opentrons 8.6.0__py3-none-any.whl
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- opentrons/__init__.py +150 -0
- opentrons/_version.py +34 -0
- opentrons/calibration_storage/__init__.py +54 -0
- opentrons/calibration_storage/deck_configuration.py +62 -0
- opentrons/calibration_storage/encoder_decoder.py +31 -0
- opentrons/calibration_storage/file_operators.py +142 -0
- opentrons/calibration_storage/helpers.py +103 -0
- opentrons/calibration_storage/ot2/__init__.py +34 -0
- opentrons/calibration_storage/ot2/deck_attitude.py +85 -0
- opentrons/calibration_storage/ot2/mark_bad_calibration.py +27 -0
- opentrons/calibration_storage/ot2/models/__init__.py +0 -0
- opentrons/calibration_storage/ot2/models/v1.py +149 -0
- opentrons/calibration_storage/ot2/pipette_offset.py +129 -0
- opentrons/calibration_storage/ot2/tip_length.py +281 -0
- opentrons/calibration_storage/ot3/__init__.py +31 -0
- opentrons/calibration_storage/ot3/deck_attitude.py +83 -0
- opentrons/calibration_storage/ot3/gripper_offset.py +156 -0
- opentrons/calibration_storage/ot3/models/__init__.py +0 -0
- opentrons/calibration_storage/ot3/models/v1.py +122 -0
- opentrons/calibration_storage/ot3/module_offset.py +138 -0
- opentrons/calibration_storage/ot3/pipette_offset.py +95 -0
- opentrons/calibration_storage/types.py +45 -0
- opentrons/cli/__init__.py +21 -0
- opentrons/cli/__main__.py +5 -0
- opentrons/cli/analyze.py +557 -0
- opentrons/config/__init__.py +631 -0
- opentrons/config/advanced_settings.py +871 -0
- opentrons/config/defaults_ot2.py +214 -0
- opentrons/config/defaults_ot3.py +499 -0
- opentrons/config/feature_flags.py +86 -0
- opentrons/config/gripper_config.py +55 -0
- opentrons/config/reset.py +203 -0
- opentrons/config/robot_configs.py +187 -0
- opentrons/config/types.py +183 -0
- opentrons/drivers/__init__.py +0 -0
- opentrons/drivers/absorbance_reader/__init__.py +11 -0
- opentrons/drivers/absorbance_reader/abstract.py +72 -0
- opentrons/drivers/absorbance_reader/async_byonoy.py +352 -0
- opentrons/drivers/absorbance_reader/driver.py +81 -0
- opentrons/drivers/absorbance_reader/hid_protocol.py +161 -0
- opentrons/drivers/absorbance_reader/simulator.py +84 -0
- opentrons/drivers/asyncio/__init__.py +0 -0
- opentrons/drivers/asyncio/communication/__init__.py +22 -0
- opentrons/drivers/asyncio/communication/async_serial.py +187 -0
- opentrons/drivers/asyncio/communication/errors.py +88 -0
- opentrons/drivers/asyncio/communication/serial_connection.py +557 -0
- opentrons/drivers/command_builder.py +102 -0
- opentrons/drivers/flex_stacker/__init__.py +13 -0
- opentrons/drivers/flex_stacker/abstract.py +214 -0
- opentrons/drivers/flex_stacker/driver.py +768 -0
- opentrons/drivers/flex_stacker/errors.py +68 -0
- opentrons/drivers/flex_stacker/simulator.py +309 -0
- opentrons/drivers/flex_stacker/types.py +367 -0
- opentrons/drivers/flex_stacker/utils.py +19 -0
- opentrons/drivers/heater_shaker/__init__.py +5 -0
- opentrons/drivers/heater_shaker/abstract.py +76 -0
- opentrons/drivers/heater_shaker/driver.py +204 -0
- opentrons/drivers/heater_shaker/simulator.py +94 -0
- opentrons/drivers/mag_deck/__init__.py +6 -0
- opentrons/drivers/mag_deck/abstract.py +44 -0
- opentrons/drivers/mag_deck/driver.py +208 -0
- opentrons/drivers/mag_deck/simulator.py +63 -0
- opentrons/drivers/rpi_drivers/__init__.py +33 -0
- opentrons/drivers/rpi_drivers/dev_types.py +94 -0
- opentrons/drivers/rpi_drivers/gpio.py +282 -0
- opentrons/drivers/rpi_drivers/gpio_simulator.py +127 -0
- opentrons/drivers/rpi_drivers/interfaces.py +15 -0
- opentrons/drivers/rpi_drivers/types.py +364 -0
- opentrons/drivers/rpi_drivers/usb.py +102 -0
- opentrons/drivers/rpi_drivers/usb_simulator.py +22 -0
- opentrons/drivers/serial_communication.py +151 -0
- opentrons/drivers/smoothie_drivers/__init__.py +4 -0
- opentrons/drivers/smoothie_drivers/connection.py +51 -0
- opentrons/drivers/smoothie_drivers/constants.py +121 -0
- opentrons/drivers/smoothie_drivers/driver_3_0.py +1933 -0
- opentrons/drivers/smoothie_drivers/errors.py +49 -0
- opentrons/drivers/smoothie_drivers/parse_utils.py +143 -0
- opentrons/drivers/smoothie_drivers/simulator.py +99 -0
- opentrons/drivers/smoothie_drivers/types.py +16 -0
- opentrons/drivers/temp_deck/__init__.py +10 -0
- opentrons/drivers/temp_deck/abstract.py +54 -0
- opentrons/drivers/temp_deck/driver.py +197 -0
- opentrons/drivers/temp_deck/simulator.py +57 -0
- opentrons/drivers/thermocycler/__init__.py +12 -0
- opentrons/drivers/thermocycler/abstract.py +99 -0
- opentrons/drivers/thermocycler/driver.py +395 -0
- opentrons/drivers/thermocycler/simulator.py +126 -0
- opentrons/drivers/types.py +107 -0
- opentrons/drivers/utils.py +222 -0
- opentrons/execute.py +742 -0
- opentrons/hardware_control/__init__.py +65 -0
- opentrons/hardware_control/__main__.py +77 -0
- opentrons/hardware_control/adapters.py +98 -0
- opentrons/hardware_control/api.py +1347 -0
- opentrons/hardware_control/backends/__init__.py +7 -0
- opentrons/hardware_control/backends/controller.py +400 -0
- opentrons/hardware_control/backends/errors.py +9 -0
- opentrons/hardware_control/backends/estop_state.py +164 -0
- opentrons/hardware_control/backends/flex_protocol.py +497 -0
- opentrons/hardware_control/backends/ot3controller.py +1930 -0
- opentrons/hardware_control/backends/ot3simulator.py +900 -0
- opentrons/hardware_control/backends/ot3utils.py +664 -0
- opentrons/hardware_control/backends/simulator.py +442 -0
- opentrons/hardware_control/backends/status_bar_state.py +240 -0
- opentrons/hardware_control/backends/subsystem_manager.py +431 -0
- opentrons/hardware_control/backends/tip_presence_manager.py +173 -0
- opentrons/hardware_control/backends/types.py +14 -0
- opentrons/hardware_control/constants.py +6 -0
- opentrons/hardware_control/dev_types.py +125 -0
- opentrons/hardware_control/emulation/__init__.py +0 -0
- opentrons/hardware_control/emulation/abstract_emulator.py +21 -0
- opentrons/hardware_control/emulation/app.py +56 -0
- opentrons/hardware_control/emulation/connection_handler.py +38 -0
- opentrons/hardware_control/emulation/heater_shaker.py +150 -0
- opentrons/hardware_control/emulation/magdeck.py +60 -0
- opentrons/hardware_control/emulation/module_server/__init__.py +8 -0
- opentrons/hardware_control/emulation/module_server/client.py +78 -0
- opentrons/hardware_control/emulation/module_server/helpers.py +130 -0
- opentrons/hardware_control/emulation/module_server/models.py +31 -0
- opentrons/hardware_control/emulation/module_server/server.py +110 -0
- opentrons/hardware_control/emulation/parser.py +74 -0
- opentrons/hardware_control/emulation/proxy.py +241 -0
- opentrons/hardware_control/emulation/run_emulator.py +68 -0
- opentrons/hardware_control/emulation/scripts/__init__.py +0 -0
- opentrons/hardware_control/emulation/scripts/run_app.py +54 -0
- opentrons/hardware_control/emulation/scripts/run_module_emulator.py +72 -0
- opentrons/hardware_control/emulation/scripts/run_smoothie.py +37 -0
- opentrons/hardware_control/emulation/settings.py +119 -0
- opentrons/hardware_control/emulation/simulations.py +133 -0
- opentrons/hardware_control/emulation/smoothie.py +192 -0
- opentrons/hardware_control/emulation/tempdeck.py +69 -0
- opentrons/hardware_control/emulation/thermocycler.py +128 -0
- opentrons/hardware_control/emulation/types.py +10 -0
- opentrons/hardware_control/emulation/util.py +38 -0
- opentrons/hardware_control/errors.py +43 -0
- opentrons/hardware_control/execution_manager.py +164 -0
- opentrons/hardware_control/instruments/__init__.py +5 -0
- opentrons/hardware_control/instruments/instrument_abc.py +39 -0
- opentrons/hardware_control/instruments/ot2/__init__.py +0 -0
- opentrons/hardware_control/instruments/ot2/instrument_calibration.py +152 -0
- opentrons/hardware_control/instruments/ot2/pipette.py +777 -0
- opentrons/hardware_control/instruments/ot2/pipette_handler.py +995 -0
- opentrons/hardware_control/instruments/ot3/__init__.py +0 -0
- opentrons/hardware_control/instruments/ot3/gripper.py +420 -0
- opentrons/hardware_control/instruments/ot3/gripper_handler.py +173 -0
- opentrons/hardware_control/instruments/ot3/instrument_calibration.py +214 -0
- opentrons/hardware_control/instruments/ot3/pipette.py +858 -0
- opentrons/hardware_control/instruments/ot3/pipette_handler.py +1030 -0
- opentrons/hardware_control/module_control.py +332 -0
- opentrons/hardware_control/modules/__init__.py +69 -0
- opentrons/hardware_control/modules/absorbance_reader.py +373 -0
- opentrons/hardware_control/modules/errors.py +7 -0
- opentrons/hardware_control/modules/flex_stacker.py +948 -0
- opentrons/hardware_control/modules/heater_shaker.py +426 -0
- opentrons/hardware_control/modules/lid_temp_status.py +35 -0
- opentrons/hardware_control/modules/magdeck.py +233 -0
- opentrons/hardware_control/modules/mod_abc.py +245 -0
- opentrons/hardware_control/modules/module_calibration.py +93 -0
- opentrons/hardware_control/modules/plate_temp_status.py +61 -0
- opentrons/hardware_control/modules/tempdeck.py +299 -0
- opentrons/hardware_control/modules/thermocycler.py +731 -0
- opentrons/hardware_control/modules/types.py +417 -0
- opentrons/hardware_control/modules/update.py +255 -0
- opentrons/hardware_control/modules/utils.py +73 -0
- opentrons/hardware_control/motion_utilities.py +318 -0
- opentrons/hardware_control/nozzle_manager.py +422 -0
- opentrons/hardware_control/ot3_calibration.py +1171 -0
- opentrons/hardware_control/ot3api.py +3227 -0
- opentrons/hardware_control/pause_manager.py +31 -0
- opentrons/hardware_control/poller.py +112 -0
- opentrons/hardware_control/protocols/__init__.py +106 -0
- opentrons/hardware_control/protocols/asyncio_configurable.py +11 -0
- opentrons/hardware_control/protocols/calibratable.py +45 -0
- opentrons/hardware_control/protocols/chassis_accessory_manager.py +90 -0
- opentrons/hardware_control/protocols/configurable.py +48 -0
- opentrons/hardware_control/protocols/event_sourcer.py +18 -0
- opentrons/hardware_control/protocols/execution_controllable.py +33 -0
- opentrons/hardware_control/protocols/flex_calibratable.py +96 -0
- opentrons/hardware_control/protocols/flex_instrument_configurer.py +52 -0
- opentrons/hardware_control/protocols/gripper_controller.py +55 -0
- opentrons/hardware_control/protocols/hardware_manager.py +51 -0
- opentrons/hardware_control/protocols/identifiable.py +16 -0
- opentrons/hardware_control/protocols/instrument_configurer.py +206 -0
- opentrons/hardware_control/protocols/liquid_handler.py +266 -0
- opentrons/hardware_control/protocols/module_provider.py +16 -0
- opentrons/hardware_control/protocols/motion_controller.py +243 -0
- opentrons/hardware_control/protocols/position_estimator.py +45 -0
- opentrons/hardware_control/protocols/simulatable.py +10 -0
- opentrons/hardware_control/protocols/stoppable.py +9 -0
- opentrons/hardware_control/protocols/types.py +27 -0
- opentrons/hardware_control/robot_calibration.py +224 -0
- opentrons/hardware_control/scripts/README.md +28 -0
- opentrons/hardware_control/scripts/__init__.py +1 -0
- opentrons/hardware_control/scripts/gripper_control.py +208 -0
- opentrons/hardware_control/scripts/ot3gripper +7 -0
- opentrons/hardware_control/scripts/ot3repl +7 -0
- opentrons/hardware_control/scripts/repl.py +187 -0
- opentrons/hardware_control/scripts/tc_control.py +97 -0
- opentrons/hardware_control/scripts/update_module_fw.py +274 -0
- opentrons/hardware_control/simulator_setup.py +260 -0
- opentrons/hardware_control/thread_manager.py +431 -0
- opentrons/hardware_control/threaded_async_lock.py +97 -0
- opentrons/hardware_control/types.py +792 -0
- opentrons/hardware_control/util.py +234 -0
- opentrons/legacy_broker.py +53 -0
- opentrons/legacy_commands/__init__.py +1 -0
- opentrons/legacy_commands/commands.py +483 -0
- opentrons/legacy_commands/helpers.py +153 -0
- opentrons/legacy_commands/module_commands.py +276 -0
- opentrons/legacy_commands/protocol_commands.py +54 -0
- opentrons/legacy_commands/publisher.py +155 -0
- opentrons/legacy_commands/robot_commands.py +51 -0
- opentrons/legacy_commands/types.py +1186 -0
- opentrons/motion_planning/__init__.py +32 -0
- opentrons/motion_planning/adjacent_slots_getters.py +168 -0
- opentrons/motion_planning/deck_conflict.py +501 -0
- opentrons/motion_planning/errors.py +35 -0
- opentrons/motion_planning/types.py +42 -0
- opentrons/motion_planning/waypoints.py +218 -0
- opentrons/ordered_set.py +138 -0
- opentrons/protocol_api/__init__.py +105 -0
- opentrons/protocol_api/_liquid.py +157 -0
- opentrons/protocol_api/_liquid_properties.py +814 -0
- opentrons/protocol_api/_nozzle_layout.py +31 -0
- opentrons/protocol_api/_parameter_context.py +300 -0
- opentrons/protocol_api/_parameters.py +31 -0
- opentrons/protocol_api/_transfer_liquid_validation.py +108 -0
- opentrons/protocol_api/_types.py +43 -0
- opentrons/protocol_api/config.py +23 -0
- opentrons/protocol_api/core/__init__.py +23 -0
- opentrons/protocol_api/core/common.py +33 -0
- opentrons/protocol_api/core/core_map.py +74 -0
- opentrons/protocol_api/core/engine/__init__.py +22 -0
- opentrons/protocol_api/core/engine/_default_labware_versions.py +179 -0
- opentrons/protocol_api/core/engine/deck_conflict.py +400 -0
- opentrons/protocol_api/core/engine/exceptions.py +19 -0
- opentrons/protocol_api/core/engine/instrument.py +2391 -0
- opentrons/protocol_api/core/engine/labware.py +238 -0
- opentrons/protocol_api/core/engine/load_labware_params.py +73 -0
- opentrons/protocol_api/core/engine/module_core.py +1027 -0
- opentrons/protocol_api/core/engine/overlap_versions.py +20 -0
- opentrons/protocol_api/core/engine/pipette_movement_conflict.py +358 -0
- opentrons/protocol_api/core/engine/point_calculations.py +64 -0
- opentrons/protocol_api/core/engine/protocol.py +1153 -0
- opentrons/protocol_api/core/engine/robot.py +139 -0
- opentrons/protocol_api/core/engine/stringify.py +74 -0
- opentrons/protocol_api/core/engine/transfer_components_executor.py +1006 -0
- opentrons/protocol_api/core/engine/well.py +241 -0
- opentrons/protocol_api/core/instrument.py +459 -0
- opentrons/protocol_api/core/labware.py +151 -0
- opentrons/protocol_api/core/legacy/__init__.py +11 -0
- opentrons/protocol_api/core/legacy/_labware_geometry.py +37 -0
- opentrons/protocol_api/core/legacy/deck.py +369 -0
- opentrons/protocol_api/core/legacy/labware_offset_provider.py +108 -0
- opentrons/protocol_api/core/legacy/legacy_instrument_core.py +709 -0
- opentrons/protocol_api/core/legacy/legacy_labware_core.py +235 -0
- opentrons/protocol_api/core/legacy/legacy_module_core.py +592 -0
- opentrons/protocol_api/core/legacy/legacy_protocol_core.py +612 -0
- opentrons/protocol_api/core/legacy/legacy_well_core.py +162 -0
- opentrons/protocol_api/core/legacy/load_info.py +67 -0
- opentrons/protocol_api/core/legacy/module_geometry.py +547 -0
- opentrons/protocol_api/core/legacy/well_geometry.py +148 -0
- opentrons/protocol_api/core/legacy_simulator/__init__.py +16 -0
- opentrons/protocol_api/core/legacy_simulator/legacy_instrument_core.py +624 -0
- opentrons/protocol_api/core/legacy_simulator/legacy_protocol_core.py +85 -0
- opentrons/protocol_api/core/module.py +484 -0
- opentrons/protocol_api/core/protocol.py +311 -0
- opentrons/protocol_api/core/robot.py +51 -0
- opentrons/protocol_api/core/well.py +116 -0
- opentrons/protocol_api/core/well_grid.py +45 -0
- opentrons/protocol_api/create_protocol_context.py +177 -0
- opentrons/protocol_api/deck.py +223 -0
- opentrons/protocol_api/disposal_locations.py +244 -0
- opentrons/protocol_api/instrument_context.py +3272 -0
- opentrons/protocol_api/labware.py +1579 -0
- opentrons/protocol_api/module_contexts.py +1447 -0
- opentrons/protocol_api/module_validation_and_errors.py +61 -0
- opentrons/protocol_api/protocol_context.py +1688 -0
- opentrons/protocol_api/robot_context.py +303 -0
- opentrons/protocol_api/validation.py +761 -0
- opentrons/protocol_engine/__init__.py +155 -0
- opentrons/protocol_engine/actions/__init__.py +65 -0
- opentrons/protocol_engine/actions/action_dispatcher.py +30 -0
- opentrons/protocol_engine/actions/action_handler.py +13 -0
- opentrons/protocol_engine/actions/actions.py +302 -0
- opentrons/protocol_engine/actions/get_state_update.py +38 -0
- opentrons/protocol_engine/clients/__init__.py +5 -0
- opentrons/protocol_engine/clients/sync_client.py +174 -0
- opentrons/protocol_engine/clients/transports.py +197 -0
- opentrons/protocol_engine/commands/__init__.py +757 -0
- opentrons/protocol_engine/commands/absorbance_reader/__init__.py +61 -0
