add byonoy luminescence and absorbance plate readers

docs/user_guide/02_analytical/plate-reading/plate-reading.ipynb

@@ -14,6 +14,7 @@
     "\n",
     "bmg-clariostar\n",
     "cytation5\n",
+    "byonoy\n",
     "```\n",
     "\n",
     "This example uses the `PlateReaderChatterboxBackend`. When using a real machine, use the corresponding backend."

pylabrobot/liquid_handling/liquid_handler.py

@@ -2109,6 +2109,9 @@ async def drop_resource(
       raise RuntimeError("No resource picked up")
     resource = self._resource_pickup.resource
 
+    if isinstance(destination, Resource):
+      destination.check_can_drop_resource_here(resource)
+
     # compute rotation based on the pickup_direction and drop_direction
     if self._resource_pickup.direction == direction:
       rotation_applied_by_move = 0
@@ -2458,7 +2461,7 @@ async def move_plate(
       **backend_kwargs,
     )
 
-  def serialize(self):
+  def serialize(self) -> dict:
     return {
       **Resource.serialize(self),
       **Machine.serialize(self),

pylabrobot/plate_reading/__init__.py

@@ -1,4 +1,10 @@
 from .biotek_backend import Cytation5Backend, Cytation5ImagingConfig
+from .byonoy import (
+  ByonoyAbsorbance96AutomateBackend,
+  ByonoyLuminescence96AutomateBackend,
+  byonoy_absorbance96_base_and_reader,
+  byonoy_absorbance_adapter,
+)
 from .chatterbox import PlateReaderChatterboxBackend
 from .clario_star_backend import CLARIOstarBackend
 from .image_reader import ImageReader

pylabrobot/plate_reading/byonoy/__init__.py

@@ -0,0 +1,2 @@
+from .byonoy import byonoy_absorbance96_base_and_reader, byonoy_absorbance_adapter
+from .byonoy_backend import ByonoyAbsorbance96AutomateBackend, ByonoyLuminescence96AutomateBackend

pylabrobot/plate_reading/byonoy/byonoy.py

@@ -0,0 +1,152 @@
+from typing import Optional, Tuple
+
+from pylabrobot.plate_reading.byonoy.byonoy_backend import ByonoyAbsorbance96AutomateBackend
+from pylabrobot.plate_reading.plate_reader import PlateReader
+from pylabrobot.resources import Coordinate, PlateHolder, Resource, ResourceHolder
+
+
+def byonoy_absorbance_adapter(name: str) -> ResourceHolder:
+  return ResourceHolder(
+    name=name,
+    size_x=127.76,  # measured
+    size_y=85.59,  # measured
+    size_z=14.07,  # measured
+    child_location=Coordinate(
+      x=-(138 - 127.76) / 2,  # measured
+      y=-(95.7 - 85.59) / 2,  # measured
+      z=14.07 - 2.45,  # measured
+    ),
+  )
+
+
+class _ByonoyAbsorbanceReaderPlateHolder(PlateHolder):
+  """Custom plate holder that checks if the reader sits on the parent base.
+  This check is used to prevent crashes (moving plate onto holder while reader is on the base)."""
+
+  def __init__(
+    self,
+    name: str,
+    size_x: float,
+    size_y: float,
+    size_z: float,
+    pedestal_size_z: float = None,  # type: ignore
+    child_location=Coordinate.zero(),
+    category="plate_holder",
+    model: Optional[str] = None,
+  ):
+    super().__init__(
+      name=name,
+      size_x=size_x,
+      size_y=size_y,
+      size_z=size_z,
+      pedestal_size_z=pedestal_size_z,
+      child_location=child_location,
+      category=category,
+      model=model,
+    )
+    self._byonoy_base: Optional["ByonoyBase"] = None
+
+  def check_can_drop_resource_here(self, resource: Resource) -> None:
+    if self._byonoy_base is None:
+      raise RuntimeError(
+        "ByonoyBase not assigned its plate holder. "
+        "Please assign a ByonoyBase instance to the plate holder."
+      )
+
+    if self._byonoy_base.reader_holder.resource is not None:
+      raise RuntimeError(
+        f"Cannot drop resource {resource.name} onto plate holder while reader is on the base. "
+        "Please remove the reader from the base before dropping a resource."
+      )
+
+    super().check_can_drop_resource_here(resource)
+
+
+class ByonoyBase(Resource):
+  def __init__(self, name, rotation=None, category=None, model=None, barcode=None):
+    super().__init__(
+      name=name,
+      size_x=138,
+      size_y=95.7,
+      size_z=27.7,
+    )
+
+    self.plate_holder = _ByonoyAbsorbanceReaderPlateHolder(
+      name=self.name + "_plate_holder",
+      size_x=127.76,
+      size_y=85.59,
+      size_z=0,
+      child_location=Coordinate(x=(138 - 127.76) / 2, y=(95.7 - 85.59) / 2, z=27.7),
+      pedestal_size_z=0,
+    )
+    self.assign_child_resource(self.plate_holder, location=Coordinate.zero())
+
+    self.reader_holder = ResourceHolder(
+      name=self.name + "_reader_holder",
+      size_x=138,
+      size_y=95.7,
+      size_z=0,
+      child_location=Coordinate(x=0, y=0, z=10.66),
+    )
+    self.assign_child_resource(self.reader_holder, location=Coordinate.zero())
+
+  def assign_child_resource(
+    self, resource: Resource, location: Optional[Coordinate], reassign=True
+  ):
+    if isinstance(resource, _ByonoyAbsorbanceReaderPlateHolder):
+      if self.plate_holder._byonoy_base is not None:
+        raise ValueError("ByonoyBase can only have one plate holder assigned.")
+      self.plate_holder._byonoy_base = self
+    return super().assign_child_resource(resource, location, reassign)
+
+  def check_can_drop_resource_here(self, resource: Resource) -> None:
+    raise RuntimeError(
+      "ByonoyBase does not support assigning child resources directly. "
+      "Use the plate_holder or reader_holder to assign plates and the reader, respectively."
+    )
+
+
+def byonoy_absorbance96_base_and_reader(name: str, assign=True) -> Tuple[ByonoyBase, PlateReader]:
+  """Creates a ByonoyBase and a PlateReader instance."""
+  byonoy_base = ByonoyBase(name=name + "_base")
+  reader = PlateReader(
+    name=name + "_reader",
+    size_x=138,
+    size_y=95.7,
+    size_z=0,
+    backend=ByonoyAbsorbance96AutomateBackend(),
+  )
+  if assign:
+    byonoy_base.reader_holder.assign_child_resource(reader)
+  return byonoy_base, reader
+
+
+# === absorbance ===
+
+# total
+
+# x: 138
+# y: 95.7
+# z: 53.35
+
+# base
+# z = 27.7
+# z without skirt 25.25
+
+# top
+# z = 41.62
+
+# adapter
+# z = 14.07
+
+# location of top wrt base
+# z = 10.66
+
+# pickup distance from top
+# z = 7.45
+
+# === lum ===
+
+# x: 155.5
+# y: 95.7
+# z: 56.9