opentrons 8.6.0__py3-none-any.whl

opentrons/protocol_engine/state/inner_well_math_utils.py

@@ -0,0 +1,548 @@
+"""Helper functions for liquid-level related calculations inside a given frustum."""
+from typing import List, Tuple
+from numpy import pi, iscomplex, roots, real
+from math import isclose
+
+from ..errors.exceptions import InvalidLiquidHeightFound, InvalidUserDefinedVolumesError
+
+from opentrons.protocol_engine.types.liquid_level_detection import (
+    LiquidTrackingType,
+    SimulatedProbeResult,
+)
+from opentrons_shared_data.labware.labware_definition import (
+    InnerWellGeometry,
+    WellSegment,
+    SphericalSegment,
+    ConicalFrustum,
+    CuboidalFrustum,
+    SquaredConeSegment,
+    UserDefinedVolumes,
+)
+
+
+def _reject_unacceptable_heights(
+    potential_heights: List[float], max_height: float
+) -> float:
+    """Reject any solutions to a polynomial equation that cannot be the height of a frustum."""
+    valid_heights: List[float] = []
+    for root in potential_heights:
+        # reject any heights that are negative or greater than the max height
+        if not iscomplex(root):
+            # take only the real component of the root and round to 4 decimal places
+            rounded_root = round(real(root), 4)
+            if (rounded_root <= max_height) and (rounded_root >= 0):
+                if not any([isclose(rounded_root, height) for height in valid_heights]):
+                    valid_heights.append(rounded_root)
+    if len(valid_heights) != 1:
+        raise InvalidLiquidHeightFound(
+            message="Unable to estimate valid liquid height from volume."
+        )
+    return valid_heights[0]
+
+
+def _cross_section_area_circular(diameter: float) -> float:
+    """Get the area of a circular cross-section."""
+    radius = diameter / 2
+    return pi * (radius**2)
+
+
+def _cross_section_area_rectangular(x_dimension: float, y_dimension: float) -> float:
+    """Get the area of a rectangular cross-section."""
+    return x_dimension * y_dimension
+
+
+def _rectangular_frustum_polynomial_roots(
+    bottom_length: float,
+    bottom_width: float,
+    top_length: float,
+    top_width: float,
+    total_frustum_height: float,
+) -> Tuple[float, float, float]:
+    """Polynomial representation of the volume of a rectangular frustum."""
+    # roots of the polynomial with shape ax^3 + bx^2 + cx
+    a = (
+        (top_length - bottom_length)
+        * (top_width - bottom_width)
+        / (3 * total_frustum_height**2)
+    )
+    b = (
+        (bottom_length * (top_width - bottom_width))
+        + (bottom_width * (top_length - bottom_length))
+    ) / (2 * total_frustum_height)
+    c = bottom_length * bottom_width
+    return a, b, c
+
+
+def _circular_frustum_polynomial_roots(
+    bottom_radius: float,
+    top_radius: float,
+    total_frustum_height: float,
+) -> Tuple[float, float, float]:
+    """Polynomial representation of the volume of a circular frustum."""
+    # roots of the polynomial with shape ax^3 + bx^2 + cx
+    a = pi * ((top_radius - bottom_radius) ** 2) / (3 * total_frustum_height**2)
+    b = pi * bottom_radius * (top_radius - bottom_radius) / total_frustum_height
+    c = pi * bottom_radius**2
+    return a, b, c
+
+
+def _volume_from_height_circular(
+    target_height: float, segment: ConicalFrustum
+) -> float:
+    return segment.volume_from_height_circular(
+        top_radius=segment.topDiameter / 2,
+        bottom_radius=segment.bottomDiameter / 2,
+        target_height=target_height,
+        total_height=segment.topHeight - segment.bottomHeight,
+    )
+
+
+def _volume_from_height_rectangular(
+    target_height: float,
+    total_frustum_height: float,
+    bottom_length: float,
+    bottom_width: float,
+    top_length: float,
+    top_width: float,
+) -> float:
+    """Find the volume given a height within a rectangular frustum."""
+    a, b, c = _rectangular_frustum_polynomial_roots(
+        bottom_length=bottom_length,
+        bottom_width=bottom_width,
+        top_length=top_length,
+        top_width=top_width,
+        total_frustum_height=total_frustum_height,
+    )
+    volume = a * (target_height**3) + b * (target_height**2) + c * target_height
+    return volume
+
+
+def _volume_from_height_spherical(
+    target_height: float,
+    radius_of_curvature: float,
+) -> float:
+    """Find the volume given a height within a spherical frustum."""
