新增simulator

unilabos/devices/liquid_handling/liquid_handler_abstract.py

@@ -1,18 +1,547 @@
 from __future__ import annotations
 
 import traceback
-from typing import List, Sequence, Optional, Literal, Union, Iterator
+from typing import List, Sequence, Optional, Literal, Union, Iterator, Dict, Any, Callable, Set
 
 import asyncio
 import time
 
-from pylabrobot.liquid_handling import LiquidHandler
+from pylabrobot.liquid_handling import LiquidHandler, LiquidHandlerBackend, LiquidHandlerChatterboxBackend, Strictness
-from pylabrobot.resources import Resource, TipRack, Container, Coordinate, Well
+from pylabrobot.liquid_handling.liquid_handler import TipPresenceProbingMethod
+from pylabrobot.liquid_handling.standard import GripDirection
+from pylabrobot.resources import (
+    Resource,
+    TipRack,
+    Container,
+    Coordinate,
+    Well,
+    Deck,
+    TipSpot,
+    Plate,
+    ResourceStack,
+    ResourceHolder,
+    Lid,
+    Trash,
+    Tip,
+)
 
 
-class LiquidHandlerAbstract(LiquidHandler):
+class LiquidHandlerMiddleware(LiquidHandler):
+    def __init__(self, backend: LiquidHandlerBackend, deck: Deck, simulator: bool = False):
+        self._simulator = simulator
+        if simulator:
+            self._simulate_backend = LiquidHandlerChatterboxBackend(8)
+            self._simulate_handler = LiquidHandlerAbstract(self._simulate_backend, deck, False)
+        super().__init__(backend, deck)
+
+    async def setup(self, **backend_kwargs):
+        if self._simulator:
+            await self._simulate_handler.setup(**backend_kwargs)
+        return await super().setup(**backend_kwargs)
+
+    def serialize_state(self) -> Dict[str, Any]:
+        if self._simulator:
+            self._simulate_handler.serialize_state()
+        return super().serialize_state()
+
+    def load_state(self, state: Dict[str, Any]):
+        if self._simulator:
+            self._simulate_handler.load_state(state)
+        super().load_state(state)
+
+    def update_head_state(self, state: Dict[int, Optional[Tip]]):
+        if self._simulator:
+            self._simulate_handler.update_head_state(state)
+        super().update_head_state(state)
+
+    def clear_head_state(self):
+        if self._simulator:
+            self._simulate_handler.clear_head_state()
+        super().clear_head_state()
+
+    def _run_async_in_thread(self, func, *args, **kwargs):
+        super()._run_async_in_thread(func, *args, **kwargs)
+
+    def _send_assigned_resource_to_backend(self, resource: Resource):
+        if self._simulator:
+            self._simulate_handler._send_assigned_resource_to_backend(resource)
+        super()._send_assigned_resource_to_backend(resource)
+
+    def _send_unassigned_resource_to_backend(self, resource: Resource):
+        if self._simulator:
+            self._simulate_handler._send_unassigned_resource_to_backend(resource)
+        super()._send_unassigned_resource_to_backend(resource)
+
+    def summary(self):
+        if self._simulator:
+            self._simulate_handler.summary()
+        super().summary()
+
+    def _assert_positions_unique(self, positions: List[str]):
+        super()._assert_positions_unique(positions)
+
+    def _assert_resources_exist(self, resources: Sequence[Resource]):
+        super()._assert_resources_exist(resources)
+
+    def _check_args(
+        self, method: Callable, backend_kwargs: Dict[str, Any], default: Set[str], strictness: Strictness
+    ) -> Set[str]:
+        return super()._check_args(method, backend_kwargs, default, strictness)
+
+    def _make_sure_channels_exist(self, channels: List[int]):
+        super()._make_sure_channels_exist(channels)
+
+    def _format_param(self, value: Any) -> Any:
+        return super()._format_param(value)
+
+    def _log_command(self, name: str, **kwargs) -> None:
+        super()._log_command(name, **kwargs)
+
+    async def pick_up_tips(
+        self,
+        tip_spots: List[TipSpot],
+        use_channels: Optional[List[int]] = None,
+        offsets: Optional[List[Coordinate]] = None,
+        **backend_kwargs,
+    ):
+        if self._simulator:
+            await self._simulate_handler.pick_up_tips(tip_spots, use_channels, offsets, **backend_kwargs)
+        return await super().pick_up_tips(tip_spots, use_channels, offsets, **backend_kwargs)
+
+    async def drop_tips(
+        self,
+        tip_spots: Sequence[Union[TipSpot, Trash]],
+        use_channels: Optional[List[int]] = None,
+        offsets: Optional[List[Coordinate]] = None,
+        allow_nonzero_volume: bool = False,
+        **backend_kwargs,
+    ):
+        if self._simulator:
+            await self._simulate_handler.drop_tips(
+                tip_spots, use_channels, offsets, allow_nonzero_volume, **backend_kwargs
+            )
+        return await super().drop_tips(tip_spots, use_channels, offsets, allow_nonzero_volume, **backend_kwargs)
+
+    async def return_tips(
+        self, use_channels: Optional[list[int]] = None, allow_nonzero_volume: bool = False, **backend_kwargs
+    ):
+        if self._simulator:
+            await self._simulate_handler.return_tips(use_channels, allow_nonzero_volume, **backend_kwargs)
