opentrons 8.6.0a1__py3-none-any.whl

opentrons/protocol_api/core/engine/overlap_versions.py

@@ -0,0 +1,20 @@
+"""Mappings between API versions and overlap versions."""
+from functools import lru_cache
+from typing_extensions import Final
+from opentrons.protocols.api_support.types import APIVersion
+
+_OVERLAP_VERSION_MAP: Final = {
+    APIVersion(2, 0): "v0",
+    APIVersion(2, 19): "v1",
+    APIVersion(2, 20): "v3",
+}
+
+
+@lru_cache(1)
+def overlap_for_api_version(api_version: APIVersion) -> str:
+    """Get the overlap version for a specific API version."""
+    defined = list(reversed(sorted(_OVERLAP_VERSION_MAP.keys())))
+    for version in defined:
+        if version <= api_version:
+            return _OVERLAP_VERSION_MAP[version]
+    return _OVERLAP_VERSION_MAP[APIVersion(2, 0)]

opentrons/protocol_api/core/engine/pipette_movement_conflict.py

@@ -0,0 +1,358 @@
+"""A Protocol-Engine-friendly wrapper for opentrons.motion_planning.deck_conflict."""
+from __future__ import annotations
+import logging
+from typing import (
+    Optional,
+    Tuple,
+    Union,
+    List,
+)
+
+from opentrons_shared_data.errors.exceptions import MotionPlanningFailureError
+from opentrons.protocol_engine.errors import LocationIsStagingSlotError
+from opentrons_shared_data.module import FLEX_TC_LID_COLLISION_ZONE
+
+from opentrons.hardware_control import CriticalPoint
+from opentrons.motion_planning import adjacent_slots_getters
+
+from opentrons.protocol_engine import (
+    StateView,
+    DeckSlotLocation,
+    OnLabwareLocation,
+    DropTipWellLocation,
+)
+from opentrons.protocol_engine.types import StagingSlotLocation, WellLocationType
+from opentrons.types import DeckSlotName, StagingSlotName, Point
+from . import point_calculations
+
+
+class PartialTipMovementNotAllowedError(MotionPlanningFailureError):
+    """Error raised when trying to perform a partial tip movement to an illegal location."""
+
+    def __init__(self, message: str) -> None:
+        super().__init__(
+            message=message,
+        )
+
+
+class UnsuitableTiprackForPipetteMotion(MotionPlanningFailureError):
+    """Error raised when trying to perform a pipette movement to a tip rack, based on adapter status."""
+
+    def __init__(self, message: str) -> None:
+        super().__init__(
+            message=message,
+        )
+
+
+_log = logging.getLogger(__name__)
+
+_FLEX_TC_LID_BACK_LEFT_PT = Point(
+    x=FLEX_TC_LID_COLLISION_ZONE["back_left"]["x"],
+    y=FLEX_TC_LID_COLLISION_ZONE["back_left"]["y"],
+    z=FLEX_TC_LID_COLLISION_ZONE["back_left"]["z"],
+)
+
+_FLEX_TC_LID_FRONT_RIGHT_PT = Point(
+    x=FLEX_TC_LID_COLLISION_ZONE["front_right"]["x"],
+    y=FLEX_TC_LID_COLLISION_ZONE["front_right"]["y"],
+    z=FLEX_TC_LID_COLLISION_ZONE["front_right"]["z"],
+)
+
+
+def check_safe_for_pipette_movement(  # noqa: C901
+    engine_state: StateView,
+    pipette_id: str,
+    labware_id: str,
+    well_name: str,
+    well_location: WellLocationType,
+) -> None:
+    """Check if the labware is safe to move to with a pipette in partial tip configuration.
+
+    Args:
+        engine_state: engine state view
+        pipette_id: ID of the pipette to be moved
+        labware_id: ID of the labware we are moving to
+        well_name: Name of the well to move to
+        well_location: exact location within the well to move to
+    """
+    # TODO (spp, 2023-02-06): remove this check after thorough testing.
+    #  This function is capable of checking for movement conflict regardless of
+    #  nozzle configuration.
