opentrons 8.6.0a1__py3-none-any.whl

opentrons/protocol_api/core/legacy/module_geometry.py

@@ -0,0 +1,547 @@
+""" opentrons.protocol_api.module_geometry: classes and functions for modules
+as deck objects
+
+This module provides things like :py:class:`ModuleGeometry` and
+:py:func:`load_module` to create and manipulate module objects as geometric
+objects on the deck (as opposed to calling commands on them, which is handled
+by :py:mod:`.module_contexts`)
+"""
+from __future__ import annotations
+
+import logging
+from enum import Enum
+from typing import TYPE_CHECKING, Optional
+
+import numpy as np
+from numpy.typing import NDArray
+
+from opentrons_shared_data import module
+from opentrons_shared_data.module.types import ModuleDefinitionV3
+from opentrons_shared_data.module import OLD_TC_GEN2_LABWARE_OFFSET
+
+from opentrons.types import Location, Point, LocationLabware
+from opentrons.motion_planning.adjacent_slots_getters import (
+    get_north_south_slots,
+    get_east_west_slots,
+    get_adjacent_slots,
+)
+
+from opentrons.drivers.types import ThermocyclerLidStatus
+from opentrons.hardware_control.modules.types import (
+    ModuleModel,
+    ModuleType,
+    module_model_from_string,
+    ThermocyclerModuleModel,
+)
+
+if TYPE_CHECKING:
+    from opentrons.protocol_api.labware import Labware
+
+
+_log = logging.getLogger(__name__)
+
+
+class ThermocyclerConfiguration(str, Enum):
+    FULL = "full"
+    SEMI = "semi"
+
+
+class NoSuchModuleError(ValueError):
+    """An error raised if a requested model does not match a known module."""
+
+
+class PipetteMovementRestrictedByHeaterShakerError(Exception):
+    """Error raised when trying to move to labware restricted by Heater-Shaker."""
+
+
+# TODO (spp, 2022-05-09): add tests
+class ModuleGeometry:
+    """
+    This class represents an active peripheral, such as an Opentrons Magnetic
+    Module, Temperature Module or Thermocycler Module. It defines the physical
+    geometry of the device (primarily the offset that modifies the position of
+    the labware mounted on top of it).
+    """
+
+    @property
+    def separate_calibration(self) -> bool:
+        _log.warning(
+            "ModuleGeometry.separate_calibrations is a deprecated internal property."
+            " It has no longer has meaning, but will always return `True`"
+        )
+        return True
+
+    def __init__(
+        self,
+        display_name: str,
+        model: ModuleModel,
+        module_type: ModuleType,
+        offset: Point,
+        overall_height: float,
+        height_over_labware: float,
+        parent: Location,
+    ) -> None:
+        """
+        Create a Module for tracking the position of a module.
+
+        Note that modules do not currently have a concept of calibration apart
+        from calibration of labware on top of the module. The practical result
+        of this is that if the module parent :py:class:`.Location` is
+        incorrect, then a correct calibration of one labware on the deck would
+        be incorrect on the module, and vice-versa. Currently, the way around
+        this would be to correct the :py:class:`.Location` so that the
+        calibrated labware is targeted accurately in both positions.
+
+        :param display_name: A human-readable display name of only the module
+                             (for instance, "Thermocycler Module" - not
+                             including parents or location)
+        :param model: The model of module this represents
+        :param offset: The offset from the slot origin at which labware loaded
+                       on this module should be placed
+        :param overall_height: The height of the module without labware
+        :param height_over_labware: The height of this module over the top of
+                                    the labware
+        :param parent: A location representing location of the front left of
+                       the outside of the module (usually the front-left corner
+                       of a slot on the deck).
