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Update prcxi.py

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This commit is contained in:
Guangxin Zhang
2025-07-16 12:52:35 +08:00
parent 0593f98f81
commit 23cf713a80
2 changed files with 265 additions and 101 deletions
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307
unilabos/devices/liquid_handling/liquid_handler_abstract.py
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@@ -119,46 +119,114 @@ class LiquidHandlerAbstract(LiquidHandler):
else: else:
if len(asp_vols) != len(targets): if len(asp_vols) != len(targets):
raise ValueError(f"Length of `asp_vols` {len(asp_vols)} must match `targets` {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)): for _ in range(len(targets)):
await self.aspirate( await self.aspirate(
resources=reagent_sources, resources=reagent_sources,
vols=[asp_vols[_]], vols=[asp_vols[_]],
use_channels=use_channels, use_channels=use_channels,
flow_rates=[flow_rates[0]] if flow_rates else None, flow_rates=[flow_rates[0]] if flow_rates else None,
offsets=[offsets[0]] if offsets else None, offsets=[offsets[0]] if offsets else None,
liquid_height=[liquid_height[0]] if liquid_height 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, 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: if delays is not None:
await self.custom_delay(seconds=delays[0]) await self.custom_delay(seconds=delays[0])
await self.dispense( await self.dispense(
resources=[targets[_]], resources=[targets[_]],
vols=[dis_vols[_]], vols=[dis_vols[_]],
use_channels=use_channels, use_channels=use_channels,
flow_rates=[flow_rates[1]] if flow_rates else None, flow_rates=[flow_rates[1]] if flow_rates else None,
offsets=[offsets[1]] if offsets 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, 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, liquid_height=[liquid_height[1]] if liquid_height else None,
spread=spread, spread=spread,
) )
if delays is not None: if delays is not None:
await self.custom_delay(seconds=delays[1]) await self.custom_delay(seconds=delays[1])
await self.mix( await self.mix(
targets=targets[_], targets=targets[_],
mix_time=mix_time, mix_time=mix_time,
mix_vol=mix_vol, mix_vol=mix_vol,
offsets=offsets if offsets else None, offsets=offsets if offsets else None,
height_to_bottom=mix_liquid_height if mix_liquid_height 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: if delays is not None:
await self.custom_delay(seconds=delays[1]) await self.custom_delay(seconds=delays[1])
await self.touch_tip(targets[_]) await self.touch_tip(targets[_])
await self.discard_tips() 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: except Exception as e:
traceback.print_exc() traceback.print_exc()
@@ -208,56 +276,126 @@ class LiquidHandlerAbstract(LiquidHandler):
""" """
try: try:
# ------------------------------------------------------------------
# 96‑channel head mode
# ------------------------------------------------------------------
if is_96_well: if is_96_well:
pass # This mode is not verified pass # This mode is not verified.
else: else:
if not (len(asp_vols) == len(sources) and len(dis_vols) == len(targets)): if len(asp_vols) != len(targets):
raise ValueError("`sources`, `targets`, and `vols` must have the same length.") raise ValueError(f"Length of `asp_vols` {len(asp_vols)} must match `targets` {len(targets)}.")
tip_iter = self.iter_tips(tip_racks) # 首先应该对任务分组，然后每次1个/8个进行操作处理
for src, tgt, asp_vol, asp_flow_rate, dis_vol, dis_flow_rate in zip( if len(use_channels) == 1:
sources, targets, asp_vols, asp_flow_rates, dis_vols, dis_flow_rates tip = []
): for _ in range(len(use_channels)):
tip = next(tip_iter) tip.extend(next(self.current_tip))
await self.pick_up_tips(tip) await self.pick_up_tips(tip)
# Aspirate from source
await self.aspirate( for _ in range(len(targets)):
resources=[src], await self.aspirate(
vols=[asp_vol], resources=sources,
use_channels=use_channels, vols=[asp_vols[_]],
flow_rates=[asp_flow_rate], use_channels=use_channels,
offsets=offsets, flow_rates=[asp_flow_rates[0]] if asp_flow_rates else None,
liquid_height=liquid_height, offsets=[offsets[0]] if offsets else None,
blow_out_air_volume=blow_out_air_volume, liquid_height=[liquid_height[0]] if liquid_height else None,
spread=spread, blow_out_air_volume=[blow_out_air_volume[0]] if blow_out_air_volume else None,
) spread=spread,
self.custom_delay(seconds=delays[0] if delays else 0) )
# Dispense into target if delays is not None:
await self.dispense( await self.custom_delay(seconds=delays[0])
resources=[tgt], await self.dispense(
vols=[dis_vol], resources=[targets[_]],
use_channels=use_channels, vols=[dis_vols[_]],
flow_rates=[dis_flow_rate], use_channels=use_channels,
offsets=offsets, flow_rates=[dis_flow_rates[1]] if dis_flow_rates else None,
liquid_height=liquid_height, offsets=[offsets[1]] if offsets else None,
blow_out_air_volume=blow_out_air_volume, blow_out_air_volume=[blow_out_air_volume[1]] if blow_out_air_volume else None,
spread=spread, liquid_height=[liquid_height[1]] if liquid_height else None,
) spread=spread,
await self.mix( )
targets=[tgt], if delays is not None:
mix_time=mix_times[0] if mix_times else None, await self.custom_delay(seconds=delays[1])
mix_vol=mix_vol[0] if mix_vol else None, await self.mix(
mix_rate=mix_rate[0] if mix_rate else None, targets=targets[_],
) mix_time=mix_times,
if touch_tip: mix_vol=mix_vol,
await self.touch_tip(tgt) 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() await self.discard_tips()
except Exception as exc: elif len(use_channels) == 8:
raise RuntimeError(f"Liquid transfer failed: {exc}") from exc 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 # Helper utilities
@@ -339,6 +477,7 @@ class LiquidHandlerAbstract(LiquidHandler):
def set_tiprack(self, tip_racks: Sequence[TipRack]): def set_tiprack(self, tip_racks: Sequence[TipRack]):
"""Set the tip racks for the liquid handler.""" """Set the tip racks for the liquid handler."""
self.tip_racks = tip_racks self.tip_racks = tip_racks
tip_iter = self.iter_tips(tip_racks) tip_iter = self.iter_tips(tip_racks)
self.current_tip = tip_iter self.current_tip = tip_iter

