open_pub/Uni-Lab-OS
1
0
Fork 0
mirror of https://github.com/dptech-corp/Uni-Lab-OS.git synced 2025-12-18 05:21:19 +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

18
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],
@@ -205,4 +209,4 @@ class LiquidHandlerBiomek(LiquidHandlerAbstract):
self.temp_protocol["steps"].append(transfer_params)
return
s
s

83
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
@@ -47,26 +43,26 @@ 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()
try:
if is_96_well:
pass # This mode is not verified
pass # This mode is not verified
else:
if len(vols) != len(sources):
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(
resources=[src],
vols=[vol],
use_channels=use_channels, # only aspirate96 used, default to None
use_channels=use_channels, # only aspirate96 used, default to None
flow_rates=[flow_rates[0]] if flow_rates else None,
offsets=[offsets[0]] if offsets else None,
liquid_height=[liquid_height[0]] if liquid_height else None,
@@ -76,15 +72,15 @@ class LiquidHandlerAbstract(LiquidHandler):
await self.custom_delay(seconds=delays[0] if delays else 0)
await self.dispense(
resources=waste_liquid,
vols=[vol],
use_channels=use_channels,
flow_rates=[flow_rates[1]] if flow_rates else None,
offsets=[offsets[1]] if offsets else None,
liquid_height=[liquid_height[1]] if liquid_height else None,
blow_out_air_volume=blow_out_air_volume[1] if blow_out_air_volume else None,
spread=spread,
)
await self.discard_tips() # For now, each of tips is discarded after use
vols=[vol],
use_channels=use_channels,
flow_rates=[flow_rates[1]] if flow_rates else None,
offsets=[offsets[1]] if offsets else None,
liquid_height=[liquid_height[1]] if liquid_height else None,
blow_out_air_volume=blow_out_air_volume[1] if blow_out_air_volume else None,
spread=spread,
)
await self.discard_tips() # For now, each of tips is discarded after use
except Exception as e:
raise RuntimeError(f"Liquid removal failed: {e}") from e
@@ -112,13 +108,13 @@ 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."""
try:
if is_96_well:
pass # This mode is not verified.
pass # This mode is not verified.
else:
if len(asp_vols) != len(targets):
raise ValueError("Length of `vols` must match `targets`.")
@@ -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*.
@@ -213,14 +210,15 @@ class LiquidHandlerAbstract(LiquidHandler):
# 96‑channel head mode
# ------------------------------------------------------------------
if is_96_well:
pass # This mode is not verified
pass # This mode is not verified
else:
if not (len(asp_vols) == len(sources) and len(dis_vols) == len(targets)):
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
@@ -259,9 +257,9 @@ class LiquidHandlerAbstract(LiquidHandler):
except Exception as exc:
raise RuntimeError(f"Liquid transfer failed: {exc}") from exc
# ---------------------------------------------------------------
# Helper utilities
# ---------------------------------------------------------------
# ---------------------------------------------------------------
# Helper utilities
# ---------------------------------------------------------------
async def custom_delay(self, seconds=0, msg=None):
"""
@@ -285,19 +283,19 @@ class LiquidHandlerAbstract(LiquidHandler):
vols=[0],
use_channels=None,
flow_rates=None,
offsets=[Coordinate(x=-targets.get_size_x()/2,y=0,z=0)],
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.custom_delay(seconds=1) # In the simulation, we do not need to wait
await self.aspirate(
resources=[targets],
vols=[0],
use_channels=None,
flow_rates=None,
offsets=[Coordinate(x=targets.get_size_x()/2,y=0,z=0)],
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(
@@ -308,9 +306,9 @@ 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
if mix_time is None: # No mixing required
return
"""Mix the liquid in the target wells."""
for _ in range(mix_time):
@@ -343,7 +341,7 @@ class LiquidHandlerAbstract(LiquidHandler):
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):
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.
@@ -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)