- opentrons/protocol_engine/commands/absorbance_reader/close_lid.py +154 -0
- opentrons/protocol_engine/commands/absorbance_reader/common.py +6 -0
- opentrons/protocol_engine/commands/absorbance_reader/initialize.py +151 -0
- opentrons/protocol_engine/commands/absorbance_reader/open_lid.py +154 -0
- opentrons/protocol_engine/commands/absorbance_reader/read.py +226 -0
- opentrons/protocol_engine/commands/air_gap_in_place.py +162 -0
- opentrons/protocol_engine/commands/aspirate.py +244 -0
- opentrons/protocol_engine/commands/aspirate_in_place.py +184 -0
- opentrons/protocol_engine/commands/aspirate_while_tracking.py +211 -0
- opentrons/protocol_engine/commands/blow_out.py +146 -0
- opentrons/protocol_engine/commands/blow_out_in_place.py +119 -0
- opentrons/protocol_engine/commands/calibration/__init__.py +60 -0
- opentrons/protocol_engine/commands/calibration/calibrate_gripper.py +166 -0
- opentrons/protocol_engine/commands/calibration/calibrate_module.py +117 -0
- opentrons/protocol_engine/commands/calibration/calibrate_pipette.py +96 -0
- opentrons/protocol_engine/commands/calibration/move_to_maintenance_position.py +156 -0
- opentrons/protocol_engine/commands/command.py +308 -0
- opentrons/protocol_engine/commands/command_unions.py +974 -0
- opentrons/protocol_engine/commands/comment.py +57 -0
- opentrons/protocol_engine/commands/configure_for_volume.py +108 -0
- opentrons/protocol_engine/commands/configure_nozzle_layout.py +115 -0
- opentrons/protocol_engine/commands/custom.py +67 -0
- opentrons/protocol_engine/commands/dispense.py +194 -0
- opentrons/protocol_engine/commands/dispense_in_place.py +179 -0
- opentrons/protocol_engine/commands/dispense_while_tracking.py +204 -0
- opentrons/protocol_engine/commands/drop_tip.py +232 -0
- opentrons/protocol_engine/commands/drop_tip_in_place.py +205 -0
- opentrons/protocol_engine/commands/flex_stacker/__init__.py +64 -0
- opentrons/protocol_engine/commands/flex_stacker/common.py +900 -0
- opentrons/protocol_engine/commands/flex_stacker/empty.py +293 -0
- opentrons/protocol_engine/commands/flex_stacker/fill.py +281 -0
- opentrons/protocol_engine/commands/flex_stacker/retrieve.py +339 -0
- opentrons/protocol_engine/commands/flex_stacker/set_stored_labware.py +328 -0
- opentrons/protocol_engine/commands/flex_stacker/store.py +339 -0
- opentrons/protocol_engine/commands/generate_command_schema.py +61 -0
- opentrons/protocol_engine/commands/get_next_tip.py +134 -0
- opentrons/protocol_engine/commands/get_tip_presence.py +87 -0
- opentrons/protocol_engine/commands/hash_command_params.py +38 -0
- opentrons/protocol_engine/commands/heater_shaker/__init__.py +102 -0
- opentrons/protocol_engine/commands/heater_shaker/close_labware_latch.py +83 -0
- opentrons/protocol_engine/commands/heater_shaker/deactivate_heater.py +82 -0
- opentrons/protocol_engine/commands/heater_shaker/deactivate_shaker.py +84 -0
- opentrons/protocol_engine/commands/heater_shaker/open_labware_latch.py +110 -0
- opentrons/protocol_engine/commands/heater_shaker/set_and_wait_for_shake_speed.py +125 -0
- opentrons/protocol_engine/commands/heater_shaker/set_target_temperature.py +90 -0
- opentrons/protocol_engine/commands/heater_shaker/wait_for_temperature.py +102 -0
- opentrons/protocol_engine/commands/home.py +100 -0
- opentrons/protocol_engine/commands/identify_module.py +86 -0
- opentrons/protocol_engine/commands/labware_handling_common.py +29 -0
- opentrons/protocol_engine/commands/liquid_probe.py +464 -0
- opentrons/protocol_engine/commands/load_labware.py +210 -0
- opentrons/protocol_engine/commands/load_lid.py +154 -0
- opentrons/protocol_engine/commands/load_lid_stack.py +272 -0
- opentrons/protocol_engine/commands/load_liquid.py +95 -0
- opentrons/protocol_engine/commands/load_liquid_class.py +144 -0
- opentrons/protocol_engine/commands/load_module.py +223 -0
- opentrons/protocol_engine/commands/load_pipette.py +167 -0
- opentrons/protocol_engine/commands/magnetic_module/__init__.py +32 -0
- opentrons/protocol_engine/commands/magnetic_module/disengage.py +97 -0
- opentrons/protocol_engine/commands/magnetic_module/engage.py +119 -0
- opentrons/protocol_engine/commands/move_labware.py +546 -0
- opentrons/protocol_engine/commands/move_relative.py +102 -0
- opentrons/protocol_engine/commands/move_to_addressable_area.py +176 -0
- opentrons/protocol_engine/commands/move_to_addressable_area_for_drop_tip.py +198 -0
- opentrons/protocol_engine/commands/move_to_coordinates.py +107 -0
- opentrons/protocol_engine/commands/move_to_well.py +119 -0
- opentrons/protocol_engine/commands/movement_common.py +338 -0
- opentrons/protocol_engine/commands/pick_up_tip.py +241 -0
- opentrons/protocol_engine/commands/pipetting_common.py +443 -0
- opentrons/protocol_engine/commands/prepare_to_aspirate.py +121 -0
- opentrons/protocol_engine/commands/pressure_dispense.py +155 -0
- opentrons/protocol_engine/commands/reload_labware.py +90 -0
- opentrons/protocol_engine/commands/retract_axis.py +75 -0
- opentrons/protocol_engine/commands/robot/__init__.py +70 -0
- opentrons/protocol_engine/commands/robot/close_gripper_jaw.py +96 -0
- opentrons/protocol_engine/commands/robot/common.py +18 -0
- opentrons/protocol_engine/commands/robot/move_axes_relative.py +101 -0
- opentrons/protocol_engine/commands/robot/move_axes_to.py +100 -0
- opentrons/protocol_engine/commands/robot/move_to.py +94 -0
- opentrons/protocol_engine/commands/robot/open_gripper_jaw.py +86 -0
- opentrons/protocol_engine/commands/save_position.py +109 -0
- opentrons/protocol_engine/commands/seal_pipette_to_tip.py +353 -0
- opentrons/protocol_engine/commands/set_rail_lights.py +67 -0
- opentrons/protocol_engine/commands/set_status_bar.py +89 -0
- opentrons/protocol_engine/commands/temperature_module/__init__.py +46 -0
- opentrons/protocol_engine/commands/temperature_module/deactivate.py +86 -0
- opentrons/protocol_engine/commands/temperature_module/set_target_temperature.py +97 -0
- opentrons/protocol_engine/commands/temperature_module/wait_for_temperature.py +104 -0
- opentrons/protocol_engine/commands/thermocycler/__init__.py +152 -0
- opentrons/protocol_engine/commands/thermocycler/close_lid.py +87 -0
- opentrons/protocol_engine/commands/thermocycler/deactivate_block.py +80 -0
- opentrons/protocol_engine/commands/thermocycler/deactivate_lid.py +80 -0
- opentrons/protocol_engine/commands/thermocycler/open_lid.py +87 -0
- opentrons/protocol_engine/commands/thermocycler/run_extended_profile.py +171 -0
- opentrons/protocol_engine/commands/thermocycler/run_profile.py +124 -0
- opentrons/protocol_engine/commands/thermocycler/set_target_block_temperature.py +140 -0
- opentrons/protocol_engine/commands/thermocycler/set_target_lid_temperature.py +100 -0
- opentrons/protocol_engine/commands/thermocycler/wait_for_block_temperature.py +93 -0
- opentrons/protocol_engine/commands/thermocycler/wait_for_lid_temperature.py +89 -0
- opentrons/protocol_engine/commands/touch_tip.py +189 -0
- opentrons/protocol_engine/commands/unsafe/__init__.py +161 -0
- opentrons/protocol_engine/commands/unsafe/unsafe_blow_out_in_place.py +100 -0
- opentrons/protocol_engine/commands/unsafe/unsafe_drop_tip_in_place.py +121 -0
- opentrons/protocol_engine/commands/unsafe/unsafe_engage_axes.py +82 -0
- opentrons/protocol_engine/commands/unsafe/unsafe_place_labware.py +208 -0
- opentrons/protocol_engine/commands/unsafe/unsafe_stacker_close_latch.py +94 -0
- opentrons/protocol_engine/commands/unsafe/unsafe_stacker_manual_retrieve.py +295 -0
- opentrons/protocol_engine/commands/unsafe/unsafe_stacker_open_latch.py +91 -0
- opentrons/protocol_engine/commands/unsafe/unsafe_stacker_prepare_shuttle.py +136 -0
- opentrons/protocol_engine/commands/unsafe/unsafe_ungrip_labware.py +77 -0
- opentrons/protocol_engine/commands/unsafe/update_position_estimators.py +90 -0
- opentrons/protocol_engine/commands/unseal_pipette_from_tip.py +153 -0
- opentrons/protocol_engine/commands/verify_tip_presence.py +100 -0
- opentrons/protocol_engine/commands/wait_for_duration.py +76 -0
- opentrons/protocol_engine/commands/wait_for_resume.py +75 -0
- opentrons/protocol_engine/create_protocol_engine.py +193 -0
- opentrons/protocol_engine/engine_support.py +28 -0
- opentrons/protocol_engine/error_recovery_policy.py +81 -0
- opentrons/protocol_engine/errors/__init__.py +191 -0
- opentrons/protocol_engine/errors/error_occurrence.py +182 -0
- opentrons/protocol_engine/errors/exceptions.py +1308 -0
- opentrons/protocol_engine/execution/__init__.py +50 -0
- opentrons/protocol_engine/execution/command_executor.py +216 -0
- opentrons/protocol_engine/execution/create_queue_worker.py +102 -0
- opentrons/protocol_engine/execution/door_watcher.py +119 -0
- opentrons/protocol_engine/execution/equipment.py +819 -0
- opentrons/protocol_engine/execution/error_recovery_hardware_state_synchronizer.py +101 -0
- opentrons/protocol_engine/execution/gantry_mover.py +686 -0
- opentrons/protocol_engine/execution/hardware_stopper.py +147 -0
- opentrons/protocol_engine/execution/heater_shaker_movement_flagger.py +207 -0
- opentrons/protocol_engine/execution/labware_movement.py +297 -0
- opentrons/protocol_engine/execution/movement.py +350 -0
- opentrons/protocol_engine/execution/pipetting.py +607 -0
- opentrons/protocol_engine/execution/queue_worker.py +86 -0
- opentrons/protocol_engine/execution/rail_lights.py +25 -0
- opentrons/protocol_engine/execution/run_control.py +33 -0
- opentrons/protocol_engine/execution/status_bar.py +34 -0
- opentrons/protocol_engine/execution/thermocycler_movement_flagger.py +188 -0
- opentrons/protocol_engine/execution/thermocycler_plate_lifter.py +81 -0
- opentrons/protocol_engine/execution/tip_handler.py +550 -0
- opentrons/protocol_engine/labware_offset_standardization.py +194 -0
- opentrons/protocol_engine/notes/__init__.py +17 -0
- opentrons/protocol_engine/notes/notes.py +59 -0
- opentrons/protocol_engine/plugins.py +104 -0
- opentrons/protocol_engine/protocol_engine.py +683 -0
- opentrons/protocol_engine/resources/__init__.py +26 -0
- opentrons/protocol_engine/resources/deck_configuration_provider.py +232 -0
- opentrons/protocol_engine/resources/deck_data_provider.py +94 -0
- opentrons/protocol_engine/resources/file_provider.py +161 -0
- opentrons/protocol_engine/resources/fixture_validation.py +68 -0
- opentrons/protocol_engine/resources/labware_data_provider.py +106 -0
- opentrons/protocol_engine/resources/labware_validation.py +73 -0
- opentrons/protocol_engine/resources/model_utils.py +32 -0
- opentrons/protocol_engine/resources/module_data_provider.py +44 -0
- opentrons/protocol_engine/resources/ot3_validation.py +21 -0
- opentrons/protocol_engine/resources/pipette_data_provider.py +379 -0
- opentrons/protocol_engine/slot_standardization.py +128 -0
- opentrons/protocol_engine/state/__init__.py +1 -0
- opentrons/protocol_engine/state/_abstract_store.py +27 -0
- opentrons/protocol_engine/state/_axis_aligned_bounding_box.py +50 -0
- opentrons/protocol_engine/state/_labware_origin_math.py +636 -0
- opentrons/protocol_engine/state/_move_types.py +83 -0
- opentrons/protocol_engine/state/_well_math.py +193 -0
- opentrons/protocol_engine/state/addressable_areas.py +699 -0
- opentrons/protocol_engine/state/command_history.py +309 -0
- opentrons/protocol_engine/state/commands.py +1164 -0
- opentrons/protocol_engine/state/config.py +39 -0
- opentrons/protocol_engine/state/files.py +57 -0
- opentrons/protocol_engine/state/fluid_stack.py +138 -0
- opentrons/protocol_engine/state/geometry.py +2408 -0
- opentrons/protocol_engine/state/inner_well_math_utils.py +548 -0
- opentrons/protocol_engine/state/labware.py +1432 -0
- opentrons/protocol_engine/state/liquid_classes.py +82 -0
- opentrons/protocol_engine/state/liquids.py +73 -0
- opentrons/protocol_engine/state/module_substates/__init__.py +45 -0
- opentrons/protocol_engine/state/module_substates/absorbance_reader_substate.py +35 -0
- opentrons/protocol_engine/state/module_substates/flex_stacker_substate.py +112 -0
- opentrons/protocol_engine/state/module_substates/heater_shaker_module_substate.py +115 -0
- opentrons/protocol_engine/state/module_substates/magnetic_block_substate.py +17 -0
- opentrons/protocol_engine/state/module_substates/magnetic_module_substate.py +65 -0
- opentrons/protocol_engine/state/module_substates/temperature_module_substate.py +67 -0
- opentrons/protocol_engine/state/module_substates/thermocycler_module_substate.py +163 -0
- opentrons/protocol_engine/state/modules.py +1515 -0
- opentrons/protocol_engine/state/motion.py +373 -0
- opentrons/protocol_engine/state/pipettes.py +905 -0
- opentrons/protocol_engine/state/state.py +421 -0
- opentrons/protocol_engine/state/state_summary.py +36 -0
- opentrons/protocol_engine/state/tips.py +420 -0
- opentrons/protocol_engine/state/update_types.py +904 -0
- opentrons/protocol_engine/state/wells.py +290 -0
- opentrons/protocol_engine/types/__init__.py +310 -0
- opentrons/protocol_engine/types/automatic_tip_selection.py +39 -0
- opentrons/protocol_engine/types/command_annotations.py +53 -0
- opentrons/protocol_engine/types/deck_configuration.py +81 -0
- opentrons/protocol_engine/types/execution.py +96 -0
- opentrons/protocol_engine/types/hardware_passthrough.py +25 -0
- opentrons/protocol_engine/types/instrument.py +47 -0
- opentrons/protocol_engine/types/instrument_sensors.py +47 -0
- opentrons/protocol_engine/types/labware.py +131 -0
- opentrons/protocol_engine/types/labware_movement.py +22 -0
- opentrons/protocol_engine/types/labware_offset_location.py +111 -0
- opentrons/protocol_engine/types/labware_offset_vector.py +16 -0
- opentrons/protocol_engine/types/liquid.py +40 -0
- opentrons/protocol_engine/types/liquid_class.py +59 -0
- opentrons/protocol_engine/types/liquid_handling.py +13 -0
- opentrons/protocol_engine/types/liquid_level_detection.py +191 -0
- opentrons/protocol_engine/types/location.py +194 -0
- opentrons/protocol_engine/types/module.py +310 -0
- opentrons/protocol_engine/types/partial_tip_configuration.py +76 -0
- opentrons/protocol_engine/types/run_time_parameters.py +133 -0
- opentrons/protocol_engine/types/tip.py +18 -0
- opentrons/protocol_engine/types/util.py +21 -0
- opentrons/protocol_engine/types/well_position.py +124 -0
- opentrons/protocol_reader/__init__.py +37 -0
- opentrons/protocol_reader/extract_labware_definitions.py +66 -0
- opentrons/protocol_reader/file_format_validator.py +152 -0
- opentrons/protocol_reader/file_hasher.py +27 -0
- opentrons/protocol_reader/file_identifier.py +284 -0
- opentrons/protocol_reader/file_reader_writer.py +90 -0
- opentrons/protocol_reader/input_file.py +16 -0
- opentrons/protocol_reader/protocol_files_invalid_error.py +6 -0
- opentrons/protocol_reader/protocol_reader.py +188 -0
- opentrons/protocol_reader/protocol_source.py +124 -0
- opentrons/protocol_reader/role_analyzer.py +86 -0
- opentrons/protocol_runner/__init__.py +26 -0
- opentrons/protocol_runner/create_simulating_orchestrator.py +118 -0
- opentrons/protocol_runner/json_file_reader.py +55 -0
- opentrons/protocol_runner/json_translator.py +314 -0
- opentrons/protocol_runner/legacy_command_mapper.py +852 -0
- opentrons/protocol_runner/legacy_context_plugin.py +116 -0
- opentrons/protocol_runner/protocol_runner.py +530 -0
- opentrons/protocol_runner/python_protocol_wrappers.py +179 -0
- opentrons/protocol_runner/run_orchestrator.py +496 -0
- opentrons/protocol_runner/task_queue.py +95 -0
- opentrons/protocols/__init__.py +6 -0
- opentrons/protocols/advanced_control/__init__.py +0 -0
- opentrons/protocols/advanced_control/common.py +38 -0
- opentrons/protocols/advanced_control/mix.py +60 -0
- opentrons/protocols/advanced_control/transfers/__init__.py +0 -0
- opentrons/protocols/advanced_control/transfers/common.py +180 -0
- opentrons/protocols/advanced_control/transfers/transfer.py +972 -0
- opentrons/protocols/advanced_control/transfers/transfer_liquid_utils.py +231 -0
- opentrons/protocols/api_support/__init__.py +0 -0
- opentrons/protocols/api_support/constants.py +8 -0
- opentrons/protocols/api_support/deck_type.py +110 -0
- opentrons/protocols/api_support/definitions.py +18 -0
- opentrons/protocols/api_support/instrument.py +151 -0
- opentrons/protocols/api_support/labware_like.py +233 -0
- opentrons/protocols/api_support/tip_tracker.py +175 -0
- opentrons/protocols/api_support/types.py +32 -0
- opentrons/protocols/api_support/util.py +403 -0
- opentrons/protocols/bundle.py +89 -0
- opentrons/protocols/duration/__init__.py +4 -0
- opentrons/protocols/duration/errors.py +5 -0