+        return await super().return_tips(use_channels, allow_nonzero_volume, **backend_kwargs)
+
+    async def discard_tips(
+        self,
+        use_channels: Optional[List[int]] = None,
+        allow_nonzero_volume: bool = True,
+        offsets: Optional[List[Coordinate]] = None,
+        **backend_kwargs,
+    ):
+        if self._simulator:
+            await self._simulate_handler.discard_tips(use_channels, allow_nonzero_volume, offsets, **backend_kwargs)
+        return await super().discard_tips(use_channels, allow_nonzero_volume, offsets, **backend_kwargs)
+
+    def _check_containers(self, resources: Sequence[Resource]):
+        super()._check_containers(resources)
+
+    async def aspirate(
+        self,
+        resources: Sequence[Container],
+        vols: List[float],
+        use_channels: Optional[List[int]] = None,
+        flow_rates: Optional[List[Optional[float]]] = None,
+        offsets: Optional[List[Coordinate]] = None,
+        liquid_height: Optional[List[Optional[float]]] = None,
+        blow_out_air_volume: Optional[List[Optional[float]]] = None,
+        spread: Literal["wide", "tight", "custom"] = "wide",
+        **backend_kwargs,
+    ):
+        if self._simulator:
+            await self._simulate_handler.aspirate(
+                resources,
+                vols,
+                use_channels,
+                flow_rates,
+                offsets,
+                liquid_height,
+                blow_out_air_volume,
+                spread,
+                **backend_kwargs,
+            )
+        return await super().aspirate(
+            resources,
+            vols,
+            use_channels,
+            flow_rates,
+            offsets,
+            liquid_height,
+            blow_out_air_volume,
+            spread,
+            **backend_kwargs,
+        )
+
+    async def dispense(
+        self,
+        resources: Sequence[Container],
+        vols: List[float],
+        use_channels: Optional[List[int]] = None,
+        flow_rates: Optional[List[Optional[float]]] = None,
+        offsets: Optional[List[Coordinate]] = None,
+        liquid_height: Optional[List[Optional[float]]] = None,
+        blow_out_air_volume: Optional[List[Optional[float]]] = None,
+        spread: Literal["wide", "tight", "custom"] = "wide",
+        **backend_kwargs,
+    ):
+        if self._simulator:
+            await self._simulate_handler.dispense(
+                resources,
+                vols,
+                use_channels,
+                flow_rates,
+                offsets,
+                liquid_height,
+                blow_out_air_volume,
+                spread,
+                **backend_kwargs,
+            )
+        return await super().dispense(
+            resources,
+            vols,
+            use_channels,
+            flow_rates,
+            offsets,
+            liquid_height,
+            blow_out_air_volume,
+            spread,
+            **backend_kwargs,
+        )
+
+    async def transfer(
+        self,
+        source: Well,
+        targets: List[Well],
+        source_vol: Optional[float] = None,
+        ratios: Optional[List[float]] = None,
+        target_vols: Optional[List[float]] = None,
+        aspiration_flow_rate: Optional[float] = None,
+        dispense_flow_rates: Optional[List[Optional[float]]] = None,
+        **backend_kwargs,
+    ):
+        if self._simulator:
+            await self._simulate_handler.transfer(
+                source,
+                targets,
+                source_vol,
+                ratios,
+                target_vols,
+                aspiration_flow_rate,
+                dispense_flow_rates,
+                **backend_kwargs,
+            )
+        return await super().transfer(
+            source,
+            targets,
+            source_vol,
+            ratios,
+            target_vols,
+            aspiration_flow_rate,
+            dispense_flow_rates,
+            **backend_kwargs,
+        )
+
+    def use_channels(self, channels: List[int]):
+        if self._simulator:
+            self._simulate_handler.use_channels(channels)
+        return super().use_channels(channels)
+
+    async def pick_up_tips96(self, tip_rack: TipRack, offset: Coordinate = Coordinate.zero(), **backend_kwargs):
+        if self._simulator:
+            await self._simulate_handler.pick_up_tips96(tip_rack, offset, **backend_kwargs)
+        return await super().pick_up_tips96(tip_rack, offset, **backend_kwargs)
+
+    async def drop_tips96(
+        self,
+        resource: Union[TipRack, Trash],
+        offset: Coordinate = Coordinate.zero(),
+        allow_nonzero_volume: bool = False,
+        **backend_kwargs,
+    ):
+        if self._simulator:
+            await self._simulate_handler.drop_tips96(resource, offset, allow_nonzero_volume, **backend_kwargs)
+        return await super().drop_tips96(resource, offset, allow_nonzero_volume, **backend_kwargs)
+
+    def _get_96_head_origin_tip_rack(self) -> Optional[TipRack]:
+        return super()._get_96_head_origin_tip_rack()
+
+    async def return_tips96(self, allow_nonzero_volume: bool = False, **backend_kwargs):