+    volume = (
+        (1 / 3) * pi * (target_height**2) * (3 * radius_of_curvature - target_height)
+    )
+    return volume
+
+
+def _volume_from_height_squared_cone(
+    target_height: float, segment: SquaredConeSegment
+) -> float:
+    """Find the volume given a height within a squared cone segment."""
+    heights = segment.height_to_volume_table.keys()
+    best_fit_height = min(heights, key=lambda x: abs(x - target_height))
+    return segment.height_to_volume_table[best_fit_height]
+
+
+def _height_from_volume_circular(
+    target_volume: float, segment: ConicalFrustum
+) -> float:
+    """Find the height given a volume within a squared cone segment."""
+    return segment.height_from_volume_search(target_volume)
+
+
+def _height_from_volume_rectangular(
+    volume: float,
+    total_frustum_height: float,
+    bottom_length: float,
+    bottom_width: float,
+    top_length: float,
+    top_width: float,
+) -> float:
+    """Find the height given a volume within a rectangular frustum."""
+    a, b, c = _rectangular_frustum_polynomial_roots(
+        bottom_length=bottom_length,
+        bottom_width=bottom_width,
+        top_length=top_length,
+        top_width=top_width,
+        total_frustum_height=total_frustum_height,
+    )
+    d = volume * -1
+    x_intercept_roots = (a, b, c, d)
+
+    height_from_volume_roots = roots(x_intercept_roots)
+    height = _reject_unacceptable_heights(
+        potential_heights=list(height_from_volume_roots),
+        max_height=total_frustum_height,
+    )
+    return height
+
+
+def _height_from_volume_spherical(
+    volume: float,
+    radius_of_curvature: float,
+    total_frustum_height: float,
+) -> float:
+    """Find the height given a volume within a spherical frustum."""
+    a = -1 * pi / 3
+    b = pi * radius_of_curvature
+    c = 0.0
+    d = volume * -1
+    x_intercept_roots = (a, b, c, d)
+
+    height_from_volume_roots = roots(x_intercept_roots)
+    height = _reject_unacceptable_heights(
+        potential_heights=list(height_from_volume_roots),
+        max_height=total_frustum_height,
+    )
+    return height
+
+
+def _height_from_volume_squared_cone(
+    target_volume: float, segment: SquaredConeSegment
+) -> float:
+    """Find the height given a volume within a squared cone segment."""
+    volumes = segment.volume_to_height_table.keys()
+    best_fit_volume = min(volumes, key=lambda x: abs(x - target_volume))
+    return segment.volume_to_height_table[best_fit_volume]
+
+
+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,
+                )
+                * 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,
+                )
+                * segment.count
+            )
+        case ConicalFrustum():
+            return (
+                _volume_from_height_circular(
+                    target_height=section_height,
+                    segment=segment,
+                )
+                * segment.count
+            )
+        case SquaredConeSegment():
+            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(
+                f"volume calculation for shape: {segment.shape} not yet implemented."
+            )
+
+
+def get_well_volumetric_capacity(
+    well_geometry: InnerWellGeometry,
+) -> List[Tuple[float, float]]:
+    """Return the volumetric capacity of a well as a list of pairs relating segment heights to volumes."""
+    #  [(top_height_0, section_0_volume), (top_height_1, section_1_volume), ...]
+    well_volume = []
+
+    # get the well segments sorted in ascending order
+    sorted_well = sorted(well_geometry.sections, key=lambda section: section.topHeight)
+
+    for segment in sorted_well:
+        section_volume = _get_segment_capacity(segment)
+        well_volume.append((segment.topHeight, section_volume))
+    return well_volume
+
+
+def height_at_volume_within_section(
+    section: WellSegment,
+    target_volume_relative: float,
+    section_height: float,
+) -> float:
+    """Calculate a height within a bounded section according to geometry."""
+    target_volume_relative = target_volume_relative / section.count
+    match section:
+        case SphericalSegment():
+            return _height_from_volume_spherical(
+                volume=target_volume_relative,
+                total_frustum_height=section_height,
+                radius_of_curvature=section.radiusOfCurvature,
+            )
+        case ConicalFrustum():
+            return _height_from_volume_circular(target_volume_relative, section)
+        case CuboidalFrustum():
+            return _height_from_volume_rectangular(
+                volume=target_volume_relative,
+                total_frustum_height=section_height,
+                bottom_width=section.bottomXDimension,
+                bottom_length=section.bottomYDimension,
+                top_width=section.topXDimension,
+                top_length=section.topYDimension,
+            )
+        case SquaredConeSegment():
+            return _height_from_volume_squared_cone(target_volume_relative, section)
+        case _:
+            raise NotImplementedError(
+                "Height from volume calculation not yet implemented for this well shape."