- opentrons/protocols/duration/estimator.py +628 -0
- opentrons/protocols/execution/__init__.py +0 -0
- opentrons/protocols/execution/dev_types.py +181 -0
- opentrons/protocols/execution/errors.py +40 -0
- opentrons/protocols/execution/execute.py +84 -0
- opentrons/protocols/execution/execute_json_v3.py +275 -0
- opentrons/protocols/execution/execute_json_v4.py +359 -0
- opentrons/protocols/execution/execute_json_v5.py +28 -0
- opentrons/protocols/execution/execute_python.py +169 -0
- opentrons/protocols/execution/json_dispatchers.py +87 -0
- opentrons/protocols/execution/types.py +7 -0
- opentrons/protocols/geometry/__init__.py +0 -0
- opentrons/protocols/geometry/planning.py +297 -0
- opentrons/protocols/labware.py +312 -0
- opentrons/protocols/models/__init__.py +0 -0
- opentrons/protocols/models/json_protocol.py +679 -0
- opentrons/protocols/parameters/__init__.py +0 -0
- opentrons/protocols/parameters/csv_parameter_definition.py +77 -0
- opentrons/protocols/parameters/csv_parameter_interface.py +96 -0
- opentrons/protocols/parameters/exceptions.py +34 -0
- opentrons/protocols/parameters/parameter_definition.py +272 -0
- opentrons/protocols/parameters/types.py +17 -0
- opentrons/protocols/parameters/validation.py +267 -0
- opentrons/protocols/parse.py +671 -0
- opentrons/protocols/types.py +159 -0
- opentrons/py.typed +0 -0
- opentrons/resources/scripts/lpc21isp +0 -0
- opentrons/resources/smoothie-edge-8414642.hex +23010 -0
- opentrons/simulate.py +1065 -0
- opentrons/system/__init__.py +6 -0
- opentrons/system/camera.py +51 -0
- opentrons/system/log_control.py +59 -0
- opentrons/system/nmcli.py +856 -0
- opentrons/system/resin.py +24 -0
- opentrons/system/smoothie_update.py +15 -0
- opentrons/system/wifi.py +204 -0
- opentrons/tools/__init__.py +0 -0
- opentrons/tools/args_handler.py +22 -0
- opentrons/tools/write_pipette_memory.py +157 -0
- opentrons/types.py +618 -0
- opentrons/util/__init__.py +1 -0
- opentrons/util/async_helpers.py +166 -0
- opentrons/util/broker.py +84 -0
- opentrons/util/change_notifier.py +47 -0
- opentrons/util/entrypoint_util.py +278 -0
- opentrons/util/get_union_elements.py +26 -0
- opentrons/util/helpers.py +6 -0
- opentrons/util/linal.py +178 -0
- opentrons/util/logging_config.py +265 -0
- opentrons/util/logging_queue_handler.py +61 -0
- opentrons/util/performance_helpers.py +157 -0
- opentrons-8.6.0.dist-info/METADATA +37 -0
- opentrons-8.6.0.dist-info/RECORD +601 -0
- opentrons-8.6.0.dist-info/WHEEL +4 -0
- opentrons-8.6.0.dist-info/entry_points.txt +3 -0
- opentrons-8.6.0.dist-info/licenses/LICENSE +202 -0
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"""Geometry state getters."""
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from logging import getLogger
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import enum
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from numpy import array, dot, double as npdouble
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from numpy.typing import NDArray
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from typing import Optional, List, Tuple, Union, cast, TypeVar, Dict, Set
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from dataclasses import dataclass
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from functools import cached_property
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from opentrons.types import (
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Point,
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DeckSlotName,
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StagingSlotName,
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MountType,
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MeniscusTrackingTarget,
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)
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from opentrons_shared_data.errors.exceptions import (
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InvalidStoredData,
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PipetteLiquidNotFoundError,
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)
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from opentrons_shared_data.labware.constants import WELL_NAME_PATTERN
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from opentrons_shared_data.labware.labware_definition import (
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LabwareDefinition,
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LabwareDefinition2,
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InnerWellGeometry,
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)
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from opentrons_shared_data.pipette import PIPETTE_X_SPAN
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from opentrons_shared_data.pipette.types import ChannelCount, LabwareUri
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from .. import errors
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LabwareNotLoadedError,
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LabwareNotLoadedOnLabwareError,
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LabwareNotLoadedOnModuleError,
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LabwareMovementNotAllowedError,
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InvalidLabwarePositionError,
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LabwareNotOnDeckError,
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)
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from ..errors.exceptions import (
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InvalidLiquidHeightFound,
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)
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from ..resources import (
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fixture_validation,
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labware_validation,
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deck_configuration_provider,
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)
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from ..types import (
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OFF_DECK_LOCATION,
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SYSTEM_LOCATION,
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LoadedLabware,
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LoadedModule,
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WellLocation,
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LiquidHandlingWellLocation,
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DropTipWellLocation,
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PickUpTipWellLocation,
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WellOrigin,
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ModuleLocation,
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OnLabwareLocation,
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LabwareLocation,
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LabwareOffsetVector,
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CurrentWell,
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CurrentPipetteLocation,
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TipGeometry,
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LabwareMovementOffsetData,
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InStackerHopperLocation,
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OnDeckLabwareLocation,
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AddressableAreaLocation,
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AddressableOffsetVector,
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LabwareOffsetLocationSequence,
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OnModuleOffsetLocationSequenceComponent,
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OnAddressableAreaOffsetLocationSequenceComponent,
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OnLabwareOffsetLocationSequenceComponent,
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OnLabwareLocationSequenceComponent,
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ModuleModel,
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PotentialCutoutFixture,
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LabwareLocationSequence,
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OnModuleLocationSequenceComponent,
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OnAddressableAreaLocationSequenceComponent,
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OnCutoutFixtureLocationSequenceComponent,
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NotOnDeckLocationSequenceComponent,
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AreaType,
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labware_location_is_off_deck,
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labware_location_is_system,
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WellLocationType,
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WellLocationFunction,
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LabwareParentDefinition,
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AddressableArea,
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)
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from ..types.liquid_level_detection import SimulatedProbeResult, LiquidTrackingType
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+
from .labware import LabwareView
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100
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+
from .wells import WellView
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101
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+
from .modules import ModuleView
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102
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+
from .pipettes import PipetteView
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103
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+
from .addressable_areas import AddressableAreaView
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104
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+
from .inner_well_math_utils import (
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105
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find_height_inner_well_geometry,
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106
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+
find_volume_inner_well_geometry,
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107
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find_height_user_defined_volumes,
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108
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+
find_volume_user_defined_volumes,
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109
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+
)
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110
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+
from ._well_math import wells_covered_by_pipette_configuration, nozzles_per_well
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111
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+
from ._labware_origin_math import get_parent_placement_origin_to_lw_origin
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112
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+
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113
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+
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114
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+
_LOG = getLogger(__name__)
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115
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+
SLOT_WIDTH = 128
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116
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+
_PIPETTE_HOMED_POSITION_Z = (
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117
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+
248.0 # Height of the bottom of the nozzle without the tip attached when homed
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118
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+
)
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119
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+
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120
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+
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121
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+
class _TipDropSection(enum.Enum):
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122
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+
"""Well sections to drop tips in."""
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123
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+
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124
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LEFT = "left"
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125
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+
RIGHT = "right"
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126
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+
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127
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+
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128
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+
class _GripperMoveType(enum.Enum):
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129
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+
"""Types of gripper movement."""
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130
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+
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131
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+
PICK_UP_LABWARE = enum.auto()
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132
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+
DROP_LABWARE = enum.auto()
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133
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+
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134
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+
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135
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+
@dataclass
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136
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+
class _AbsoluteRobotExtents:
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137
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+
front_left: Dict[MountType, Point]
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138
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+
back_right: Dict[MountType, Point]
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139
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+
deck_extents: Point
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140
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+
padding_rear: float
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141
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+
padding_front: float
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142
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+
padding_left_side: float
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143
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+
padding_right_side: float
|
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144
|
+
|
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145
|
+
|
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146
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+
_LabwareLocation = TypeVar("_LabwareLocation", bound=LabwareLocation)
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147
|
+
|
|
148
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+
|
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149
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+
# TODO(mc, 2021-06-03): continue evaluation of which selectors should go here
|
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150
|
+
# vs which selectors should be in LabwareView
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151
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+
class GeometryView:
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152
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+
"""Geometry computed state getters."""