+        :type parent: :py:class:`.Location`
+        """
+        self._parent = parent
+        self._module_type = module_type
+
+        self._display_name = display_name
+        self._model = model
+        self._offset = offset
+        self._height = overall_height + self._parent.point.z
+        self._over_labware = height_over_labware
+        self._labware: Optional[Labware] = None
+        self._location = Location(point=self._offset + self._parent.point, labware=self)
+
+    def add_labware(self, labware: Labware) -> Labware:
+        if self._labware is not None:
+            raise RuntimeError(f"{self._labware} is already on this module")
+        self._labware = labware
+        return self._labware
+
+    def reset_labware(self) -> None:
+        self._labware = None
+
+    @property
+    def display_name(self) -> str:
+        return self._display_name
+
+    @property
+    def model(self) -> ModuleModel:
+        return self._model
+
+    @property
+    def load_name(self) -> str:
+        # Mypy (at the time of writing, v0.910) incorrectly types self.model.value as
+        # Any. It seems to have trouble with it being a union of enums.
+        assert isinstance(self.model.value, str)
+        return self.model.value
+
+    @property
+    def module_type(self) -> ModuleType:
+        """The Moduletype"""
+        return self._module_type
+
+    @property
+    def parent(self) -> LocationLabware:
+        return self._parent.labware.object
+
+    @property
+    def labware(self) -> Optional[Labware]:
+        return self._labware
+
+    @property
+    def location(self) -> Location:
+        """
+        :return: a :py:class:`.Location` representing the top of the module
+        """
+        return self._location
+
+    @property
+    def labware_offset(self) -> Point:
+        """
+        :return: a :py:class:`.Point` representing the transformation
+        between the critical point of the module and the critical
+        point of its contained labware
+        """
+        return self._offset
+
+    @property
+    def highest_z(self) -> float:
+        if self.labware:
+            return self.labware.highest_z + self._over_labware
+        else:
+            return self._height
+
+    def __repr__(self) -> str:
+        location = f" on {self.parent}" if isinstance(self.parent, str) else ""
+        return f"{self._display_name}{location}"
+
+
+class ThermocyclerGeometry(ModuleGeometry):
+    def __init__(
+        self,
+        display_name: str,
+        model: ModuleModel,
+        module_type: ModuleType,
+        offset: Point,
+        overall_height: float,
+        height_over_labware: float,
+        lid_height: float,
+        parent: Location,
+        configuration: ThermocyclerConfiguration = ThermocyclerConfiguration.FULL,
+    ) -> None:
+        """
+        Create a Module for tracking the position of a module.
+
+        Note that modules do not currently have a concept of calibration apart
+        from calibration of labware on top of the module. The practical result
+        of this is that if the module parent :py:class:`.Location` is
+        incorrect, then a correct calibration of one labware on the deck would
+        be incorrect on the module, and vice-versa. Currently, the way around
+        this would be to correct the :py:class:`.Location` so that the
+        calibrated labware is targeted accurately in both positions.
+
+        :param display_name: A human-readable display name of only the module
+                             (for instance, "Thermocycler Module" - not
+                             including parents or location)
+        :param model: The model of module this represents
+        :param offset: The offset from the slot origin at which labware loaded
+                       on this module should be placed
+        :param overall_height: The height of the module without labware
+        :param height_over_labware: The height of this module over the top of
+                                    the labware
+        :param parent: A location representing location of the front left of
+                       the outside of the module (usually the front-left corner
+                       of a slot on the deck).
+        :type parent: :py:class:`.Location`
+        :param configuration: Used to specify the slot configuration of
+                              the Thermocycler. It should by of type
+                              :py:class:`.ThermocyclerConfiguration` and can
+                              either be FULL or SEMI.
+        """
+        super().__init__(
+            display_name,
+            model,
+            module_type,
+            offset,
+            overall_height,
+            height_over_labware,
+            parent,
+        )
+        self._lid_height = lid_height
+        self._lid_status = ThermocyclerLidStatus.OPEN  # Needs to reflect true status
+        self._configuration = configuration
+        if self.is_semi_configuration:
+            self._offset = self._offset + Point(-23.28, 0, 0)
+
+    @property
+    def highest_z(self) -> float:
+        # TODO: BC 2019-08-27 this highest_z value represents the distance
+        # from the top of the open TC chassis to the base. Once we have a
+        # more robust collision detection system in place, the collision
+        # model for the TC should change based on it's lid_status
+        # (open or closed). A prerequisite for that check will be
+        # path-specific highest z calculations, as opposed to the current
+        # global check on instrument.move_to. For example: a move from slot 1
+        # to slot 3 should only check the highest z of all deck items between
+        # the source and destination in the x,y plane.
