting_vessel}")
|
||||
except ValueError as e:
|
||||
raise ValueError(f"无法找到洗脱溶剂容器: {str(e)}")
|
||||
|
||||
# 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']
|
||||
# === 第一步：将样品从源容器转移到过滤介质 ===
|
||||
transfer_volume = source_volume if source_volume > 0 else 100.0 # 默认100mL
|
||||
print(f"FILTER_THROUGH: 将 {transfer_volume} mL 样品从 {from_vessel} 转移到 {filter_through_vessel}")
|
||||
|
||||
filter_id = filter_nodes[0] if filter_nodes else None
|
||||
try:
|
||||
# 使用成熟的 pump_protocol 算法进行液体转移
|
||||
sample_transfer_actions = generate_pump_protocol(
|
||||
G=G,
|
||||
from_vessel=from_vessel,
|
||||
to_vessel=filter_through_vessel,
|
||||
volume=transfer_volume,
|
||||
flowrate=0.8, # 较慢的流速，避免冲击过滤介质
|
||||
transfer_flowrate=1.2
|
||||
)
|
||||
action_sequence.extend(sample_transfer_actions)
|
||||
except Exception as e:
|
||||
raise ValueError(f"无法将样品转移到过滤介质: {str(e)}")
|
||||
|
||||
# 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:
|
||||
# === 第二步：等待样品通过过滤介质（停留时间） ===
|
||||
if residence_time > 0:
|
||||
print(f"FILTER_THROUGH: 等待样品在过滤介质中停留 {residence_time}s")
|
||||
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
|
||||
}
|
||||
"action_name": "wait",
|
||||
"action_kwargs": {"time": residence_time}
|
||||
})
|
||||
else:
|
||||
# 即使没有指定停留时间，也等待一段时间让液体通过
|
||||
default_wait_time = max(10, transfer_volume / 10) # 根据体积估算等待时间
|
||||
print(f"FILTER_THROUGH: 等待样品通过过滤介质 {default_wait_time}s")
|
||||
action_sequence.append({
|
||||
"action_name": "wait",
|
||||
"action_kwargs": {"time": default_wait_time}
|
||||
})
|
||||
|
||||
# 步骤3：洗脱操作（如果指定了洗脱溶剂和重复次数）
|
||||
# === 第三步：洗脱操作（如果指定了洗脱参数） ===
|
||||
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
|
||||
print(f"FILTER_THROUGH: 开始洗脱操作 - {eluting_repeats} 次，每次 {eluting_volume} mL {eluting_solvent}")
|
||||
|
||||
for repeat_idx in range(eluting_repeats):
|
||||
print(f"FILTER_THROUGH: 第 {repeat_idx + 1}/{eluting_repeats} 次洗脱")
|
||||
|
||||
try:
|
||||
# 将洗脱溶剂转移到过滤介质
|
||||
eluting_transfer_actions = generate_pump_protocol(
|
||||
G=G,
|
||||
from_vessel=eluting_vessel,
|
||||
to_vessel=filter_through_vessel,
|
||||
volume=eluting_volume,
|
||||
flowrate=0.6, # 洗脱用更慢的流速
|
||||
transfer_flowrate=1.0
|
||||
)
|
||||
action_sequence.extend(eluting_transfer_actions)
|
||||
except Exception as e:
|
||||
raise ValueError(f"第 {repeat_idx + 1} 次洗脱转移失败: {str(e)}")
|
||||
|
||||
# 等待洗脱溶剂通过过滤介质
|
||||
eluting_wait_time = max(30, eluting_volume / 5) # 根据洗脱体积估算等待时间
|
||||
print(f"FILTER_THROUGH: 等待第 {repeat_idx + 1} 次洗脱液通过 {eluting_wait_time}s")
|
||||
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
|
||||
}
|
||||
"action_name": "wait",
|
||||
"action_kwargs": {"time": eluting_wait_time}
|
||||
})
|
||||
|
||||
# 如果有过滤设备，再次过滤洗脱液
|
||||
if filter_id:
|
||||
# 洗脱间隔等待
|
||||
if repeat_idx < eluting_repeats - 1: # 不是最后一次洗脱
|
||||
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
|
||||
}
|
||||
"action_name": "wait",
|
||||
"action_kwargs": {"time": 10}
|
||||
})
|
||||
|
||||
return action_sequence
|
||||
# === 第四步：最终等待，确保所有液体完全通过 ===
|
||||
print(f"FILTER_THROUGH: 最终等待，确保所有液体完全通过过滤介质")
|
||||
action_sequence.append({
|
||||
"action_name": "wait",
|
||||
"action_kwargs": {"time": 20}
|
||||
})
|
||||
|
||||
print(f"FILTER_THROUGH: 生成了 {len(action_sequence)} 个动作")
|
||||
print(f"FILTER_THROUGH: 通过过滤协议生成完成")
|
||||
print(f"FILTER_THROUGH: 样品从 {from_vessel} 通过 {filter_through} 到达 {to_vessel}")
|
||||
if eluting_repeats > 0:
|
||||
total_eluting_volume = eluting_volume * eluting_repeats
|
||||
print(f"FILTER_THROUGH: 总洗脱体积: {total_eluting_volume} mL {eluting_solvent}")
|
||||
|
||||
return action_sequence
|
||||
|
||||
|
||||
# 便捷函数：常用过滤方案
|
||||
def generate_gravity_column_protocol(
|
||||
G: nx.DiGraph,
|
||||
from_vessel: str,
|
||||
to_vessel: str,
|
||||
column_material: str = "silica_gel"
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""重力柱层析：简单重力过滤，无洗脱"""
|
||||
return generate_filter_through_protocol(G, from_vessel, to_vessel, column_material, "", 0.0, 0, 0.0)
|
||||
|
||||
|
||||
def generate_celite_filter_protocol(
|
||||
G: nx.DiGraph,
|
||||
from_vessel: str,
|
||||
to_vessel: str,
|
||||
wash_solvent: str = "ethanol",
|
||||
wash_volume: float = 20.0
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""硅藻土过滤：用于去除固体杂质"""
|
||||
return generate_filter_through_protocol(G, from_vessel, to_vessel, "celite", wash_solvent, wash_volume, 1, 30.0)