+    if not engine_state.pipettes.get_is_partially_configured(pipette_id):
+        return
+
+    if isinstance(well_location, DropTipWellLocation):
+        # convert to WellLocation
+        well_location = engine_state.geometry.get_checked_tip_drop_location(
+            pipette_id=pipette_id,
+            labware_id=labware_id,
+            well_location=well_location,
+            partially_configured=True,
+        )
+    well_location_point = engine_state.geometry.get_well_position(
+        labware_id=labware_id,
+        well_name=well_name,
+        well_location=well_location,
+        pipette_id=pipette_id,
+    )
+    primary_nozzle = engine_state.pipettes.get_primary_nozzle(pipette_id)
+
+    destination_cp = _get_critical_point_to_use(engine_state, labware_id)
+    pipette_bounds_at_well_location = (
+        engine_state.pipettes.get_pipette_bounds_at_specified_move_to_position(
+            pipette_id=pipette_id,
+            destination_position=well_location_point,
+            critical_point=destination_cp,
+        )
+    )
+    if not _is_within_pipette_extents(
+        engine_state=engine_state,
+        pipette_id=pipette_id,
+        pipette_bounding_box_at_loc=pipette_bounds_at_well_location,
+    ):
+        raise PartialTipMovementNotAllowedError(
+            f"Requested motion with the {primary_nozzle} nozzle partial configuration"
+            f" is outside of robot bounds for the pipette."
+        )
+    ancestor = engine_state.geometry.get_ancestor_slot_name(labware_id)
+    if isinstance(ancestor, StagingSlotName):
+        raise LocationIsStagingSlotError(
+            "Cannot perform pipette actions on labware in Staging Area Slot."
+        )
+    labware_slot = ancestor
+
+    surrounding_slots = adjacent_slots_getters.get_surrounding_slots(
+        slot=labware_slot.as_int(), robot_type=engine_state.config.robot_type
+    )
+
+    if _will_collide_with_thermocycler_lid(
+        engine_state=engine_state,
+        pipette_bounds=pipette_bounds_at_well_location,
+        surrounding_regular_slots=surrounding_slots.regular_slots,
+    ):
+        raise PartialTipMovementNotAllowedError(
+            f"Moving to {engine_state.labware.get_display_name(labware_id)} in slot"
+            f" {labware_slot} with {primary_nozzle} nozzle partial configuration"
+            f" will result in collision with thermocycler lid in deck slot A1."
+        )
+
+    for regular_slot in surrounding_slots.regular_slots:
+        if _slot_has_potential_colliding_object(
+            engine_state=engine_state,
+            pipette_bounds=pipette_bounds_at_well_location,
+            surrounding_slot=regular_slot,
+        ):
+            raise PartialTipMovementNotAllowedError(
+                f"Moving to {engine_state.labware.get_display_name(labware_id)} in slot"
+                f" {labware_slot} with {primary_nozzle} nozzle partial configuration"
+                f" will result in collision with items in deck slot {regular_slot}."
+            )
+    for staging_slot in surrounding_slots.staging_slots:
+        if _slot_has_potential_colliding_object(
+            engine_state=engine_state,
+            pipette_bounds=pipette_bounds_at_well_location,
+            surrounding_slot=staging_slot,
+        ):
+            raise PartialTipMovementNotAllowedError(
+                f"Moving to {engine_state.labware.get_display_name(labware_id)} in slot"
+                f" {labware_slot} with {primary_nozzle} nozzle partial configuration"
+                f" will result in collision with items in staging slot {staging_slot}."
+            )
+
+
+def _get_critical_point_to_use(
+    engine_state: StateView, labware_id: str
+) -> Optional[CriticalPoint]:
+    """Return the critical point to use when accessing the given labware."""
+    # TODO (spp, 2024-09-17): looks like Y_CENTER of column is the same as its XY_CENTER.
+    #   I'm using this if-else ladder to be consistent with what we do in
+    #   `MotionPlanning.get_movement_waypoints_to_well()`.
+    #   We should probably use only XY_CENTER in both places.