+        return super().highest_z
+
+    @property
+    def lid_status(self) -> ThermocyclerLidStatus:
+        return self._lid_status
+
+    @lid_status.setter
+    def lid_status(self, status: ThermocyclerLidStatus) -> None:
+        self._lid_status = status
+
+    @property
+    def is_semi_configuration(self) -> bool:
+        return bool(self._configuration == ThermocyclerConfiguration.SEMI)
+
+    # TODO(mc, 2022-11-16): this method causes bugs and should not be used;
+    # Thermocycler `configuration="semi"` does not work properly and should be removed
+    # https://opentrons.atlassian.net/browse/RSS-106
+    def labware_accessor(self, labware: Labware) -> Labware:
+        from opentrons.protocol_api.labware import Labware
+        from opentrons.protocol_api.core.legacy.legacy_labware_core import (
+            LegacyLabwareCore,
+        )
+
+        definition = labware._core.get_definition()
+
+        # For type checking. This should always pass because
+        # opentrons.protocol_api.core.legacy should only load labware with schema 2.
+        assert definition["schemaVersion"] == 2
+
+        # Block first three columns from being accessed
+        definition["ordering"] = definition["ordering"][2::]
+        return Labware(
+            core=LegacyLabwareCore(definition, super().location),
+            api_version=labware.api_version,
+            protocol_core=None,  # type: ignore[arg-type]
+            core_map=None,  # type: ignore[arg-type]
+        )
+
+    def add_labware(self, labware: Labware) -> Labware:
+        if self._labware is not None:
+            raise RuntimeError(f"{self._labware} is already on this module")
+        if self.lid_status == "closed":
+            raise RuntimeError("Cannot place labware in closed module")
+        if self.is_semi_configuration:
+            self._labware = self.labware_accessor(labware)
+        else:
+            self._labware = labware
+        return self._labware
+
+    def flag_unsafe_move(
+        self,
+        to_loc: Location,
+        from_loc: Location,
+        lid_position: Optional[str],
+    ) -> None:
+        to_lw, to_well = to_loc.labware.get_parent_labware_and_well()
+        from_lw, from_well = from_loc.labware.get_parent_labware_and_well()
+
+        if (
+            self.labware is not None
+            and (self.labware == to_lw or self.labware == from_lw)
+            and lid_position != "open"
+        ):
+            raise RuntimeError(
+                "Cannot move to labware loaded in Thermocycler"
+                " when lid is not fully open."
+            )
+
+
+class HeaterShakerGeometry(ModuleGeometry):
+    """Class holding the state of a Heater-Shaker's physical geometry."""
+
+    def flag_unsafe_move(
+        self,
+        to_slot: int,
+        is_tiprack: bool,
+        is_using_multichannel: bool,
+        is_labware_latch_closed: bool,
+        is_plate_shaking: bool,
+    ) -> None:
+        """Raise error if unsafe to move pipette due to Heater-Shaker placement."""