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153
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+
|
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154
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+
def __init__(
|
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155
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+
self,
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156
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+
config: Config,
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157
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+
labware_view: LabwareView,
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158
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+
well_view: WellView,
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159
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+
module_view: ModuleView,
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160
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+
pipette_view: PipetteView,
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161
|
+
addressable_area_view: AddressableAreaView,
|
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162
|
+
) -> None:
|
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163
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+
"""Initialize a GeometryView instance."""
|
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164
|
+
self._config = config
|
|
165
|
+
self._labware = labware_view
|
|
166
|
+
self._wells = well_view
|
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167
|
+
self._modules = module_view
|
|
168
|
+
self._pipettes = pipette_view
|
|
169
|
+
self._addressable_areas = addressable_area_view
|
|
170
|
+
self._last_drop_tip_location_spot: Dict[str, _TipDropSection] = {}
|
|
171
|
+
|
|
172
|
+
@cached_property
|
|
173
|
+
def absolute_deck_extents(self) -> _AbsoluteRobotExtents:
|
|
174
|
+
"""The absolute deck extents for a given robot deck."""
|
|
175
|
+
left_offset = self._addressable_areas.mount_offsets["left"]
|
|
176
|
+
right_offset = self._addressable_areas.mount_offsets["right"]
|
|
177
|
+
|
|
178
|
+
front_left_abs = {
|
|
179
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+
MountType.LEFT: Point(left_offset.x, -1 * left_offset.y, left_offset.z),
|
|
180
|
+
MountType.RIGHT: Point(right_offset.x, -1 * right_offset.y, right_offset.z),
|
|
181
|
+
}
|
|
182
|
+
back_right_abs = {
|
|
183
|
+
MountType.LEFT: self._addressable_areas.deck_extents + left_offset,
|
|
184
|
+
MountType.RIGHT: self._addressable_areas.deck_extents + right_offset,
|
|
185
|
+
}
|
|
186
|
+
return _AbsoluteRobotExtents(
|
|
187
|
+
front_left=front_left_abs,
|
|
188
|
+
back_right=back_right_abs,
|
|
189
|
+
deck_extents=self._addressable_areas.deck_extents,
|
|
190
|
+
padding_rear=self._addressable_areas.padding_offsets["rear"],
|
|
191
|
+
padding_front=self._addressable_areas.padding_offsets["front"],
|
|
192
|
+
padding_left_side=self._addressable_areas.padding_offsets["left_side"],
|
|
193
|
+
padding_right_side=self._addressable_areas.padding_offsets["right_side"],
|
|
194
|
+
)
|
|
195
|
+
|
|
196
|
+
def get_labware_highest_z(self, labware_id: str) -> float:
|
|
197
|
+
"""Get the highest Z-point of a labware."""
|
|
198
|
+
labware_data = self._labware.get(labware_id)
|
|
199
|
+
return self._get_highest_z_from_labware_data(labware_data)
|
|
200
|
+
|
|
201
|
+
def _is_obstacle_labware(self, labware_id: str) -> bool:
|
|
202
|
+
"""Check if the labware is a deck obstacle."""
|
|
203
|
+
for loc in self.get_location_sequence(labware_id):
|
|
204
|
+
if isinstance(loc, InStackerHopperLocation) or isinstance(
|
|
205
|
+
loc, NotOnDeckLocationSequenceComponent
|
|
206
|
+
):
|
|
207
|
+
return False
|
|
208
|
+
return True
|
|
209
|
+
|
|
210
|
+
def _get_tallest_obstacle_labware(self) -> float:
|
|
211
|
+
"""Get the highest Z-point of all labware on the deck."""
|
|
212
|
+
return max(
|
|
213
|
+
(
|
|
214
|
+
self._get_highest_z_from_labware_data(lw_data)
|
|
215
|
+
for lw_data in self._labware.get_all()
|
|
216
|
+
if self._is_obstacle_labware(lw_data.id)
|
|
217
|
+
),
|
|
218
|
+
default=0.0,
|
|
219
|
+
)
|
|
220
|
+
|
|
221
|
+
def _get_tallest_obstacle_module(self) -> float:
|
|
222
|
+
"""Get the highest Z-point of all modules on the deck."""
|
|
223
|
+
return max(
|
|
224
|
+
(
|
|
225
|
+
self._modules.get_module_highest_z(module.id, self._addressable_areas)
|
|
226
|
+
for module in self._modules.get_all()
|
|
227
|
+
),
|
|
228
|
+
default=0.0,
|
|
229
|
+
)
|
|
230
|
+
|
|
231
|
+
def _get_tallest_obstacle_fixture(self) -> float:
|
|
232
|
+
"""Get the highest Z-point of all fixtures on the deck."""
|
|
233
|
+
all_fixtures = self._addressable_areas.get_all_cutout_fixtures()
|
|
234
|
+
if all_fixtures is None:
|
|
235
|
+
# We're using a simulated deck config (see `Config.use_simulated_deck_config`).
|
|
236
|
+
# We only know the addressable areas referenced by the protocol, not the fixtures
|
|
237
|
+
# providing them. And there is more than one possible configuration of fixtures
|
|
238
|
+
# to provide them. So, we can't know what the highest fixture is. Default to 0.
|
|
239
|
+
#
|
|
240
|
+
# Defaulting to 0 may not be the right thing to do here.
|
|
241
|
+
# For example, suppose a protocol references an addressable area that implies a tall
|
|
242
|
+
# fixture must be on the deck, and then it uses long tips that wouldn't be able to
|
|
243
|
+
# clear the top of that fixture. We should perhaps raise an analysis error for that,
|
|
244
|
+
# but defaulting to 0 here means we won't.
|
|
245
|
+
return 0.0
|
|
246
|
+
return max(
|
|
247
|
+
(
|
|
248
|
+
self._addressable_areas.get_fixture_height(cutout_fixture_name)
|
|
249
|
+
for cutout_fixture_name in all_fixtures
|
|
250
|
+
),
|
|
251
|
+
default=0.0,
|
|
252
|
+
)
|
|
253
|
+
|
|
254
|
+
def get_all_obstacle_highest_z(self) -> float:
|
|
255
|
+
"""Get the highest Z-point across all obstacles that the instruments need to fly over."""
|
|
256
|
+
return max(
|
|
257
|
+
self._get_tallest_obstacle_labware(),
|
|
258
|
+
self._get_tallest_obstacle_module(),
|
|
259
|
+
self._get_tallest_obstacle_fixture(),
|
|
260
|
+
)
|
|
261
|
+
|
|
262
|
+
def get_highest_z_in_slot(
|
|
263
|
+
self, slot: Union[DeckSlotLocation, StagingSlotLocation]
|
|
264
|
+
) -> float:
|
|
265
|
+
"""Get the highest Z-point of all items stacked in the given deck slot.
|
|
266
|
+
|
|
267
|
+
This height includes the height of any module that occupies the given slot
|
|
268
|
+
even if it wasn't loaded in that slot (e.g., thermocycler).
|
|
269
|
+
"""
|
|
270
|
+
slot_item = self.get_slot_item(slot.slotName)
|
|
271
|
+
if isinstance(slot_item, LoadedModule):
|
|
272
|
+
# get height of module + all labware on it
|
|
273
|
+
module_id = slot_item.id
|
|
274
|
+
try:
|
|
275
|
+
labware_id = self._labware.get_id_by_module(module_id=module_id)
|
|
276
|
+
except LabwareNotLoadedOnModuleError:
|
|
277
|
+
return self._modules.get_module_highest_z(
|
|
278
|
+
module_id=module_id,
|
|
279
|
+
addressable_areas=self._addressable_areas,
|
|
280
|
+
)
|
|
281
|
+
else:
|
|
282
|
+
return self.get_highest_z_of_labware_stack(labware_id)
|
|
283
|
+
elif isinstance(slot_item, LoadedLabware):
|
|
284
|
+
# get stacked heights of all labware in the slot
|
|
285
|
+
return self.get_highest_z_of_labware_stack(slot_item.id)
|
|
286
|
+
elif type(slot_item) is dict:
|
|
287
|
+
# TODO (cb, 2024-02-05): Eventually this logic should become the responsibility of bounding box
|
|
288
|
+
# conflict checking, as fixtures may not always be considered as items from slots.
|
|
289
|
+
return self._addressable_areas.get_fixture_height(slot_item["id"])
|
|
290
|
+
else:
|
|
291
|
+
return 0
|
|
292
|
+
|
|
293
|
+
def get_highest_z_of_labware_stack(self, labware_id: str) -> float:
|
|
294
|
+
"""Get the highest Z-point of the topmost labware in the stack of labware on the given labware.
|
|
295
|
+
|
|
296
|
+
If there is no labware on the given labware, returns highest z of the given labware.
|
|
297
|
+
"""
|
|
298
|
+
try:
|
|
299
|
+
stacked_labware_id = self._labware.get_id_by_labware(labware_id)
|
|
300
|
+
except LabwareNotLoadedOnLabwareError:
|
|
301
|
+
return self.get_labware_highest_z(labware_id)
|
|
302
|
+
return self.get_highest_z_of_labware_stack(stacked_labware_id)
|
|
303
|
+
|
|
304
|
+
def get_min_travel_z(
|
|
305
|
+
self,
|
|
306
|
+
pipette_id: str,
|
|
307
|
+
labware_id: str,
|
|
308
|
+
location: Optional[CurrentPipetteLocation],
|
|
309
|
+
minimum_z_height: Optional[float],
|
|
310
|
+
) -> float:
|
|
311
|
+
"""Get the minimum allowed travel height of an arc move."""
|
|
312
|
+
if (
|
|
313
|
+
isinstance(location, CurrentWell)
|
|
314
|
+
and pipette_id == location.pipette_id
|
|
315
|
+
and labware_id == location.labware_id
|
|
316
|
+
):
|
|
317
|
+
min_travel_z = self.get_labware_highest_z(labware_id)
|
|
318
|
+
else:
|
|
319
|
+
min_travel_z = self.get_all_obstacle_highest_z()
|
|
320
|
+
if minimum_z_height:
|
|
321
|
+
min_travel_z = max(min_travel_z, minimum_z_height)
|
|
322
|
+
return min_travel_z
|
|
323
|
+
|
|
324
|
+
def _normalize_module_calibration_offset(
|
|
325
|
+
self,
|
|
326
|
+
module_location: DeckSlotLocation,
|
|
327
|
+
offset_data: Optional[ModuleOffsetData],
|
|
328
|
+
) -> Point:
|
|
329
|
+
"""Normalize the module calibration offset depending on the module location."""
|
|
330
|
+
if not offset_data:
|
|
331
|
+
return Point(x=0, y=0, z=0)
|
|
332
|
+
offset = Point.from_xyz_attrs(offset_data.moduleOffsetVector)
|
|
333
|
+
calibrated_slot = offset_data.location.slotName
|
|
334
|
+
calibrated_slot_column = self.get_slot_column(calibrated_slot)
|
|
335
|
+
current_slot_column = self.get_slot_column(module_location.slotName)
|
|
336
|
+
# make sure that we have valid colums since we cant have modules in the middle of the deck
|
|
337
|
+
assert set([calibrated_slot_column, current_slot_column]).issubset(
|
|
338
|
+
{1, 3}
|
|
339
|
+
), f"Module calibration offset is an invalid slot {calibrated_slot}"
|
|
340
|
+
|
|
341
|
+
# Check if the module has moved from one side of the deck to the other
|
|
342
|
+
if calibrated_slot_column != current_slot_column:
|
|
343
|
+
# Since the module was rotated, the calibration offset vector needs to be rotated by 180 degrees along the z axis
|
|
344
|
+
saved_offset: NDArray[npdouble] = array([offset.x, offset.y, offset.z])
|
|
345
|
+
rotation_matrix: NDArray[npdouble] = array(
|
|
346
|
+
[[-1, 0, 0], [0, -1, 0], [0, 0, 1]]
|
|
347
|
+
)
|
|
348
|
+
new_offset = dot(saved_offset, rotation_matrix)
|
|
349
|
+
offset = Point(x=new_offset[0], y=new_offset[1], z=new_offset[2])
|
|
350
|
+
return offset
|
|
351
|
+
|
|
352
|
+
def _get_calibrated_module_offset(self, location: LabwareLocation) -> Point:
|
|
353
|
+
"""Get a labware location's underlying calibrated module offset, if it is on a module."""
|
|
354
|
+
if isinstance(location, ModuleLocation):
|
|
355
|
+
module_id = location.moduleId
|
|
356
|
+
module_location = self._modules.get_location(module_id)
|
|
357
|
+
offset_data = self._modules.get_module_calibration_offset(module_id)
|
|
358
|
+
return self._normalize_module_calibration_offset(
|
|
359
|
+
module_location, offset_data
|
|
360
|
+
)
|
|
361
|
+
elif isinstance(location, (DeckSlotLocation, AddressableAreaLocation)):
|
|
362
|
+
# TODO we might want to do a check here to make sure addressable area location is a standard deck slot
|
|
363
|
+
# and raise if its not (or maybe we don't actually care since modules will never be loaded elsewhere)
|
|
364
|
+
return Point(x=0, y=0, z=0)
|
|
365
|
+
elif isinstance(location, OnLabwareLocation):
|
|
366
|
+
labware_data = self._labware.get(location.labwareId)
|
|
367
|
+
return self._get_calibrated_module_offset(labware_data.location)
|
|
368
|
+
elif (
|
|
369
|
+
location == OFF_DECK_LOCATION
|
|
370
|
+
or location == SYSTEM_LOCATION
|
|
371
|
+
or isinstance(location, InStackerHopperLocation)
|
|
372
|
+
):
|
|
373
|
+
raise errors.LabwareNotOnDeckError(
|
|
374
|
+
"Labware does not have a slot or module associated with it"
|
|
375
|
+
" since it is no longer on the deck."
|
|
376
|
+
)
|
|
377
|
+
|
|
378
|
+
def get_labware_origin_position(self, labware_id: str) -> Point:
|
|
379
|
+
"""Get the deck coordinates of a labware's origin.
|
|
380
|
+
|
|
381
|
+
This includes module calibration but excludes the calibration of the given labware.
|
|
382
|
+
"""
|
|
383
|
+
location = self._labware.get(labware_id).location
|
|
384
|
+
definition = self._labware.get_definition(labware_id)
|
|
385
|
+
|
|
386
|
+
slot_front_left = self._get_labware_ancestor_position(labware_id)
|
|
387
|
+
stackup_origin_to_lw_origin = self._get_stackup_placement_origin_to_lw_origin(
|
|
388
|
+
location=location, definition=definition, is_topmost_labware=True
|
|
389
|
+
)
|
|
390
|
+
module_cal_offset = self._get_calibrated_module_offset(location)
|
|
391
|
+
|
|
392
|
+
return slot_front_left + stackup_origin_to_lw_origin + module_cal_offset
|
|
393
|
+
|
|
394
|
+
def _get_labware_ancestor_position(self, labware_id: str) -> Point:
|
|
395
|
+
"""Get the position of the labware's underlying ancestor."""
|
|
396
|
+
slot_name = self._get_underlying_addressable_area_name(
|
|
397
|
+
self._labware.get(labware_id).location
|
|
398
|
+
)
|
|
399
|
+
parent_pos = self._addressable_areas.get_addressable_area_position(slot_name)
|
|
400
|
+
|
|
401
|
+
return parent_pos
|
|
402
|
+
|
|
403
|
+
def _get_stackup_placement_origin_to_lw_origin(
|
|
404
|
+
self,
|
|
405
|
+
location: LabwareLocation,
|
|
406
|
+
definition: LabwareDefinition,
|
|
407
|
+
is_topmost_labware: bool,
|
|
408
|
+
) -> Point:
|
|
409
|
+
"""Get the offset vector from the lowest entity in a stackup to the labware."""
|
|
410
|
+
if isinstance(
|
|
411
|
+
location, (AddressableAreaLocation, DeckSlotLocation, ModuleLocation)
|
|
412
|
+
):
|
|
413
|
+
return self._get_parent_placement_origin_to_lw_origin(
|
|
414
|
+
labware_location=location,
|
|
415
|
+
labware_definition=definition,
|
|
416
|
+
is_topmost_labware=is_topmost_labware,
|
|
417
|
+
)
|
|
418
|
+
elif isinstance(location, OnLabwareLocation):
|
|
419
|
+
parent_id = location.labwareId
|
|
420
|
+
parent_location = self._labware.get(parent_id).location
|
|
421
|
+
parent_definition = self._labware.get_definition(parent_id)
|
|
422
|
+
|
|
423
|
+
parent_placement_origin_to_lw_origin = (
|
|
424
|
+
self._get_parent_placement_origin_to_lw_origin(
|
|
425
|
+
labware_location=location,
|
|
426
|
+
labware_definition=definition,
|
|
427
|
+
is_topmost_labware=is_topmost_labware,
|
|
428
|
+
)
|
|
429
|
+
)
|
|
430
|
+
|
|
431
|
+
return (
|
|
432
|
+
parent_placement_origin_to_lw_origin
|
|
433
|
+
+ self._get_stackup_placement_origin_to_lw_origin(
|
|
434
|
+
location=parent_location,
|
|
435
|
+
definition=parent_definition,
|
|
436
|
+
is_topmost_labware=False,
|
|
437
|
+
)
|
|
438
|
+
)
|
|
439
|
+
else:
|
|
440
|
+
raise errors.LabwareNotOnDeckError(
|
|
441
|
+
"Cannot access labware since it is not on the deck. "
|
|
442
|
+
"Either it has been loaded off-deck or its been moved off-deck."
