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feat(shared-data): Add the ability to handle sub wells in labware geometry #16658

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merged 5 commits into from
Nov 1, 2024
Merged

feat(shared-data): Add the ability to handle sub wells in labware geometry #16658

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3e3f503
add the math/schema updates
ryanthecoder Oct 31, 2024
c763085
implement the subwells in the labware we have defs for
ryanthecoder Oct 31, 2024
d841ddf
forgot to add count to the 1 well subwells
ryanthecoder Oct 31, 2024
df6a0c7
update the defs to be x and y but give them a property of count to co…
ryanthecoder Nov 1, 2024
20474ef
update the defs with x and y count
ryanthecoder Nov 1, 2024
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89 changes: 57 additions & 32 deletions api/src/opentrons/protocol_engine/state/frustum_helpers.py
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Original file line number Diff line number Diff line change
Expand Up @@ -220,28 +220,40 @@ def _get_segment_capacity(segment: WellSegment) -> float:
section_height = segment.topHeight - segment.bottomHeight
match segment:
case SphericalSegment():
return _volume_from_height_spherical(
target_height=segment.topHeight,
radius_of_curvature=segment.radiusOfCurvature,
return (
_volume_from_height_spherical(
target_height=segment.topHeight,
radius_of_curvature=segment.radiusOfCurvature,
)
* segment.count
)
case CuboidalFrustum():
return _volume_from_height_rectangular(
target_height=section_height,
bottom_length=segment.bottomYDimension,
bottom_width=segment.bottomXDimension,
top_length=segment.topYDimension,
top_width=segment.topXDimension,
total_frustum_height=section_height,
return (
_volume_from_height_rectangular(
target_height=section_height,
bottom_length=segment.bottomYDimension,
bottom_width=segment.bottomXDimension,
top_length=segment.topYDimension,
top_width=segment.topXDimension,
total_frustum_height=section_height,
)
* segment.count
)
case ConicalFrustum():
return _volume_from_height_circular(
target_height=section_height,
total_frustum_height=section_height,
bottom_radius=(segment.bottomDiameter / 2),
top_radius=(segment.topDiameter / 2),
return (
_volume_from_height_circular(
target_height=section_height,
total_frustum_height=section_height,
bottom_radius=(segment.bottomDiameter / 2),
top_radius=(segment.topDiameter / 2),
)
* segment.count
)
case SquaredConeSegment():
return _volume_from_height_squared_cone(section_height, segment)
return (
_volume_from_height_squared_cone(section_height, segment)
* segment.count
)
case _:
# TODO: implement volume calculations for truncated circular and rounded rectangular segments
raise NotImplementedError(
Expand Down Expand Up @@ -272,6 +284,7 @@ def height_at_volume_within_section(
section_height: float,
) -> float:
"""Calculate a height within a bounded section according to geometry."""
target_volume_relative = target_volume_relative / section.count
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@caila-marashaj caila-marashaj Oct 31, 2024 •
edited
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I think we may not have to do this for height to volume ? In the two cases where height is given, either:

  • The height is not in the subwell: the calculation doesnt change
  • the height is within the subwells: the volume we're trying to find is contained only within the one subwell we're getting the liquid height from

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@ryanthecoder ryanthecoder Nov 1, 2024 •
edited
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This is still correct, if we want to be say 24ul above the bottom and there are 8 subwells, we need to find the height in 1 subwell that equals (24/8)=3ul if we didn't do the division, then we would be trying to find where it would be 24ul in 1 subwell

