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24 high level liquidhandler (#28)
* unify liquid_handler definition * remove default values * Dev Sync (#25) * 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 --------- Co-authored-by: Harvey Que <Q-Query@outlook.com> Co-authored-by: zhangshixiang <@zhangshixiang> Co-authored-by: q434343 <73513873+q434343@users.noreply.github.com> * remove default behavior for visualization * change liquidhandler name * resource create from outer easy * add easy resource creation * easy resource creation logic * remove wrongly debug msg from others * remove wrongly debug msg from others * add missing action clients * fix device_id * fix slot_on_deck * fix registry typo * complete require packages msg converter support array string implements create resource logic * 修复port输入 * fix: remove dirty actions --------- Co-authored-by: Junhan Chang <changjh@pku.edu.cn> Co-authored-by: Harvey Que <Q-Query@outlook.com> Co-authored-by: q434343 <73513873+q434343@users.noreply.github.com>
This commit is contained in:
Xuwznln
GitHub
355
unilabos/devices/liquid_handling/liquid_handler_abstract.py
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355
unilabos/devices/liquid_handling/liquid_handler_abstract.py
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@@ -0,0 +1,355 @@
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from __future__ import annotations
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from typing import List, Sequence, Optional, Literal, Union, Iterator
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import asyncio
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import time
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from pylabrobot.liquid_handling import LiquidHandler
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from pylabrobot.resources import (
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Resource,
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TipRack,
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Container,
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Coordinate,
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Well
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)
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class LiquidHandlerAbstract(LiquidHandler):
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"""Extended LiquidHandler with additional operations."""
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# ---------------------------------------------------------------
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# REMOVE LIQUID --------------------------------------------------
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# ---------------------------------------------------------------
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async def remove_liquid(
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self,
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vols: List[float],
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sources: Sequence[Container],
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waste_liquid: Optional[Container] = None,
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*,
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use_channels: Optional[List[int]] = None,
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flow_rates: Optional[List[Optional[float]]] = None,
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offsets: Optional[List[Coordinate]] = None,
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liquid_height: Optional[List[Optional[float]]] = None,
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blow_out_air_volume: Optional[List[Optional[float]]] = None,
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spread: Optional[Literal["wide", "tight", "custom"]] = "wide",
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delays: Optional[List[int]] = None,
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is_96_well: Optional[bool] = False,
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top: Optional[List(float)] = None,
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none_keys: List[str] = []
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):
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"""A complete *remove* (aspirate → waste) operation."""
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trash = self.deck.get_trash_area()
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try:
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if is_96_well:
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pass # This mode is not verified
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else:
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if len(vols) != len(sources):
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raise ValueError("Length of `vols` must match `sources`.")
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for src, vol in zip(sources, vols):
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self.move_to(src, dis_to_top=top[0] if top else 0)
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tip = next(self.current_tip)
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await self.pick_up_tips(tip)
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await self.aspirate(
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resources=[src],
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vols=[vol],
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use_channels=use_channels, # only aspirate96 used, default to None
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flow_rates=[flow_rates[0]] if flow_rates else None,
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offsets=[offsets[0]] if offsets else None,
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liquid_height=[liquid_height[0]] if liquid_height else None,
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blow_out_air_volume=blow_out_air_volume[0] if blow_out_air_volume else None,
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spread=spread,
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)
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await self.custom_delay(seconds=delays[0] if delays else 0)
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await self.dispense(
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resources=waste_liquid,
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vols=[vol],
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use_channels=use_channels,
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flow_rates=[flow_rates[1]] if flow_rates else None,
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offsets=[offsets[1]] if offsets else None,
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liquid_height=[liquid_height[1]] if liquid_height else None,
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blow_out_air_volume=blow_out_air_volume[1] if blow_out_air_volume else None,
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spread=spread,
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)
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await self.discard_tips() # For now, each of tips is discarded after use
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except Exception as e:
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raise RuntimeError(f"Liquid removal failed: {e}") from e
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# ---------------------------------------------------------------
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# ADD LIQUID -----------------------------------------------------
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# ---------------------------------------------------------------
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async def add_liquid(
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self,
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asp_vols: Union[List[float], float],
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dis_vols: Union[List[float], float],
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reagent_sources: Sequence[Container],
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targets: Sequence[Container],
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*,
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use_channels: Optional[List[int]] = None,
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flow_rates: Optional[List[Optional[float]]] = None,
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offsets: Optional[List[Coordinate]] = None,
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liquid_height: Optional[List[Optional[float]]] = None,
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blow_out_air_volume: Optional[List[Optional[float]]] = None,
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spread: Optional[Literal["wide", "tight", "custom"]] = "wide",
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is_96_well: bool = False,
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delays: Optional[List[int]] = None,
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mix_time: Optional[int] = None,
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mix_vol: Optional[int] = None,
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mix_rate: Optional[int] = None,
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mix_liquid_height: Optional[float] = None,
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none_keys: List[str] = []
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):
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"""A complete *add* (aspirate reagent → dispense into targets) operation."""