|
|
443
|
+
)
|
|
444
|
+
|
|
445
|
+
def _get_parent_placement_origin_to_lw_origin(
|
|
446
|
+
self,
|
|
447
|
+
labware_location: LabwareLocation,
|
|
448
|
+
labware_definition: LabwareDefinition,
|
|
449
|
+
is_topmost_labware: bool,
|
|
450
|
+
) -> Point:
|
|
451
|
+
parent_deck_item = self._get_parent_definition(labware_location)
|
|
452
|
+
|
|
453
|
+
if isinstance(labware_location, ModuleLocation):
|
|
454
|
+
module_parent_to_child_offset = (
|
|
455
|
+
self._modules.get_nominal_offset_to_child_from_addressable_area(
|
|
456
|
+
module_id=labware_location.moduleId,
|
|
457
|
+
)
|
|
458
|
+
)
|
|
459
|
+
return get_parent_placement_origin_to_lw_origin(
|
|
460
|
+
child_labware=labware_definition,
|
|
461
|
+
parent_deck_item=parent_deck_item, # type: ignore[arg-type]
|
|
462
|
+
module_parent_to_child_offset=module_parent_to_child_offset,
|
|
463
|
+
deck_definition=self._addressable_areas.deck_definition,
|
|
464
|
+
is_topmost_labware=is_topmost_labware,
|
|
465
|
+
labware_location=labware_location,
|
|
466
|
+
)
|
|
467
|
+
elif isinstance(labware_location, OnLabwareLocation):
|
|
468
|
+
return get_parent_placement_origin_to_lw_origin(
|
|
469
|
+
child_labware=labware_definition,
|
|
470
|
+
parent_deck_item=parent_deck_item, # type: ignore[arg-type]
|
|
471
|
+
module_parent_to_child_offset=None,
|
|
472
|
+
deck_definition=self._addressable_areas.deck_definition,
|
|
473
|
+
is_topmost_labware=is_topmost_labware,
|
|
474
|
+
labware_location=labware_location,
|
|
475
|
+
)
|
|
476
|
+
elif isinstance(labware_location, (DeckSlotLocation, AddressableAreaLocation)):
|
|
477
|
+
return get_parent_placement_origin_to_lw_origin(
|
|
478
|
+
child_labware=labware_definition,
|
|
479
|
+
parent_deck_item=parent_deck_item, # type: ignore[arg-type]
|
|
480
|
+
module_parent_to_child_offset=None,
|
|
481
|
+
deck_definition=self._addressable_areas.deck_definition,
|
|
482
|
+
is_topmost_labware=is_topmost_labware,
|
|
483
|
+
labware_location=labware_location,
|
|
484
|
+
)
|
|
485
|
+
else:
|
|
486
|
+
raise ValueError(f"Invalid labware location: {labware_location}")
|
|
487
|
+
|
|
488
|
+
def _get_parent_definition(
|
|
489
|
+
self, location: LabwareLocation
|
|
490
|
+
) -> LabwareParentDefinition:
|
|
491
|
+
"""Get the parent's definition given the labware's location."""
|
|
492
|
+
if isinstance(location, DeckSlotLocation):
|
|
493
|
+
addressable_area_name = location.slotName.id
|
|
494
|
+
return self._addressable_areas.get_slot_definition(addressable_area_name)
|
|
495
|
+
|
|
496
|
+
elif isinstance(location, AddressableAreaLocation):
|
|
497
|
+
addressable_area_name = location.addressableAreaName
|
|
498
|
+
return self._addressable_areas.get_addressable_area(addressable_area_name)
|
|
499
|
+
|
|
500
|
+
elif isinstance(location, ModuleLocation):
|
|
501
|
+
module_id = location.moduleId
|
|
502
|
+
return self._modules.get_definition(module_id)
|
|
503
|
+
|
|
504
|
+
elif isinstance(location, OnLabwareLocation):
|
|
505
|
+
below_labware_id = location.labwareId
|
|
506
|
+
return self._labware.get_definition(below_labware_id)
|
|
507
|
+
|
|
508
|
+
elif location == OFF_DECK_LOCATION or location == SYSTEM_LOCATION:
|
|
509
|
+
raise errors.LabwareNotOnDeckError(
|
|
510
|
+
f"Labware location {location} does not have a slot associated with it"
|
|
511
|
+
f" since it is no longer on the deck."
|
|
512
|
+
)
|
|
513
|
+
|
|
514
|
+
elif isinstance(location, InStackerHopperLocation):
|
|
515
|
+
raise errors.LabwareNotOnDeckError(
|
|
516
|
+
"Labware does not have a slot or module associated with it"
|
|
517
|
+
" since it is no longer on the deck."
|
|
518
|
+
)
|
|
519
|
+
|
|
520
|
+
else:
|
|
521
|
+
raise errors.InvalidLabwarePositionError(
|
|
522
|
+
f"Cannot get ancestor from location {location}"
|
|
523
|
+
)
|
|
524
|
+
|
|
525
|
+
def _get_underlying_addressable_area_name(self, location: LabwareLocation) -> str:
|
|
526
|
+
if isinstance(location, DeckSlotLocation):
|
|
527
|
+
return location.slotName.id
|
|
528
|
+
elif isinstance(location, AddressableAreaLocation):
|
|
529
|
+
return location.addressableAreaName
|
|
530
|
+
elif isinstance(location, ModuleLocation):
|
|
531
|
+
return self._modules.get_provided_addressable_area(location.moduleId)
|
|
532
|
+
elif isinstance(location, OnLabwareLocation):
|
|
533
|
+
return self.get_ancestor_addressable_area_name(location.labwareId)
|
|
534
|
+
else:
|
|
535
|
+
raise errors.InvalidLabwarePositionError(
|
|
536
|
+
f"Cannot get ancestor slot of location {location}"
|
|
537
|
+
)
|
|
538
|
+
|
|
539
|
+
def get_labware_position(self, labware_id: str) -> Point:
|
|
540
|
+
"""Get the calibrated origin of the labware."""
|
|
541
|
+
origin_pos = self.get_labware_origin_position(labware_id)
|
|
542
|
+
cal_offset = self._labware.get_labware_offset_vector(labware_id)
|
|
543
|
+
return Point(
|
|
544
|
+
x=origin_pos.x + cal_offset.x,
|
|
545
|
+
y=origin_pos.y + cal_offset.y,
|
|
546
|
+
z=origin_pos.z + cal_offset.z,
|
|
547
|
+
)
|
|
548
|
+
|
|
549
|
+
def _validate_well_position(
|
|
550
|
+
self,
|
|
551
|
+
target_height: LiquidTrackingType, # height in mm inside a well relative to the bottom
|
|
552
|
+
well_max_height: float,
|
|
553
|
+
pipette_id: str,
|
|
554
|
+
) -> LiquidTrackingType:
|
|
555
|
+
"""If well offset would be outside the bounds of a well, silently bring it back to the boundary."""
|
|
556
|
+
if isinstance(target_height, SimulatedProbeResult):
|
|
557
|
+
return target_height
|
|
558
|
+
lld_min_height = self._pipettes.get_current_tip_lld_settings(
|
|
559
|
+
pipette_id=pipette_id
|
|
560
|
+
)
|
|
561
|
+
if target_height < lld_min_height:
|
|
562
|
+
target_height = lld_min_height
|
|
563
|
+
elif target_height > well_max_height:
|
|
564
|
+
target_height = well_max_height
|
|
565
|
+
return target_height
|
|
566
|
+
|
|
567
|
+
def validate_probed_height(
|
|
568
|
+
self,
|
|
569
|
+
labware_id: str,
|
|
570
|
+
well_name: str,
|
|
571
|
+
pipette_id: str,
|
|
572
|
+
probed_height: LiquidTrackingType,
|
|
573
|
+
) -> None:
|
|
574
|
+
"""Raise an error if a probed liquid height is not within well bounds."""
|
|
575
|
+
if isinstance(probed_height, SimulatedProbeResult):
|
|
576
|
+
return
|
|
577
|
+
lld_min_height = self._pipettes.get_current_tip_lld_settings(
|
|
578
|
+
pipette_id=pipette_id
|
|
579
|
+
)
|
|
580
|
+
well_def = self._labware.get_well_definition(labware_id, well_name)
|
|
581
|
+
well_depth = well_def.depth
|
|
582
|
+
if probed_height < lld_min_height:
|
|
583
|
+
raise PipetteLiquidNotFoundError(
|
|
584
|
+
f"Liquid Height of {probed_height} mm is lower minumum allowed lld height {lld_min_height} mm."
|
|
585
|
+
)
|
|
586
|
+
if probed_height > well_depth:
|
|
587
|
+
raise PipetteLiquidNotFoundError(
|
|
588
|
+
f"Liquid Height of {probed_height} mm is greater than maximum well height {well_depth} mm."
|
|
589
|
+
)
|
|
590
|
+
|
|
591
|
+
def get_well_position(
|
|
592
|
+
self,
|
|
593
|
+
labware_id: str,
|
|
594
|
+
well_name: str,
|
|
595
|
+
well_location: Optional[WellLocationType] = None,
|
|
596
|
+
operation_volume: Optional[float] = None,
|
|
597
|
+
pipette_id: Optional[str] = None,
|
|
598
|
+
) -> Point:
|
|
599
|
+
"""Given relative well location in a labware, get absolute position."""
|
|
600
|
+
labware_pos = self.get_labware_position(labware_id)
|
|
601
|
+
well_def = self._labware.get_well_definition(labware_id, well_name)
|
|
602
|
+
well_depth = well_def.depth
|
|
603
|
+
|
|
604
|
+
offset = WellOffset(x=0, y=0, z=well_depth)
|
|
605
|
+
if well_location is not None:
|
|
606
|
+
offset = well_location.offset # location of the bottom of the well
|
|
607
|
+
offset_adjustment = self.get_well_offset_adjustment(
|
|
608
|
+
labware_id=labware_id,
|
|
609
|
+
well_name=well_name,
|
|
610
|
+
well_location=well_location,
|
|
611
|
+
well_depth=well_depth,
|
|
612
|
+
operation_volume=operation_volume,
|
|
613
|
+
pipette_id=pipette_id,
|
|
614
|
+
)
|
|
615
|
+
if not isinstance(offset_adjustment, SimulatedProbeResult):
|
|
616
|
+
offset = offset.model_copy(update={"z": offset.z + offset_adjustment})
|
|
617
|
+
return Point(
|
|
618
|
+
x=labware_pos.x + offset.x + well_def.x,
|
|
619
|
+
y=labware_pos.y + offset.y + well_def.y,
|
|
620
|
+
z=labware_pos.z + offset.z + well_def.z,
|
|
621
|
+
)
|
|
622
|
+
|
|
623
|
+
def _get_relative_liquid_handling_well_location(
|
|
624
|
+
self,
|
|
625
|
+
labware_id: str,
|
|
626
|
+
well_name: str,
|
|
627
|
+
absolute_point: Point,
|
|
628
|
+
delta: Point,
|
|
629
|
+
meniscus_tracking: Optional[MeniscusTrackingTarget] = None,
|
|
630
|
+
) -> Tuple[WellLocationType, bool]:
|
|
631
|
+
"""Given absolute position, get relative location of a well in a labware."""
|
|
632
|
+
dynamic_liquid_tracking = False
|
|
633
|
+
if meniscus_tracking:
|
|
634
|
+
location = LiquidHandlingWellLocation(
|
|
635
|
+
origin=WellOrigin.MENISCUS,
|
|
636
|
+
offset=WellOffset(x=0, y=0, z=absolute_point.z),
|
|
637
|
+
)
|
|
638
|
+
# TODO(cm): handle operationVolume being a float other than 0
|
|
639
|
+
if meniscus_tracking == MeniscusTrackingTarget.END:
|
|
640
|
+
location.volumeOffset = "operationVolume"
|
|
641
|
+
elif meniscus_tracking == MeniscusTrackingTarget.DYNAMIC:
|
|
642
|
+
dynamic_liquid_tracking = True
|
|
643
|
+
else:
|
|
644
|
+
location = LiquidHandlingWellLocation(
|
|
645
|
+
offset=WellOffset(x=delta.x, y=delta.y, z=delta.z)
|
|
646
|
+
)
|
|
647
|
+
return location, dynamic_liquid_tracking
|
|
648
|
+
|
|
649
|
+
def get_relative_well_location(
|
|
650
|
+
self,
|
|
651
|
+
labware_id: str,
|
|
652
|
+
well_name: str,
|
|
653
|
+
absolute_point: Point,
|
|
654
|
+
location_type: WellLocationFunction,
|
|
655
|
+
meniscus_tracking: Optional[MeniscusTrackingTarget] = None,
|
|
656
|
+
) -> Tuple[WellLocationType, bool]:
|
|
657
|
+
"""Given absolute position, get relative location of a well in a labware."""
|
|
658
|
+
well_absolute_point = self.get_well_position(labware_id, well_name)
|
|
659
|
+
delta = absolute_point - well_absolute_point
|
|
660
|
+
match location_type:
|
|
661
|
+
case WellLocationFunction.BASE | WellLocationFunction.DROP_TIP:
|
|
662
|
+
return (
|
|
663
|
+
WellLocation(offset=WellOffset(x=delta.x, y=delta.y, z=delta.z)),
|
|
664
|
+
False,
|
|
665
|
+
)
|
|
666
|
+
case WellLocationFunction.PICK_UP_TIP:
|
|
667
|
+
return (
|
|
668
|
+
PickUpTipWellLocation(
|
|
669
|
+
offset=WellOffset(x=delta.x, y=delta.y, z=delta.z)
|
|
670
|
+
),
|
|
671
|
+
False,
|
|
672
|
+
)
|
|
673
|
+
case WellLocationFunction.LIQUID_HANDLING:
|
|
674
|
+
return self._get_relative_liquid_handling_well_location(
|
|
675
|
+
labware_id=labware_id,
|
|
676
|
+
well_name=well_name,
|
|
677
|
+
absolute_point=absolute_point,
|
|
678
|
+
delta=delta,
|
|
679
|
+
meniscus_tracking=meniscus_tracking,
|
|
680
|
+
)
|
|
681
|
+
|
|
682
|
+
def get_well_height(
|
|
683
|
+
self,
|
|
684
|
+
labware_id: str,
|
|
685
|
+
well_name: str,
|
|
686
|
+
) -> float:
|
|
687
|
+
"""Get the height of a specified well for a labware."""
|
|
688
|
+
well_def = self._labware.get_well_definition(labware_id, well_name)
|
|
689
|
+
return well_def.depth
|
|
690
|
+
|
|
691
|
+
def _get_highest_z_from_labware_data(self, lw_data: LoadedLabware) -> float:
|
|
692
|
+
labware_pos = self.get_labware_position(lw_data.id)
|
|
693
|
+
z_dim = self._labware.get_dimensions(labware_id=lw_data.id).z
|
|
694
|
+
height_over_labware: float = 0
|
|
695
|
+
if isinstance(lw_data.location, ModuleLocation):
|
|
696
|
+
# Note: when calculating highest z of stacked labware, height-over-labware
|
|
697
|
+
# gets accounted for only if the top labware is directly on the module.
|
|
698
|
+
# So if there's a labware on an adapter on a module, then this
|
|
699
|
+
# over-module-height gets ignored. We currently do not have any modules
|
|
700
|
+
# that use an adapter and has height over labware so this doesn't cause
|
|
701
|
+
# any issues yet. But if we add one in the future then this calculation
|
|
702
|
+
# should be updated.
|
|
703
|
+
module_id = lw_data.location.moduleId
|
|
704
|
+
height_over_labware = self._modules.get_height_over_labware(module_id)
|
|
705
|
+
# todo(mm, 2025-07-31): This math needs updating for schema 2:
|
|
706
|
+
# labware_pos.z is not necessarily the bottom of the labware.
|
|
707
|
+
return labware_pos.z + z_dim + height_over_labware
|
|
708
|
+
|
|
709
|
+
def get_nominal_effective_tip_length(
|
|
710
|
+
self,
|
|
711
|
+
pipette_id: str,
|
|
712
|
+
labware_id: str,
|
|
713
|
+
) -> float:
|
|
714
|
+
"""Given a labware and a pipette's config, get the nominal effective tip length.
|
|
715
|
+
|
|
716
|
+
Effective tip length is the nominal tip length less the distance the
|
|
717
|
+
tip overlaps with the pipette nozzle. This does not take calibrated
|
|
718
|
+
tip lengths into account.