match section:
case SphericalSegment():
return _height_from_volume_spherical(
Expand Down Expand Up @@ -311,28 +324,40 @@ def volume_at_height_within_section(
"""Calculate a volume within a bounded section according to geometry."""
match section:
case SphericalSegment():
return _volume_from_height_spherical(
target_height=target_height_relative,
radius_of_curvature=section.radiusOfCurvature,
return (
_volume_from_height_spherical(
target_height=target_height_relative,
radius_of_curvature=section.radiusOfCurvature,
)
* section.count
)
case ConicalFrustum():
return _volume_from_height_circular(
target_height=target_height_relative,
total_frustum_height=section_height,
bottom_radius=(section.bottomDiameter / 2),
top_radius=(section.topDiameter / 2),
return (
_volume_from_height_circular(
target_height=target_height_relative,
total_frustum_height=section_height,
bottom_radius=(section.bottomDiameter / 2),
top_radius=(section.topDiameter / 2),
)
* section.count
)
case CuboidalFrustum():
return _volume_from_height_rectangular(
target_height=target_height_relative,
total_frustum_height=section_height,
bottom_width=section.bottomXDimension,
bottom_length=section.bottomYDimension,
top_width=section.topXDimension,
top_length=section.topYDimension,
return (
_volume_from_height_rectangular(
target_height=target_height_relative,
total_frustum_height=section_height,
bottom_width=section.bottomXDimension,
bottom_length=section.bottomYDimension,
top_width=section.topXDimension,
top_length=section.topYDimension,
)
* section.count
)
case SquaredConeSegment():
return _volume_from_height_squared_cone(target_height_relative, section)
return (
_volume_from_height_squared_cone(target_height_relative, section)
* section.count
)
case _:
# TODO(cm): this would be the NEST-96 2uL wells referenced in EXEC-712
# we need to input the math attached to that issue
Expand Down
22 changes: 21 additions & 1 deletion shared-data/labware/definitions/3/agilent_1_reservoir_290ml/2.json
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Original file line number Diff line number Diff line change
Expand Up @@ -54,7 +54,27 @@
},
"innerLabwareGeometry": {
"cuboidalWell": {
"sections": []
"sections": [
{
"shape": "cuboidal",
"topXDimension": 107.25,
"topYDimension": 8,
"bottomXDimension": 101.25,
"bottomYDimension": 1.66,
"topHeight": 2,
"bottomHeight": 8,
"yCount": 8
},
{
"shape": "cuboidal",
"topXDimension": 107.5,
"topYDimension": 71.25,
"bottomXDimension": 107.25,
"bottomYDimension": 71.0,
"topHeight": 39.22,
"bottomHeight": 2
}
]
}
}
}
23 changes: 22 additions & 1 deletion shared-data/labware/definitions/3/nest_1_reservoir_195ml/3.json
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Original file line number Diff line number Diff line change
Expand Up @@ -56,7 +56,28 @@
},
"innerLabwareGeometry": {
"cuboidalWell": {
"sections": []
"sections": [
{
"shape": "cuboidal",
"topXDimension": 9,
"topYDimension": 9,
"bottomXDimension": 1.93,
"bottomYDimension": 1.93,
"topHeight": 2,
"bottomHeight": 0,
"xCount": 12,
"yCount": 8
},
{
"shape": "cuboidal",
"topXDimension": 71.3,
"topYDimension": 70.6,
"bottomXDimension": 107.3,
"bottomYDimension": 106.8,
"topHeight": 26.85,
"bottomHeight": 2
}
]
}
}
}
22 changes: 21 additions & 1 deletion shared-data/labware/definitions/3/usascientific_12_reservoir_22ml/2.json
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Original file line number Diff line number Diff line change
Expand Up @@ -203,7 +203,27 @@
},
"innerLabwareGeometry": {
"cuboidalWell": {
"sections": []
"sections": [
{
"shape": "squaredcone",
"bottomCrossSection": "circular",
"circleDiameter": 2.5,
"rectangleXDimension": 7.98,
"rectangleYDimension": 70.98,
"topHeight": 4.05,
"bottomHeight": 0.0,
"yCount": 8
},
{
"shape": "cuboidal",
"topXDimension": 8.34,
"topYDimension": 71.85,
"bottomXDimension": 7.98,
"bottomYDimension": 70.98,
"topHeight": 41.75,
"bottomHeight": 4.05
}
]
}
}
}
30 changes: 30 additions & 0 deletions shared-data/labware/schemas/3.json
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Original file line number Diff line number Diff line change
Expand Up @@ -83,6 +83,12 @@
},
"bottomHeight": {
"type": "number"
},
"xCount": {
"type": "integer"
},
"yCount": {
"type": "integer"
}
}
},
Expand Down Expand Up @@ -112,6 +118,12 @@
},
"bottomHeight": {
"type": "number"
},
"xCount": {
"type": "integer"
},
"yCount": {
"type": "integer"
}
}
},
Expand Down Expand Up @@ -149,6 +161,12 @@
},
"bottomHeight": {
"type": "number"
},
"xCount": {
"type": "integer"
},
"yCount": {
"type": "integer"
}
}
},
Expand Down Expand Up @@ -187,6 +205,12 @@
},
"bottomHeight": {
"type": "number"
},
"xCount": {
"type": "integer"
},
"yCount": {
"type": "integer"
}
}
},
Expand Down Expand Up @@ -225,6 +249,12 @@
},
"bottomHeight": {
"type": "number"
},
"xCount": {
"type": "integer"
},
"yCount": {
"type": "integer"
}
}
},
Expand Down
72 changes: 72 additions & 0 deletions shared-data/python/opentrons_shared_data/labware/labware_definition.py
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Original file line number Diff line number Diff line change
Expand Up @@ -256,6 +256,21 @@ class SphericalSegment(BaseModel):
...,
description="Height of the bottom of the segment, must be 0.0",
)
xCount: _StrictNonNegativeInt = Field(
default=1,
description="Number of instances of this shape in the stackup, used for wells that have multiple sub-wells",
)
yCount: _StrictNonNegativeInt = Field(
default=1,
description="Number of instances of this shape in the stackup, used for wells that have multiple sub-wells",
)