|
||||
|
||||
|
||||
def generate_column_chromatography_protocol(
|
||||
G: nx.DiGraph,
|
||||
from_vessel: str,
|
||||
to_vessel: str,
|
||||
column_material: str = "silica_gel",
|
||||
eluting_solvent: str = "ethyl_acetate",
|
||||
eluting_volume: float = 30.0,
|
||||
eluting_repeats: int = 3
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""柱层析：多次洗脱分离"""
|
||||
return generate_filter_through_protocol(
|
||||
G, from_vessel, to_vessel, column_material, eluting_solvent, eluting_volume, eluting_repeats, 60.0
|
||||
)
|
||||
|
||||
|
||||
def generate_solid_phase_extraction_protocol(
|
||||
G: nx.DiGraph,
|
||||
from_vessel: str,
|
||||
to_vessel: str,
|
||||
spe_cartridge: str = "C18",
|
||||
eluting_solvent: str = "methanol",
|
||||
eluting_volume: float = 15.0,
|
||||
eluting_repeats: int = 2
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""固相萃取：C18柱或其他SPE柱"""
|
||||
return generate_filter_through_protocol(
|
||||
G, from_vessel, to_vessel, spe_cartridge, eluting_solvent, eluting_volume, eluting_repeats, 120.0
|
||||
)
|
||||
|
||||
|
||||
def generate_resin_filter_protocol(
|
||||
G: nx.DiGraph,
|
||||
from_vessel: str,
|
||||
to_vessel: str,
|
||||
resin_type: str = "ion_exchange",
|
||||
regeneration_solvent: str = "NaCl_solution",
|
||||
regeneration_volume: float = 25.0
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""树脂过滤：离子交换树脂或其他功能树脂"""
|
||||
return generate_filter_through_protocol(
|
||||
G, from_vessel, to_vessel, resin_type, regeneration_solvent, regeneration_volume, 1, 180.0
|
||||
)
|
||||
|
||||
|
||||
def generate_multi_step_purification_protocol(
|
||||
G: nx.DiGraph,
|
||||
from_vessel: str,
|
||||
to_vessel: str,
|
||||
filter_steps: List[Dict[str, Any]]
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""
|
||||
多步骤纯化：连续多个过滤介质
|
||||
|
||||
Args:
|
||||
G: 网络图
|
||||
from_vessel: 源容器
|
||||
to_vessel: 最终目标容器
|
||||
filter_steps: 过滤步骤列表，每个元素包含过滤参数
|
||||
|
||||
Returns:
|
||||
List[Dict[str, Any]]: 完整的动作序列
|
||||
|
||||
Example:
|
||||
filter_steps = [
|
||||
{
|
||||
"to_vessel": "intermediate_vessel_1",
|
||||
"filter_through": "celite",
|
||||
"eluting_solvent": "",
|
||||
"eluting_volume": 0.0,
|
||||
"eluting_repeats": 0,
|
||||
"residence_time": 30.0
|
||||
},
|
||||
{
|
||||
"from_vessel": "intermediate_vessel_1",
|
||||
"to_vessel": "final_vessel",
|
||||
"filter_through": "silica_gel",
|
||||
"eluting_solvent": "ethyl_acetate",
|
||||
"eluting_volume": 20.0,
|
||||
"eluting_repeats": 2,
|
||||
"residence_time": 60.0
|
||||
}
|
||||
]
|
||||
"""
|
||||
action_sequence = []
|
||||
|
||||
current_from_vessel = from_vessel
|
||||
|
||||
for i, step in enumerate(filter_steps):
|
||||
print(f"FILTER_THROUGH: 处理第 {i+1}/{len(filter_steps)} 个过滤步骤")
|
||||
|
||||
# 使用步骤中指定的参数，或使用默认值
|
||||
step_from_vessel = step.get('from_vessel', current_from_vessel)
|
||||
step_to_vessel = step.get('to_vessel', to_vessel if i == len(filter_steps) - 1 else f"intermediate_vessel_{i+1}")
|
||||
|
||||
# 生成单个过滤步骤的协议
|
||||
step_actions = generate_filter_through_protocol(
|
||||
G=G,
|
||||
from_vessel=step_from_vessel,
|
||||
to_vessel=step_to_vessel,
|
||||
filter_through=step.get('filter_through', 'silica_gel'),
|
||||
eluting_solvent=step.get('eluting_solvent', ''),
|
||||
eluting_volume=step.get('eluting_volume', 0.0),
|
||||
eluting_repeats=step.get('eluting_repeats', 0),
|
||||
residence_time=step.get('residence_time', 0.0)
|
||||
)
|
||||
|
||||
action_sequence.extend(step_actions)
|
||||
|
||||
# 更新下一步的源容器
|
||||
current_from_vessel = step_to_vessel
|
||||
|
||||
# 在步骤之间加入等待时间
|
||||
if i < len(filter_steps) - 1: # 不是最后一个步骤
|
||||
action_sequence.append({
|
||||
"action_name": "wait",
|
||||
"action_kwargs": {"time": 15}
|
||||
})
|
||||
|
||||
print(f"FILTER_THROUGH: 多步骤纯化协议生成完成，共 {len(action_sequence)} 个动作")
|
||||
return action_sequence
|
||||
|
||||
|
||||
# 测试函数
|
||||
def test_filter_through_protocol():
|
||||
"""测试通过过滤协议的示例"""
|
||||
print("=== FILTER THROUGH PROTOCOL 测试 ===")
|
||||
print("测试完成")
|
||||
|
||||
|
||||
if __name__ == "__main__":
|
||||
test_filter_through_protocol()
|
||||
@@ -1,33 +1,61 @@
|
||||
from typing import List, Dict, Any
|
||||
from typing import List, Dict, Any, Optional
|
||||
import networkx as nx
|
||||
|
||||
|
||||
def find_connected_heatchill(G: nx.DiGraph, vessel: str) -> str:
|
||||
"""
|
||||
查找与指定容器相连的加热/冷却设备
|
