mirror of
https://github.com/dptech-corp/Uni-Lab-OS.git
synced 2026-02-04 13:25:13 +00:00
Update prcxi.py
This commit is contained in:
Guangxin Zhang
@@ -119,46 +119,114 @@ class LiquidHandlerAbstract(LiquidHandler):
|
||||
else:
|
||||
if len(asp_vols) != len(targets):
|
||||
raise ValueError(f"Length of `asp_vols` {len(asp_vols)} must match `targets` {len(targets)}.")
|
||||
tip = next(self.current_tip)
|
||||
await self.pick_up_tips(tip)
|
||||
|
||||
# 首先应该对任务分组，然后每次1个/8个进行操作处理
|
||||
if len(use_channels) == 1:
|
||||
tip = []
|
||||
for _ in range(len(use_channels)):
|
||||
tip.extend(next(self.current_tip))
|
||||
await self.pick_up_tips(tip)
|
||||
|
||||
for _ in range(len(targets)):
|
||||
await self.aspirate(
|
||||
resources=reagent_sources,
|
||||
vols=[asp_vols[_]],
|
||||
use_channels=use_channels,
|
||||
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,
|
||||
blow_out_air_volume=[blow_out_air_volume[0]] if blow_out_air_volume else None,
|
||||
spread=spread,
|
||||
)
|
||||
if delays is not None:
|
||||
await self.custom_delay(seconds=delays[0])
|
||||
await self.dispense(
|
||||
resources=[targets[_]],
|
||||
vols=[dis_vols[_]],
|
||||
use_channels=use_channels,
|
||||
flow_rates=[flow_rates[1]] if flow_rates else None,
|
||||
offsets=[offsets[1]] if offsets else None,
|
||||
blow_out_air_volume=[blow_out_air_volume[1]] if blow_out_air_volume else None,
|
||||
liquid_height=[liquid_height[1]] if liquid_height else None,
|
||||
spread=spread,
|
||||
)
|
||||
if delays is not None:
|
||||
await self.custom_delay(seconds=delays[1])
|
||||
await self.mix(
|
||||
targets=targets[_],
|
||||
mix_time=mix_time,
|
||||
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,
|
||||
)
|
||||
if delays is not None:
|
||||
await self.custom_delay(seconds=delays[1])
|
||||
await self.touch_tip(targets[_])
|
||||
await self.discard_tips()
|
||||
for _ in range(len(targets)):
|
||||
await self.aspirate(
|
||||
resources=reagent_sources,
|
||||
vols=[asp_vols[_]],
|
||||
use_channels=use_channels,
|
||||
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,
|
||||
blow_out_air_volume=[blow_out_air_volume[0]] if blow_out_air_volume else None,
|
||||
spread=spread,
|
||||
)
|
||||
if delays is not None:
|
||||
await self.custom_delay(seconds=delays[0])
|
||||
await self.dispense(
|
||||
resources=[targets[_]],
|
||||
vols=[dis_vols[_]],
|
||||
use_channels=use_channels,
|
||||
flow_rates=[flow_rates[1]] if flow_rates else None,
|
||||
offsets=[offsets[1]] if offsets else None,
|
||||
blow_out_air_volume=[blow_out_air_volume[1]] if blow_out_air_volume else None,
|
||||
liquid_height=[liquid_height[1]] if liquid_height else None,
|
||||
spread=spread,
|
||||
)
|
||||
if delays is not None:
|
||||
await self.custom_delay(seconds=delays[1])
|
||||
await self.mix(
|
||||
targets=targets[_],
|
||||
mix_time=mix_time,
|
||||
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,
|
||||
)
|
||||
if delays is not None:
|
||||
await self.custom_delay(seconds=delays[1])
|
||||
await self.touch_tip(targets[_])
|
||||
await self.discard_tips()
|
||||
elif len(use_channels) == 8:
|
||||
tip = []
|
||||
for _ in range(len(use_channels)):
|
||||
tip.extend(next(self.current_tip))
|
||||
await self.pick_up_tips(tip)
|
||||
|
||||
# 对于8个的情况，需要判断此时任务是不是能被8通道移液站来成功处理
|
||||
if len(targets) % 8 != 0:
|
||||
raise ValueError(f"Length of `targets` {len(targets)} must be a multiple of 8 for 8-channel mode.")