+        if self._simulator:
+            await self._simulate_handler.return_tips96(allow_nonzero_volume, **backend_kwargs)
+        return await super().return_tips96(allow_nonzero_volume, **backend_kwargs)
+
+    async def discard_tips96(self, allow_nonzero_volume: bool = True, **backend_kwargs):
+        if self._simulator:
+            await self._simulate_handler.discard_tips96(allow_nonzero_volume, **backend_kwargs)
+        return await super().discard_tips96(allow_nonzero_volume, **backend_kwargs)
+
+    async def aspirate96(
+        self,
+        resource: Union[Plate, Container, List[Well]],
+        volume: float,
+        offset: Coordinate = Coordinate.zero(),
+        flow_rate: Optional[float] = None,
+        blow_out_air_volume: Optional[float] = None,
+        **backend_kwargs,
+    ):
+        if self._simulator:
+            await self._simulate_handler.aspirate96(
+                resource, volume, offset, flow_rate, blow_out_air_volume, **backend_kwargs
+            )
+        return await super().aspirate96(resource, volume, offset, flow_rate, blow_out_air_volume, **backend_kwargs)
+
+    async def dispense96(
+        self,
+        resource: Union[Plate, Container, List[Well]],
+        volume: float,
+        offset: Coordinate = Coordinate.zero(),
+        flow_rate: Optional[float] = None,
+        blow_out_air_volume: Optional[float] = None,
+        **backend_kwargs,
+    ):
+        if self._simulator:
+            await self._simulate_handler.dispense96(
+                resource, volume, offset, flow_rate, blow_out_air_volume, **backend_kwargs
+            )
+        return await super().dispense96(resource, volume, offset, flow_rate, blow_out_air_volume, **backend_kwargs)
+
+    async def stamp(
+        self,
+        source: Plate,
+        target: Plate,
+        volume: float,
+        aspiration_flow_rate: Optional[float] = None,
+        dispense_flow_rate: Optional[float] = None,
+    ):
+        if self._simulator:
+            await self._simulate_handler.stamp(source, target, volume, aspiration_flow_rate, dispense_flow_rate)
+        return await super().stamp(source, target, volume, aspiration_flow_rate, dispense_flow_rate)
+
+    async def pick_up_resource(
+        self,
+        resource: Resource,
+        offset: Coordinate = Coordinate.zero(),
+        pickup_distance_from_top: float = 0,
+        direction: GripDirection = GripDirection.FRONT,
+        **backend_kwargs,
+    ):
+        if self._simulator:
+            await self._simulate_handler.pick_up_resource(
+                resource, offset, pickup_distance_from_top, direction, **backend_kwargs
+            )
+        return await super().pick_up_resource(resource, offset, pickup_distance_from_top, direction, **backend_kwargs)
+
+    async def move_picked_up_resource(
+        self,
+        to: Coordinate,
+        offset: Coordinate = Coordinate.zero(),
+        direction: Optional[GripDirection] = None,
+        **backend_kwargs,
+    ):
+        if self._simulator:
+            await self._simulate_handler.move_picked_up_resource(to, offset, direction, **backend_kwargs)
+        return await super().move_picked_up_resource(to, offset, direction, **backend_kwargs)
+
+    async def drop_resource(
+        self,
+        destination: Union[ResourceStack, ResourceHolder, Resource, Coordinate],
+        offset: Coordinate = Coordinate.zero(),
+        direction: GripDirection = GripDirection.FRONT,
+        **backend_kwargs,
+    ):
+        if self._simulator:
+            await self._simulate_handler.drop_resource(destination, offset, direction, **backend_kwargs)
+        return await super().drop_resource(destination, offset, direction, **backend_kwargs)
+
+    async def move_resource(
+        self,
+        resource: Resource,
+        to: Union[ResourceStack, ResourceHolder, Resource, Coordinate],
+        intermediate_locations: Optional[List[Coordinate]] = None,
+        pickup_offset: Coordinate = Coordinate.zero(),
+        destination_offset: Coordinate = Coordinate.zero(),
+        pickup_distance_from_top: float = 0,
+        pickup_direction: GripDirection = GripDirection.FRONT,
+        drop_direction: GripDirection = GripDirection.FRONT,
+        **backend_kwargs,
+    ):
+        if self._simulator:
+            await self._simulate_handler.move_resource(
+                resource,
+                to,
+                intermediate_locations,
+                pickup_offset,
+                destination_offset,
+                pickup_distance_from_top,
+                pickup_direction,
+                drop_direction,
+                **backend_kwargs,
+            )
+        return await super().move_resource(
+            resource,
+            to,
+            intermediate_locations,
+            pickup_offset,
+            destination_offset,
+            pickup_distance_from_top,
+            pickup_direction,
+            drop_direction,
+            **backend_kwargs,
+        )
+
+    async def move_lid(
+        self,
+        lid: Lid,
+        to: Union[Plate, ResourceStack, Coordinate],