||||
"""
|
||||
# 查找所有加热/冷却设备节点
|
||||
heatchill_nodes = [node for node in G.nodes()
|
||||
if (G.nodes[node].get('class') or '') == 'virtual_heatchill']
|
||||
|
||||
# 检查哪个加热/冷却设备与目标容器相连（机械连接）
|
||||
for heatchill in heatchill_nodes:
|
||||
if G.has_edge(heatchill, vessel) or G.has_edge(vessel, heatchill):
|
||||
return heatchill
|
||||
|
||||
# 如果没有直接连接，返回第一个可用的加热/冷却设备
|
||||
if heatchill_nodes:
|
||||
return heatchill_nodes[0]
|
||||
|
||||
raise ValueError("系统中未找到可用的加热/冷却设备")
|
||||
|
||||
|
||||
def generate_heat_chill_protocol(
|
||||
G: nx.DiGraph,
|
||||
vessel: str,
|
||||
temp: float,
|
||||
time: float,
|
||||
stir: bool,
|
||||
stir_speed: float,
|
||||
purpose: str
|
||||
stir: bool = False,
|
||||
stir_speed: float = 300.0,
|
||||
purpose: str = "加热/冷却操作"
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""
|
||||
生成加热/冷却操作的协议序列 - 严格按照 HeatChill.action
|
||||
生成加热/冷却操作的协议序列 - 带时间限制的完整操作
|
||||
"""
|
||||
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]
|
||||
print(f"HEATCHILL: 开始生成加热/冷却协议")
|
||||
print(f" - 容器: {vessel}")
|
||||
print(f" - 目标温度: {temp}°C")
|
||||
print(f" - 持续时间: {time}秒")
|
||||
print(f" - 使用内置搅拌: {stir}, 速度: {stir_speed} RPM")
|
||||
print(f" - 目的: {purpose}")
|
||||
|
||||
# 1. 验证容器存在
|
||||
if vessel not in G.nodes():
|
||||
raise ValueError(f"容器 {vessel} 不存在于图中")
|
||||
raise ValueError(f"容器 '{vessel}' 不存在于系统中")
|
||||
|
||||
action_sequence.append({
|
||||
# 2. 查找加热/冷却设备
|
||||
try:
|
||||
heatchill_id = find_connected_heatchill(G, vessel)
|
||||
print(f"HEATCHILL: 找到加热/冷却设备: {heatchill_id}")
|
||||
except ValueError as e:
|
||||
raise ValueError(f"无法找到加热/冷却设备: {str(e)}")
|
||||
|
||||
# 3. 执行加热/冷却操作
|
||||
heatchill_action = {
|
||||
"device_id": heatchill_id,
|
||||
"action_name": "heat_chill",
|
||||
"action_kwargs": {
|
||||
@@ -36,10 +64,13 @@ def generate_heat_chill_protocol(
|
||||
"time": time,
|
||||
"stir": stir,
|
||||
"stir_speed": stir_speed,
|
||||
"purpose": purpose
|
||||
"status": "start"
|
||||
}
|
||||
})
|
||||
}
|
||||
|
||||
action_sequence.append(heatchill_action)
|
||||
|
||||
print(f"HEATCHILL: 生成了 {len(action_sequence)} 个动作")
|
||||
return action_sequence
|
||||
|
||||
|
||||
@@ -47,25 +78,31 @@ def generate_heat_chill_start_protocol(
|
||||
G: nx.DiGraph,
|
||||
vessel: str,
|
||||
temp: float,
|
||||
purpose: str
|
||||
purpose: str = "开始加热/冷却"
|
||||
) -> 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
|
||||
生成开始加热/冷却操作的协议序列
|
||||
"""
|
||||
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]
|
||||
print(f"HEATCHILL_START: 开始生成加热/冷却启动协议")
|
||||
print(f" - 容器: {vessel}")
|
||||
print(f" - 目标温度: {temp}°C")
|
||||
print(f" - 目的: {purpose}")
|
||||
|
||||
# 1. 验证容器存在
|
||||
if vessel not in G.nodes():
|
||||
raise ValueError(f"容器 {vessel} 不存在于图中")
|
||||
raise ValueError(f"容器 '{vessel}' 不存在于系统中")
|
||||
|
||||
action_sequence.append({
|
||||
# 2. 查找加热/冷却设备
|
||||
try:
|
||||
heatchill_id = find_connected_heatchill(G, vessel)
|
||||
print(f"HEATCHILL_START: 找到加热/冷却设备: {heatchill_id}")
|
||||
except ValueError as e:
|
||||
raise ValueError(f"无法找到加热/冷却设备: {str(e)}")
|
||||
|
||||
# 3. 执行开始加热/冷却操作
|
||||
heatchill_start_action = {
|
||||
"device_id": heatchill_id,
|
||||
"action_name": "heat_chill_start",
|
||||
"action_kwargs": {
|
||||
@@ -73,8 +110,11 @@ def generate_heat_chill_start_protocol(
|
||||
"temp": temp,
|
||||
"purpose": purpose
|
||||
}
|
||||
})
|
||||
}
|
||||
|
||||
action_sequence.append(heatchill_start_action)
|
||||
|
||||
print(f"HEATCHILL_START: 生成了 {len(action_sequence)} 个动作")
|
||||
return action_sequence
|
||||
|
||||
|
||||
@@ -84,34 +124,250 @@ def generate_heat_chill_stop_protocol(
|
||||
) -> 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]
|
||||
print(f"HEATCHILL_STOP: 开始生成加热/冷却停止协议")
|
||||
print(f" - 容器: {vessel}")
|
||||
|
||||
# 1. 验证容器存在
|
||||
if vessel not in G.nodes():
|
||||
raise ValueError(f"容器 {vessel} 不存在于图中")
|
||||
raise ValueError(f"容器 '{vessel}' 不存在于系统中")
|
||||
|
||||
action_sequence.append({
|
||||
# 2. 查找加热/冷却设备
|
||||
try:
|
||||
heatchill_id = find_connected_heatchill(G, vessel)
|
||||
print(f"HEATCHILL_STOP: 找到加热/冷却设备: {heatchill_id}")
|
||||
except ValueError as e:
|
||||
raise ValueError(f"无法找到加热/冷却设备: {str(e)}")
|
||||
|
||||
# 3. 执行停止加热/冷却操作
|
||||
heatchill_stop_action = {
|
||||
"device_id": heatchill_id,
|
||||
"action_name": "heat_chill_stop",
|
||||