|
||||
|
||||
# 8个8个来取任务序列
|
||||
|
||||
for i in range(0, len(targets), 8):
|
||||
# 取出8个任务
|
||||
current_targets = targets[i:i + 8]
|
||||
current_reagent_sources = reagent_sources[i:i + 8]
|
||||
current_asp_vols = asp_vols[i:i + 8]
|
||||
current_dis_vols = dis_vols[i:i + 8]
|
||||
current_asp_flow_rates = flow_rates[i:i + 8] if flow_rates else [None] * 8
|
||||
current_dis_flow_rates = flow_rates[i+8 :i + 16] if flow_rates else [None] * 8
|
||||
current_asp_offset = offsets[i:i + 8] if offsets else [None] * 8
|
||||
current_dis_offset = offsets[i+8 :i + 16] if offsets else [None] * 8
|
||||
current_asp_liquid_height = liquid_height[i:i + 8] if liquid_height else [None] * 8
|
||||
current_dis_liquid_height = liquid_height[i+8 :i + 16] if liquid_height else [None] * 8
|
||||
current_asp_blow_out_air_volume = blow_out_air_volume[i:i + 8] if blow_out_air_volume else [None] * 8
|
||||
current_dis_blow_out_air_volume = blow_out_air_volume[i+8 :i + 16] if blow_out_air_volume else [None] * 8
|
||||
|
||||
await self.aspirate(
|
||||
resources=current_reagent_sources,
|
||||
vols=current_asp_vols,
|
||||
use_channels=use_channels,
|
||||
flow_rates=current_asp_flow_rates,
|
||||
offsets=current_asp_offset,
|
||||
liquid_height=current_asp_liquid_height,
|
||||
blow_out_air_volume=current_asp_blow_out_air_volume,
|
||||
spread=spread,
|
||||
)
|
||||
if delays is not None:
|
||||
await self.custom_delay(seconds=delays[0])
|
||||
await self.dispense(
|
||||
resources=current_targets,
|
||||
vols=current_dis_vols,
|
||||
use_channels=use_channels,
|
||||
flow_rates=current_dis_flow_rates,
|
||||
offsets=current_dis_offset,
|
||||
liquid_height=current_dis_liquid_height,
|
||||
blow_out_air_volume=current_dis_blow_out_air_volume,
|
||||
spread=spread,
|
||||
)
|
||||
if delays is not None:
|
||||
await self.custom_delay(seconds=delays[1])
|
||||
|
||||
await self.mix(
|
||||
targets=current_targets,
|
||||
mix_time=mix_time,
|
||||
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,
|
||||
)
|
||||
if delays is not None:
|
||||
await self.custom_delay(seconds=delays[1])
|
||||
#await self.touch_tip(current_targets)
|
||||
|
||||
except Exception as e:
|
||||
traceback.print_exc()
|
||||
@@ -208,56 +276,126 @@ class LiquidHandlerAbstract(LiquidHandler):
|
||||
"""
|
||||
|
||||
try:
|
||||
# ------------------------------------------------------------------
|
||||
# 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
|
||||
):
|
||||
tip = next(tip_iter)
|
||||
if len(asp_vols) != len(targets):
|
||||
raise ValueError(f"Length of `asp_vols` {len(asp_vols)} must match `targets` {len(targets)}.")