+    if engine_state.labware.get_should_center_column_on_target_well(labware_id):
+        return CriticalPoint.Y_CENTER
+    elif engine_state.labware.get_should_center_pipette_on_target_well(labware_id):
+        return CriticalPoint.XY_CENTER
+    return None
+
+
+def _slot_has_potential_colliding_object(
+    engine_state: StateView,
+    pipette_bounds: Tuple[Point, Point, Point, Point],
+    surrounding_slot: Union[DeckSlotName, StagingSlotName],
+) -> bool:
+    """Return the slot, if any, that has an item that the pipette might collide into."""
+    # Check if slot overlaps with pipette position
+    slot_pos = engine_state.addressable_areas.get_addressable_area_position(
+        addressable_area_name=surrounding_slot.id,
+        do_compatibility_check=False,
+    )
+    slot_bounds = engine_state.addressable_areas.get_addressable_area_bounding_box(
+        addressable_area_name=surrounding_slot.id,
+        do_compatibility_check=False,
+    )
+    slot_back_left_coords = Point(slot_pos.x, slot_pos.y + slot_bounds.y, slot_pos.z)
+    slot_front_right_coords = Point(slot_pos.x + slot_bounds.x, slot_pos.y, slot_pos.z)
+
+    # If slot overlaps with pipette bounds
+    if point_calculations.are_overlapping_rectangles(
+        rectangle1=(pipette_bounds[0], pipette_bounds[1]),
+        rectangle2=(slot_back_left_coords, slot_front_right_coords),
+    ):
+        # Check z-height of items in overlapping slot
+        if isinstance(surrounding_slot, DeckSlotName):
+            slot_highest_z = engine_state.geometry.get_highest_z_in_slot(
+                DeckSlotLocation(slotName=surrounding_slot)
+            )
+        else:
+            slot_highest_z = engine_state.geometry.get_highest_z_in_slot(
+                StagingSlotLocation(slotName=surrounding_slot)
+            )
+        return slot_highest_z >= pipette_bounds[0].z
+    return False
+
+
+def _will_collide_with_thermocycler_lid(
+    engine_state: StateView,
+    pipette_bounds: Tuple[Point, Point, Point, Point],
+    surrounding_regular_slots: List[DeckSlotName],
+) -> bool:
+    """Return whether the pipette might collide with thermocycler's lid/clips on a Flex.
+
+    If any of the pipette's bounding vertices lie inside the no-go zone of the thermocycler-
+    which is the area that's to the left, back and below the thermocycler's lid's
+    protruding clips, then we will mark the movement for possible collision.
+
+    This could cause false raises for the case where an 8-channel is accessing the
+    thermocycler labware in a location such that the pipette is in the area between
+    the clips but not touching either clips. But that's a tradeoff we'll need to make
+    between a complicated check involving accurate positions of all entities involved
+    and a crude check that disallows all partial tip movements around the thermocycler.
+    """
+    # TODO (spp, 2024-02-27): Improvements:
+    #  - make the check dynamic according to lid state:
+    #     - if lid is open, check if pipette is in no-go zone
+    #     - if lid is closed, use the closed lid height to check for conflict
+    if (
+        DeckSlotName.SLOT_A1 in surrounding_regular_slots
+        and engine_state.modules.is_flex_deck_with_thermocycler()
+    ):
+        return (
+            point_calculations.are_overlapping_rectangles(
+                rectangle1=(_FLEX_TC_LID_BACK_LEFT_PT, _FLEX_TC_LID_FRONT_RIGHT_PT),
+                rectangle2=(pipette_bounds[0], pipette_bounds[1]),
+            )
+            and pipette_bounds[0].z <= _FLEX_TC_LID_BACK_LEFT_PT.z
+        )
+
+    return False
+
+
+def check_safe_for_tip_pickup_and_return(
+    engine_state: StateView,
+    pipette_id: str,
+    labware_id: str,
+) -> None:
+    """Check if the presence or absence of a tiprack adapter might cause any pipette movement issues.
