Merge branch 'PyLabRobot:main' into nimbus8

Author: cmoscy

docs/resources/library/celltreat.md

@@ -8,6 +8,7 @@
 | Same as 229590 (229590 is sold with lids) 'CellTreat_96_wellplate_350ul_Ub'<br>Part no.: 229591<br>[manufacturer website](https://www.celltreat.com/product/229591/) | ![](img/celltreat/CellTreat_96_wellplate_350ul_Ub.jpg) | `CellTreat_96_wellplate_350ul_Ub`  |
 | 229195 and 229196 'CellTreat_96_wellplate_350ul_Fb'<br>Part no.: 229195<br>[manufacturer website](https://www.celltreat.com/product/229195/) <br>  are treated | ![](img/celltreat/CellTreat_96_wellplate_350ul_Fb.jpg) | `CellTreat_96_wellplate_350ul_Fb`  |
 | 229562 (not sterile), 229566 (sterile) 'CellTreat_12_troughplate_15000ul_Vb'<br>[manufacturer website](https://www.celltreat.com/product/229562) <br>  are treated | ![](img/celltreat/CellTreat_12_troughplate_15000ul_Vb.jpg) | `CellTreat_12_troughplate_15000ul_Vb`  |
+| 229123, 229124<br>[manufacturer website](https://www.celltreat.com/product/229123) | ![](img/celltreat/CellTreat_24_wellplate_3300ul_Fb.jpg) | `CellTreat_24_wellplate_3300ul_Fb`  |
 
 
 ## Tubes

docs/resources/library/hamilton.md

@@ -50,7 +50,7 @@ Sometimes called "sample carriers" in Hamilton jargon.
 | Description | Image | PLR definition |
 | - | - | - |
 | 'Tube_CAR_24_A00'<br>Part no.: 173400<br>[manufacturer website](https://www.hamiltoncompany.com/automated-liquid-handling/other-robotics/173400) <br>Carries 24 "sample" tubes with 14.5–18 mm outer diameter, 60–120 mm high. Occupies one track. | ![](img/hamilton/Tube_CAR_24_A00.png) | `Tube_CAR_24_A00` |
-| 'Tube_CAR_32_A00'<br>Part no.: 173410<br>[manufacturer website](https://www.hamiltoncompany.com/other-robotics/173410) <br>Carries 32 "sample" tubes with 11–14 mm outer diameter, 60–120 mm high. Occupies one track. | ![](img/hamilton/Tube_CAR_32_A00.png.avif) | `Tube_CAR_32_A00` |
+| 'hamilton_tube_carrier_32_a00_insert_eppendorf_1_5mL'<br>Part no.: 173410<br>[manufacturer website](https://www.hamiltoncompany.com/other-robotics/173410) <br>Carries 32 `Eppendorf_DNA_LoBind_1_5ml_Vb` or `Eppendorf_Protein_LoBind_1_5ml_Vb` tubes. Occupies one track. | ![](img/hamilton/Tube_CAR_32_A00.png.avif) | `hamilton_tube_carrier_32_a00_insert_eppendorf_1_5mL` |
 | 'hamilton_tube_carrier_12_b00'<br>Part no.: 182045<br>[manufacturer website](https://www.hamiltoncompany.com/other-robotics/50-ml-falcon-tube-carrier) <br>Carries 12 "sample" tubes with 30 mm outer diameter, 115 mm high. Occupies two tracks. | ![](img/hamilton/hamilton_tube_carrier_12_b00.jpg) | `hamilton_tube_carrier_12_b00` |
 
 ### Trough carriers

docs/resources/library/img/celltreat/CellTreat_24_wellplate_3300ul_Fb.jpg

@@ -3415,6 +3415,9 @@ async def pick_up_resource(
       if use_unsafe_hotel:
         raise ValueError("Cannot use iswap hotel mode with core grippers")
 