59
unilabos/devices/liquid_handling/prcxi/prcxi.py
View File

@@ -392,7 +392,7 @@ class PRCXI9300Backend(LiquidHandlerBackend):
async def pick_up_tips(self, ops: List[Pickup], use_channels: List[int] = None): async def pick_up_tips(self, ops: List[Pickup], use_channels: List[int] = None):
"""Pick up tips from the specified resource.""" """Pick up tips from the specified resource."""
if len(ops) != 8: if len(ops) != 8:
raise ValueError(f"PRCXI9300Backend pick_up_tips: Expected 8 pickups, got {len(ops)}") 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) self.steps_todo_list.append(step)
async def drop_tips(self, ops: List[Drop], use_channels: List[int] = None): async def drop_tips(self, ops: List[Drop], use_channels: List[int] = None):
"""Pick up tips from the specified resource.""" """Pick up tips from the specified resource."""
@@ -569,6 +568,7 @@ class PRCXI9300Backend(LiquidHandlerBackend):
hole_numbers="1,2,3,4,5,6,7,8", hole_numbers="1,2,3,4,5,6,7,8",
) )
self.steps_todo_list.append(step) self.steps_todo_list.append(step)
async def dispense(self, ops: List[SingleChannelDispense], use_channels: List[int] = None): 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 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.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.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.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.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.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.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)) # 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 #print(json.dumps(handler._unilabos_backend.steps_todo_list, indent=2)) # Print matrix info
asyncio.run(handler.add_liquid( asyncio.run(handler.add_liquid(
asp_vols=[100]*8, asp_vols=[100]*16,
dis_vols=[100]*8, dis_vols=[100]*16,
reagent_sources=well_containers.children[-8:], reagent_sources=well_containers.children[-16:],
targets=well_containers.children[:8], targets=well_containers.children[:16],
use_channels=[0, 1, 2, 3, 4, 5, 6, 7], use_channels=[0, 1, 2, 3, 4, 5, 6, 7],
flow_rates=[None] * 8, flow_rates=[None] * 16,
offsets=[Coordinate(0, 0, 0)] * 8, offsets=[Coordinate(0, 0, 0)] * 16,
liquid_height=[None] * 8, liquid_height=[None] * 16,
blow_out_air_volume=[None] * 8, blow_out_air_volume=[None] * 16,
delays=None,
mix_time=3,
mix_vol=50,
spread="wide", 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") # 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("Running protocol...")
# input("Press Enter to continue...") # Wait for user input before proceeding # input("Press Enter to continue...") # Wait for user input before proceeding
# print("PRCXI9300Handler initialized with deck and host settings.") # print("PRCXI9300Handler initialized with deck and host settings.")
# 但是怎么丢tip？这个需要手动设置一下？