|
||||
|
||||
# 首先应该对任务分组，然后每次1个/8个进行操作处理
|
||||
if len(use_channels) == 1:
|
||||
tip = []
|
||||
for _ in range(len(use_channels)):
|
||||
tip.extend(next(self.current_tip))
|
||||
await self.pick_up_tips(tip)
|
||||
# Aspirate from source
|
||||
await self.aspirate(
|
||||
resources=[src],
|
||||
vols=[asp_vol],
|
||||
use_channels=use_channels,
|
||||
flow_rates=[asp_flow_rate],
|
||||
offsets=offsets,
|
||||
liquid_height=liquid_height,
|
||||
blow_out_air_volume=blow_out_air_volume,
|
||||
spread=spread,
|
||||
)
|
||||
self.custom_delay(seconds=delays[0] if delays else 0)
|
||||
# Dispense into target
|
||||
await self.dispense(
|
||||
resources=[tgt],
|
||||
vols=[dis_vol],
|
||||
use_channels=use_channels,
|
||||
flow_rates=[dis_flow_rate],
|
||||
offsets=offsets,
|
||||
liquid_height=liquid_height,
|
||||
blow_out_air_volume=blow_out_air_volume,
|
||||
spread=spread,
|
||||
)
|
||||
await self.mix(
|
||||
targets=[tgt],
|
||||
mix_time=mix_times[0] if mix_times else None,
|
||||
mix_vol=mix_vol[0] if mix_vol else None,
|
||||
mix_rate=mix_rate[0] if mix_rate else None,
|
||||
)
|
||||
if touch_tip:
|
||||
await self.touch_tip(tgt)
|
||||
|
||||
for _ in range(len(targets)):
|
||||
await self.aspirate(
|
||||
resources=sources,
|
||||
vols=[asp_vols[_]],
|
||||
use_channels=use_channels,
|
||||
flow_rates=[asp_flow_rates[0]] if asp_flow_rates else None,
|
||||
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,
|
||||
)
|
||||
if delays is not None:
|
||||
await self.custom_delay(seconds=delays[0])
|
||||
await self.dispense(
|
||||
resources=[targets[_]],
|
||||
vols=[dis_vols[_]],
|
||||
use_channels=use_channels,
|
||||
flow_rates=[dis_flow_rates[1]] if dis_flow_rates else None,
|
||||
offsets=[offsets[1]] if offsets else None,
|
||||
blow_out_air_volume=[blow_out_air_volume[1]] if blow_out_air_volume else None,
|
||||
liquid_height=[liquid_height[1]] if liquid_height else None,
|
||||
spread=spread,
|
||||
)
|
||||
if delays is not None:
|
||||
await self.custom_delay(seconds=delays[1])
|
||||
await self.mix(
|
||||
targets=targets[_],
|
||||
mix_time=mix_times,
|
||||
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,
|
||||
)
|
||||
if delays is not None:
|
||||
await self.custom_delay(seconds=delays[1])
|
||||
await self.touch_tip(targets[_])
|
||||
await self.discard_tips()
|
||||
|
||||
except Exception as exc:
|
||||
raise RuntimeError(f"Liquid transfer failed: {exc}") from exc
|
||||
elif len(use_channels) == 8:
|
||||
tip = []
|
||||
for _ in range(len(use_channels)):
|
||||
tip.extend(next(self.current_tip))
|
||||
await self.pick_up_tips(tip)
|
||||
|
||||
# 对于8个的情况，需要判断此时任务是不是能被8通道移液站来成功处理
|
||||
if len(targets) % 8 != 0:
|
||||
raise ValueError(f"Length of `targets` {len(targets)} must be a multiple of 8 for 8-channel mode.")
