open_pub/Uni-Lab-OS
1
0
Fork 0
mirror of https://github.com/dptech-corp/Uni-Lab-OS.git synced 2025-12-18 13:31:20 +00:00
Code Issues Packages Projects Releases Wiki Activity

Merge branch '37-biomek-i5i7' of https://github.com/dptech-corp/Uni-Lab-OS into 37-biomek-i5i7

Browse Source
This commit is contained in:
Guangxin Zhang
2025-05-30 17:11:23 +08:00
parent 208540b307 ea2e9c3e3a
commit d2dda6ee03
6 changed files with 143 additions and 60 deletions
Download Patch File Download Diff File Expand all files Collapse all files

16
unilabos/devices/liquid_handling/biomek.py
View File

@@ -1,6 +1,9 @@
import requests
from typing import List, Sequence, Optional, Union, Literal
from geometry_msgs.msg import Point
from unilabos_msgs.msg import Resource
from unilabos.ros.nodes.resource_tracker import DeviceNodeResourceTracker # type: ignore
from .liquid_handler_abstract import LiquidHandlerAbstract
@@ -20,12 +23,14 @@ class LiquidHandlerBiomek(LiquidHandlerAbstract):
self.temp_protocol = {}
self.py32_path = "/opt/py32" # Biomek的Python 3.2路径
def create_protocol(self,
def create_protocol(
self,
protocol_name: str,
protocol_description: str,
protocol_version: str,
protocol_author: str,
protocol_date: str,
none_keys: List[str] = [],
):
"""
创建一个新的协议。
@@ -79,11 +84,10 @@ class LiquidHandlerBiomek(LiquidHandlerAbstract):
def create_resource(
self,
device_id: str,
res_id: str,
class_name: str,
parent: str,
bind_locations: Point,
resource_tracker: DeviceNodeResourceTracker,
resources: list[Resource],
bind_parent_id: str,
bind_location: dict[str, float],
liquid_input_slot: list[int],
liquid_type: list[str],
liquid_volume: list[int],

41
unilabos/devices/liquid_handling/liquid_handler_abstract.py
View File

@@ -6,13 +6,8 @@ import asyncio
import time
from pylabrobot.liquid_handling import LiquidHandler
from pylabrobot.resources import (
Resource,
TipRack,
Container,
Coordinate,
Well
)
from pylabrobot.resources import Resource, TipRack, Container, Coordinate, Well
class LiquidHandlerAbstract(LiquidHandler):
"""Extended LiquidHandler with additional operations."""
@@ -21,14 +16,15 @@ class LiquidHandlerAbstract(LiquidHandler):
# REMOVE LIQUID --------------------------------------------------
# ---------------------------------------------------------------
async def create_protocol(self,
async def create_protocol(
self,
protocol_name: str,
protocol_description: str,
protocol_version: str,
protocol_author: str,
protocol_date: str,
protocol_type: str,
none_keys: List[str] = []
none_keys: List[str] = [],
):
"""Create a new protocol with the given metadata."""
pass
@@ -47,8 +43,8 @@ class LiquidHandlerAbstract(LiquidHandler):
spread: Optional[Literal["wide", "tight", "custom"]] = "wide",
delays: Optional[List[int]] = None,
is_96_well: Optional[bool] = False,
top: Optional[List(float)] = None,
none_keys: List[str] = []
top: Optional[List[float]] = None,
none_keys: List[str] = [],
):
"""A complete *remove* (aspirate → waste) operation."""
trash = self.deck.get_trash_area()
@@ -60,7 +56,7 @@ class LiquidHandlerAbstract(LiquidHandler):
raise ValueError("Length of `vols` must match `sources`.")
for src, vol in zip(sources, vols):
self.move_to(src, dis_to_top=top[0] if top else 0)
await self.move_to(src, dis_to_top=top[0] if top else 0)
tip = next(self.current_tip)
await self.pick_up_tips(tip)
await self.aspirate(
@@ -112,7 +108,7 @@ class LiquidHandlerAbstract(LiquidHandler):
mix_vol: Optional[int] = None,
mix_rate: Optional[int] = None,
mix_liquid_height: Optional[float] = None,
none_keys: List[str] = []
none_keys: List[str] = [],
):
"""A complete *add* (aspirate reagent → dispense into targets) operation."""
@@ -134,7 +130,7 @@ class LiquidHandlerAbstract(LiquidHandler):
offsets=[offsets[0]] if offsets else None,
liquid_height=[liquid_height[0]] if liquid_height else None,
blow_out_air_volume=[blow_out_air_volume[0]] if blow_out_air_volume else None,
spread=spread
spread=spread,
)
if delays is not None:
await self.custom_delay(seconds=delays[0])
@@ -156,7 +152,8 @@ class LiquidHandlerAbstract(LiquidHandler):
mix_vol=mix_vol,
offsets=offsets if offsets else None,
height_to_bottom=mix_liquid_height if mix_liquid_height else None,
mix_rate=mix_rate if mix_rate else None)
mix_rate=mix_rate if mix_rate else None,
)
if delays is not None:
await self.custom_delay(seconds=delays[1])
await self.touch_tip(targets[_])
@@ -191,7 +188,7 @@ class LiquidHandlerAbstract(LiquidHandler):
mix_rate: Optional[int] = None,
mix_liquid_height: Optional[float] = None,
delays: Optional[List[int]] = None,
none_keys: List[str] = []
none_keys: List[str] = [],
):
"""Transfer liquid from each *source* well/plate to the corresponding *target*.
@@ -219,8 +216,9 @@ class LiquidHandlerAbstract(LiquidHandler):
raise ValueError("`sources`, `targets`, and `vols` must have the same length.")
tip_iter = self.iter_tips(tip_racks)
for src, tgt, asp_vol, asp_flow_rate, dis_vol, dis_flow_rate in (
zip(sources, targets, asp_vols, asp_flow_rates, dis_vols, dis_flow_rates)):
for src, tgt, asp_vol, asp_flow_rate, dis_vol, dis_flow_rate in zip(
sources, targets, asp_vols, asp_flow_rates, dis_vols, dis_flow_rates
):
tip = next(tip_iter)
await self.pick_up_tips(tip)
# Aspirate from source
@@ -287,7 +285,7 @@ class LiquidHandlerAbstract(LiquidHandler):
flow_rates=None,
offsets=[Coordinate(x=-targets.get_size_x() / 2, y=0, z=0)],
liquid_height=None,
blow_out_air_volume=None
blow_out_air_volume=None,
)
# await self.custom_delay(seconds=1) # In the simulation, we do not need to wait
await self.aspirate(
@@ -297,7 +295,7 @@ class LiquidHandlerAbstract(LiquidHandler):
flow_rates=None,
offsets=[Coordinate(x=targets.get_size_x() / 2, y=0, z=0)],
liquid_height=None,
blow_out_air_volume=None
blow_out_air_volume=None,
)
async def mix(
@@ -308,7 +306,7 @@ class LiquidHandlerAbstract(LiquidHandler):
height_to_bottom: Optional[float] = None,
offsets: Optional[Coordinate] = None,
mix_rate: Optional[float] = None,
none_keys: List[str] = []
none_keys: List[str] = [],
):
if mix_time is None: # No mixing required
return
@@ -362,4 +360,3 @@ class LiquidHandlerAbstract(LiquidHandler):
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)