+        intermediate_locations: Optional[List[Coordinate]] = None,
+        pickup_offset: Coordinate = Coordinate.zero(),
+        destination_offset: Coordinate = Coordinate.zero(),
+        pickup_direction: GripDirection = GripDirection.FRONT,
+        drop_direction: GripDirection = GripDirection.FRONT,
+        pickup_distance_from_top: float = 5.7 - 3.33,
+        **backend_kwargs,
+    ):
+        if self._simulator:
+            await self._simulate_handler.move_lid(
+                lid,
+                to,
+                intermediate_locations,
+                pickup_offset,
+                destination_offset,
+                pickup_direction,
+                drop_direction,
+                pickup_distance_from_top,
+                **backend_kwargs,
+            )
+        return await super().move_lid(
+            lid,
+            to,
+            intermediate_locations,
+            pickup_offset,
+            destination_offset,
+            pickup_direction,
+            drop_direction,
+            pickup_distance_from_top,
+            **backend_kwargs,
+        )
+
+    async def move_plate(
+        self,
+        plate: Plate,
+        to: Union[ResourceStack, ResourceHolder, Resource, Coordinate],
+        intermediate_locations: Optional[List[Coordinate]] = None,
+        pickup_offset: Coordinate = Coordinate.zero(),
+        destination_offset: Coordinate = Coordinate.zero(),
+        drop_direction: GripDirection = GripDirection.FRONT,
+        pickup_direction: GripDirection = GripDirection.FRONT,
+        pickup_distance_from_top: float = 13.2 - 3.33,
+        **backend_kwargs,
+    ):
+        if self._simulator:
+            await self._simulate_handler.move_plate(
+                plate,
+                to,
+                intermediate_locations,
+                pickup_offset,
+                destination_offset,
+                drop_direction,
+                pickup_direction,
+                pickup_distance_from_top,
+                **backend_kwargs,
+            )
+        return await super().move_plate(
+            plate,
+            to,
+            intermediate_locations,
+            pickup_offset,
+            destination_offset,
+            drop_direction,
+            pickup_direction,
+            pickup_distance_from_top,
+            **backend_kwargs,
+        )
+
+    def serialize(self):
+        if self._simulator:
+            self._simulate_handler.serialize()
+        return super().serialize()
+
+    @classmethod
+    def deserialize(cls, data: dict, allow_marshal: bool = False) -> LiquidHandler:
+        return super().deserialize(data, allow_marshal)
+
+    @classmethod
+    def load(cls, path: str) -> LiquidHandler:
+        return super().load(path)
+
+    async def prepare_for_manual_channel_operation(self, channel: int):
+        if self._simulator:
+            await self._simulate_handler.prepare_for_manual_channel_operation(channel)
+        return await super().prepare_for_manual_channel_operation(channel)
+
+    async def move_channel_x(self, channel: int, x: float):
+        if self._simulator:
+            await self._simulate_handler.move_channel_x(channel, x)
+        return await super().move_channel_x(channel, x)
+
+    async def move_channel_y(self, channel: int, y: float):
+        if self._simulator:
+            await self._simulate_handler.move_channel_y(channel, y)
+        return await super().move_channel_y(channel, y)
+
+    async def move_channel_z(self, channel: int, z: float):
+        if self._simulator:
+            await self._simulate_handler.move_channel_z(channel, z)
+        return await super().move_channel_z(channel, z)
+
+    def assign_child_resource(self, resource: Resource, location: Optional[Coordinate], reassign: bool = True):
+        if self._simulator:
+            self._simulate_handler.assign_child_resource(resource, location, reassign)
+        pass
+
+    async def probe_tip_presence_via_pickup(
+        self, tip_spots: List[TipSpot], use_channels: Optional[List[int]] = None
+    ) -> Dict[str, bool]:
+        if self._simulator:
+            await self._simulate_handler.probe_tip_presence_via_pickup(tip_spots, use_channels)
+        return await super().probe_tip_presence_via_pickup(tip_spots, use_channels)
+
+    async def probe_tip_inventory(
+        self,
+        tip_spots: List[TipSpot],
+        probing_fn: Optional[TipPresenceProbingMethod] = None,
+        use_channels: Optional[List[int]] = None,
+    ) -> Dict[str, bool]:
+        if self._simulator:
+            await self._simulate_handler.probe_tip_inventory(tip_spots, probing_fn, use_channels)
+        return await super().probe_tip_inventory(tip_spots, probing_fn, use_channels)
+
+    async def consolidate_tip_inventory(self, tip_racks: List[TipRack], use_channels: Optional[List[int]] = None):
+        if self._simulator:
+            await self._simulate_handler.consolidate_tip_inventory(tip_racks, use_channels)
+        return await super().consolidate_tip_inventory(tip_racks, use_channels)
+
+
+class LiquidHandlerAbstract(LiquidHandlerMiddleware):
     """Extended LiquidHandler with additional operations."""
 