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try:
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if is_96_well:
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pass # This mode is not verified.
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else:
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if len(asp_vols) != len(targets):
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raise ValueError("Length of `vols` must match `targets`.")
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tip = next(self.current_tip)
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await self.pick_up_tips(tip)
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for _ in range(len(targets)):
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await self.aspirate(
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resources=reagent_sources,
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vols=[asp_vols[_]],
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use_channels=use_channels,
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flow_rates=[flow_rates[0]] if flow_rates else None,
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offsets=[offsets[0]] if offsets else None,
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liquid_height=[liquid_height[0]] if liquid_height else None,
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blow_out_air_volume=[blow_out_air_volume[0]] if blow_out_air_volume else None,
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spread=spread
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)
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if delays is not None:
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await self.custom_delay(seconds=delays[0])
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await self.dispense(
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resources=[targets[_]],
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vols=[dis_vols[_]],
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use_channels=use_channels,
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flow_rates=[flow_rates[1]] if flow_rates else None,
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offsets=[offsets[1]] if offsets else None,
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blow_out_air_volume=[blow_out_air_volume[1]] if blow_out_air_volume else None,
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liquid_height=[liquid_height[1]] if liquid_height else None,
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spread=spread,
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)
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if delays is not None:
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await self.custom_delay(seconds=delays[1])
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await self.mix(
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targets=targets[_],
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mix_time=mix_time,
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mix_vol=mix_vol,
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offsets=offsets if offsets else None,
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height_to_bottom=mix_liquid_height if mix_liquid_height else None,
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mix_rate=mix_rate if mix_rate else None)
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if delays is not None:
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await self.custom_delay(seconds=delays[1])
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await self.touch_tip(targets[_])
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await self.discard_tips()
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except Exception as e:
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raise RuntimeError(f"Liquid addition failed: {e}") from e
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# ---------------------------------------------------------------
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# TRANSFER LIQUID ------------------------------------------------
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# ---------------------------------------------------------------
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async def transfer_liquid(
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self,
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asp_vols: Union[List[float], float],
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dis_vols: Union[List[float], float],
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sources: Sequence[Container],
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targets: Sequence[Container],
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tip_racks: Sequence[TipRack],
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*,
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use_channels: Optional[List[int]] = None,
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asp_flow_rates: Optional[List[Optional[float]]] = None,
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dis_flow_rates: Optional[List[Optional[float]]] = None,
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offsets: Optional[List[Coordinate]] = None,
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touch_tip: bool = False,
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liquid_height: Optional[List[Optional[float]]] = None,
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blow_out_air_volume: Optional[List[Optional[float]]] = None,
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spread: Literal["wide", "tight", "custom"] = "wide",
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is_96_well: bool = False,
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mix_stage: Optional[Literal["none", "before", "after", "both"]] = "none",
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mix_times: Optional[List(int)] = None,
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mix_vol: Optional[int] = None,
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mix_rate: Optional[int] = None,
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mix_liquid_height: Optional[float] = None,
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delays: Optional[List[int]] = None,
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none_keys: List[str] = []
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):
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"""Transfer liquid from each *source* well/plate to the corresponding *target*.
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Parameters
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----------
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asp_vols, dis_vols
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Single volume (µL) or list matching the number of transfers.
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sources, targets
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Same‑length sequences of containers (wells or plates). In 96‑well mode
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each must contain exactly one plate.
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tip_racks
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One or more TipRacks providing fresh tips.
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is_96_well
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Set *True* to use the 96‑channel head.
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"""
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try:
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# ------------------------------------------------------------------
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# 96‑channel head mode
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# ------------------------------------------------------------------
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if is_96_well:
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pass # This mode is not verified
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else:
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if not (len(asp_vols) == len(sources) and len(dis_vols) == len(targets)):
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raise ValueError("`sources`, `targets`, and `vols` must have the same length.")