57
unilabos/registry/devices/liquid_handler.yaml
View File

@@ -272,3 +272,60 @@ liquid_handler.revvity:
status: status
result:
success: success
liquid_handler.biomek:
description: Biomek液体处理器设备，基于pylabrobot控制
icon: icon_yiyezhan.webp
class:
module: unilabos.devices.liquid_handling.biomek:LiquidHandlerBiomek
type: python
status_types: {}
action_value_mappings:
create_protocol:
type: LiquidHandlerProtocolCreation
goal:
protocol_name: protocol_name
protocol_description: protocol_description
protocol_version: protocol_version
protocol_author: protocol_author
protocol_date: protocol_date
protocol_type: protocol_type
none_keys: none_keys
feedback: {}
result: {}
run_protocol:
type: EmptyIn
goal: {}
feedback: {}
result: {}
transfer_liquid:
type: LiquidHandlerTransfer
goal:
asp_vols: asp_vols
dis_vols: dis_vols
sources: sources
targets: targets
tip_racks: tip_racks
use_channels: use_channels
asp_flow_rates: asp_flow_rates
dis_flow_rates: dis_flow_rates
offsets: offsets
touch_tip: touch_tip
liquid_height: liquid_height
blow_out_air_volume: blow_out_air_volume
spread: spread
is_96_well: is_96_well
mix_stage: mix_stage
mix_times: mix_times
mix_vol: mix_vol
mix_rate: mix_rate
mix_liquid_height: mix_liquid_height
delays: delays
none_keys: none_keys
feedback: {}
result: {}
schema:
type: object
properties: {}
required: []
additionalProperties: false

14
unilabos/ros/nodes/base_device_node.py
View File

@@ -349,6 +349,20 @@ class BaseROS2DeviceNode(Node, Generic[T]):
response = rclient.call(request)
# 应该先add_resource了
res.response = "OK"
# 如果driver自己就有assign的方法，那就使用driver自己的assign方法
if hasattr(self.driver_instance, "create_resource"):
create_resource_func = getattr(self.driver_instance, "create_resource")
create_resource_func(
resource_tracker=self.resource_tracker,
resources=request.resources,
bind_parent_id=bind_parent_id,
bind_location=location,
liquid_input_slot=LIQUID_INPUT_SLOT,
liquid_type=ADD_LIQUID_TYPE,
liquid_volume=LIQUID_VOLUME,
slot_on_deck=slot,
)
return res
# 接下来该根据bind_parent_id进行assign了，目前只有plr可以进行assign，不然没有办法输入到物料系统中
resource = self.resource_tracker.figure_resource({"name": bind_parent_id})
# request.resources = [convert_to_ros_msg(Resource, resources)]

2
unilabos_msgs/CMakeLists.txt
View File

@@ -29,6 +29,8 @@ set(action_files
"action/HeatChillStart.action"
"action/HeatChillStop.action"
"action/LiquidHandlerProtocolCreation.action"
"action/LiquidHandlerAspirate.action"
"action/LiquidHandlerDiscardTips.action"
"action/LiquidHandlerDispense.action"

9
unilabos_msgs/action/LiquidHandlerProtocolCreation.action Normal file
View File

@@ -0,0 +1,9 @@
string protocol_name
string protocol_description
string protocol_version
string protocol_author
string protocol_date
string protocol_type
string[] none_keys
---
---