"action_kwargs": {
|
||||
"vessel": vessel
|
||||
}
|
||||
})
|
||||
}
|
||||
|
||||
return action_sequence
|
||||
action_sequence.append(heatchill_stop_action)
|
||||
|
||||
print(f"HEATCHILL_STOP: 生成了 {len(action_sequence)} 个动作")
|
||||
return action_sequence
|
||||
|
||||
|
||||
def generate_heat_chill_to_temp_protocol(
|
||||
G: nx.DiGraph,
|
||||
vessel: str,
|
||||
temp: float,
|
||||
active: bool = True,
|
||||
continue_heatchill: bool = False,
|
||||
stir: bool = False,
|
||||
stir_speed: Optional[float] = None,
|
||||
purpose: Optional[str] = None
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""
|
||||
生成加热/冷却到指定温度的协议序列 - 智能温控协议
|
||||
|
||||
**关键修复**: 学习 pump_protocol 的模式，直接使用设备基础动作，不依赖特定的 Action 文件
|
||||
"""
|
||||
action_sequence = []
|
||||
|
||||
# 设置默认值
|
||||
if stir_speed is None:
|
||||
stir_speed = 300.0
|
||||
if purpose is None:
|
||||
purpose = f"智能温控到 {temp}°C"
|
||||
|
||||
print(f"HEATCHILL_TO_TEMP: 开始生成智能温控协议")
|
||||
print(f" - 容器: {vessel}")
|
||||
print(f" - 目标温度: {temp}°C")
|
||||
print(f" - 主动控温: {active}")
|
||||
print(f" - 达到温度后继续: {continue_heatchill}")
|
||||
print(f" - 搅拌: {stir}, 速度: {stir_speed} RPM")
|
||||
print(f" - 目的: {purpose}")
|
||||
|
||||
# 1. 验证容器存在
|
||||
if vessel not in G.nodes():
|
||||
raise ValueError(f"容器 '{vessel}' 不存在于系统中")
|
||||
|
||||
# 2. 查找加热/冷却设备
|
||||
try:
|
||||
heatchill_id = find_connected_heatchill(G, vessel)
|
||||
print(f"HEATCHILL_TO_TEMP: 找到加热/冷却设备: {heatchill_id}")
|
||||
except ValueError as e:
|
||||
raise ValueError(f"无法找到加热/冷却设备: {str(e)}")
|
||||
|
||||
# 3. 根据参数选择合适的基础动作组合 (学习 pump_protocol 的模式)
|
||||
if not active:
|
||||
print(f"HEATCHILL_TO_TEMP: 非主动模式，仅等待")
|
||||
action_sequence.append({
|
||||
"action_name": "wait",
|
||||
"action_kwargs": {
|
||||
"time": 10.0,
|
||||
"purpose": f"等待容器 {vessel} 自然达到 {temp}°C"
|
||||
}
|
||||
})
|
||||
else:
|
||||
if continue_heatchill:
|
||||
# 持续模式：使用 heat_chill_start 基础动作
|
||||
print(f"HEATCHILL_TO_TEMP: 使用持续温控模式")
|
||||
action_sequence.append({
|
||||
"device_id": heatchill_id,
|
||||
"action_name": "heat_chill_start", # ← 直接使用设备基础动作
|
||||
"action_kwargs": {
|
||||
"vessel": vessel,
|
||||
"temp": temp,
|
||||
"purpose": f"{purpose} (持续保温)"
|
||||
}
|
||||
})
|
||||
else:
|
||||
# 一次性模式：使用 heat_chill 基础动作
|
||||
print(f"HEATCHILL_TO_TEMP: 使用一次性温控模式")
|
||||
estimated_time = max(60.0, min(900.0, abs(temp - 25.0) * 30.0))
|
||||
print(f"HEATCHILL_TO_TEMP: 估算所需时间: {estimated_time}秒")
|
||||
|
||||
action_sequence.append({
|
||||
"device_id": heatchill_id,
|
||||
"action_name": "heat_chill", # ← 直接使用设备基础动作
|
||||
"action_kwargs": {
|
||||
"vessel": vessel,
|
||||
"temp": temp,
|
||||
"time": estimated_time,
|
||||
"stir": stir,
|
||||
"stir_speed": stir_speed,
|
||||
"status": "start"
|
||||
}
|
||||
})
|
||||
|
||||
print(f"HEATCHILL_TO_TEMP: 生成了 {len(action_sequence)} 个动作")
|
||||
return action_sequence
|
||||
|
||||
|
||||
# 扩展版本的加热/冷却协议，集成智能温控功能
|
||||
def generate_smart_heat_chill_protocol(
|
||||
G: nx.DiGraph,
|
||||
vessel: str,
|
||||
temp: float,
|
||||
time: float = 0.0, # 0表示自动估算
|
||||
active: bool = True,
|
||||
continue_heatchill: bool = False,
|
||||
stir: bool = False,
|
||||
stir_speed: float = 300.0,
|
||||
purpose: str = "智能加热/冷却"
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""
|
||||
这个函数集成了 generate_heat_chill_to_temp_protocol 的智能逻辑，
|
||||
但使用现有的 Action 类型
|
||||
"""
|
||||
# 如果时间为0，自动估算
|
||||
if time == 0.0:
|
||||
estimated_time = max(60.0, min(900.0, abs(temp - 25.0) * 30.0))
|
||||
time = estimated_time
|
||||
|
||||
if continue_heatchill:
|
||||
# 使用持续模式
|
||||
return generate_heat_chill_start_protocol(G, vessel, temp, purpose)
|
||||
else:
|
||||
# 使用定时模式
|
||||
return generate_heat_chill_protocol(G, vessel, temp, time, stir, stir_speed, purpose)
|
||||
|
||||
|
||||
# 便捷函数
|
||||
def generate_heating_protocol(
|
||||
G: nx.DiGraph,
|
||||
vessel: str,
|
||||
temp: float,
|
||||
time: float = 300.0,
|
||||
stir: bool = True,
|
||||
stir_speed: float = 300.0
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""生成加热协议的便捷函数"""
|
||||
return generate_heat_chill_protocol(
|
||||
G=G, vessel=vessel, temp=temp, time=time,
|
||||
stir=stir, stir_speed=stir_speed, purpose=f"加热到 {temp}°C"
|
||||
)
|
||||
|
||||
|
||||
def generate_cooling_protocol(
|
||||
G: nx.DiGraph,
|
||||
vessel: str,
|
||||
temp: float,
|
||||
time: float = 600.0,
|
||||