+      if pickup.direction != GripDirection.FRONT:
+        raise NotImplementedError("Core grippers only support FRONT (default)")
+
       if channel_1 is not None or channel_2 is not None:
         warnings.warn(
           "The channel_1 and channel_2 parameters are deprecated and will be removed in future versions. "
@@ -3545,7 +3548,7 @@ async def drop_resource(
           hotel_center_z_direction=0 if z >= 0 else 1,
           clearance_height=round(hotel_clearance_height * 10),
           hotel_depth=round(hotel_depth * 10),
-          grip_direction=drop.drop_direction,
+          grip_direction=drop.direction,
           open_gripper_position=round(open_gripper_position * 10),
           traverse_height_at_beginning=round(traversal_height_start * 10),
           z_position_at_end=round(z_position_at_the_command_end * 10),
@@ -3565,7 +3568,7 @@ async def drop_resource(
             GripDirection.RIGHT: 2,
             GripDirection.BACK: 3,
             GripDirection.LEFT: 4,
-          }[drop.drop_direction],
+          }[drop.direction],
           minimum_traverse_height_at_beginning_of_a_command=round(traversal_height_start * 10),
           z_position_at_the_command_end=round(z_position_at_the_command_end * 10),
           open_gripper_position=round(open_gripper_position * 10),
@@ -3576,6 +3579,9 @@ async def drop_resource(
       if use_unsafe_hotel:
         raise ValueError("Cannot use iswap hotel mode with core grippers")
 
+      if drop.direction != GripDirection.FRONT:
+        raise NotImplementedError("Core grippers only support FRONT direction (default)")
+
       await self.core_release_picked_up_resource(
         location=Coordinate(x, y, z),
         resource=drop.resource,

pylabrobot/liquid_handling/backends/hamilton/STAR_backend.py

@@ -213,7 +213,7 @@ async def drop_resource(self, drop: ResourceDrop, **backend_kwargs):
         "offset": serialize(drop.offset),
         "pickup_distance_from_top": drop.pickup_distance_from_top,
         "pickup_direction": serialize(drop.pickup_direction),
-        "drop_direction": serialize(drop.drop_direction),
+        "drop_direction": serialize(drop.direction),
         "rotation": drop.rotation,
       },
       **backend_kwargs,

pylabrobot/liquid_handling/backends/serializing_backend.py

@@ -387,7 +387,7 @@ async def test_move_resource(self):
       offset=Coordinate.zero(),
       pickup_distance_from_top=13.2,
       pickup_direction=GripDirection.FRONT,
-      drop_direction=GripDirection.FRONT,
+      direction=GripDirection.FRONT,
       rotation=0,
     )
 

pylabrobot/liquid_handling/backends/tecan/EVO_tests.py

@@ -2221,7 +2221,7 @@ async def drop_resource(
       offset=offset,
       pickup_distance_from_top=self._resource_pickup.pickup_distance_from_top,
       pickup_direction=self._resource_pickup.direction,
-      drop_direction=direction,
+      direction=direction,
       rotation=rotation_applied_by_move,
     )
     result = await self.backend.drop_resource(drop=drop, **backend_kwargs)

pylabrobot/liquid_handling/liquid_handler.py

@@ -169,7 +169,7 @@ class ResourceDrop:
   offset: Coordinate
   pickup_distance_from_top: float
   pickup_direction: GripDirection
-  drop_direction: GripDirection
+  direction: GripDirection
   rotation: float
 
 

pylabrobot/liquid_handling/standard.py

@@ -94,6 +94,8 @@ def CellTreat_6_wellplate_16300ul_Fb(name: str, lid: Optional[Lid] = None) -> Pl
   CellTreat cat. no.: 229105
   - Material: Polystyrene
   - Tissue culture treated: No
+
+  https://www.celltreat.com/wp-content/uploads/6-Well-Plate.pdf
   """
   UPPER_WELL_RADIUS = 17.75  # from plate specs/drawing
   LOWER_WELL_RADIUS = 17.35  # from plate specs/drawing
@@ -222,3 +224,49 @@ def CellTreat_12_troughplate_15000ul_Vb(name: str) -> Plate:
       **well_kwargs,
     ),
   )
+
+
+def CellTreat_24_wellplate_3300ul_Fb_Lid(name: str) -> Lid:
+  return Lid(
+    name=name,
+    size_x=127.61,  # from spec
+    size_y=85.24,  # from spec
+    size_z=9.94,  # measured
+    nesting_z_height=8.94,  # measured as height of plate "plateau"
+    model=CellTreat_24_wellplate_3300ul_Fb_Lid.__name__,
+  )
+
+
+def CellTreat_24_wellplate_3300ul_Fb(name: str, with_lid: bool = False) -> Plate:
+  """
+  CellTreat cat. no.: 229123, 229124
+  https://www.celltreat.com/wp-content/uploads/24-Well-Plate.pdf
+  """
+  well_kwargs = {
+    "size_x": 16.6,  # from spec
+    "size_y": 16.6,  # from spec
+    "size_z": 17.2,  # from spec
+    "bottom_type": WellBottomType.FLAT,
+    "material_z_thickness": 2.3,
+    "cross_section_type": CrossSectionType.CIRCLE,
+    "max_volume": 3300,
+  }
+  return Plate(
+    name=name,
+    size_x=128.02,  # from spec
+    size_y=85.74,  # from spec
+    size_z=20.2,  # from spec, without lid
+    lid=CellTreat_24_wellplate_3300ul_Fb_Lid(name + "_lid") if with_lid else None,
+    model=CellTreat_24_wellplate_3300ul_Fb.__name__,
+    ordered_items=create_ordered_items_2d(
+      Well,
+      num_items_x=6,
+      num_items_y=4,
+      dx=16.01 - 15.7 / 2,  # from spec
+      dy=14.06 - 15.7 / 2,  # from spec
+      dz=20.2 - 17.2 - 2.3,  # from spec
+      item_dx=19.2,  # from spec
+      item_dy=19.2,  # from spec
+      **well_kwargs,
+    ),
+  )