+        assert isinstance(self.parent, str), "Could not determine module slot location"
+
+        heater_shaker_slot = int(self.parent)
+        dest_east_west = to_slot in get_east_west_slots(heater_shaker_slot)
+        dest_north_south = to_slot in get_north_south_slots(heater_shaker_slot)
+        dest_heater_shaker = to_slot == heater_shaker_slot
+
+        # If Heater-Shaker is running, can't move to or around it
+        if (
+            any([dest_east_west, dest_north_south, dest_heater_shaker])
+            and is_plate_shaking
+        ):
+            raise PipetteMovementRestrictedByHeaterShakerError(
+                "Cannot move pipette to Heater-Shaker or adjacent slot while module is shaking"
+            )
+
+        # If Heater-Shaker's latch is open, can't move to it or east and west of it
+        elif (dest_east_west or dest_heater_shaker) and not is_labware_latch_closed:
+            raise PipetteMovementRestrictedByHeaterShakerError(
+                "Cannot move pipette to Heater-Shaker or adjacent slot to the left or right while labware latch is open"
+            )
+
+        elif is_using_multichannel:
+            # Can't go to east/west slot under any circumstances if pipette is multi-channel
+            if dest_east_west:
+                raise PipetteMovementRestrictedByHeaterShakerError(
+                    "Cannot move 8-Channel pipette to slot adjacent to the left or right of Heater-Shaker"
+                )
+            # Can only go north/south if the labware is a tip rack
+            elif dest_north_south and not is_tiprack:
+                raise PipetteMovementRestrictedByHeaterShakerError(
+                    "Cannot move 8-Channel pipette to non-tip-rack labware directly in front of or behind a Heater-Shaker"
+                )
+
+    def is_pipette_blocking_shake_movement(
+        self, pipette_location: Optional[Location]
+    ) -> bool:
+        """Check whether pipette is parked adjacent to Heater-Shaker.
+
+        Returns True if pipette's last known location was in a slot adjacent to or
+        on the Heater-Shaker. Also returns True if last location is not known or is
+        not associated with a slot.
+        """
+        if pipette_location is None:
+            # If we don't know the pipette's latest location then let's be extra
+            # cautious and call it blocking
+            return True
+
+        pipette_location_slot = pipette_location.labware.first_parent()
+        if pipette_location_slot is None:
+            # If a location is not associated w/ a slot (e.g., if it has labware=None)
+            # then we don't know if it's close to the h/s, so, we will be cautious
+            # and call it blocking
+            return True
+
+        heater_shaker_slot = self.parent
+
+        assert isinstance(
+            heater_shaker_slot, str
+        ), "Could not determine module slot location"
+
+        return heater_shaker_slot == pipette_location_slot or int(
+            pipette_location_slot
+        ) in get_adjacent_slots(int(heater_shaker_slot))
+
+    def is_pipette_blocking_latch_movement(
+        self, pipette_location: Optional[Location]
+    ) -> bool:
+        """Check whether pipette is parked left or right of Heater-Shaker.
+
+        Returns True is pipette's last known location was on the Heater-Shaker
+        or in a slot adjacent to its left or right. Also returns True if last
+        location is not known or is not associated with a slot.
+        """
+        if pipette_location is None:
+            # If we don't know the pipette's latest location then let's be extra
+            # cautious and call it blocking
+            return True
+
+        pipette_location_slot = pipette_location.labware.first_parent()
+        if pipette_location_slot is None:
+            # If a location is not associated w/ a slot (e.g., if it has labware=None)
+            # then we don't know if it's close to the h/s, so, we will be cautious
+            # and call it blocking
+            return True
+
+        heater_shaker_slot = self.parent
+
+        assert isinstance(
+            heater_shaker_slot, str
+        ), "Could not determine module slot location"
+
+        return heater_shaker_slot == pipette_location_slot or int(
+            pipette_location_slot
+        ) in get_east_west_slots(int(heater_shaker_slot))
+
+
+def create_geometry(
+    definition: ModuleDefinitionV3,
+    parent: Location,
+    configuration: Optional[str],
+) -> ModuleGeometry:
+    """Create a module geometry object from the module's definition and location.
+
+    The definition should be schema checked before being passed to this
+    function; all definitions passed here are assumed to be valid.
