From 0c4d3717c7742d4ead6e8fc61f26fa0f478785b2 Mon Sep 17 00:00:00 2001 From: Sanniti Date: Tue, 8 Oct 2024 16:24:16 -0400 Subject: [PATCH 1/2] moved pipette movement conflict to separate file --- .../protocol_api/core/engine/deck_conflict.py | 297 --------------- .../protocol_api/core/engine/instrument.py | 18 +- .../core/engine/pipette_movement_conflict.py | 348 ++++++++++++++++++ .../core/engine/test_deck_conflict.py | 22 +- .../core/engine/test_instrument_core.py | 26 +- .../test_pipette_movement_deck_conflicts.py | 2 +- 6 files changed, 383 insertions(+), 330 deletions(-) create mode 100644 api/src/opentrons/protocol_api/core/engine/pipette_movement_conflict.py diff --git a/api/src/opentrons/protocol_api/core/engine/deck_conflict.py b/api/src/opentrons/protocol_api/core/engine/deck_conflict.py index abf47212dac..ee724ea5ca3 100644 --- a/api/src/opentrons/protocol_api/core/engine/deck_conflict.py +++ b/api/src/opentrons/protocol_api/core/engine/deck_conflict.py @@ -10,16 +10,13 @@ overload, Union, TYPE_CHECKING, - List, ) from opentrons_shared_data.errors.exceptions import MotionPlanningFailureError from opentrons_shared_data.module import FLEX_TC_LID_COLLISION_ZONE -from opentrons.hardware_control import CriticalPoint from opentrons.hardware_control.modules.types import ModuleType from opentrons.motion_planning import deck_conflict as wrapped_deck_conflict -from opentrons.motion_planning import adjacent_slots_getters from opentrons.protocol_engine import ( StateView, @@ -28,16 +25,10 @@ OnLabwareLocation, AddressableAreaLocation, OFF_DECK_LOCATION, - WellLocation, - DropTipWellLocation, ) from opentrons.protocol_engine.errors.exceptions import LabwareNotLoadedOnModuleError -from opentrons.protocol_engine.types import ( - StagingSlotLocation, -) from opentrons.types import DeckSlotName, StagingSlotName, Point from ...disposal_locations import TrashBin, WasteChute -from . import point_calculations if TYPE_CHECKING: from ...labware import Labware @@ -193,294 +184,6 @@ def check( ) -# TODO (spp, 2023-02-16): move pipette movement safety checks to its own separate file. -def check_safe_for_pipette_movement( - engine_state: StateView, - pipette_id: str, - labware_id: str, - well_name: str, - well_location: Union[WellLocation, DropTipWellLocation], -) -> 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 - ) - 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." - ) - - labware_slot = engine_state.geometry.get_ancestor_slot_name(labware_id) - - 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).z - adapter_height = engine_state.labware.get_dimensions(tiprack_parent.labwareId).z - 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 - ) - - def _map_labware( engine_state: StateView, labware_id: str, diff --git a/api/src/opentrons/protocol_api/core/engine/instrument.py b/api/src/opentrons/protocol_api/core/engine/instrument.py index 55519e7899c..8fe2b8d7f6e 100644 --- a/api/src/opentrons/protocol_api/core/engine/instrument.py +++ b/api/src/opentrons/protocol_api/core/engine/instrument.py @@ -34,7 +34,7 @@ from opentrons.protocol_api._nozzle_layout import NozzleLayout from opentrons.hardware_control.nozzle_manager import NozzleConfigurationType from opentrons.hardware_control.nozzle_manager import NozzleMap -from . import deck_conflict, overlap_versions +from . import overlap_versions, pipette_movement_conflict from ..instrument import AbstractInstrument from .well import WellCore @@ -153,7 +153,7 @@ def aspirate( absolute_point=location.point, ) ) - deck_conflict.check_safe_for_pipette_movement( + pipette_movement_conflict.check_safe_for_pipette_movement( engine_state=self._engine_client.state, pipette_id=self._pipette_id, labware_id=labware_id, @@ -244,7 +244,7 @@ def dispense( absolute_point=location.point, ) ) - deck_conflict.check_safe_for_pipette_movement( + pipette_movement_conflict.check_safe_for_pipette_movement( engine_state=self._engine_client.state, pipette_id=self._pipette_id, labware_id=labware_id, @@ -321,7 +321,7 @@ def blow_out( absolute_point=location.point, ) ) - deck_conflict.check_safe_for_pipette_movement( + pipette_movement_conflict.check_safe_for_pipette_movement( engine_state=self._engine_client.state, pipette_id=self._pipette_id, labware_id=labware_id, @@ -371,7 +371,7 @@ def touch_tip( well_location = WellLocation( origin=WellOrigin.TOP, offset=WellOffset(x=0, y=0, z=z_offset) ) - deck_conflict.check_safe_for_pipette_movement( + pipette_movement_conflict.check_safe_for_pipette_movement( engine_state=self._engine_client.state, pipette_id=self._pipette_id, labware_id=labware_id, @@ -421,12 +421,12 @@ def pick_up_tip( well_name=well_name, absolute_point=location.point, ) - deck_conflict.check_safe_for_tip_pickup_and_return( + pipette_movement_conflict.check_safe_for_tip_pickup_and_return( engine_state=self._engine_client.state, pipette_id=self._pipette_id, labware_id=labware_id, ) - deck_conflict.check_safe_for_pipette_movement( + pipette_movement_conflict.check_safe_for_pipette_movement( engine_state=self._engine_client.state, pipette_id=self._pipette_id, labware_id=labware_id, @@ -486,12 +486,12 @@ def drop_tip( well_location = DropTipWellLocation() if self._engine_client.state.labware.is_tiprack(labware_id): - deck_conflict.check_safe_for_tip_pickup_and_return( + pipette_movement_conflict.check_safe_for_tip_pickup_and_return( engine_state=self._engine_client.state, pipette_id=self._pipette_id, labware_id=labware_id, ) - deck_conflict.check_safe_for_pipette_movement( + pipette_movement_conflict.check_safe_for_pipette_movement( engine_state=self._engine_client.state, pipette_id=self._pipette_id, labware_id=labware_id, diff --git a/api/src/opentrons/protocol_api/core/engine/pipette_movement_conflict.py b/api/src/opentrons/protocol_api/core/engine/pipette_movement_conflict.py new file mode 100644 index 00000000000..bfe98e1f217 --- /dev/null +++ b/api/src/opentrons/protocol_api/core/engine/pipette_movement_conflict.py @@ -0,0 +1,348 @@ +"""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_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, + WellLocation, + DropTipWellLocation, +) +from opentrons.protocol_engine.types import ( + StagingSlotLocation, +) +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( + engine_state: StateView, + pipette_id: str, + labware_id: str, + well_name: str, + well_location: Union[WellLocation, DropTipWellLocation], +) -> 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 + ) + 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." + ) + + labware_slot = engine_state.geometry.get_ancestor_slot_name(labware_id) + + 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).z + adapter_height = engine_state.labware.get_dimensions(tiprack_parent.labwareId).z + 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 + ) diff --git a/api/tests/opentrons/protocol_api/core/engine/test_deck_conflict.py b/api/tests/opentrons/protocol_api/core/engine/test_deck_conflict.py index 9a46318c8b8..42e17983018 100644 --- a/api/tests/opentrons/protocol_api/core/engine/test_deck_conflict.py +++ b/api/tests/opentrons/protocol_api/core/engine/test_deck_conflict.py @@ -19,7 +19,7 @@ _TRASH_BIN_CUTOUT_FIXTURE, ) from opentrons.protocol_api.labware import Labware -from opentrons.protocol_api.core.engine import deck_conflict +from opentrons.protocol_api.core.engine import deck_conflict, pipette_movement_conflict from opentrons.protocol_engine import ( Config, DeckSlotLocation, @@ -441,7 +441,7 @@ def test_maps_trash_bins( Point(x=50, y=50, z=40), ), pytest.raises( - deck_conflict.PartialTipMovementNotAllowedError, + pipette_movement_conflict.PartialTipMovementNotAllowedError, match="collision with items in deck slot D1", ), 0, @@ -454,7 +454,7 @@ def test_maps_trash_bins( Point(x=101, y=50, z=40), ), pytest.raises( - deck_conflict.PartialTipMovementNotAllowedError, + pipette_movement_conflict.PartialTipMovementNotAllowedError, match="collision with items in deck slot D2", ), 