open_pub/Uni-Lab-OS
1
0
Fork 0
mirror of https://github.com/deepmodeling/Uni-Lab-OS synced 2026-03-24 04:10:33 +00:00
Code Issues Packages Projects Releases Wiki Activity

修改tracker的问题，在volumetracker报错时，禁用并进行下一步

Browse Source
This commit is contained in:
q434343
2026-03-17 20:29:15 +08:00
parent b11f6eac55
commit 1a267729e4
1 changed files with 119 additions and 90 deletions
Download Patch File Download Diff File Expand all files Collapse all files

209
unilabos/devices/liquid_handling/liquid_handler_abstract.py
View File

@@ -10,6 +10,7 @@ from pylabrobot.liquid_handling import LiquidHandler, LiquidHandlerBackend, Liqu
from pylabrobot.liquid_handling.liquid_handler import TipPresenceProbingMethod
from pylabrobot.liquid_handling.standard import GripDirection
from pylabrobot.resources.errors import TooLittleLiquidError, TooLittleVolumeError
from pylabrobot.resources.volume_tracker import no_volume_tracking
from pylabrobot.resources import (
Resource,
TipRack,
@@ -213,60 +214,60 @@ class LiquidHandlerMiddleware(LiquidHandler):
if spread == "":
spread = "custom"
def _safe_aspirate_volumes(_resources: Sequence[Container], _vols: List[float]) -> List[float]:
"""将 aspirate 体积裁剪到源容器当前液量及 tip 剩余容量范围内，避免 volume tracker 报错。"""
safe: List[float] = []
_head_owner = getattr(self, '_simulate_handler', None) or self
_head = getattr(_head_owner, 'head', {})
_channels = use_channels or list(range(len(_resources)))
for i, (res, vol) in enumerate(zip(_resources, _vols)):
req = max(float(vol), 0.0)
tracker_disabled = False
for res in resources:
tracker = getattr(res, "tracker", None)
if tracker is None or getattr(tracker, "is_disabled", False):
continue
history = getattr(tracker, "liquid_history", None)
if tracker.get_used_volume() <= 0 and isinstance(history, list) and len(history) == 0:
fill_vol = tracker.max_volume if tracker.max_volume > 0 else 50000
try:
tracker = getattr(res, "tracker", None)
tracker_disabled = bool(getattr(tracker, "is_disabled", False))
if not tracker_disabled:
get_used = getattr(tracker, "get_used_volume", None)
if callable(get_used):
used_volume = get_used()
if isinstance(used_volume, (int, float)) and used_volume > 0:
req = min(req, float(used_volume))
tracker.add_liquid(fill_vol)
except Exception:
pass
tracker.liquid_history.append(("auto_init", fill_vol))
if not tracker_disabled:
try:
ch = _channels[i] if i < len(_channels) else i
if ch in _head and _head[ch].has_tip:
_tip = _head[ch].get_tip()
_tip_free = _tip.maximal_volume - _tip.tracker.get_used_volume()
if _tip_free >= 0:
req = min(req, _tip_free)
except Exception:
pass
safe.append(req)
return safe
actual_vols = _safe_aspirate_volumes(resources, vols)
if actual_vols != vols and hasattr(self, "_ros_node") and self._ros_node is not None:
self._ros_node.lab_logger().warning(f"[aspirate] volume adjusted, requested_vols={vols}, actual_vols={actual_vols}")
if self._simulator:
return await self._simulate_handler.aspirate(
resources,
actual_vols,
use_channels,
flow_rates,
offsets,
liquid_height,
blow_out_air_volume,
spread,
**backend_kwargs,
)
try:
return await self._simulate_handler.aspirate(
resources,
vols,
use_channels,
flow_rates,
offsets,
liquid_height,
blow_out_air_volume,
spread,
**backend_kwargs,
)
except (TooLittleLiquidError, TooLittleVolumeError) as e:
tracker_info = []
for r in resources:
t = r.tracker
tracker_info.append(
f"{r.name}(used={t.get_used_volume():.1f}, "
f"free={t.get_free_volume():.1f}, max={r.max_volume})"
)
if hasattr(self, "_ros_node") and self._ros_node is not None:
self._ros_node.lab_logger().warning(
f"[aspirate] volume tracker error, bypassing tracking. "
f"error={e}, vols={vols}, trackers={tracker_info}"
)
with no_volume_tracking():
return await self._simulate_handler.aspirate(
resources,
vols,
use_channels,
flow_rates,
offsets,
liquid_height,
blow_out_air_volume,
spread,
**backend_kwargs,
)
try:
await super().aspirate(
resources,
actual_vols,
vols,
use_channels,
flow_rates,
offsets,
@@ -279,7 +280,7 @@ class LiquidHandlerMiddleware(LiquidHandler):
if "Resource is too small to space channels" in str(e) and spread != "custom":
await super().aspirate(
resources,
actual_vols,
vols,
use_channels,
flow_rates,
offsets,
@@ -290,35 +291,15 @@ class LiquidHandlerMiddleware(LiquidHandler):
)
else:
raise
except TooLittleLiquidError:
# 再兜底一次：按实时可用液量重算后重试，避免状态更新竞争导致的瞬时不足
retry_vols = _safe_aspirate_volumes(resources, actual_vols)
if any(v > 0 for v in retry_vols):
await super().aspirate(
resources,
retry_vols,
use_channels,
flow_rates,
offsets,
liquid_height,
blow_out_air_volume,
spread,
**backend_kwargs,
)
actual_vols = retry_vols
else:
actual_vols = retry_vols
res_samples = []
res_volumes = []
# 处理 use_channels 为 None 的情况（通常用于单通道操作）
if use_channels is None:
# 对于单通道操作，推断通道为 [0]
channels_to_use = [0] * len(resources)
else:
channels_to_use = use_channels
for resource, volume, channel in zip(resources, actual_vols, channels_to_use):