|
|
719
|
+
"""
|
|
720
|
+
labware_uri = self._labware.get_definition_uri(labware_id)
|
|
721
|
+
nominal_overlap = self._pipettes.get_nominal_tip_overlap(
|
|
722
|
+
pipette_id=pipette_id, labware_uri=labware_uri
|
|
723
|
+
)
|
|
724
|
+
|
|
725
|
+
return self._labware.get_tip_length(
|
|
726
|
+
labware_id=labware_id, overlap=nominal_overlap
|
|
727
|
+
)
|
|
728
|
+
|
|
729
|
+
def get_nominal_tip_geometry(
|
|
730
|
+
self,
|
|
731
|
+
pipette_id: str,
|
|
732
|
+
labware_id: str,
|
|
733
|
+
well_name: Optional[str],
|
|
734
|
+
) -> TipGeometry:
|
|
735
|
+
"""Given a labware, well, and hardware pipette config, get the tip geometry.
|
|
736
|
+
|
|
737
|
+
Tip geometry includes effective tip length, tip diameter, and tip volume,
|
|
738
|
+
which is all data required by the hardware controller for proper tip handling.
|
|
739
|
+
|
|
740
|
+
This geometry data is based solely on labware and pipette definitions and
|
|
741
|
+
does not take calibrated tip lengths into account.
|
|
742
|
+
"""
|
|
743
|
+
effective_length = self.get_nominal_effective_tip_length(
|
|
744
|
+
pipette_id=pipette_id,
|
|
745
|
+
labware_id=labware_id,
|
|
746
|
+
)
|
|
747
|
+
well_def = self._labware.get_well_definition(labware_id, well_name)
|
|
748
|
+
|
|
749
|
+
if well_def.shape != "circular":
|
|
750
|
+
raise errors.LabwareIsNotTipRackError(
|
|
751
|
+
f"Well {well_name} in labware {labware_id} is not circular."
|
|
752
|
+
)
|
|
753
|
+
|
|
754
|
+
return TipGeometry(
|
|
755
|
+
length=effective_length,
|
|
756
|
+
diameter=well_def.diameter,
|
|
757
|
+
# TODO(mc, 2020-11-12): WellDefinition type says totalLiquidVolume
|
|
758
|
+
# is a float, but hardware controller expects an int
|
|
759
|
+
volume=int(well_def.totalLiquidVolume),
|
|
760
|
+
)
|
|
761
|
+
|
|
762
|
+
def get_checked_tip_drop_location(
|
|
763
|
+
self,
|
|
764
|
+
pipette_id: str,
|
|
765
|
+
labware_id: str,
|
|
766
|
+
well_location: DropTipWellLocation,
|
|
767
|
+
partially_configured: bool = False,
|
|
768
|
+
override_default_offset: float | None = None,
|
|
769
|
+
) -> WellLocation:
|
|
770
|
+
"""Get tip drop location given labware and hardware pipette.
|
|
771
|
+
|
|
772
|
+
This makes sure that the well location has an appropriate origin & offset
|
|
773
|
+
if one is not already set previously.
|
|
774
|
+
"""
|
|
775
|
+
if (
|
|
776
|
+
self._labware.get_definition(labware_id).parameters.isTiprack
|
|
777
|
+
and partially_configured
|
|
778
|
+
):
|
|
779
|
+
raise errors.UnexpectedProtocolError(
|
|
780
|
+
"Cannot return tip to a tiprack while the pipette is configured for partial tip."
|
|
781
|
+
)
|
|
782
|
+
if well_location.origin != DropTipWellOrigin.DEFAULT:
|
|
783
|
+
return WellLocation(
|
|
784
|
+
origin=WellOrigin(well_location.origin.value),
|
|
785
|
+
offset=well_location.offset,
|
|
786
|
+
)
|
|
787
|
+
if override_default_offset is not None:
|
|
788
|
+
z_offset = override_default_offset
|
|
789
|
+
elif self._labware.get_definition(labware_id).parameters.isTiprack:
|
|
790
|
+
z_offset = self._labware.get_tip_drop_z_offset(
|
|
791
|
+
labware_id=labware_id,
|
|
792
|
+
length_scale=self._pipettes.get_return_tip_scale(pipette_id),
|
|
793
|
+
additional_offset=well_location.offset.z,
|
|
794
|
+
)
|
|
795
|
+
else:
|
|
796
|
+
# return to top if labware is not tip rack
|
|
797
|
+
z_offset = well_location.offset.z
|
|
798
|
+
|
|
799
|
+
return WellLocation(
|
|
800
|
+
origin=WellOrigin.TOP,
|
|
801
|
+
offset=WellOffset(
|
|
802
|
+
x=well_location.offset.x,
|
|
803
|
+
y=well_location.offset.y,
|
|
804
|
+
z=z_offset,
|
|
805
|
+
),
|
|
806
|
+
)
|
|
807
|
+
|
|
808
|
+
def convert_pick_up_tip_well_location(
|
|
809
|
+
self, well_location: PickUpTipWellLocation
|
|
810
|
+
) -> WellLocation:
|
|
811
|
+
"""Convert PickUpTipWellLocation to WellLocation."""
|
|
812
|
+
return WellLocation(
|
|
813
|
+
origin=WellOrigin(well_location.origin.value), offset=well_location.offset
|
|
814
|
+
)
|
|
815
|
+
|
|
816
|
+
def get_ancestor_slot_name(
|
|
817
|
+
self, labware_id: str
|
|
818
|
+
) -> Union[DeckSlotName, StagingSlotName]:
|
|
819
|
+
"""Get the slot name of the labware or the module that the labware is on."""
|
|
820
|
+
labware = self._labware.get(labware_id)
|
|
821
|
+
slot_name: Union[DeckSlotName, StagingSlotName]
|
|
822
|
+
if isinstance(labware.location, DeckSlotLocation):
|
|
823
|
+
slot_name = labware.location.slotName
|
|
824
|
+
elif isinstance(labware.location, ModuleLocation):
|
|
825
|
+
module_id = labware.location.moduleId
|
|
826
|
+
slot_name = self._modules.get_location(module_id).slotName
|
|
827
|
+
elif isinstance(labware.location, OnLabwareLocation):
|
|
828
|
+
below_labware_id = labware.location.labwareId
|
|
829
|
+
slot_name = self.get_ancestor_slot_name(below_labware_id)
|
|
830
|
+
elif isinstance(labware.location, AddressableAreaLocation):
|
|
831
|
+
area_name = labware.location.addressableAreaName
|
|
832
|
+
if self._labware.is_absorbance_reader_lid(labware_id):
|
|
833
|
+
raise errors.LocationIsLidDockSlotError(
|
|
834
|
+
"Cannot get ancestor slot name for labware on lid dock slot."
|
|
835
|
+
)
|
|
836
|
+
elif fixture_validation.is_staging_slot(area_name):
|
|
837
|
+
slot_name = StagingSlotName.from_primitive(area_name)
|
|
838
|
+
else:
|
|
839
|
+
slot_name = DeckSlotName.from_primitive(area_name)
|
|
840
|
+
elif labware.location == OFF_DECK_LOCATION:
|
|
841
|
+
raise errors.LabwareNotOnDeckError(
|
|
842
|
+
f"Labware {labware_id} does not have a slot associated with it"
|
|
843
|
+
f" since it is no longer on the deck."
|
|
844
|
+
)
|
|
845
|
+
else:
|
|
846
|
+
_LOG.error(
|
|
847
|
+
f"Unhandled location type in get_ancestor_slot_name: {labware.location}"
|
|
848
|
+
)
|
|
849
|
+
raise errors.InvalidLabwarePositionError(
|
|
850
|
+
f"Cannot get ancestor slot of {self._labware.get_display_name(labware_id)} with location {labware.location}"
|
|
851
|
+
)
|
|
852
|
+
|
|
853
|
+
return slot_name
|
|
854
|
+
|
|
855
|
+
def get_ancestor_addressable_area_name(self, labware_id: str) -> str:
|
|
856
|
+
"""Get the name of the addressable area the labware is eventually on."""
|
|
857
|
+
labware = self._labware.get(labware_id)
|
|
858
|
+
original_display_name = self._labware.get_display_name(labware_id)
|
|
859
|
+
seen: Set[str] = set((labware_id,))
|
|
860
|
+
while isinstance(labware.location, OnLabwareLocation):
|
|
861
|
+
labware = self._labware.get(labware.location.labwareId)
|
|
862
|
+
if labware.id in seen:
|
|
863
|
+
raise InvalidLabwarePositionError(
|
|
864
|
+
f"Cycle detected in labware positioning for {original_display_name}"
|
|
865
|
+
)
|
|
866
|
+
seen.add(labware.id)
|
|
867
|
+
if isinstance(labware.location, DeckSlotLocation):
|
|
868
|
+
return labware.location.slotName.id
|
|
869
|
+
elif isinstance(labware.location, AddressableAreaLocation):
|
|
870
|
+
return labware.location.addressableAreaName
|
|
871
|
+
elif isinstance(labware.location, ModuleLocation):
|
|
872
|
+
return self._modules.get_provided_addressable_area(
|
|
873
|
+
labware.location.moduleId
|
|
874
|
+
)
|
|
875
|
+
else:
|
|
876
|
+
raise LabwareNotOnDeckError(
|
|
877
|
+
f"Labware {original_display_name} is not loaded on deck",
|
|
878
|
+
details={"eventual-location": repr(labware.location)},
|
|
879
|
+
)
|
|
880
|
+
|
|
881
|
+
def ensure_location_not_occupied(
|
|
882
|
+
self,
|
|
883
|
+
location: _LabwareLocation,
|
|
884
|
+
desired_addressable_area: Optional[str] = None,
|
|
885
|
+
) -> _LabwareLocation:
|
|
886
|
+
"""Ensure that the location does not already have either Labware or a Module in it."""
|
|
887
|
+
# Collect set of existing fixtures, if any
|
|
888
|
+
existing_fixtures = self._get_potential_fixtures_for_location_occupation(
|
|
889
|
+
location
|
|
890
|
+
)
|
|
891
|
+
potential_fixtures = (
|
|
892
|
+
self._get_potential_fixtures_for_location_occupation(
|
|
893
|
+
AddressableAreaLocation(addressableAreaName=desired_addressable_area)
|
|
894
|
+
)
|
|
895
|
+
if desired_addressable_area is not None
|
|
896
|
+
else None
|
|
897
|
+
)
|
|
898
|
+
|
|
899
|
+
# Handle the checking conflict on an incoming fixture
|
|
900
|
+
if potential_fixtures is not None and isinstance(location, DeckSlotLocation):
|
|
901
|
+
if (
|
|
902
|
+
existing_fixtures is not None
|
|
903
|
+
and not any(
|
|
904
|
+
location.slotName.id in fixture.provided_addressable_areas
|
|
905
|
+
for fixture in potential_fixtures[1].intersection(
|
|
906
|
+
existing_fixtures[1]
|
|
907
|
+
)
|
|
908
|
+
)
|
|
909
|
+
) or (
|
|
910
|
+
self._labware.get_by_slot(location.slotName) is not None
|
|
911
|
+
and not any(
|
|
912
|
+
location.slotName.id in fixture.provided_addressable_areas
|
|
913
|
+
for fixture in potential_fixtures[1]
|
|
914
|
+
)
|
|
915
|
+
):
|
|
916
|
+
self._labware.raise_if_labware_in_location(location)
|
|
917
|
+
|
|
918
|
+
else:
|
|
919
|
+
self._modules.raise_if_module_in_location(location)
|
|
920
|
+
|
|
921
|
+
# Otherwise handle standard conflict checking
|
|
922
|
+
else:
|
|
923
|
+
if isinstance(
|
|
924
|
+
location,
|
|
925
|
+
(
|
|
926
|
+
DeckSlotLocation,
|
|
927
|
+
ModuleLocation,
|
|
928
|
+
OnLabwareLocation,
|
|
929
|
+
AddressableAreaLocation,
|
|
930
|
+
),
|
|
931
|
+
):
|
|
932
|
+
self._labware.raise_if_labware_in_location(location)
|
|
933
|
+
|
|
934
|
+
area = (
|
|
935
|
+
location.slotName.id
|
|
936
|
+
if isinstance(location, DeckSlotLocation)
|
|
937
|
+
else (
|
|
938
|
+
location.addressableAreaName
|
|
939
|
+
if isinstance(location, AddressableAreaLocation)
|
|
940
|
+
else None
|
|
941
|
+
)
|
|
942
|
+
)
|
|
943
|
+
if area is not None and (
|
|
944
|
+
existing_fixtures is None
|
|
945
|
+
or not any(
|
|
946
|
+
area in fixture.provided_addressable_areas
|
|
947
|
+
for fixture in existing_fixtures[1]
|
|
948
|
+
)
|
|
949
|
+
):
|
|
950
|
+
if isinstance(location, DeckSlotLocation):
|
|
951
|
+
self._modules.raise_if_module_in_location(location)
|
|
952
|
+
elif isinstance(location, AddressableAreaLocation):
|
|
953
|
+
self._modules.raise_if_module_in_location(
|
|
954
|
+
DeckSlotLocation(
|
|
955
|
+
slotName=self._addressable_areas.get_addressable_area_base_slot(
|
|
956
|
+
location.addressableAreaName
|
|
957
|
+
)
|
|
958
|
+
)
|
|
959
|
+
)
|
|
960
|
+
|
|
961
|
+
return location
|
|
962
|
+
|
|
963
|
+
def _get_potential_fixtures_for_location_occupation(
|
|
964
|
+
self, location: _LabwareLocation
|
|
965
|
+
) -> Tuple[str, Set[PotentialCutoutFixture]] | None:
|
|
966
|
+
loc: DeckSlotLocation | AddressableAreaLocation | None = None
|
|
967
|
+
if isinstance(location, AddressableAreaLocation):
|
|
968
|
+
# Convert the addressable area into a staging slot if applicable
|
|
969
|
+
slots = StagingSlotName._value2member_map_
|
|
970
|
+
for slot in slots:
|
|
971
|
+
if location.addressableAreaName == slot:
|
|
972
|
+
loc = DeckSlotLocation(
|
|
973
|
+
slotName=DeckSlotName(location.addressableAreaName[0] + "3")
|
|
974
|
+
)
|
|
975
|
+
if loc is None:
|
|
976
|
+
loc = location
|
|
977
|
+
elif isinstance(location, DeckSlotLocation):
|
|
978
|
+
loc = location
|
|
979
|
+
|
|
980
|
+
if isinstance(loc, DeckSlotLocation):
|
|
981
|
+
module = self._modules.get_by_slot(loc.slotName)
|
|
982
|
+
if module is not None and self._config.robot_type != "OT-2 Standard":
|
|
983
|
+
fixtures = deck_configuration_provider.get_potential_cutout_fixtures(
|
|
984
|
+
addressable_area_name=self._modules.ensure_and_convert_module_fixture_location(
|
|
985
|
+
deck_slot=loc.slotName,
|
|
986
|
+
model=module.model,
|
|
987
|
+
),
|
|
988
|
+
deck_definition=self._addressable_areas.deck_definition,
|
|
989
|
+
)
|
|
990
|
+
else:
|
|
991
|
+
fixtures = None
|
|
992
|
+
elif isinstance(loc, AddressableAreaLocation):
|
|
993
|
+
fixtures = deck_configuration_provider.get_potential_cutout_fixtures(
|
|
994
|
+
addressable_area_name=loc.addressableAreaName,
|
|
995
|
+
deck_definition=self._addressable_areas.deck_definition,
|
|
996
|
+
)
|
|
997
|
+
else:
|
|
998
|
+
fixtures = None
|
|
999
|
+
return fixtures
|
|
1000
|
+
|
|
1001
|
+
def _get_potential_disposal_location_cutout_fixtures(
|
|
1002
|
+
self, slot_name: DeckSlotName
|
|
1003
|
+
) -> CutoutFixture | None:
|
|
1004
|
+
for area in self._addressable_areas.get_all():
|
|
1005
|
+
if (
|
|
1006
|
+
self._addressable_areas.get_addressable_area(area).area_type
|
|
1007
|
+
== AreaType.WASTE_CHUTE
|
|
1008
|
+
or self._addressable_areas.get_addressable_area(area).area_type
|
|
1009
|
+
== AreaType.MOVABLE_TRASH
|
|
1010
|
+
) and slot_name == self._addressable_areas.get_addressable_area_base_slot(
|
|
1011
|
+
area
|
|
1012
|
+
):
|
|
1013
|
+
# Given we only have one Waste Chute fixture and one type of Trash bin fixture it's
|
|
1014
|
+
# fine to return the first result of our potential fixtures here. This will need to
|
|
1015
|
+
# change in the future if there multiple trash fixtures that share the same area type.
|
|
1016
|
+
potential_fixture = (
|
|
1017
|
+
deck_configuration_provider.get_potential_cutout_fixtures(
|
|
1018
|
+
area, self._addressable_areas.deck_definition
|
|
1019
|
+
)[1].pop()
|
|
1020
|
+
)
|
|
1021
|
+
return deck_configuration_provider.get_cutout_fixture(
|
|
1022
|
+
potential_fixture.cutout_fixture_id,
|
|
1023
|
+
self._addressable_areas.deck_definition,
|
|
1024
|
+
)
|
|
1025
|
+
return None
|
|
1026
|
+
|
|
1027
|
+
def get_labware_grip_point(
|
|
1028
|
+
self,
|
|
1029
|
+
labware_definition: LabwareDefinition,
|
|
1030
|
+
location: Union[
|
|
1031
|
+
DeckSlotLocation, ModuleLocation, OnLabwareLocation, AddressableAreaLocation
|
|
1032
|
+
],
|
|
1033
|
+
) -> Point:
|
|
1034
|
+
"""Get the grip point of the labware as placed on the given location.