0, @@ -467,7 +467,7 @@ def test_maps_trash_bins( Point(x=250, y=150, z=40), ), pytest.raises( - deck_conflict.PartialTipMovementNotAllowedError, + pipette_movement_conflict.PartialTipMovementNotAllowedError, match="will result in collision with items in staging slot C4.", ), 170, @@ -623,7 +623,7 @@ def test_deck_conflict_raises_for_bad_pipette_move( ).then_return(Dimensions(90, 90, 0)) with expected_raise: - deck_conflict.check_safe_for_pipette_movement( + pipette_movement_conflict.check_safe_for_pipette_movement( engine_state=mock_state_view, pipette_id="pipette-id", labware_id="destination-labware-id", @@ -726,10 +726,10 @@ def test_deck_conflict_raises_for_collision_with_tc_lid( True ) with pytest.raises( - deck_conflict.PartialTipMovementNotAllowedError, + pipette_movement_conflict.PartialTipMovementNotAllowedError, match="Requested motion with the A12 nozzle partial configuration is outside of robot bounds for the pipette.", ): - deck_conflict.check_safe_for_pipette_movement( + pipette_movement_conflict.check_safe_for_pipette_movement( engine_state=mock_state_view, pipette_id="pipette-id", labware_id="destination-labware-id", @@ -829,7 +829,7 @@ class PipetteMovementSpec(NamedTuple): is_on_flex_adapter=False, is_partial_config=False, expected_raise=pytest.raises( - deck_conflict.UnsuitableTiprackForPipetteMotion, + pipette_movement_conflict.UnsuitableTiprackForPipetteMotion, match="A cool tiprack must be on an Opentrons Flex 96 Tip Rack Adapter", ), ), @@ -846,7 +846,7 @@ class PipetteMovementSpec(NamedTuple): is_on_flex_adapter=False, is_partial_config=False, expected_raise=pytest.raises( - deck_conflict.UnsuitableTiprackForPipetteMotion, + pipette_movement_conflict.UnsuitableTiprackForPipetteMotion, match="A cool tiprack must be on an Opentrons Flex 96 Tip Rack Adapter", ), ), @@ -856,7 +856,7 @@ class PipetteMovementSpec(NamedTuple): is_on_flex_adapter=True, is_partial_config=True, expected_raise=pytest.raises( - deck_conflict.PartialTipMovementNotAllowedError, + pipette_movement_conflict.PartialTipMovementNotAllowedError, match="A cool tiprack cannot be on an adapter taller than the tip rack", ), ), @@ -918,7 +918,7 @@ def test_valid_96_pipette_movement_for_tiprack_and_adapter( ).then_return(is_on_flex_adapter) with expected_raise: - deck_conflict.check_safe_for_tip_pickup_and_return( + pipette_movement_conflict.check_safe_for_tip_pickup_and_return( engine_state=mock_state_view, pipette_id="pipette-id", labware_id="labware-id", diff --git a/api/tests/opentrons/protocol_api/core/engine/test_instrument_core.py b/api/tests/opentrons/protocol_api/core/engine/test_instrument_core.py index 8854c070ef0..bd3cebe94d7 100644 --- a/api/tests/opentrons/protocol_api/core/engine/test_instrument_core.py +++ b/api/tests/opentrons/protocol_api/core/engine/test_instrument_core.py @@ -44,7 +44,7 @@ InstrumentCore, WellCore, ProtocolCore, - deck_conflict, + pipette_movement_conflict, ) from opentrons.protocols.api_support.definitions import MAX_SUPPORTED_VERSION from opentrons.protocols.api_support.types import APIVersion @@ -76,8 +76,10 @@ def patch_mock_pipette_movement_safety_check( decoy: Decoy, monkeypatch: pytest.MonkeyPatch ) -> None: """Replace deck_conflict.check() with a mock.""" - mock = decoy.mock(func=deck_conflict.check_safe_for_pipette_movement) - monkeypatch.setattr(deck_conflict, "check_safe_for_pipette_movement", mock) + mock = decoy.mock(func=pipette_movement_conflict.check_safe_for_pipette_movement) + monkeypatch.setattr( + pipette_movement_conflict, "check_safe_for_pipette_movement", mock + ) @pytest.fixture @@ -271,12 +273,12 @@ def test_pick_up_tip( ) decoy.verify( - deck_conflict.check_safe_for_tip_pickup_and_return( + pipette_movement_conflict.check_safe_for_tip_pickup_and_return( engine_state=mock_engine_client.state, pipette_id="abc123", labware_id="labware-id", ), - deck_conflict.check_safe_for_pipette_movement( + pipette_movement_conflict.check_safe_for_pipette_movement( engine_state=mock_engine_client.state, pipette_id="abc123", labware_id="labware-id", @@ -325,7 +327,7 @@ def test_drop_tip_no_location( subject.drop_tip(location=None, well_core=well_core, home_after=True) decoy.verify( - deck_conflict.check_safe_for_pipette_movement( + pipette_movement_conflict.check_safe_for_pipette_movement( engine_state=mock_engine_client.state, pipette_id="abc123", labware_id="labware-id", @@ -376,12 +378,12 @@ def test_drop_tip_with_location( subject.drop_tip(location=location, well_core=well_core, home_after=True) decoy.verify( - deck_conflict.check_safe_for_tip_pickup_and_return( + pipette_movement_conflict.check_safe_for_tip_pickup_and_return( engine_state=mock_engine_client.state, pipette_id="abc123", labware_id="labware-id", ), - deck_conflict.check_safe_for_pipette_movement( + pipette_movement_conflict.check_safe_for_pipette_movement( engine_state=mock_engine_client.state, pipette_id="abc123", labware_id="labware-id", @@ -504,7 +506,7 @@ def test_aspirate_from_well( ) decoy.verify( - deck_conflict.check_safe_for_pipette_movement( + pipette_movement_conflict.check_safe_for_pipette_movement( engine_state=mock_engine_client.state, pipette_id="abc123", labware_id="123abc", @@ -618,7 +620,7 @@ def test_blow_out_to_well( subject.blow_out(location=location, well_core=well_core, in_place=False) decoy.verify( - deck_conflict.check_safe_for_pipette_movement( + pipette_movement_conflict.check_safe_for_pipette_movement( engine_state=mock_engine_client.state, pipette_id="abc123", labware_id="123abc", @@ -729,7 +731,7 @@ def test_dispense_to_well( ) decoy.verify( - deck_conflict.check_safe_for_pipette_movement( + pipette_movement_conflict.check_safe_for_pipette_movement( engine_state=mock_engine_client.state, pipette_id="abc123", labware_id="123abc", @@ -1113,7 +1115,7 @@ def test_touch_tip( ) decoy.verify( - deck_conflict.check_safe_for_pipette_movement( + pipette_movement_conflict.check_safe_for_pipette_movement( engine_state=mock_engine_client.state, pipette_id="abc123", labware_id="123abc", diff --git a/api/tests/opentrons/protocol_api_integration/test_pipette_movement_deck_conflicts.py b/api/tests/opentrons/protocol_api_integration/test_pipette_movement_deck_conflicts.py index ebaf5e49971..cad2bffddf9 100644 --- a/api/tests/opentrons/protocol_api_integration/test_pipette_movement_deck_conflicts.py +++ b/api/tests/opentrons/protocol_api_integration/test_pipette_movement_deck_conflicts.py @@ -4,7 +4,7 @@ from opentrons import simulate from opentrons.protocol_api import COLUMN, ALL, SINGLE, ROW -from opentrons.protocol_api.core.engine.deck_conflict import ( +from opentrons.protocol_api.core.engine.pipette_movement_conflict import ( PartialTipMovementNotAllowedError, ) From 5212d3f3bc551a08934c51f576a681fd7088d988 Mon Sep 17 00:00:00 2001 From: Sanniti Date: Wed, 9 Oct 2024 14:10:08 -0400 Subject: [PATCH 2/2] update pipette movement conflict path in hardware-testing --- hardware-testing/hardware_testing/gravimetric/helpers.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/hardware-testing/hardware_testing/gravimetric/helpers.py b/hardware-testing/hardware_testing/gravimetric/helpers.py index eaadca2c6a9..b3533a002b0 100644 --- a/hardware-testing/hardware_testing/gravimetric/helpers.py +++ b/hardware-testing/hardware_testing/gravimetric/helpers.py @@ -41,7 +41,7 @@ WellLocation, DropTipWellLocation, ) -from opentrons.protocol_api.core.engine import deck_conflict as DeckConflit +from opentrons.protocol_api.core.engine import pipette_movement_conflict def _add_fake_simulate( @@ -455,8 +455,8 @@ def _load_pipette( front_right_nozzle="A1", back_left_nozzle="A1", ) - # override deck conflict checking cause we specially lay out our tipracks - DeckConflit.check_safe_for_pipette_movement = ( + # override pipette movement conflict checking 'cause we specially lay out our tipracks + pipette_movement_conflict.check_safe_for_pipette_movement = ( _override_check_safe_for_pipette_movement ) pipette.trash_container = trash