@cached_property
def count(self) -> int:
return self.xCount * self.yCount

class Config:
keep_untouched = (cached_property,)


class ConicalFrustum(BaseModel):
Expand All @@ -276,6 +291,21 @@ class ConicalFrustum(BaseModel):
...,
description="The height at the bottom of a bounded subsection of a well, relative to the bottom of the well",
)
xCount: _StrictNonNegativeInt = Field(
default=1,
description="Number of instances of this shape in the stackup, used for wells that have multiple sub-wells",
)
yCount: _StrictNonNegativeInt = Field(
default=1,
description="Number of instances of this shape in the stackup, used for wells that have multiple sub-wells",
)

@cached_property
def count(self) -> int:
return self.xCount * self.yCount

class Config:
keep_untouched = (cached_property,)


class CuboidalFrustum(BaseModel):
Expand Down Expand Up @@ -305,6 +335,21 @@ class CuboidalFrustum(BaseModel):
...,
description="The height at the bottom of a bounded subsection of a well, relative to the bottom of the well",
)
xCount: _StrictNonNegativeInt = Field(
default=1,
description="Number of instances of this shape in the stackup, used for wells that have multiple sub-wells",
)
yCount: _StrictNonNegativeInt = Field(
default=1,
description="Number of instances of this shape in the stackup, used for wells that have multiple sub-wells",
)

@cached_property
def count(self) -> int:
return self.xCount * self.yCount

class Config:
keep_untouched = (cached_property,)


# A squared cone is the intersection of a cube and a cone that both
Expand Down Expand Up @@ -354,6 +399,14 @@ class SquaredConeSegment(BaseModel):
...,
description="The height at the bottom of a bounded subsection of a well, relative to the bottom of the well",
)
xCount: _StrictNonNegativeInt = Field(
default=1,
description="Number of instances of this shape in the stackup, used for wells that have multiple sub-wells",
)
yCount: _StrictNonNegativeInt = Field(
default=1,
description="Number of instances of this shape in the stackup, used for wells that have multiple sub-wells",
)

@staticmethod
def _area_trap_points(
Expand Down Expand Up @@ -433,6 +486,10 @@ def height_to_volume_table(self) -> Dict[float, float]:
def volume_to_height_table(self) -> Dict[float, float]:
return dict((v, k) for k, v in self.height_to_volume_table.items())

@cached_property
def count(self) -> int:
return self.xCount * self.yCount

class Config:
keep_untouched = (cached_property,)

Expand Down Expand Up @@ -546,6 +603,21 @@ class RoundedCuboidSegment(BaseModel):
...,
description="The height at the bottom of a bounded subsection of a well, relative to the bottom of the well",
)
xCount: _StrictNonNegativeInt = Field(
default=1,
description="Number of instances of this shape in the stackup, used for wells that have multiple sub-wells",
)
yCount: _StrictNonNegativeInt = Field(
default=1,
description="Number of instances of this shape in the stackup, used for wells that have multiple sub-wells",
)

@cached_property
def count(self) -> int:
return self.xCount * self.yCount

class Config:
keep_untouched = (cached_property,)


class Metadata1(BaseModel):
Expand Down
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