|
|
1035
|
+
|
|
1036
|
+
Returns the absolute position of the labware's gripping point as if
|
|
1037
|
+
it were placed on the specified location. Labware offset (LPC offset) not included.
|
|
1038
|
+
|
|
1039
|
+
Grip point is the location where critical point of the gripper should move to
|
|
1040
|
+
in order to pick/drop the given labware in the specified location.
|
|
1041
|
+
It is calculated as the xy center of the slot with z as the point indicated by
|
|
1042
|
+
z-position of labware bottom + grip height from labware bottom.
|
|
1043
|
+
"""
|
|
1044
|
+
grip_z_from_lw_origin = self._labware.get_grip_z(labware_definition)
|
|
1045
|
+
aa_name = self._get_underlying_addressable_area_name(location)
|
|
1046
|
+
parent_to_lw_offset = self._get_stackup_placement_origin_to_lw_origin(
|
|
1047
|
+
location=location,
|
|
1048
|
+
definition=labware_definition,
|
|
1049
|
+
is_topmost_labware=True, # We aren't concerned with entities above the gripped labware.
|
|
1050
|
+
)
|
|
1051
|
+
addressable_area = self._addressable_areas.get_addressable_area(aa_name)
|
|
1052
|
+
lw_origin_to_parent = self._get_lw_origin_to_parent(
|
|
1053
|
+
labware_definition=labware_definition, addressable_area=addressable_area
|
|
1054
|
+
)
|
|
1055
|
+
mod_cal_offset = self._get_calibrated_module_offset(location)
|
|
1056
|
+
location_center = self._addressable_areas.get_addressable_area_center(aa_name)
|
|
1057
|
+
|
|
1058
|
+
return (
|
|
1059
|
+
location_center
|
|
1060
|
+
+ parent_to_lw_offset
|
|
1061
|
+
+ lw_origin_to_parent
|
|
1062
|
+
+ mod_cal_offset
|
|
1063
|
+
+ Point(0, 0, grip_z_from_lw_origin)
|
|
1064
|
+
)
|
|
1065
|
+
|
|
1066
|
+
def _get_lw_origin_to_parent(
|
|
1067
|
+
self, labware_definition: LabwareDefinition, addressable_area: AddressableArea
|
|
1068
|
+
) -> Point:
|
|
1069
|
+
if isinstance(labware_definition, LabwareDefinition2):
|
|
1070
|
+
return Point(0, 0, 0)
|
|
1071
|
+
else:
|
|
1072
|
+
bb_y = addressable_area.bounding_box.y
|
|
1073
|
+
bb_z = addressable_area.bounding_box.z
|
|
1074
|
+
return (
|
|
1075
|
+
Point(
|
|
1076
|
+
x=0,
|
|
1077
|
+
y=bb_y,
|
|
1078
|
+
z=bb_z,
|
|
1079
|
+
)
|
|
1080
|
+
* -1
|
|
1081
|
+
)
|
|
1082
|
+
|
|
1083
|
+
def get_extra_waypoints(
|
|
1084
|
+
self,
|
|
1085
|
+
location: Optional[CurrentPipetteLocation],
|
|
1086
|
+
to_slot: Union[DeckSlotName, StagingSlotName],
|
|
1087
|
+
) -> List[Tuple[float, float]]:
|
|
1088
|
+
"""Get extra waypoints for movement if thermocycler needs to be dodged."""
|
|
1089
|
+
if location is not None:
|
|
1090
|
+
if isinstance(location, CurrentWell):
|
|
1091
|
+
from_slot = self.get_ancestor_slot_name(location.labware_id)
|
|
1092
|
+
else:
|
|
1093
|
+
from_slot = self._addressable_areas.get_addressable_area_base_slot(
|
|
1094
|
+
location.addressable_area_name
|
|
1095
|
+
)
|
|
1096
|
+
if self._modules.should_dodge_thermocycler(
|
|
1097
|
+
from_slot=from_slot, to_slot=to_slot
|
|
1098
|
+
):
|
|
1099
|
+
|
|
1100
|
+
middle_slot_fixture = (
|
|
1101
|
+
self._addressable_areas.get_fixture_by_deck_slot_name(
|
|
1102
|
+
DeckSlotName.SLOT_C2.to_equivalent_for_robot_type(
|
|
1103
|
+
self._config.robot_type
|
|
1104
|
+
)
|
|
1105
|
+
)
|
|
1106
|
+
)
|
|
1107
|
+
if middle_slot_fixture is None:
|
|
1108
|
+
middle_slot = DeckSlotName.SLOT_5.to_equivalent_for_robot_type(
|
|
1109
|
+
self._config.robot_type
|
|
1110
|
+
)
|
|
1111
|
+
middle_slot_center = (
|
|
1112
|
+
self._addressable_areas.get_addressable_area_center(
|
|
1113
|
+
addressable_area_name=middle_slot.id,
|
|
1114
|
+
)
|
|
1115
|
+
)
|
|
1116
|
+
else:
|
|
1117
|
+
# todo(chb, 2025-07-30): For now we're defaulting to the first addressable area for these center slot fixtures, but
|
|
1118
|
+
# if we ever introduce a fixture in the center slot with many addressable areas that aren't "centered" over the deck
|
|
1119
|
+
# slot we will enter up generating a pretty whacky movement path (potentially dangerous).
|
|
1120
|
+
middle_slot_center = self._addressable_areas.get_addressable_area_center(
|
|
1121
|
+
addressable_area_name=middle_slot_fixture[
|
|
1122
|
+
"providesAddressableAreas"
|
|
1123
|
+
][
|
|
1124
|
+
deck_configuration_provider.get_cutout_id_by_deck_slot_name(
|
|
1125
|
+
DeckSlotName.SLOT_C2.to_equivalent_for_robot_type(
|
|
1126
|
+
self._config.robot_type
|
|
1127
|
+
)
|
|
1128
|
+
)
|
|
1129
|
+
][
|
|
1130
|
+
0
|
|
1131
|
+
],
|
|
1132
|
+
)
|
|
1133
|
+
return [(middle_slot_center.x, middle_slot_center.y)]
|
|
1134
|
+
return []
|
|
1135
|
+
|
|
1136
|
+
def get_slot_item(
|
|
1137
|
+
self, slot_name: Union[DeckSlotName, StagingSlotName]
|
|
1138
|
+
) -> Union[LoadedLabware, LoadedModule, CutoutFixture, None]:
|
|
1139
|
+
"""Get the top-most item present in a deck slot, if any.
|
|
1140
|
+
|
|
1141
|
+
This includes any module that occupies the given slot even if it wasn't loaded
|
|
1142
|
+
in that slot (e.g., thermocycler).
|
|
1143
|
+
"""
|
|
1144
|
+
maybe_labware = self._labware.get_by_slot(
|
|
1145
|
+
slot_name=slot_name,
|
|
1146
|
+
)
|
|
1147
|
+
|
|
1148
|
+
if isinstance(slot_name, DeckSlotName):
|
|
1149
|
+
maybe_fixture = self._addressable_areas.get_fixture_by_deck_slot_name(
|
|
1150
|
+
slot_name
|
|
1151
|
+
)
|
|
1152
|
+
|
|
1153
|
+
# Ignore generic single slot fixtures
|
|
1154
|
+
if maybe_fixture and maybe_fixture["id"] in {
|
|
1155
|
+
"singleLeftSlot",
|
|
1156
|
+
"singleCenterSlot",
|
|
1157
|
+
"singleRightSlot",
|
|
1158
|
+
}:
|
|
1159
|
+
maybe_fixture = None
|
|
1160
|
+
|
|
1161
|
+
maybe_module = self._modules.get_by_slot(
|
|
1162
|
+
slot_name=slot_name,
|
|
1163
|
+
) or self._modules.get_overflowed_module_in_slot(slot_name=slot_name)
|
|
1164
|
+
|
|
1165
|
+
# For situations in which the deck config is none
|
|
1166
|
+
if maybe_fixture is None and maybe_labware is None and maybe_module is None:
|
|
1167
|
+
# todo(chb 2025-03-19): This can go away once we solve the problem of no deck config in analysis
|
|
1168
|
+
maybe_fixture = self._get_potential_disposal_location_cutout_fixtures(
|
|
1169
|
+
slot_name
|
|
1170
|
+
)
|
|
1171
|
+
else:
|
|
1172
|
+
# Modules and fixtures can't be loaded on staging slots
|
|
1173
|
+
maybe_fixture = None
|
|
1174
|
+
maybe_module = None
|
|
1175
|
+
|
|
1176
|
+
return maybe_labware or maybe_module or maybe_fixture or None
|
|
1177
|
+
|
|
1178
|
+
@staticmethod
|
|
1179
|
+
def get_slot_column(slot_name: Union[DeckSlotName, StagingSlotName]) -> int:
|
|
1180
|
+
"""Get the column number for the specified slot."""
|
|
1181
|
+
if isinstance(slot_name, StagingSlotName):
|
|
1182
|
+
return 4
|
|
1183
|
+
row_col_name = slot_name.to_ot3_equivalent()
|
|
1184
|
+
slot_name_match = WELL_NAME_PATTERN.match(row_col_name.value)
|
|
1185
|
+
assert (
|
|
1186
|
+
slot_name_match is not None
|
|
1187
|
+
), f"Slot name {row_col_name} did not match required pattern; please check labware location."
|
|
1188
|
+
|
|
1189
|
+
row_name, column_name = slot_name_match.group(1, 2)
|
|
1190
|
+
return int(column_name)
|
|
1191
|
+
|
|
1192
|
+
def get_next_tip_drop_location(
|
|
1193
|
+
self, labware_id: str, well_name: str, pipette_id: str
|
|
1194
|
+
) -> DropTipWellLocation:
|
|
1195
|
+
"""Get the next location within the specified well to drop the tip into.
|
|
1196
|
+
|
|
1197
|
+
In order to prevent tip stacking, we will alternate between two tip drop locations:
|
|
1198
|
+
1. location in left section: a safe distance from left edge of the well
|
|
1199
|
+
2. location in right section: a safe distance from right edge of the well
|
|
1200
|
+
|
|
1201
|
+
This safe distance for most cases would be a location where all tips drop
|
|
1202
|
+
reliably inside the labware's well. This can be calculated based off of the
|
|
1203
|
+
span of a pipette, including all its tips, in the x-direction.
|
|
1204
|
+
|
|
1205
|
+
But we also need to account for the not-so-uncommon case of a left pipette
|
|
1206
|
+
trying to drop tips in a labware in the rightmost deck column and vice versa.
|
|
1207
|
+
If this labware extends beyond a regular deck slot, like the Flex's default trash,
|
|
1208
|
+
then even after keeping a margin for x-span of a pipette, we will get
|
|
1209
|
+
a location that's unreachable for the pipette. In such cases, we try to drop tips
|
|
1210
|
+
at the rightmost location that a left pipette is able to reach,
|
|
1211
|
+
and leftmost location that a right pipette is able to reach respectively.
|
|
1212
|
+
|
|
1213
|
+
In these calculations we assume that the critical point of a pipette
|
|
1214
|
+
is considered to be the midpoint of the pipette's tip for single channel,
|
|
1215
|
+
and the midpoint of the entire tip assembly for multi-channel pipettes.
|
|
1216
|
+
We also assume that the pipette_x_span includes any safety margins required.
|
|
1217
|
+
"""
|
|
1218
|
+
if not self._labware.is_fixed_trash(labware_id=labware_id):
|
|
1219
|
+
# In order to avoid the complexity of finding tip drop locations for
|
|
1220
|
+
# variety of labware with different well configs, we will allow
|
|
1221
|
+
# location cycling only for fixed trash labware right now.
|
|
1222
|
+
# TODO (spp, 2023-09-12): update this to possibly a labware-width based check,
|
|
1223
|
+
# or a 'trash' quirk check, once movable trash is implemented.
|
|
1224
|
+
return DropTipWellLocation(
|
|
1225
|
+
origin=DropTipWellOrigin.DEFAULT,
|
|
1226
|
+
offset=WellOffset(x=0, y=0, z=0),
|
|
1227
|
+
)
|
|
1228
|
+
|
|
1229
|
+
well_x_dim = self._labware.get_well_size(
|
|
1230
|
+
labware_id=labware_id, well_name=well_name
|
|
1231
|
+
)[0]
|
|
1232
|
+
pipette_channels = self._pipettes.get_config(pipette_id).channels
|
|
1233
|
+
pipette_mount = self._pipettes.get_mount(pipette_id)
|
|
1234
|
+
|
|
1235
|
+
labware_slot_column = self.get_slot_column(
|
|
1236
|
+
slot_name=self.get_ancestor_slot_name(labware_id)
|
|
1237
|
+
)
|
|
1238
|
+
|
|
1239
|
+
if self._last_drop_tip_location_spot.get(labware_id) == _TipDropSection.RIGHT:
|
|
1240
|
+
# Drop tip in LEFT section
|
|
1241
|
+
x_offset = self._get_drop_tip_well_x_offset(
|
|
1242
|
+
tip_drop_section=_TipDropSection.LEFT,
|
|
1243
|
+
well_x_dim=well_x_dim,
|
|
1244
|
+
pipette_channels=pipette_channels,
|
|
1245
|
+
pipette_mount=pipette_mount,
|
|
1246
|
+
labware_slot_column=labware_slot_column,
|
|
1247
|
+
)
|
|
1248
|
+
self._last_drop_tip_location_spot[labware_id] = _TipDropSection.LEFT
|
|
1249
|
+
else:
|
|
1250
|
+
# Drop tip in RIGHT section
|
|
1251
|
+
x_offset = self._get_drop_tip_well_x_offset(
|
|
1252
|
+
tip_drop_section=_TipDropSection.RIGHT,
|
|
1253
|
+
well_x_dim=well_x_dim,
|
|
1254
|
+
pipette_channels=pipette_channels,
|
|
1255
|
+
pipette_mount=pipette_mount,
|
|
1256
|
+
labware_slot_column=labware_slot_column,
|
|
1257
|
+
)
|
|
1258
|
+
self._last_drop_tip_location_spot[labware_id] = _TipDropSection.RIGHT
|
|
1259
|
+
|
|
1260
|
+
return DropTipWellLocation(
|
|
1261
|
+
origin=DropTipWellOrigin.TOP,
|
|
1262
|
+
offset=WellOffset(
|
|
1263
|
+
x=x_offset,
|
|
1264
|
+
y=0,
|
|
1265
|
+
z=0,
|
|
1266
|
+
),
|
|
1267
|
+
)
|
|
1268
|
+
|
|
1269
|
+
# TODO find way to combine this with above
|
|
1270
|
+
def get_next_tip_drop_location_for_addressable_area(
|
|
1271
|
+
self,
|
|
1272
|
+
addressable_area_name: str,
|
|
1273
|
+
pipette_id: str,
|
|
1274
|
+
) -> AddressableOffsetVector:
|
|
1275
|
+
"""Get the next location within the specified well to drop the tip into.
