Add agilent_96_wellplate_150uL_Vb

docs/resources/library/agilent.md

@@ -6,4 +6,4 @@
 
 | Description | Image | PLR definition |
 |-|-|-|
-| 'agilent_96_wellplate_150uL_Ub'<br>Part no.: 5042-8502<br>[manufacturer website](https://www.agilent.com/store/en_US/Prod-5042-8502/5042-8502) | ![](img/agilent/agilent_96_wellplate_150uL_Ub.jpg) | `agilent_96_wellplate_150uL_Ub` |
+| 'agilent_96_wellplate_150uL_Vb'<br>Part no.: 5042-8502<br>[manufacturer website](https://www.agilent.com/store/en_US/Prod-5042-8502/5042-8502) | ![](img/agilent/agilent_96_wellplate_150uL_Vb.jpg) | `agilent_96_wellplate_150uL_Vb` |

pylabrobot/resources/agilent/plates.py

@@ -1,12 +1,69 @@
+import warnings
+
+from pylabrobot.resources.height_volume_functions import (
+  calculate_liquid_height_container_1segment_round_vbottom,
+  calculate_liquid_volume_container_1segment_round_vbottom,
+)
 from pylabrobot.resources.plate import Plate
 from pylabrobot.resources.utils import create_ordered_items_2d
 from pylabrobot.resources.well import Well, WellBottomType
 
 
-def agilent_96_wellplate_150uL_Ub(name: str) -> Plate:
+def _compute_volume_from_height_agilent_96_wellplate_150uL_Vb(
+  h: float,
+):
+  # well depth: 12.5 mm
+  # well diameter at the top: 6.0 mm
+  if h > 12.5:
+    raise ValueError(f"Height {h} is too large for agilent_96_wellplate_150uL_Vb")
+  return calculate_liquid_volume_container_1segment_round_vbottom(
+    d=6.4, h_pyramid=12.5, liquid_height=h
+  )
+
+
+def _compute_height_from_volume_agilent_96_wellplate_150uL_Vb(
+  v: float,
+):
+  if v > 150:
+    raise ValueError(f"Volume {v} is too large for agilent_96_wellplate_150uL_Vb")
+  return calculate_liquid_height_container_1segment_round_vbottom(
+    d=6.4, h_pyramid=12.5, liquid_volume=v
+  )
+
+
+def agilent_96_wellplate_150uL_Vb(name: str) -> Plate:
   """
   Part number: 5042-8502
 
+  Well Number                  | 96
+  Well Form                    | Round
+  Well Diameter (A)            | 6.4 mm
+  Well Bottom Shape            | Conical
+  Well Volume                  | 150 µL
+  Well Working Volume          | 120 µL
+  Well Depth (B)               | 14.0 mm
+  Plate Height (C)             | 15.9 mm
+  Plate Width (D)              | 85.5 mm
+  Plate Length (E)             | 127.8 mm
+  Row Distance (F)             | 9 mm
+  Column Distance (G)          | 9 mm
+  Row Offset (H)               | 11.2 mm
+  Column Offset (I)            | 14.4 mm
+  Frame Footprint              | SBS
+  Frame Numbering              | Alphanumeric
+  Skirted                      | Yes
+  Color                        | Clear
+  Material                     | Well: polypropylene
+                               | Frame: polycarbonate
+  Temperature Range            | -80 to 120 °C
+  Autoclavable                 | Yes
+  Sterile                      | Nonsterile
+  Stackable                    | Yes
+  Pack Size                    | 25, p/n 5042-8502
+  Compatible Closing Mat       | p/n 5067-5154 (not recommended for
+                               | chromatography autosamplers)
+  Agilent Instrument Definition| Not applicable
+
   https://www.agilent.com/cs/library/datasheets/public/ds-well-plate-specifications-5994-6035en-agilent.pdf
   """
 