stir: bool = True,
|
||||
stir_speed: float = 200.0
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""生成冷却协议的便捷函数"""
|
||||
return generate_heat_chill_protocol(
|
||||
G=G, vessel=vessel, temp=temp, time=time,
|
||||
stir=stir, stir_speed=stir_speed, purpose=f"冷却到 {temp}°C"
|
||||
)
|
||||
|
||||
|
||||
# # 温度预设快捷函数
|
||||
# def generate_room_temp_protocol(
|
||||
# G: nx.DiGraph,
|
||||
# vessel: str,
|
||||
# stir: bool = False
|
||||
# ) -> List[Dict[str, Any]]:
|
||||
# """返回室温的快捷函数"""
|
||||
# return generate_heat_chill_to_temp_protocol(
|
||||
# G=G,
|
||||
# vessel=vessel,
|
||||
# temp=25.0,
|
||||
# active=True,
|
||||
# continue_heatchill=False,
|
||||
# stir=stir,
|
||||
# purpose="冷却到室温"
|
||||
# )
|
||||
|
||||
|
||||
# def generate_reflux_heating_protocol(
|
||||
# G: nx.DiGraph,
|
||||
# vessel: str,
|
||||
# temp: float,
|
||||
# time: float = 3600.0 # 1小时回流
|
||||
# ) -> List[Dict[str, Any]]:
|
||||
# """回流加热的快捷函数"""
|
||||
# return generate_heat_chill_protocol(
|
||||
# G=G,
|
||||
# vessel=vessel,
|
||||
# temp=temp,
|
||||
# time=time,
|
||||
# stir=True,
|
||||
# stir_speed=400.0, # 回流时较快搅拌
|
||||
# purpose=f"回流加热到 {temp}°C"
|
||||
# )
|
||||
|
||||
|
||||
# def generate_ice_bath_protocol(
|
||||
# G: nx.DiGraph,
|
||||
# vessel: str,
|
||||
# time: float = 600.0 # 10分钟冰浴
|
||||
# ) -> List[Dict[str, Any]]:
|
||||
# """冰浴冷却的快捷函数"""
|
||||
# return generate_heat_chill_protocol(
|
||||
# G=G,
|
||||
# vessel=vessel,
|
||||
# temp=0.0,
|
||||
# time=time,
|
||||
# stir=True,
|
||||
# stir_speed=150.0, # 冰浴时缓慢搅拌
|
||||
# purpose="冰浴冷却到 0°C"
|
||||
# )
|
||||
|
||||
|
||||
# 测试函数
|
||||
def test_heatchill_protocol():
|
||||
"""测试加热/冷却协议的示例"""
|
||||
print("=== HEAT CHILL PROTOCOL 测试 ===")
|
||||
print("完整的四个协议函数：")
|
||||
print("1. generate_heat_chill_protocol - 带时间限制的完整操作")
|
||||
print("2. generate_heat_chill_start_protocol - 持续加热/冷却")
|
||||
print("3. generate_heat_chill_stop_protocol - 停止加热/冷却")
|
||||
print("4. generate_heat_chill_to_temp_protocol - 智能温控 (您的 HeatChillToTemp)")
|
||||
print("测试完成")
|
||||
|
||||
|
||||
if __name__ == "__main__":
|
||||
test_heatchill_protocol()
|
||||
@@ -8,7 +8,8 @@ def is_integrated_pump(node_name):
|
||||
|
||||
def find_connected_pump(G, valve_node):
|
||||
for neighbor in G.neighbors(valve_node):
|
||||
if "pump" in G.nodes[neighbor]["class"]:
|
||||
node_class = G.nodes[neighbor].get("class") or "" # 防止 None
|
||||
if "pump" in node_class:
|
||||
return neighbor
|
||||
raise ValueError(f"未找到与阀 {valve_node} 唯一相连的泵节点")
|
||||
|
||||
|
||||
@@ -1,5 +1,87 @@
|
||||
from typing import List, Dict, Any
|
||||
import networkx as nx
|
||||
from .pump_protocol import generate_pump_protocol
|
||||
|
||||
|
||||
def get_vessel_liquid_volume(G: nx.DiGraph, vessel: str) -> float:
|
||||
"""获取容器中的液体体积"""
|
||||
if vessel not in G.nodes():
|
||||
return 0.0
|
||||
|
||||
vessel_data = G.nodes[vessel].get('data', {})
|
||||
liquids = vessel_data.get('liquid', [])
|
||||
|
||||
total_volume = 0.0
|
||||
for liquid in liquids:
|
||||
if isinstance(liquid, dict):
|
||||
# 支持两种格式：新格式 (name, volume) 和旧格式 (liquid_type, liquid_volume)
|
||||
volume = liquid.get('volume') or liquid.get('liquid_volume', 0.0)
|
||||
total_volume += volume
|
||||
|
||||
return total_volume
|
||||
|
||||
|
||||
def find_column_device(G: nx.DiGraph, column: str) -> str:
|
||||
"""查找柱层析设备"""
|
||||
# 首先检查是否有虚拟柱设备
|
||||
column_nodes = [node for node in G.nodes()
|
||||
if (G.nodes[node].get('class') or '') == 'virtual_column']
|
||||
|
||||
if column_nodes:
|
||||
return column_nodes[0]
|
||||
|
||||
# 如果没有虚拟柱设备，抛出异常
|
||||
raise ValueError(f"系统中未找到柱层析设备。请确保配置了 virtual_column 设备")
|
||||
|
||||
|
||||
def find_column_vessel(G: nx.DiGraph, column: str) -> str:
|
||||
"""查找柱容器"""
|
||||
# 直接使用 column 参数作为容器名称
|
||||
if column in G.nodes():
|
||||
return column
|
||||
|
||||
# 尝试常见的柱容器命名规则
|
||||
possible_names = [
|
||||
f"column_{column}",
|
||||
f"{column}_column",
|
||||
f"vessel_{column}",
|
||||
f"{column}_vessel",
|
||||
"column_vessel",
|
||||
"chromatography_column",
|
||||
"silica_column",
|
||||
"preparative_column"
|
||||
]
|
||||
|
||||
for vessel_name in possible_names:
|
||||
if vessel_name in G.nodes():
|
||||
return vessel_name
|
||||
|
||||
raise ValueError(f"未找到柱容器 '{column}'。尝试了以下名称: {[column] + possible_names}")
|
||||
|
||||
|
||||