+    def __init__(self, backend: LiquidHandlerBackend, deck: Deck, simulator: bool):
+        """Initialize a LiquidHandler.
+
+        Args:
+          backend: Backend to use.
+          deck: Deck to use.
+        """
+        self._simulator = simulator
+        super().__init__(backend, deck, simulator)
+
     # ---------------------------------------------------------------
     # REMOVE LIQUID --------------------------------------------------
     # ---------------------------------------------------------------
@@ -52,7 +581,7 @@ class LiquidHandlerAbstract(LiquidHandler):
         try:
             if is_96_well:
                 pass  # This mode is not verified.
-            else:           
+            else:
                 # 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 = []
@@ -175,7 +704,7 @@ 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)}.")
-                
+
                 # 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 = []
@@ -229,7 +758,7 @@ class LiquidHandlerAbstract(LiquidHandler):
                     # 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):
@@ -337,7 +866,7 @@ 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)}.")
-                
+
                 # 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 = []
@@ -392,7 +921,7 @@ class LiquidHandlerAbstract(LiquidHandler):
                     # 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):
@@ -401,7 +930,7 @@ class LiquidHandlerAbstract(LiquidHandler):
                         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_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*8-8:len(offsets)-i*8] if offsets else [None] * 8
                         current_asp_liquid_height = liquid_height[i:i + 8] if liquid_height else [None] * 8
@@ -420,7 +949,7 @@ class LiquidHandlerAbstract(LiquidHandler):
                             liquid_height=current_asp_liquid_height,
                             spread=spread,
                         )
-                        
+
                         if delays is not None:
                             await self.custom_delay(seconds=delays[0])
                         await self.dispense(
@@ -446,7 +975,7 @@ class LiquidHandlerAbstract(LiquidHandler):
                         )
                         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()

unilabos/devices/liquid_handling/prcxi/prcxi.py

@@ -14,7 +14,7 @@ from pylabrobot.liquid_handling import (
     SingleChannelDispense,
     PickupTipRack,
     DropTipRack,
-    MultiHeadAspirationPlate,
+    MultiHeadAspirationPlate, ChatterBoxBackend, LiquidHandlerChatterboxBackend,
 )
 from pylabrobot.liquid_handling.standard import (
     MultiHeadAspirationContainer,
@@ -105,7 +105,7 @@ class PRCXI9300Handler(LiquidHandlerAbstract):
                     WorkTablets(Number=count, Code=f"T{count}", Material=child._unilabos_state["Material"])
                 )
         self._unilabos_backend = PRCXI9300Backend(tablets_info, host, port, timeout, setup, debug)
-        super().__init__(backend=self._unilabos_backend, deck=deck)
+        super().__init__(backend=self._unilabos_backend, deck=deck, simulator=True)
 
     async def create_protocol(
         self,