|
||||
|
||||
# 8个8个来取任务序列
|
||||
|
||||
for i in range(0, len(targets), 8):
|
||||
# 取出8个任务
|
||||
current_targets = targets[i:i + 8]
|
||||
current_reagent_sources = sources[i:i + 8]
|
||||
current_asp_vols = asp_vols[i:i + 8]
|
||||
current_dis_vols = dis_vols[i:i + 8]
|
||||
current_asp_flow_rates = asp_flow_rates[i:i + 8]
|
||||
current_asp_offset = offsets[i:i + 8] if offsets else [None] * 8
|
||||
current_dis_offset = offsets[i+8 :i + 16] if offsets else [None] * 8
|
||||
current_asp_liquid_height = liquid_height[i:i + 8] if liquid_height else [None] * 8
|
||||
current_dis_liquid_height = liquid_height[i+8 :i + 16] if liquid_height else [None] * 8
|
||||
current_asp_blow_out_air_volume = blow_out_air_volume[i:i + 8] if blow_out_air_volume else [None] * 8
|
||||
current_dis_blow_out_air_volume = blow_out_air_volume[i+8 :i + 16] if blow_out_air_volume else [None] * 8
|
||||
current_dis_flow_rates = dis_flow_rates[i:i + 8] if dis_flow_rates else [None] * 8
|
||||
|
||||
await self.aspirate(
|
||||
resources=current_reagent_sources,
|
||||
vols=current_asp_vols,
|
||||
use_channels=use_channels,
|
||||
flow_rates=current_asp_flow_rates,
|
||||
offsets=current_asp_offset,
|
||||
blow_out_air_volume=current_asp_blow_out_air_volume,
|
||||
liquid_height=current_asp_liquid_height,
|
||||
spread=spread,
|
||||
)
|
||||
|
||||
if delays is not None:
|
||||
await self.custom_delay(seconds=delays[0])
|
||||
await self.dispense(
|
||||
resources=current_targets,
|
||||
vols=current_dis_vols,
|
||||
use_channels=use_channels,
|
||||
flow_rates=current_dis_flow_rates,
|
||||
offsets=current_dis_offset,
|
||||
blow_out_air_volume=current_dis_blow_out_air_volume,
|
||||
liquid_height=current_dis_liquid_height,
|
||||
spread=spread,
|
||||
)
|
||||
if delays is not None:
|
||||
await self.custom_delay(seconds=delays[1])
|
||||
|
||||
await self.mix(
|
||||
targets=current_targets,
|
||||
mix_time=mix_times,
|
||||
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,
|
||||
)
|
||||
if delays is not None:
|
||||
await self.custom_delay(seconds=delays[1])
|
||||
|
||||
#await self.touch_tip(current_targets)
|
||||
except Exception as e:
|
||||
traceback.print_exc()
|
||||
raise RuntimeError(f"Liquid addition failed: {e}") from e
|
||||
|
||||
|
||||
# ---------------------------------------------------------------
|
||||
# Helper utilities
|
||||
@@ -339,6 +477,7 @@ class LiquidHandlerAbstract(LiquidHandler):
|
||||
|
||||
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
|
||||
|
||||
@@ -392,7 +392,7 @@ class PRCXI9300Backend(LiquidHandlerBackend):
|
||||
|
||||
async def pick_up_tips(self, ops: List[Pickup], use_channels: List[int] = None):
|
||||
"""Pick up tips from the specified resource."""
|
||||
|
||||
|
||||
if len(ops) != 8:
|
||||
raise ValueError(f"PRCXI9300Backend pick_up_tips: Expected 8 pickups, got {len(ops)}")
|
||||
|
||||
@@ -430,7 +430,6 @@ class PRCXI9300Backend(LiquidHandlerBackend):
|
||||
)
|
||||
self.steps_todo_list.append(step)
|
||||
|
||||
|
||||
async def drop_tips(self, ops: List[Drop], use_channels: List[int] = None):
|
||||
|
||||
"""Pick up tips from the specified resource."""