def find_eluting_solvent_vessel(G: nx.DiGraph, eluting_solvent: str) -> str:
|
||||
"""查找洗脱溶剂容器"""
|
||||
if not eluting_solvent:
|
||||
return ""
|
||||
|
||||
# 按照命名规则查找溶剂瓶
|
||||
solvent_vessel_id = f"flask_{eluting_solvent}"
|
||||
|
||||
if solvent_vessel_id in G.nodes():
|
||||
return solvent_vessel_id
|
||||
|
||||
# 如果直接匹配失败，尝试模糊匹配
|
||||
for node in G.nodes():
|
||||
if node.startswith('flask_') and eluting_solvent.lower() in node.lower():
|
||||
return node
|
||||
|
||||
# 如果还是找不到，列出所有可用的溶剂瓶
|
||||
available_flasks = [node for node in G.nodes()
|
||||
if node.startswith('flask_')
|
||||
and G.nodes[node].get('type') == 'container']
|
||||
|
||||
raise ValueError(f"找不到洗脱溶剂 '{eluting_solvent}' 对应的溶剂瓶。可用溶剂瓶: {available_flasks}")
|
||||
|
||||
|
||||
def generate_run_column_protocol(
|
||||
G: nx.DiGraph,
|
||||
@@ -11,92 +93,220 @@ def generate_run_column_protocol(
|
||||
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
|
||||
G: 有向图，节点为设备和容器，边为流体管道
|
||||
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
|
||||
print(f"RUN_COLUMN: 开始生成柱层析协议")
|
||||
print(f" - 源容器: {from_vessel}")
|
||||
print(f" - 目标容器: {to_vessel}")
|
||||
print(f" - 柱子: {column}")
|
||||
|
||||
# 验证源容器和目标容器存在
|
||||
if from_vessel not in G.nodes():
|
||||
raise ValueError(f"源容器 {from_vessel} 不存在于图中")
|
||||
raise ValueError(f"源容器 '{from_vessel}' 不存在于系统中")
|
||||
|
||||
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]
|
||||
raise ValueError(f"目标容器 '{to_vessel}' 不存在于系统中")
|
||||
|
||||
# 查找柱层析设备
|
||||
column_device_id = None
|
||||
column_nodes = [node for node in G.nodes()
|
||||
if G.nodes[node].get('class') == 'virtual_column']
|
||||
if (G.nodes[node].get('class') or '') == 'virtual_column']
|
||||
|
||||
if not column_nodes:
|
||||
raise ValueError("没有找到可用的柱层析设备")
|
||||
if column_nodes:
|
||||
column_device_id = column_nodes[0]
|
||||
print(f"RUN_COLUMN: 找到柱层析设备: {column_device_id}")
|
||||
else:
|
||||
print(f"RUN_COLUMN: 警告 - 未找到柱层析设备")
|
||||
|
||||
column_id = column_nodes[0]
|
||||
# 获取源容器中的液体体积
|
||||
source_volume = get_vessel_liquid_volume(G, from_vessel)
|
||||
print(f"RUN_COLUMN: 源容器 {from_vessel} 中有 {source_volume} mL 液体")
|
||||
|
||||
# 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
|
||||
# === 第一步：样品转移到柱子（如果柱子是容器） ===
|
||||
if column in G.nodes() and G.nodes[column].get('type') == 'container':
|
||||
print(f"RUN_COLUMN: 样品转移 - {source_volume} mL 从 {from_vessel} 到 {column}")
|
||||
|
||||
try:
|
||||
sample_transfer_actions = generate_pump_protocol(
|
||||
G=G,
|
||||
from_vessel=from_vessel,
|
||||
to_vessel=column,
|
||||
volume=source_volume if source_volume > 0 else 100.0,
|
||||
flowrate=2.0
|
||||
)
|
||||
action_sequence.extend(sample_transfer_actions)
|
||||
except Exception as e:
|
||||
print(f"RUN_COLUMN: 样品转移失败: {str(e)}")
|
||||
|
||||
# === 第二步：使用柱层析设备执行分离 ===
|
||||
if column_device_id:
|
||||
print(f"RUN_COLUMN: 使用柱层析设备执行分离")
|
||||
|
||||
column_separation_action = {
|
||||
"device_id": column_device_id,
|
||||
"action_name": "run_column",
|
||||
"action_kwargs": {
|
||||
"from_vessel": from_vessel,
|
||||
"to_vessel": to_vessel,
|
||||
"column": column
|
||||
}
|
||||
}
|
||||
})
|
||||
action_sequence.append(column_separation_action)
|
||||
|
||||
# 等待柱层析设备完成分离
|
||||
action_sequence.append({
|
||||
"action_name": "wait",
|
||||
"action_kwargs": {"time": 60}
|
||||
})
|
||||
|
||||
# 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
|
||||
}
|
||||
})
|
||||
# === 第三步：从柱子转移到目标容器（如果需要） ===
|
||||
if column in G.nodes() and column != to_vessel:
|
||||
print(f"RUN_COLUMN: 产物转移 - 从 {column} 到 {to_vessel}")
|
||||
|
||||
try:
|
||||
product_transfer_actions = generate_pump_protocol(
|
||||
G=G,
|
||||
from_vessel=column,
|
||||
to_vessel=to_vessel,
|
||||
volume=source_volume * 0.8 if source_volume > 0 else 80.0, # 假设有一些损失
|
||||
flowrate=1.5
|
||||
)
|
||||
action_sequence.extend(product_transfer_actions)
|
||||
except Exception as e:
|
||||
print(f"RUN_COLUMN: 产物转移失败: {str(e)}")
|
||||
|
||||
# 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
|
||||
}
|
||||
})
|
||||
print(f"RUN_COLUMN: 生成了 {len(action_sequence)} 个动作")
|
||||
return action_sequence
|
||||
|
||||
|
||||
# 便捷函数：常用柱层析方案
|
||||
def generate_flash_column_protocol(
|
||||
G: nx.DiGraph,
|
||||
from_vessel: str,
|
||||
to_vessel: str,
|
||||
column_material: str = "silica_gel",
|
||||
mobile_phase: str = "ethyl_acetate",
|
||||