+            )
+
+
+def volume_at_height_within_section(
+    section: WellSegment,
+    target_height_relative: float,
+    section_height: float,
+) -> float:
+    """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,
+                )
+                * section.count
+            )
+        case ConicalFrustum():
+            return (
+                _volume_from_height_circular(
+                    target_height=target_height_relative, segment=section
+                )
+                * 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,
+                )
+                * section.count
+            )
+        case SquaredConeSegment():
+            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
+            raise NotImplementedError(
+                "Height from volume calculation not yet implemented for this well shape."
+            )
+
+
+def _find_volume_in_partial_frustum(
+    sorted_well: List[WellSegment],
+    target_height: float,
+) -> float:
+    """Look through a sorted list of frusta for a target height, and find the volume at that height."""
+    for segment in sorted_well:
+        if segment.bottomHeight <= target_height <= segment.topHeight:
+            relative_target_height = target_height - segment.bottomHeight
+            section_height = segment.topHeight - segment.bottomHeight
+            return volume_at_height_within_section(
+                section=segment,
+                target_height_relative=relative_target_height,
+                section_height=section_height,
+            )
+    # if we've looked through all sections and can't find the target volume, raise an error
+    # this code should never be reached- an error should be raised by find_volume_at_well_height
+    raise InvalidLiquidHeightFound(
+        f"Target height {target_height} mm exceeds the well height."
+    )
+
+
+def _linear_interpolation(
+    interpolating_from: List[float], to_interpolate: List[float], target_val: float
+) -> float:
+    if len(interpolating_from) != len(to_interpolate):
+        raise InvalidUserDefinedVolumesError(
+            "Height and volume data have unequal sizes"
+        )
+    if not (interpolating_from[0] == to_interpolate[0] == 0.0):
+        raise ValueError("linear interpolation datasets must start with 0.0")
+
+    if target_val == 0.0:
+        return 0.0
+    for i in range(1, len(interpolating_from)):
+        if target_val == interpolating_from[i]:
+            return to_interpolate[i]
+        if interpolating_from[i - 1] < target_val < interpolating_from[i]:
+            proportional_diff = (target_val - interpolating_from[i - 1]) / (
+                interpolating_from[i] - interpolating_from[i - 1]
+            )
+            addend = proportional_diff * (to_interpolate[i] - to_interpolate[i - 1])
+            result = to_interpolate[i - 1] + addend
+            return result
+    raise ValueError("linear interpolation failed")
+
+
+def find_volume_user_defined_volumes(
+    target_height: LiquidTrackingType, well_geometry: UserDefinedVolumes
+) -> LiquidTrackingType:
+    """Return a linear interpolation of volume based on target height."""
+    if isinstance(target_height, SimulatedProbeResult):
+        return target_height
+    sorted_volume_map = sorted(
+        well_geometry.heightToVolumeMap, key=lambda section: section.height
+    )
+    max_height = sorted_volume_map[-1].height
+    if target_height < 0 or target_height > max_height:
+        raise InvalidLiquidHeightFound(
+            f"Invalid target height {target_height} mm; greatest well height in InnerLabwareGeometry is {max_height} mm."
+        )
+    volumes = [0.0]
+    heights = [0.0]
+    for pair in sorted_volume_map:
+        volumes.append(pair.volume)
+        heights.append(pair.height)
+
+    try:
+        return _linear_interpolation(
+            interpolating_from=heights, to_interpolate=volumes, target_val=target_height
+        )
+    except ValueError:
+        raise InvalidLiquidHeightFound(
+            f"Unable to find volume at target volume {target_height}."
+        )
+
+
+def find_height_user_defined_volumes(
+    target_volume: LiquidTrackingType,
+    well_geometry: UserDefinedVolumes,
+) -> LiquidTrackingType:
+    """Return a linear interpolation of height based on target volume."""
+    if isinstance(target_volume, SimulatedProbeResult):
+        return target_volume
+    sorted_volume_map = sorted(
+        well_geometry.heightToVolumeMap, key=lambda section: section.height
+    )
+    max_volume = sorted_volume_map[-1].volume
+    if target_volume < 0 or target_volume > max_volume:
+        raise InvalidLiquidHeightFound(
+            f"Invalid target volume {target_volume}µL; greatest well volume in InnerLabwareGeometry is {max_volume}µL."