+    """
+    module_type = ModuleType(definition["moduleType"])
+    module_model = module_model_from_string(definition["model"])
+    overall_height = definition["dimensions"]["bareOverallHeight"]
+    height_over_labware = definition["dimensions"]["overLabwareHeight"]
+    display_name = definition["displayName"]
+
+    if module_model == ThermocyclerModuleModel.THERMOCYCLER_V2:
+        pre_transform: NDArray[np.double] = np.array(
+            (
+                OLD_TC_GEN2_LABWARE_OFFSET["x"],
+                OLD_TC_GEN2_LABWARE_OFFSET["y"],
+                OLD_TC_GEN2_LABWARE_OFFSET["z"],
+                1,
+            )
+        )
+    else:
+        pre_transform = np.array(
+            (
+                definition["labwareOffset"]["x"],
+                definition["labwareOffset"]["y"],
+                definition["labwareOffset"]["z"],
+                1,
+            )
+        )
+    if not parent.labware.is_slot:
+        par = ""
+        _log.warning(
+            f"module location parent labware was {parent.labware} which is"
+            "not a slot name; slot transforms will not be loaded"
+        )
+    else:
+        par = str(parent.labware.object)
+
+    # This ModuleGeometry class is only used in Python Protocol API versions <=2.13,
+    # which only support the OT-2, so we can ignore OT-3s and hard-code "ot2_standard."
+    # We also assume that "ot2_short_trash" has the same transforms as "ot2_standard."
+    xforms_ser = (
+        definition["slotTransforms"]
+        .get("ot2_standard", {})
+        .get(
+            par,
+            {"labwareOffset": [[1, 0, 0, 0], [0, 1, 0, 0], [0, 0, 1, 0], [0, 0, 0, 1]]},
+        )
+    )
+    xform_ser = xforms_ser["labwareOffset"]
+
+    # apply the slot transform if any
+    xform: NDArray[np.double] = np.array(xform_ser)
+    xformed = np.dot(xform, pre_transform)
+    labware_offset = Point(xformed[0], xformed[1], xformed[2])
+
+    if module_type == ModuleType.MAGNETIC or module_type == ModuleType.TEMPERATURE:
+        return ModuleGeometry(
+            parent=parent,
+            offset=labware_offset,
+            overall_height=overall_height,
+            height_over_labware=height_over_labware,
+            model=module_model,
+            module_type=module_type,
+            display_name=display_name,
+        )
+    elif module_type == ModuleType.THERMOCYCLER:
+        return ThermocyclerGeometry(
+            parent=parent,
+            offset=labware_offset,
+            overall_height=overall_height,
+            height_over_labware=height_over_labware,
+            model=module_model,
+            module_type=module_type,
+            display_name=display_name,
+            lid_height=definition["dimensions"]["lidHeight"],
+            configuration=(
+                ThermocyclerConfiguration(configuration)
+                if configuration is not None
+                else ThermocyclerConfiguration.FULL
+            ),
+        )
+    elif module_type == ModuleType.HEATER_SHAKER:
+        return HeaterShakerGeometry(
+            parent=parent,
+            offset=labware_offset,
+            overall_height=overall_height,
+            height_over_labware=height_over_labware,
+            model=module_model,
+            module_type=module_type,
+            display_name=display_name,
+        )
+    else:
+        raise AssertionError(f"Module type {module_type} is invalid")
+
+
+def load_definition(model: str) -> ModuleDefinitionV3:
+    """Load the geometry definition of a given module by model."""
+    try:
+        return module.load_definition("3", model)
+    except module.ModuleNotFoundError:
+        raise NoSuchModuleError(f'Could not find a module with model "{model}"')
+
+
+def models_compatible(
+    requested_model: ModuleModel, candidate_definition: ModuleDefinitionV3
+) -> bool:
+    """Check if a requested model is compatible with a given definition."""
+    return (
+        requested_model.value == candidate_definition["model"]
+        or requested_model.value in candidate_definition["compatibleWith"]
+    )

opentrons/protocol_api/core/legacy/well_geometry.py

@@ -0,0 +1,148 @@
+from __future__ import annotations
+
+from typing import Optional, cast, TYPE_CHECKING
+
+from opentrons.types import Point
+from opentrons_shared_data.labware.types import (
+    WellDefinition2 as WellDefinition,
+    CircularWellDefinition2 as CircularWellDefinition,
+    RectangularWellDefinition2 as RectangularWellDefinition,
+)
+
+if TYPE_CHECKING:
+    from .legacy_labware_core import LegacyLabwareCore
+
+
+class WellGeometry:
+    def __init__(
+        self,
+        well_props: WellDefinition,
+        parent_point: Point,
+        parent_object: LegacyLabwareCore,
+    ):
+        """
+        Construct a well geometry object.