|
||||
@@ -569,6 +568,7 @@ class PRCXI9300Backend(LiquidHandlerBackend):
|
||||
hole_numbers="1,2,3,4,5,6,7,8",
|
||||
)
|
||||
self.steps_todo_list.append(step)
|
||||
|
||||
|
||||
|
||||
async def dispense(self, ops: List[SingleChannelDispense], use_channels: List[int] = None):
|
||||
@@ -1027,26 +1027,51 @@ if __name__ == "__main__":
|
||||
handler.set_tiprack([tip_rack]) # Set the tip rack for the handler
|
||||
asyncio.run(handler.setup()) # Initialize the handler and setup the connection
|
||||
asyncio.run(handler.create_protocol(protocol_name="Test Protocol")) # Initialize the backend and setup the connection
|
||||
asyncio.run(handler.pick_up_tips(tip_rack.children[:8],[0,1,2,3,4,5,6,7]))
|
||||
asyncio.run(handler.aspirate(well_containers.children[:8],[50]*8, [0,1,2,3,4,5,6,7]))
|
||||
asyncio.run(handler.dispense(well_containers.children[:8],[50]*8,[0,1,2,3,4,5,6,7]))
|
||||
asyncio.run(handler.drop_tips(tip_rack.children[8:16],[0,1,2,3,4,5,6,7]))
|
||||
asyncio.run(handler.mix(well_containers.children[:8], mix_time=3, mix_vol=50, height_to_bottom=0.5, offsets=Coordinate(0, 0, 0), mix_rate=100))
|
||||
print(json.dumps(handler._unilabos_backend.steps_todo_list, indent=2)) # Print matrix info
|
||||
# asyncio.run(handler.pick_up_tips(tip_rack.children[:8],[0,1,2,3,4,5,6,7]))
|
||||
# asyncio.run(handler.aspirate(well_containers.children[:8],[50]*8, [0,1,2,3,4,5,6,7]))
|
||||
# asyncio.run(handler.dispense(well_containers.children[:8],[50]*8,[0,1,2,3,4,5,6,7]))
|
||||
# asyncio.run(handler.drop_tips(tip_rack.children[8:16],[0,1,2,3,4,5,6,7]))
|
||||
# asyncio.run(handler.mix(well_containers.children[:8], mix_time=3, mix_vol=50, height_to_bottom=0.5, offsets=Coordinate(0, 0, 0), mix_rate=100))
|
||||
#print(json.dumps(handler._unilabos_backend.steps_todo_list, indent=2)) # Print matrix info
|
||||
asyncio.run(handler.add_liquid(
|
||||
asp_vols=[100]*8,
|
||||
dis_vols=[100]*8,
|
||||
reagent_sources=well_containers.children[-8:],
|
||||
targets=well_containers.children[:8],
|
||||
asp_vols=[100]*16,
|
||||
dis_vols=[100]*16,
|
||||
reagent_sources=well_containers.children[-16:],
|
||||
targets=well_containers.children[:16],
|
||||
use_channels=[0, 1, 2, 3, 4, 5, 6, 7],
|
||||
flow_rates=[None] * 8,
|
||||
offsets=[Coordinate(0, 0, 0)] * 8,
|
||||
liquid_height=[None] * 8,
|
||||
blow_out_air_volume=[None] * 8,
|
||||
flow_rates=[None] * 16,
|
||||
offsets=[Coordinate(0, 0, 0)] * 16,
|
||||
liquid_height=[None] * 16,
|
||||
blow_out_air_volume=[None] * 16,
|
||||
delays=None,
|
||||
mix_time=3,
|
||||
mix_vol=50,
|
||||
spread="wide",
|
||||
))
|
||||
|
||||
# asyncio.run(handler.transfer_liquid(
|
||||
# asp_vols=[100]*16,
|
||||
# dis_vols=[100]*16,
|
||||
# tip_racks=[tip_rack],
|
||||
# sources=well_containers.children[-16:],
|
||||
# targets=well_containers.children[:16],
|
||||
# use_channels=[0, 1, 2, 3, 4, 5, 6, 7],
|
||||
# offsets=[Coordinate(0, 0, 0)] * 32,
|
||||
# asp_flow_rates=[None] * 16,
|
||||
# dis_flow_rates=[None] * 16,
|
||||
# liquid_height=[None] * 32,
|
||||
# blow_out_air_volume=[None] * 32,
|
||||
# mix_times=3,
|
||||
# mix_vol=50,
|
||||
# spread="wide",
|
||||
# ))
|
||||
print(json.dumps(handler._unilabos_backend.steps_todo_list, indent=2)) # Print matrix info
|
||||
# input("pick_up_tips add step")
|
||||
asyncio.run(handler.run_protocol()) # Run the protocol
|
||||
#asyncio.run(handler.run_protocol()) # Run the protocol
|
||||
# input("Running protocol...")
|
||||
# input("Press Enter to continue...") # Wait for user input before proceeding
|
||||
# print("PRCXI9300Handler initialized with deck and host settings.")
|
||||
|
||||
|
||||
|
||||
# 但是怎么丢tip？这个需要手动设置一下？
|
||||
Reference in New Issue
Block a user