@@ -19,6 +76,8 @@ def agilent_96_wellplate_150uL_Ub(name: str) -> Plate:
     "bottom_type": WellBottomType.U,
     "material_z_thickness": 0.88,  # measured using z-probing
     "max_volume": 150,
+    "compute_volume_from_height": _compute_volume_from_height_agilent_96_wellplate_150uL_Vb,
+    "compute_height_from_volume": _compute_height_from_volume_agilent_96_wellplate_150uL_Vb,
   }
 
   return Plate(
@@ -27,17 +86,26 @@ def agilent_96_wellplate_150uL_Ub(name: str) -> Plate:
     size_y=85.5,  # standard
     size_z=15.9,  # from spec
     lid=None,
-    model=agilent_96_wellplate_150uL_Ub.__name__,
+    model=agilent_96_wellplate_150uL_Vb.__name__,
     ordered_items=create_ordered_items_2d(
       Well,
       num_items_x=12,
       num_items_y=8,
       dx=14.4 - diameter / 2,  # from spec
       dy=11.2 - diameter / 2,  # from spec
-      dz=16.0 - 14.0 - 0.88,  # spec - spec - measured
+      dz=15.9 - 14.0 - 0.88,  # spec - spec - measured manually
       item_dx=9.0,  # standard
       item_dy=9.0,  # standard
       **well_kwargs,
     ),
     plate_type="skirted",
   )
+
+
+def agilent_96_wellplate_150uL_Ub(name: str) -> Plate:
+  """Deprecated for agilent_96_wellplate_150uL_Vb. Use that one instead."""
+  warnings.warn(
+    "agilent_96_wellplate_150uL_Ub is deprecated. Use agilent_96_wellplate_150uL_Vb instead.",
+    DeprecationWarning,
+  )
+  return agilent_96_wellplate_150uL_Vb(name)

pylabrobot/resources/height_volume_functions.py

@@ -434,6 +434,33 @@ def calculate_liquid_height_container_1segment_round_fbottom(
   return liquid_height
 
 
+def calculate_liquid_height_container_1segment_round_vbottom(
+  d: float, h_pyramid: float, liquid_volume: float
+) -> float:
+  """Calculate the height of liquid in a container with a cylindrical pyramid (cone) shape.
+
+  Parameters:
+    d: The diameter of the base of the cone in mm.
+    h_pyramid: The height of the cone in mm.
+    liquid_volume: The volume of the liquid in the container in cubic millimeters.
+
+  Returns:
+    The height of the liquid in the container in mm.
+  """
+  r = d / 2
+  max_volume = (1 / 3) * math.pi * r**2 * h_pyramid
+
+  if liquid_volume > max_volume:
+    raise ValueError(
+      """WARNING: Liquid overflow detected;
+    check your labware definition and/or that you are using the right labware."""
+    )
+
+  scale_factor: float = (liquid_volume / max_volume) ** (1 / 3)
+  liquid_height = scale_factor * h_pyramid
+  return liquid_height
+
+
 def calculate_liquid_volume_container_1segment_round_fbottom(
   d: float, h_cylinder: float, liquid_height: float
 ) -> float:
@@ -458,6 +485,31 @@ def calculate_liquid_volume_container_1segment_round_fbottom(
   return cylinder_liquid_volume
 
 
+def calculate_liquid_volume_container_1segment_round_vbottom(
+  d: float, h_pyramid: float, liquid_height: float
+) -> float:
+  """Calculate the volume of liquid in a container with a cylindrical pyramid (cone) shape.
+
+  Parameters:
+    d: The diameter of the base of the cone in mm.
+    h_pyramid: The height of the cone in mm.
+    liquid_height: The height of the liquid in the container in mm.
+
+  Returns:
+    The volume of the liquid in cubic millimeters.
+  """
+  r = d / 2
+  if liquid_height > h_pyramid:
+    raise ValueError(
+      """WARNING: Liquid overflow detected;
+    check your labware definition and/or that you are using the right labware."""
+    )
+
+  scale_factor = liquid_height / h_pyramid
+  liquid_volume = (1 / 3) * math.pi * r**2 * h_pyramid * (scale_factor**3)
+  return liquid_volume
+
+
 ### Example of usage using a lambda function:
 # def Rectangular_Reservoir(name: str) -> Plate:
 #   """ An 8 well reservoir with a 30mL volume. """