+
+    A 96 channel pipette will pick up tips using cam action when it's configured
+    to use ALL nozzles. For this, the tiprack needs to be on the Flex 96 channel tiprack adapter
+    or similar or the tips will not be picked up.
+
+    On the other hand, if the pipette is configured with partial nozzle configuration,
+    it uses the usual pipette presses to pick the tips up, in which case, having the tiprack
+    on the Flex 96 channel tiprack adapter (or similar) will cause the pipette to
+    crash against the adapter posts.
+
+    In order to check if the 96-channel can move and pickup/drop tips safely, this method
+    checks for the height attribute of the tiprack adapter rather than checking for the
+    specific official adapter since users might create custom labware &/or definitions
+    compatible with the official adapter.
+    """
+    if not engine_state.pipettes.get_channels(pipette_id) == 96:
+        # Adapters only matter to 96 ch.
+        return
+
+    is_partial_config = engine_state.pipettes.get_is_partially_configured(pipette_id)
+    tiprack_name = engine_state.labware.get_display_name(labware_id)
+    tiprack_parent = engine_state.labware.get_location(labware_id)
+    if isinstance(tiprack_parent, OnLabwareLocation):  # tiprack is on an adapter
+        is_96_ch_tiprack_adapter = engine_state.labware.get_has_quirk(
+            labware_id=tiprack_parent.labwareId, quirk="tiprackAdapterFor96Channel"
+        )
+        tiprack_height = engine_state.labware.get_dimensions(labware_id=labware_id).z
+        adapter_height = engine_state.labware.get_dimensions(
+            labware_id=tiprack_parent.labwareId
+        ).z
+        # todo(mm, 2025-07-31): This looks like it needs to be something like
+        # `tiprack_top_plane < adapter_top_plane` instead of `tiprack_height < adapter_height`.
+        # In other words, take into account the stacking offset between the tip rack
+        # and its adapter.
+        if is_partial_config and tiprack_height < adapter_height:
+            raise PartialTipMovementNotAllowedError(
+                f"{tiprack_name} cannot be on an adapter taller than the tip rack"
+                f" when picking up fewer than 96 tips."
+            )
+        elif not is_partial_config and not is_96_ch_tiprack_adapter:
+            raise UnsuitableTiprackForPipetteMotion(
+                f"{tiprack_name} must be on an Opentrons Flex 96 Tip Rack Adapter"
+                f" in order to pick up or return all 96 tips simultaneously."
+            )
+
+    elif (
+        not is_partial_config
+    ):  # tiprack is not on adapter and pipette is in full config
+        raise UnsuitableTiprackForPipetteMotion(
+            f"{tiprack_name} must be on an Opentrons Flex 96 Tip Rack Adapter"
+            f" in order to pick up or return all 96 tips simultaneously."
+        )
+
+
+def _is_within_pipette_extents(
+    engine_state: StateView,
+    pipette_id: str,
+    pipette_bounding_box_at_loc: Tuple[Point, Point, Point, Point],
+) -> bool:
+    """Whether a given point is within the extents of a configured pipette on the specified robot."""