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tip_iter = self.iter_tips(tip_racks)
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for src, tgt, asp_vol, asp_flow_rate, dis_vol, dis_flow_rate in (
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zip(sources, targets, asp_vols, asp_flow_rates, dis_vols, dis_flow_rates)):
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tip = next(tip_iter)
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await self.pick_up_tips(tip)
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# Aspirate from source
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await self.aspirate(
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resources=[src],
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vols=[asp_vol],
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use_channels=use_channels,
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flow_rates=[asp_flow_rate],
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offsets=offsets,
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liquid_height=liquid_height,
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blow_out_air_volume=blow_out_air_volume,
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spread=spread,
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)
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self.custom_delay(seconds=delays[0] if delays else 0)
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# Dispense into target
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await self.dispense(
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resources=[tgt],
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vols=[dis_vol],
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use_channels=use_channels,
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flow_rates=[dis_flow_rate],
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offsets=offsets,
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liquid_height=liquid_height,
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blow_out_air_volume=blow_out_air_volume,
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spread=spread,
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)
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await self.mix(
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targets=[tgt],
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mix_time=mix_times[0] if mix_times else None,
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mix_vol=mix_vol[0] if mix_vol else None,
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mix_rate=mix_rate[0] if mix_rate else None,
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)
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if touch_tip:
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await self.touch_tip(tgt)
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await self.discard_tips()
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except Exception as exc:
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raise RuntimeError(f"Liquid transfer failed: {exc}") from exc
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# ---------------------------------------------------------------
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# Helper utilities
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# ---------------------------------------------------------------
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async def custom_delay(self, seconds=0, msg=None):
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"""
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seconds: seconds to wait
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msg: information to be printed
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"""
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if seconds != None and seconds > 0:
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if msg:
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print(f"Waiting time: {msg}")
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print(f"Current time: {time.strftime('%H:%M:%S')}")
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print(f"Time to finish: {time.strftime('%H:%M:%S', time.localtime(time.time() + seconds))}")
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await asyncio.sleep(seconds)
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if msg:
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print(f"Done: {msg}")
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print(f"Current time: {time.strftime('%H:%M:%S')}")
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async def touch_tip(self,
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targets: Sequence[Container],
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):
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"""Touch the tip to the side of the well."""
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await self.aspirate(
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resources=[targets],
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vols=[0],
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use_channels=None,
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flow_rates=None,
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offsets=[Coordinate(x=-targets.get_size_x()/2,y=0,z=0)],
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liquid_height=None,
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blow_out_air_volume=None
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)
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#await self.custom_delay(seconds=1) # In the simulation, we do not need to wait
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await self.aspirate(
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resources=[targets],
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vols=[0],
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use_channels=None,
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flow_rates=None,
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offsets=[Coordinate(x=targets.get_size_x()/2,y=0,z=0)],
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liquid_height=None,
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blow_out_air_volume=None
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)
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async def mix(
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self,
|
||||
targets: Sequence[Container],
|
||||
mix_time: int = None,
|
||||
mix_vol: Optional[int] = None,
|
||||
height_to_bottom: Optional[float] = None,
|
||||
offsets: Optional[Coordinate] = None,
|
||||
mix_rate: Optional[float] = None,
|
||||
none_keys: List[str] = []
|
||||
):
|
||||
if mix_time is None: # No mixing required
|
||||
return
|
||||
"""Mix the liquid in the target wells."""
|
||||
for _ in range(mix_time):
|
||||
await self.aspirate(
|
||||
resources=[targets],
|
||||
vols=[mix_vol],
|
||||
flow_rates=[mix_rate] if mix_rate else None,
|
||||
offsets=[offsets] if offsets else None,
|
||||
liquid_height=[height_to_bottom] if height_to_bottom else None,
|
||||
)
|
||||
await self.custom_delay(seconds=1)
|
||||
await self.dispense(
|
||||
resources=[targets],
|
||||
vols=[mix_vol],
|
||||
flow_rates=[mix_rate] if mix_rate else None,
|
||||
offsets=[offsets] if offsets else None,
|
||||
liquid_height=[height_to_bottom] if height_to_bottom else None,
|
||||
)
|
||||
|
||||
def iter_tips(self, tip_racks: Sequence[TipRack]) -> Iterator[Resource]:
|
||||
"""Yield tips from a list of TipRacks one-by-one until depleted."""
|
||||
for rack in tip_racks:
|
||||
for tip in rack:
|
||||
yield tip
|
||||
raise RuntimeError("Out of tips!")
|
||||
|
||||
def set_tiprack(self, tip_racks: Sequence[TipRack]):
|
||||
"""Set the tip racks for the liquid handler."""
|
||||
self.tip_racks = tip_racks
|
||||
tip_iter = self.iter_tips(tip_racks)
|
||||
self.current_tip = tip_iter
|
||||
|
||||
async def move_to(self, well: Well, dis_to_top: float = 0 , channel: int = 0):
|
||||
"""
|
||||
Move a single channel to a specific well with a given z-height.
|
||||
|
||||
Parameters
|
||||
----------
|
||||
well : Well
|
||||
The target well.
|
||||
dis_to_top : float
|
||||
Height in mm to move to relative to the well top.
|
||||
channel : int
|
||||
Pipetting channel to move (default: 0).
|
||||
"""
|
||||
await self.prepare_for_manual_channel_operation(channel=channel)
|
||||
abs_loc = well.get_absolute_location()
|
||||
well_height = well.get_absolute_size_z()
|
||||
await self.move_channel_x(channel, abs_loc.x)
|
||||
await self.move_channel_y(channel, abs_loc.y)
|
||||
await self.move_channel_z(channel, abs_loc.z + well_height + dis_to_top)
|
||||
|
||||
Reference in New Issue
Block a user