+        )
+
+    volumes = [0.0]
+    heights = [0.0]
+    for pair in sorted_volume_map:
+        volumes.append(pair.volume)
+        heights.append(pair.height)
+
+    try:
+        return _linear_interpolation(
+            interpolating_from=volumes, to_interpolate=heights, target_val=target_volume
+        )
+    except ValueError:
+        raise InvalidLiquidHeightFound(
+            f"Unable to find volume at target volume {target_volume}."
+        )
+
+
+def find_volume_inner_well_geometry(
+    target_height: LiquidTrackingType,
+    well_geometry: InnerWellGeometry,
+) -> LiquidTrackingType:
+    """Find the volume within a well, at a known height."""
+    # comparisons with SimulatedProbeResult objects aren't meaningful, just return
+    if isinstance(target_height, SimulatedProbeResult):
+        return target_height
+    volumetric_capacity = get_well_volumetric_capacity(well_geometry)
+    max_height = volumetric_capacity[-1][0]
+    if target_height < 0 or target_height > max_height:
+        raise InvalidLiquidHeightFound(
+            f"Invalid target height {target_height} mm; max well height is {max_height} mm."
+        )
+    # volumes in volumetric_capacity are relative to each frustum,
+    # so we have to find the volume of all the full sections enclosed
+    # beneath the target height
+    closed_section_volume = 0.0
+    for boundary_height, section_volume in volumetric_capacity:
+        if boundary_height > target_height:
+            break
+        closed_section_volume += section_volume
+        # if target height is a boundary cross-section, we already know the volume
+        if target_height == boundary_height:
+            return closed_section_volume
+    # find the section the target height is in and compute the volume
+
+    sorted_well = sorted(well_geometry.sections, key=lambda section: section.topHeight)
+    partial_volume = _find_volume_in_partial_frustum(
+        sorted_well=sorted_well,
+        target_height=target_height,
+    )
+    return partial_volume + closed_section_volume
+
+
+def _find_height_in_partial_frustum(
+    sorted_well: List[WellSegment],
+    volumetric_capacity: List[Tuple[float, float]],
+    target_volume: float,
+) -> float:
+    """Look through a sorted list of frusta for a target volume, and find the height at that volume."""
+    bottom_section_volume = 0.0
+    if target_volume == 0.0:
+        return 0.0
+    for section, capacity in zip(sorted_well, volumetric_capacity):
+        section_top_height, section_volume = capacity
+        if target_volume == section_volume + bottom_section_volume:
+            return section_top_height
+        if (
+            bottom_section_volume
+            <= target_volume
+            <= (bottom_section_volume + section_volume)
+        ):
+            relative_target_volume = target_volume - bottom_section_volume
+            section_height = section.topHeight - section.bottomHeight
+            partial_height = height_at_volume_within_section(
+                section=section,
+                target_volume_relative=relative_target_volume,
+                section_height=section_height,
+            )
+            return partial_height + section.bottomHeight
+        # bottom section volume should always be the volume enclosed in the previously
+        # viewed section
+        bottom_section_volume += section_volume
+
+    # if we finish looping through the whole well, bottom_section will be the well's volume
+    total_well_volume = bottom_section_volume
+    # if we've looked through all sections and can't find the target volume, raise an error
+    # also this code should never be reached bc an invalid target volume should be changed
+    # by find_height_at_well_volume
+    raise InvalidLiquidHeightFound(
+        f"Target volume {target_volume}µL exceeds the well volume {total_well_volume}µL."
+    )
+
+
+def find_height_inner_well_geometry(
+    target_volume: LiquidTrackingType,
+    well_geometry: InnerWellGeometry,
+) -> LiquidTrackingType:
+    """Find the height within a well, at a known volume."""
+    # comparisons with SimulatedProbeResult objects aren't meaningful, just
+    # return if we have one of those
+    if isinstance(target_volume, SimulatedProbeResult):
+        return target_volume
+
+    volumetric_capacity = get_well_volumetric_capacity(well_geometry)
+    max_volume = sum(row[1] for row in volumetric_capacity)
+
+    if target_volume < 0:
+        target_volume = 0
+    elif target_volume > max_volume:
+        target_volume = max_volume
+    sorted_well = sorted(well_geometry.sections, key=lambda section: section.topHeight)
+    # find the section the target volume is in and compute the height
+    return _find_height_in_partial_frustum(
+        sorted_well=sorted_well,
+        volumetric_capacity=volumetric_capacity,
+        target_volume=target_volume,
+    )