+    channels = engine_state.pipettes.get_channels(pipette_id)
+    robot_extents = engine_state.geometry.absolute_deck_extents
+    (
+        pip_back_left_bound,
+        pip_front_right_bound,
+        pip_back_right_bound,
+        pip_front_left_bound,
+    ) = pipette_bounding_box_at_loc
+
+    # Given the padding values accounted for against the deck extents,
+    # a pipette is within extents when all of the following are true:
+
+    # Each corner slot full pickup case:
+    # A1: Front right nozzle is within the rear and left-side padding limits
+    # D1: Back right nozzle is within the front and left-side padding limits
+    # A3 Front left nozzle is within the rear and right-side padding limits
+    # D3: Back left nozzle is within the front and right-side padding limits
+    # Thermocycler Column A2: Front right nozzle is within padding limits
+
+    if channels == 96:
+        return (
+            pip_front_right_bound.y
+            <= robot_extents.deck_extents.y + robot_extents.padding_rear
+            and pip_front_right_bound.x >= robot_extents.padding_left_side
+            and pip_back_right_bound.y >= robot_extents.padding_front
+            and pip_back_right_bound.x >= robot_extents.padding_left_side
+            and pip_front_left_bound.y
+            <= robot_extents.deck_extents.y + robot_extents.padding_rear
+            and pip_front_left_bound.x
+            <= robot_extents.deck_extents.x + robot_extents.padding_right_side
+            and pip_back_left_bound.y >= robot_extents.padding_front
+            and pip_back_left_bound.x
+            <= robot_extents.deck_extents.x + robot_extents.padding_right_side
+        )
+    # For 8ch pipettes we only check the rear and front extents
+    return (
+        pip_front_right_bound.y
+        <= robot_extents.deck_extents.y + robot_extents.padding_rear
+        and pip_back_right_bound.y >= robot_extents.padding_front
+        and pip_front_left_bound.y
+        <= robot_extents.deck_extents.y + robot_extents.padding_rear
+        and pip_back_left_bound.y >= robot_extents.padding_front
+    )

opentrons/protocol_api/core/engine/point_calculations.py

@@ -0,0 +1,64 @@
+from typing import Tuple
+
+from opentrons.types import Point
+
+
+def get_relative_offset(
+    point: Point,
+    size: Tuple[float, float, float],
+    x_ratio: float,
+    y_ratio: float,
+    z_ratio: float,
+) -> Point:
+    """Gets a relative offset for a deck coordinate based on percentage of the radius of each axis."""
+    x_size, y_size, z_size = size
+
+    x_offset = x_size / 2.0 * x_ratio
+    y_offset = y_size / 2.0 * y_ratio
+    z_offset = z_size / 2.0 * z_ratio
+
+    return Point(
+        x=point.x + x_offset,
+        y=point.y + y_offset,
+        z=point.z + z_offset,
+    )
+
+
+def are_overlapping_rectangles(
+    rectangle1: Tuple[Point, Point],
+    rectangle2: Tuple[Point, Point],
+) -> bool:
+    """Return whether the two provided rectangles are overlapping in 2D space.
+
+    The rectangles are assumed to be coplanar and represented by tuples of
+    the back-left and front right vertices (in that order) of the respective rectangles.
+    The z-coordinate of each point will be ignored.
+
+    We determine if the rectangles overlap by comparing projections of the sides of
+    the rectangles on each of the 2 axes (x & y). If the projections on each axis overlap,
+    then we can conclude that the rectangles overlap.
+
+    The projection on an axis overlaps if the distance between the first projected point
+    and the last projected point is less than the sum of the lengths of the projected sides
+    of the two rectangles. For example, if we have two rectangles with vertices:
+    Rect1 -> BL: (x1, y1), FR: (x2, y2)
+    Rect2 -> BL: (x3, y3), FR: (x4, y4)
+
+    Then for the two rectangles to be overlapping, they should satisfy:
+    max(x1, x2, x3, x4) - min(x1, x2, x3, x4) < (x2 - x1) + (x4 - x3)
+    AND
+    max(y1, y2, y3, y4) - min(y1, y2, y3, y4) < (y2 - y1) + (y4 - y3)
+    """
+    x_coordinates = [rectangle1[0].x, rectangle1[1].x, rectangle2[0].x, rectangle2[1].x]
+    x_length_rect1 = abs(rectangle1[1].x - rectangle1[0].x)
+    x_length_rect2 = abs(rectangle2[1].x - rectangle2[0].x)
+    overlapping_in_x = (
+        abs(max(x_coordinates) - min(x_coordinates)) < x_length_rect1 + x_length_rect2
+    )
+    y_coordinates = [rectangle1[0].y, rectangle1[1].y, rectangle2[0].y, rectangle2[1].y]
+    y_length_rect1 = abs(rectangle1[1].y - rectangle1[0].y)
+    y_length_rect2 = abs(rectangle2[1].y - rectangle2[0].y)
+    overlapping_in_y = (
+        abs(max(y_coordinates) - min(y_coordinates)) < y_length_rect1 + y_length_rect2
+    )
+    return overlapping_in_x and overlapping_in_y