+
+        :param well_props: Properties from the labware definition
+        :param parent_point: The coordinate of parent labware
+        :param parent_object: The parent labware
+        """
+
+        self._position = (
+            Point(
+                well_props["x"], well_props["y"], well_props["z"] + well_props["depth"]
+            )
+            + parent_point
+        )
+
+        if not parent_object:
+            raise ValueError("Wells must have a parent")
+
+        self._parent = parent_object
+
+        self._length: Optional[float] = None
+        self._width: Optional[float] = None
+        self._diameter: Optional[float] = None
+
+        shape = well_props["shape"]
+        if shape == "rectangular":
+            rect_props = cast(RectangularWellDefinition, well_props)
+            self._length = rect_props["xDimension"]
+            self._width = rect_props["yDimension"]
+            self._x_size = self._length
+            self._y_size = self._width
+        elif shape == "circular":
+            circular_props = cast(CircularWellDefinition, well_props)
+            self._diameter = circular_props["diameter"]
+            self._x_size = self._y_size = self._diameter
+        else:
+            raise ValueError(f'Shape "{shape}" is not a supported well shape')
+
+        self._max_volume = well_props["totalLiquidVolume"]
+        self._depth = well_props["depth"]
+
+    @property
+    def parent(self) -> LegacyLabwareCore:
+        return self._parent
+
+    @property
+    def position(self) -> Point:
+        return self._position
+
+    @property
+    def diameter(self) -> Optional[float]:
+        return self._diameter
+
+    @property
+    def length(self) -> Optional[float]:
+        return self._length
+
+    @property
+    def width(self) -> Optional[float]:
+        return self._width
+
+    @property
+    def depth(self) -> float:
+        return self._depth
+
+    def top(self, z: float = 0.0) -> Point:
+        return self._position + Point(0, 0, z)
+
+    def bottom(self, z: float = 0.0) -> Point:
+        top = self.top()
+        bottom_z = top.z - self._depth + z
+        return Point(x=top.x, y=top.y, z=bottom_z)
+
+    def center(self) -> Point:
+        top = self.top()
+        center_z = top.z - (self._depth / 2.0)
+        return Point(x=top.x, y=top.y, z=center_z)
+
+    @property
+    def max_volume(self) -> float:
+        return self._max_volume
+
+    def from_center_cartesian(self, x: float, y: float, z: float) -> Point:
+        """
+        Specifies an arbitrary point in deck coordinates based
+        on percentages of the radius in each axis. For example, to specify the
+        back-right corner of a well at 1/4 of the well depth from the bottom,
+        the call would be `from_center_cartesian(1, 1, -0.5)`.
+
+        No checks are performed to ensure that the resulting position will be
+        inside of the well.
+
+        To use this point in a liquid handling command, you must create a
+        location object using the well such as,
+
+        .. code-block:: python
+
+            from opentrons import types
+
+            # Cannot be passed into a liquid handling function
+            point = well.from_center_cartesian(1, 1, -0.5)
+
+            # Can be passed into a liquid handling function
+            location = types.Location(
+                well.from_center_cartesian(1, 1, -0.5), well)
+
+        :param x: a float in the range [-1.0, 1.0] for a percentage of half of
+            the radius/length in the X axis
+        :param y: a float in the range [-1.0, 1.0] for a percentage of half of
+            the radius/width in the Y axis
+        :param z: a float in the range [-1.0, 1.0] for a percentage of half of
+            the height above/below the center
+
+        :return: a Point representing the specified location in absolute deck
+        coordinates
+        """
+        center = self.center()
+        x_size = self._x_size
+        y_size = self._y_size
+        z_size = self._depth
+
+        return Point(
+            x=center.x + (x * (x_size / 2.0)),
+            y=center.y + (y * (y_size / 2.0)),
+            z=center.z + (z * (z_size / 2.0)),
+        )