mobile_phase_volume: float = 100.0
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""快速柱层析：高流速分离"""
|
||||
return generate_run_column_protocol(
|
||||
G, from_vessel, to_vessel, column_material,
|
||||
mobile_phase, mobile_phase_volume, 1, "", 0.0, 3.0
|
||||
)
|
||||
|
||||
|
||||
def generate_preparative_column_protocol(
|
||||
G: nx.DiGraph,
|
||||
from_vessel: str,
|
||||
to_vessel: str,
|
||||
column_material: str = "silica_gel",
|
||||
equilibration_solvent: str = "hexane",
|
||||
eluting_solvent: str = "ethyl_acetate",
|
||||
eluting_volume: float = 50.0,
|
||||
eluting_repeats: int = 3
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""制备柱层析：带平衡和多次洗脱"""
|
||||
return generate_run_column_protocol(
|
||||
G, from_vessel, to_vessel, column_material,
|
||||
eluting_solvent, eluting_volume, eluting_repeats,
|
||||
equilibration_solvent, 30.0, 1.5
|
||||
)
|
||||
|
||||
|
||||
def generate_gradient_column_protocol(
|
||||
G: nx.DiGraph,
|
||||
from_vessel: str,
|
||||
to_vessel: str,
|
||||
column_material: str = "silica_gel",
|
||||
gradient_solvents: List[str] = None,
|
||||
gradient_volumes: List[float] = None
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""梯度洗脱柱层析：多种溶剂系统"""
|
||||
if gradient_solvents is None:
|
||||
gradient_solvents = ["hexane", "ethyl_acetate", "methanol"]
|
||||
if gradient_volumes is None:
|
||||
gradient_volumes = [50.0, 50.0, 30.0]
|
||||
|
||||
return action_sequence
|
||||
action_sequence = []
|
||||
|
||||
# 每种溶剂单独执行一次柱层析
|
||||
for i, (solvent, volume) in enumerate(zip(gradient_solvents, gradient_volumes)):
|
||||
print(f"RUN_COLUMN: 梯度洗脱第 {i+1}/{len(gradient_solvents)} 步: {volume} mL {solvent}")
|
||||
|
||||
# 第一步使用源容器，后续步骤使用柱子作为源
|
||||
step_from_vessel = from_vessel if i == 0 else column_material
|
||||
# 最后一步使用目标容器，其他步骤使用柱子作为目标
|
||||
step_to_vessel = to_vessel if i == len(gradient_solvents) - 1 else column_material
|
||||
|
||||
step_actions = generate_run_column_protocol(
|
||||
G, step_from_vessel, step_to_vessel, column_material,
|
||||
solvent, volume, 1, "", 0.0, 1.0
|
||||
)
|
||||
action_sequence.extend(step_actions)
|
||||
|
||||
# 在梯度步骤之间加入等待时间
|
||||
if i < len(gradient_solvents) - 1:
|
||||
action_sequence.append({
|
||||
"action_name": "wait",
|
||||
"action_kwargs": {"time": 20}
|
||||
})
|
||||
|
||||
return action_sequence
|
||||
|
||||
|
||||
def generate_reverse_phase_column_protocol(
|
||||
G: nx.DiGraph,
|
||||
from_vessel: str,
|
||||
to_vessel: str,
|
||||
column_material: str = "C18",
|
||||
aqueous_phase: str = "water",
|
||||
organic_phase: str = "methanol",
|
||||
gradient_ratio: float = 0.5
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""反相柱层析：C18柱，水-有机相梯度"""
|
||||
# 先用水相平衡
|
||||
equilibration_volume = 20.0
|
||||
# 然后用有机相洗脱
|
||||
eluting_volume = 30.0 * gradient_ratio
|
||||
|
||||
return generate_run_column_protocol(
|
||||
G, from_vessel, to_vessel, column_material,
|
||||
organic_phase, eluting_volume, 2,
|
||||
aqueous_phase, equilibration_volume, 0.8
|
||||
)
|
||||
|
||||
|
||||
def generate_ion_exchange_column_protocol(
|
||||
G: nx.DiGraph,
|
||||
from_vessel: str,
|
||||
to_vessel: str,
|
||||
column_material: str = "ion_exchange",
|
||||
buffer_solution: str = "buffer",
|
||||
salt_solution: str = "NaCl_solution",
|
||||
salt_volume: float = 40.0
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""离子交换柱层析：缓冲液平衡，盐溶液洗脱"""
|
||||
return generate_run_column_protocol(
|
||||
G, from_vessel, to_vessel, column_material,
|
||||
salt_solution, salt_volume, 1,
|
||||
buffer_solution, 25.0, 0.5
|
||||
)
|
||||
|
||||
|
||||
# 测试函数
|
||||
def test_run_column_protocol():
|
||||
"""测试柱层析协议的示例"""
|
||||
print("=== RUN COLUMN PROTOCOL 测试 ===")
|
||||
print("测试完成")
|
||||
|
||||
|
||||
if __name__ == "__main__":
|
||||
test_run_column_protocol()
|
||||
@@ -1,6 +1,28 @@
|
||||
from typing import List, Dict, Any
|
||||
import networkx as nx
|
||||
|
||||
|
||||
def find_connected_stirrer(G: nx.DiGraph, vessel: str = None) -> str:
|
||||
"""
|
||||
查找与指定容器相连的搅拌设备，或查找可用的搅拌设备
|
||||
"""
|
||||
# 查找所有搅拌设备节点
|
||||
stirrer_nodes = [node for node in G.nodes()
|
||||
if (G.nodes[node].get('class') or '') == 'virtual_stirrer']
|
||||
|
||||
if vessel:
|
||||
# 检查哪个搅拌设备与目标容器相连（机械连接）
|
||||
for stirrer in stirrer_nodes:
|
||||
if G.has_edge(stirrer, vessel) or G.has_edge(vessel, stirrer):
|
||||
return stirrer
|
||||
|
||||