for resource, volume, channel in zip(resources, vols, channels_to_use):
sample_uuid_value = getattr(resource, "unilabos_extra", {}).get(EXTRA_SAMPLE_UUID, None)
res_samples.append({"name": resource.name, "sample_uuid": sample_uuid_value})
res_volumes.append(volume)
@@ -365,17 +346,43 @@ class LiquidHandlerMiddleware(LiquidHandler):
actual_vols = _safe_dispense_volumes(resources, vols)
if self._simulator:
return await self._simulate_handler.dispense(
resources,
actual_vols,
use_channels,
flow_rates,
offsets,
liquid_height,
blow_out_air_volume,
spread,
**backend_kwargs,
)
try:
return await self._simulate_handler.dispense(
resources,
actual_vols,
use_channels,
flow_rates,
offsets,
liquid_height,
blow_out_air_volume,
spread,
**backend_kwargs,
)
except (TooLittleLiquidError, TooLittleVolumeError) as e:
tracker_info = []
for r in resources:
t = r.tracker
tracker_info.append(
f"{r.name}(used={t.get_used_volume():.1f}, "
f"free={t.get_free_volume():.1f}, max={r.max_volume})"
)
if hasattr(self, "_ros_node") and self._ros_node is not None:
self._ros_node.lab_logger().warning(
f"[dispense] volume tracker error, bypassing tracking. "
f"error={e}, vols={actual_vols}, trackers={tracker_info}"
)
with no_volume_tracking():
return await self._simulate_handler.dispense(
resources,
actual_vols,
use_channels,
flow_rates,
offsets,
liquid_height,
blow_out_air_volume,
spread,
**backend_kwargs,
)
try:
await super().dispense(
resources,
@@ -859,6 +866,14 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware):
local = cast(Union[Container, TipRack], plr)
if hasattr(plr, "unilabos_extra") and hasattr(local, "unilabos_extra"):
local.unilabos_extra = getattr(plr, "unilabos_extra", {}).copy()
if local is not plr and hasattr(plr, "tracker") and hasattr(local, "tracker"):
local_tracker = local.tracker
plr_tracker = plr.tracker
local_history = getattr(local_tracker, "liquid_history", None)
plr_history = getattr(plr_tracker, "liquid_history", None)
if (isinstance(local_history, list) and len(local_history) == 0
and isinstance(plr_history, list) and len(plr_history) > 0):
local_tracker.liquid_history = list(plr_history)
resolved.append(local)
if len(resolved) != len(uuids):
raise ValueError(
@@ -868,8 +883,18 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware):
resolved = _resolve_from_local_by_uuids()
result = list(items)
for (idx, _), plr in zip(dict_items, resolved):
result[idx] = plr
for (idx, orig_dict), res in zip(dict_items, resolved):
if isinstance(orig_dict, dict) and hasattr(res, "tracker"):
tracker = res.tracker
local_history = getattr(tracker, "liquid_history", None)
if isinstance(local_history, list) and len(local_history) == 0:
data = orig_dict.get("data") or {}
dict_history = data.get("liquid_history")
if isinstance(dict_history, list) and len(dict_history) > 0:
tracker.liquid_history = [
(name, float(vol)) for name, vol in dict_history
]
result[idx] = res
return result
@classmethod
@@ -1070,7 +1095,7 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware):
for _ in range(len(sources)):
tip = []
for __ in range(len(use_channels)):
tip.extend(self._get_next_tip())
tip.append(self._get_next_tip())
await self.pick_up_tips(tip)
await self.aspirate(
resources=[sources[_]],
@@ -1110,7 +1135,7 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware):
for i in range(0, len(sources), 8):
tip = []
for _ in range(len(use_channels)):
tip.extend(self._get_next_tip())
tip.append(self._get_next_tip())
await self.pick_up_tips(tip)
current_targets = waste_liquid[i : i + 8]
current_reagent_sources = sources[i : i + 8]
@@ -1204,7 +1229,7 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware):
for _ in range(len(targets)):
tip = []
for x in range(len(use_channels)):
tip.extend(self._get_next_tip())
tip.append(self._get_next_tip())
await self.pick_up_tips(tip)
await self.aspirate(
@@ -1256,7 +1281,7 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware):
for i in range(0, len(targets), 8):
tip = []
for _ in range(len(use_channels)):
tip.extend(self._get_next_tip())
tip.append(self._get_next_tip())
await self.pick_up_tips(tip)
current_targets = targets[i : i + 8]
current_reagent_sources = reagent_sources[i : i + 8]
@@ -1538,7 +1563,7 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware):
delays = kwargs.get('delays')
tip = []
tip.extend(self._get_next_tip())
tip.append(self._get_next_tip())
await self.pick_up_tips(tip)
blow_out_air_volume_before_vol = 0.0
if blow_out_air_volume_before is not None and len(blow_out_air_volume_before) > 0:
@@ -1741,9 +1766,13 @@ class LiquidHandlerAbstract(LiquidHandlerMiddleware):
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!")
if isinstance(rack, TipSpot):
yield rack
elif hasattr(rack, "get_all_items"):
yield from rack.get_all_items()
else:
for tip in rack:
yield tip
def _get_next_tip(self):
"""从 current_tip 迭代器获取下一个 tip，耗尽时抛出明确错误而非 StopIteration"""