pylabrobot/resources/celltreat/plates.py

@@ -1,3 +1,5 @@
+import warnings
+
 from pylabrobot.resources.carrier import (
   Coordinate,
   ResourceHolder,
@@ -31,25 +33,42 @@ def Tube_CAR_24_A00(name: str) -> TubeCarrier:
 
 
 def Tube_CAR_32_A00(name: str) -> TubeCarrier:
-  """Hamilton cat. no.: 173410
+  warnings.warn(
+    "The true dimensions of a Tube_CAR_32_A00 (SMP_CAR_32_A00) are not known. "
+    "The hamilton definitions are with inserts. "
+    "Do you want to use `hamilton_tube_carrier_32_a00_insert_eppendorf_1_5mL` instead?",
+    DeprecationWarning,
+  )
+  return hamilton_tube_carrier_32_a00_insert_eppendorf_1_5mL(name)
+
+
+def hamilton_tube_carrier_32_a00_insert_eppendorf_1_5mL(name: str) -> TubeCarrier:
+  """Hamilton cat. no.: 173410 with inserts cat no. 187350.
   Hamilton name: 'SMP_CAR_32_A00'.
   'Sample' carrier for 32 tubes
   1 track(T) wide.
+  For use with `Eppendorf_DNA_LoBind_1_5ml_Vb` and `Eppendorf_Protein_LoBind_1_5ml_Vb`.
   """
+  hole_diameter = 10.8
   return TubeCarrier(
     name=name,
-    size_x=22.5,
-    size_y=497.0,
-    size_z=71.5,
+    size_x=22.5,  # 1 track
+    size_y=497.0,  # standard
+    size_z=60.2,  # caliper
     sites=create_homogeneous_resources(
       klass=ResourceHolder,
-      locations=[Coordinate(5, 6.5 + x * 15, 24.0) for x in range(32)],
+      locations=[
+        Coordinate(14.5 - hole_diameter / 2, 14.5 - hole_diameter / 2 + x * 15, 25.88)
+        for x in range(
+          32
+        )  # SMP_CAR_32_A00 in venus, verified with caliper, custom z from z probing
+      ],
       # should fix container
-      resource_size_x=13.0,
-      resource_size_y=13.0,
+      resource_size_x=hole_diameter,  # venus
+      resource_size_y=hole_diameter,  # venus
       name_prefix=name,
     ),
-    model="Tube_CAR_32_A00",
+    model=hamilton_tube_carrier_32_a00_insert_eppendorf_1_5mL.__name__,
   )
 
 
@@ -59,6 +78,7 @@ def hamilton_tube_carrier_12_b00(name: str) -> TubeCarrier:
   'Sample' carrier for 12 50mL falcon tubes (Cor_Falcon_tube_50mL_Vb).
   2 track(T) wide.
   """
+  hole_diameter = 29.0
   return TubeCarrier(
     name=name,
     size_x=45,  # 2 tracks
@@ -67,11 +87,11 @@ def hamilton_tube_carrier_12_b00(name: str) -> TubeCarrier:
     sites=create_homogeneous_resources(
       klass=ResourceHolder,
       locations=[
-        Coordinate(26.05 - 29 / 2, 41.74 - 29 / 2 + i * 36.5, 18.9)
+        Coordinate(26.05 - hole_diameter / 2, 41.74 - hole_diameter / 2 + i * 36.5, 18.9)
         for i in range(12)  # SMP_CAR_12_A00 in venus, verified with caliper, custom z
       ],
-      resource_size_x=29.0,
-      resource_size_y=29.0,
+      resource_size_x=hole_diameter,
+      resource_size_y=hole_diameter,
       name_prefix=name,
     ),
     model=hamilton_tube_carrier_12_b00.__name__,