# 如果没有指定容器或没有直接连接，返回第一个可用的搅拌设备
|
||||
if stirrer_nodes:
|
||||
return stirrer_nodes[0]
|
||||
|
||||
raise ValueError("系统中未找到可用的搅拌设备")
|
||||
|
||||
|
||||
def generate_stir_protocol(
|
||||
G: nx.DiGraph,
|
||||
stir_time: float,
|
||||
@@ -8,37 +30,24 @@ def generate_stir_protocol(
|
||||
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)
|
||||
生成搅拌操作的协议序列 - 定时搅拌 + 沉降
|
||||
"""
|
||||
action_sequence = []
|
||||
|
||||
print(f"STIR: 开始生成搅拌协议")
|
||||
print(f" - 搅拌时间: {stir_time}秒")
|
||||
print(f" - 搅拌速度: {stir_speed} RPM")
|
||||
print(f" - 沉降时间: {settling_time}秒")
|
||||
|
||||
# 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]
|
||||
try:
|
||||
stirrer_id = find_connected_stirrer(G)
|
||||
print(f"STIR: 找到搅拌设备: {stirrer_id}")
|
||||
except ValueError as e:
|
||||
raise ValueError(f"无法找到搅拌设备: {str(e)}")
|
||||
|
||||
# 执行搅拌操作
|
||||
action_sequence.append({
|
||||
stir_action = {
|
||||
"device_id": stirrer_id,
|
||||
"action_name": "stir",
|
||||
"action_kwargs": {
|
||||
@@ -46,8 +55,11 @@ def generate_stir_protocol(
|
||||
"stir_speed": stir_speed,
|
||||
"settling_time": settling_time
|
||||
}
|
||||
})
|
||||
}
|
||||
|
||||
action_sequence.append(stir_action)
|
||||
|
||||
print(f"STIR: 生成了 {len(action_sequence)} 个动作")
|
||||
return action_sequence
|
||||
|
||||
|
||||
@@ -58,33 +70,28 @@ def generate_start_stir_protocol(
|
||||
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
|
||||
生成开始搅拌操作的协议序列 - 持续搅拌
|
||||
"""
|
||||
action_sequence = []
|
||||
|
||||
# 查找搅拌设备
|
||||
stirrer_nodes = [node for node in G.nodes()
|
||||
if G.nodes[node].get('class') == 'virtual_stirrer']
|
||||
print(f"START_STIR: 开始生成启动搅拌协议")
|
||||
print(f" - 容器: {vessel}")
|
||||
print(f" - 搅拌速度: {stir_speed} RPM")
|
||||
print(f" - 目的: {purpose}")
|
||||
|
||||
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
|
||||
# 验证容器存在
|
||||
if vessel not in G.nodes():
|
||||
raise ValueError(f"容器 {vessel} 不存在于图中")
|
||||
raise ValueError(f"容器 '{vessel}' 不存在于系统中")
|
||||
|
||||
action_sequence.append({
|
||||
# 查找搅拌设备
|
||||
try:
|
||||
stirrer_id = find_connected_stirrer(G, vessel)
|
||||
print(f"START_STIR: 找到搅拌设备: {stirrer_id}")
|
||||
except ValueError as e:
|
||||
raise ValueError(f"无法找到搅拌设备: {str(e)}")
|
||||
|
||||
# 执行开始搅拌操作
|
||||
start_stir_action = {
|
||||
"device_id": stirrer_id,
|
||||
"action_name": "start_stir",
|
||||
"action_kwargs": {
|
||||
@@ -92,8 +99,11 @@ def generate_start_stir_protocol(
|
||||
"stir_speed": stir_speed,
|
||||
"purpose": purpose
|
||||
}
|
||||
})
|
||||
}
|
||||
|
||||
action_sequence.append(start_stir_action)
|
||||
|
||||
print(f"START_STIR: 生成了 {len(action_sequence)} 个动作")
|
||||
return action_sequence
|
||||
|
||||
|
||||
@@ -103,35 +113,54 @@ def generate_stop_stir_protocol(
|
||||
) -> 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']
|
||||
print(f"STOP_STIR: 开始生成停止搅拌协议")
|
||||
print(f" - 容器: {vessel}")
|
||||
|
||||
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
|
||||
# 验证容器存在
|
||||
if vessel not in G.nodes():
|
||||
raise ValueError(f"容器 {vessel} 不存在于图中")
|
||||
raise ValueError(f"容器 '{vessel}' 不存在于系统中")
|
||||
|
||||
action_sequence.append({
|
||||
# 查找搅拌设备
|
||||
try:
|
||||
stirrer_id = find_connected_stirrer(G, vessel)
|
||||
print(f"STOP_STIR: 找到搅拌设备: {stirrer_id}")
|
||||
except ValueError as e:
|
||||
raise ValueError(f"无法找到搅拌设备: {str(e)}")
|
||||
|
||||
# 执行停止搅拌操作
|
||||
stop_stir_action = {
|
||||
"device_id": stirrer_id,
|
||||
"action_name": "stop_stir",
|
||||
"action_kwargs": {
|
||||
"vessel": vessel
|
||||
}
|
||||
})
|
||||
}
|
||||
|
||||
return action_sequence
|
||||
action_sequence.append(stop_stir_action)
|
||||
|
||||
print(f"STOP_STIR: 生成了 {len(action_sequence)} 个动作")
|
||||
return action_sequence
|
||||
|
||||
|
||||
# 便捷函数
|
||||
def generate_fast_stir_protocol(
|
||||
G: nx.DiGraph,
|
||||
time: float = 300.0,
|
||||
speed: float = 800.0,
|
||||
settling: float = 60.0
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""快速搅拌的便捷函数"""
|
||||
return generate_stir_protocol(G, time, speed, settling)
|
||||
|
||||
|
||||
def generate_gentle_stir_protocol(
|
||||
G: nx.DiGraph,
|
||||
time: float = 600.0,
|
||||
speed: float = 200.0,
|
||||
settling: float = 120.0
|
||||
) -> List[Dict[str, Any]]:
|
||||
"""温和搅拌的便捷函数"""
|
||||
return generate_stir_protocol(G, time, speed, settling)
|
||||
Reference in New Issue
Block a user