|
|
1276
|
+
|
|
1277
|
+
See the doc-string for `get_next_tip_drop_location` for more info on execution.
|
|
1278
|
+
"""
|
|
1279
|
+
area_x_dim = self._addressable_areas.get_addressable_area(
|
|
1280
|
+
addressable_area_name
|
|
1281
|
+
).bounding_box.x
|
|
1282
|
+
|
|
1283
|
+
pipette_channels = self._pipettes.get_config(pipette_id).channels
|
|
1284
|
+
pipette_mount = self._pipettes.get_mount(pipette_id)
|
|
1285
|
+
|
|
1286
|
+
labware_slot_column = self.get_slot_column(
|
|
1287
|
+
slot_name=self._addressable_areas.get_addressable_area_base_slot(
|
|
1288
|
+
addressable_area_name
|
|
1289
|
+
)
|
|
1290
|
+
)
|
|
1291
|
+
|
|
1292
|
+
if (
|
|
1293
|
+
self._last_drop_tip_location_spot.get(addressable_area_name)
|
|
1294
|
+
== _TipDropSection.RIGHT
|
|
1295
|
+
):
|
|
1296
|
+
# Drop tip in LEFT section
|
|
1297
|
+
x_offset = self._get_drop_tip_well_x_offset(
|
|
1298
|
+
tip_drop_section=_TipDropSection.LEFT,
|
|
1299
|
+
well_x_dim=area_x_dim,
|
|
1300
|
+
pipette_channels=pipette_channels,
|
|
1301
|
+
pipette_mount=pipette_mount,
|
|
1302
|
+
labware_slot_column=labware_slot_column,
|
|
1303
|
+
)
|
|
1304
|
+
self._last_drop_tip_location_spot[
|
|
1305
|
+
addressable_area_name
|
|
1306
|
+
] = _TipDropSection.LEFT
|
|
1307
|
+
else:
|
|
1308
|
+
# Drop tip in RIGHT section
|
|
1309
|
+
x_offset = self._get_drop_tip_well_x_offset(
|
|
1310
|
+
tip_drop_section=_TipDropSection.RIGHT,
|
|
1311
|
+
well_x_dim=area_x_dim,
|
|
1312
|
+
pipette_channels=pipette_channels,
|
|
1313
|
+
pipette_mount=pipette_mount,
|
|
1314
|
+
labware_slot_column=labware_slot_column,
|
|
1315
|
+
)
|
|
1316
|
+
self._last_drop_tip_location_spot[
|
|
1317
|
+
addressable_area_name
|
|
1318
|
+
] = _TipDropSection.RIGHT
|
|
1319
|
+
|
|
1320
|
+
return AddressableOffsetVector(x=x_offset, y=0, z=0)
|
|
1321
|
+
|
|
1322
|
+
@staticmethod
|
|
1323
|
+
def _get_drop_tip_well_x_offset(
|
|
1324
|
+
tip_drop_section: _TipDropSection,
|
|
1325
|
+
well_x_dim: float,
|
|
1326
|
+
pipette_channels: int,
|
|
1327
|
+
pipette_mount: MountType,
|
|
1328
|
+
labware_slot_column: int,
|
|
1329
|
+
) -> float:
|
|
1330
|
+
"""Get the well x offset for DropTipWellLocation."""
|
|
1331
|
+
drop_location_margin_from_labware_edge = (
|
|
1332
|
+
PIPETTE_X_SPAN[cast(ChannelCount, pipette_channels)] / 2
|
|
1333
|
+
)
|
|
1334
|
+
if tip_drop_section == _TipDropSection.LEFT:
|
|
1335
|
+
if (
|
|
1336
|
+
well_x_dim > SLOT_WIDTH
|
|
1337
|
+
and pipette_channels != 96
|
|
1338
|
+
and pipette_mount == MountType.RIGHT
|
|
1339
|
+
and labware_slot_column == 1
|
|
1340
|
+
):
|
|
1341
|
+
# Pipette might not reach the default left spot so use a different left spot
|
|
1342
|
+
x_well_offset = (
|
|
1343
|
+
-well_x_dim / 2 + drop_location_margin_from_labware_edge * 2
|
|
1344
|
+
)
|
|
1345
|
+
else:
|
|
1346
|
+
x_well_offset = -well_x_dim / 2 + drop_location_margin_from_labware_edge
|
|
1347
|
+
if x_well_offset > 0:
|
|
1348
|
+
x_well_offset = 0
|
|
1349
|
+
else:
|
|
1350
|
+
if (
|
|
1351
|
+
well_x_dim > SLOT_WIDTH
|
|
1352
|
+
and pipette_channels != 96
|
|
1353
|
+
and pipette_mount == MountType.LEFT
|
|
1354
|
+
and labware_slot_column == 3
|
|
1355
|
+
):
|
|
1356
|
+
# Pipette might not reach the default right spot so use a different right spot
|
|
1357
|
+
x_well_offset = (
|
|
1358
|
+
-well_x_dim / 2
|
|
1359
|
+
+ SLOT_WIDTH
|
|
1360
|
+
- drop_location_margin_from_labware_edge
|
|
1361
|
+
)
|
|
1362
|
+
else:
|
|
1363
|
+
x_well_offset = well_x_dim / 2 - drop_location_margin_from_labware_edge
|
|
1364
|
+
if x_well_offset < 0:
|
|
1365
|
+
x_well_offset = 0
|
|
1366
|
+
return x_well_offset
|
|
1367
|
+
|
|
1368
|
+
def get_final_labware_movement_offset_vectors(
|
|
1369
|
+
self,
|
|
1370
|
+
from_location: OnDeckLabwareLocation,
|
|
1371
|
+
to_location: OnDeckLabwareLocation,
|
|
1372
|
+
additional_pick_up_offset: Point,
|
|
1373
|
+
additional_drop_offset: Point,
|
|
1374
|
+
current_labware: LabwareDefinition,
|
|
1375
|
+
) -> LabwareMovementOffsetData:
|
|
1376
|
+
"""Calculate the final labware offset vector to use in labware movement."""
|
|
1377
|
+
pick_up_offset = (
|
|
1378
|
+
self.get_total_nominal_gripper_offset_for_move_type(
|
|
1379
|
+
location=from_location,
|
|
1380
|
+
move_type=_GripperMoveType.PICK_UP_LABWARE,
|
|
1381
|
+
current_labware=current_labware,
|
|
1382
|
+
)
|
|
1383
|
+
+ additional_pick_up_offset
|
|
1384
|
+
)
|
|
1385
|
+
drop_offset = (
|
|
1386
|
+
self.get_total_nominal_gripper_offset_for_move_type(
|
|
1387
|
+
location=to_location,
|
|
1388
|
+
move_type=_GripperMoveType.DROP_LABWARE,
|
|
1389
|
+
current_labware=current_labware,
|
|
1390
|
+
)
|
|
1391
|
+
+ additional_drop_offset
|
|
1392
|
+
)
|
|
1393
|
+
|
|
1394
|
+
return LabwareMovementOffsetData(
|
|
1395
|
+
pickUpOffset=LabwareOffsetVector(
|
|
1396
|
+
x=pick_up_offset.x, y=pick_up_offset.y, z=pick_up_offset.z
|
|
1397
|
+
),
|
|
1398
|
+
dropOffset=LabwareOffsetVector(
|
|
1399
|
+
x=drop_offset.x, y=drop_offset.y, z=drop_offset.z
|
|
1400
|
+
),
|
|
1401
|
+
)
|
|
1402
|
+
|
|
1403
|
+
@staticmethod
|
|
1404
|
+
def ensure_valid_gripper_location(
|
|
1405
|
+
location: LabwareLocation,
|
|
1406
|
+
) -> Union[
|
|
1407
|
+
DeckSlotLocation, ModuleLocation, OnLabwareLocation, AddressableAreaLocation
|
|
1408
|
+
]:
|
|
1409
|
+
"""Ensure valid on-deck location for gripper, otherwise raise error."""
|
|
1410
|
+
if not isinstance(
|
|
1411
|
+
location,
|
|
1412
|
+
(
|
|
1413
|
+
DeckSlotLocation,
|
|
1414
|
+
ModuleLocation,
|
|
1415
|
+
OnLabwareLocation,
|
|
1416
|
+
AddressableAreaLocation,
|
|
1417
|
+
),
|
|
1418
|
+
):
|
|
1419
|
+
raise errors.LabwareMovementNotAllowedError(
|
|
1420
|
+
"Off-deck labware movements are not supported using the gripper."
|
|
1421
|
+
)
|
|
1422
|
+
return location
|
|
1423
|
+
|
|
1424
|
+
def get_total_nominal_gripper_offset_for_move_type(
|
|
1425
|
+
self,
|
|
1426
|
+
location: OnDeckLabwareLocation,
|
|
1427
|
+
move_type: _GripperMoveType,
|
|
1428
|
+
current_labware: LabwareDefinition,
|
|
1429
|
+
) -> Point:
|
|
1430
|
+
"""Get the total of the offsets to be used to pick up labware in its current location."""
|
|
1431
|
+
if move_type == _GripperMoveType.PICK_UP_LABWARE:
|
|
1432
|
+
if isinstance(
|
|
1433
|
+
location, (ModuleLocation, DeckSlotLocation, AddressableAreaLocation)
|
|
1434
|
+
):
|
|
1435
|
+
return Point.from_xyz_attrs(
|
|
1436
|
+
self._nominal_gripper_offsets_for_location(location).pickUpOffset
|
|
1437
|
+
)
|
|
1438
|
+
else:
|
|
1439
|
+
# If it's a labware on a labware (most likely an adapter),
|
|
1440
|
+
# we calculate the offset as sum of offsets for the direct parent labware
|
|
1441
|
+
# and the underlying non-labware parent location.
|
|
1442
|
+
direct_parent_offset = self._nominal_gripper_offsets_for_location(
|
|
1443
|
+
location
|
|
1444
|
+
)
|
|
1445
|
+
ancestor = self._labware.get_parent_location(location.labwareId)
|
|
1446
|
+
extra_offset = Point(x=0, y=0, z=0)
|
|
1447
|
+
if (
|
|
1448
|
+
isinstance(ancestor, ModuleLocation)
|
|
1449
|
+
# todo(mm, 2025-06-20): Avoid this private attribute access.
|
|
1450
|
+
and self._modules._state.requested_model_by_id[ancestor.moduleId]
|
|
1451
|
+
== ModuleModel.THERMOCYCLER_MODULE_V2
|
|
1452
|
+
and labware_validation.validate_definition_is_lid(current_labware)
|
|
1453
|
+
):
|
|
1454
|
+
if "lidOffsets" in current_labware.gripperOffsets.keys():
|
|
1455
|
+
extra_offset = Point(
|
|
1456
|
+
x=current_labware.gripperOffsets[
|
|
1457
|
+
"lidOffsets"
|
|
1458
|
+
].pickUpOffset.x,
|
|
1459
|
+
y=current_labware.gripperOffsets[
|
|
1460
|
+
"lidOffsets"
|
|
1461
|
+
].pickUpOffset.y,
|
|
1462
|
+
z=current_labware.gripperOffsets[
|
|
1463
|
+
"lidOffsets"
|
|
1464
|
+
].pickUpOffset.z,
|
|
1465
|
+
)
|
|
1466
|
+
else:
|
|
1467
|
+
raise errors.LabwareOffsetDoesNotExistError(
|
|
1468
|
+
f"Labware Definition {current_labware.parameters.loadName} does not contain required field 'lidOffsets' of 'gripperOffsets'."
|
|
1469
|
+
)
|
|
1470
|
+
|
|
1471
|
+
assert isinstance(
|
|
1472
|
+
ancestor,
|
|
1473
|
+
(
|
|
1474
|
+
DeckSlotLocation,
|
|
1475
|
+
ModuleLocation,
|
|
1476
|
+
OnLabwareLocation,
|
|
1477
|
+
AddressableAreaLocation,
|
|
1478
|
+
),
|
|
1479
|
+
), "No gripper offsets for off-deck labware"
|
|
1480
|
+
return (
|
|
1481
|
+
Point.from_xyz_attrs(direct_parent_offset.pickUpOffset)
|
|
1482
|
+
+ Point.from_xyz_attrs(
|
|
1483
|
+
self._nominal_gripper_offsets_for_location(
|
|
1484
|
+
location=ancestor
|
|
1485
|
+
).pickUpOffset
|
|
1486
|
+
)
|
|
1487
|
+
+ extra_offset
|
|
1488
|
+
)
|
|
1489
|
+
else:
|
|
1490
|
+
if isinstance(
|
|
1491
|
+
location, (ModuleLocation, DeckSlotLocation, AddressableAreaLocation)
|
|
1492
|
+
):
|
|
1493
|
+
return Point.from_xyz_attrs(
|
|
1494
|
+
self._nominal_gripper_offsets_for_location(location).dropOffset
|
|
1495
|
+
)
|
|
1496
|
+
else:
|
|
1497
|
+
# If it's a labware on a labware (most likely an adapter),
|
|
1498
|
+
# we calculate the offset as sum of offsets for the direct parent labware
|
|
1499
|
+
# and the underlying non-labware parent location.
|
|
1500
|
+
direct_parent_offset = self._nominal_gripper_offsets_for_location(
|
|
1501
|
+
location
|
|
1502
|
+
)
|
|
1503
|
+
ancestor = self._labware.get_parent_location(location.labwareId)
|
|
1504
|
+
extra_offset = Point(x=0, y=0, z=0)
|
|
1505
|
+
if (
|
|
1506
|
+
isinstance(ancestor, ModuleLocation)
|
|
1507
|
+
# todo(mm, 2024-11-06): Do not access private module state; only use public ModuleView methods.
|
|
1508
|
+
and self._modules._state.requested_model_by_id[ancestor.moduleId]
|
|
1509
|
+
== ModuleModel.THERMOCYCLER_MODULE_V2
|
|
1510
|
+
and labware_validation.validate_definition_is_lid(current_labware)
|
|
1511
|
+
):
|
|
1512
|
+
if "lidOffsets" in current_labware.gripperOffsets.keys():
|
|
1513
|
+
extra_offset = Point(
|
|
1514
|
+
x=current_labware.gripperOffsets[
|
|
1515
|
+
"lidOffsets"
|
|
1516
|
+
].pickUpOffset.x,
|
|
1517
|
+
y=current_labware.gripperOffsets[
|
|
1518
|
+
"lidOffsets"
|
|
1519
|
+
].pickUpOffset.y,
|
|
1520
|
+
z=current_labware.gripperOffsets[
|
|
1521
|
+
"lidOffsets"
|
|
1522
|
+
].pickUpOffset.z,
|
|
1523
|
+
)
|
|
1524
|
+
else:
|
|
1525
|
+
raise errors.LabwareOffsetDoesNotExistError(
|
|
1526
|
+
f"Labware Definition {current_labware.parameters.loadName} does not contain required field 'lidOffsets' of 'gripperOffsets'."
|
|
1527
|
+
)
|
|
1528
|
+
|
|
1529
|
+
assert isinstance(
|
|
1530
|
+
ancestor,
|
|
1531
|
+
(
|
|
1532
|
+
DeckSlotLocation,
|
|
1533
|
+
ModuleLocation,
|
|
1534
|
+
OnLabwareLocation,
|
|
1535
|
+
AddressableAreaLocation,
|
|
1536
|
+
),
|
|
1537
|
+
), "No gripper offsets for off-deck labware"
|
|
1538
|
+
return (
|
|
1539
|
+
Point.from_xyz_attrs(direct_parent_offset.dropOffset)
|
|
1540
|
+
+ Point.from_xyz_attrs(
|
|
1541
|
+
self._nominal_gripper_offsets_for_location(
|
|
1542
|
+
location=ancestor
|
|
1543
|
+
).dropOffset
|
|
1544
|
+
)
|
|
1545
|
+
+ extra_offset
|
|
1546
|
+
)
|
|
1547
|
+
|
|
1548
|
+
# todo(mm, 2024-11-05): This may be incorrect because it does not take the following
|
|
1549
|
+
# offsets into account, which *are* taken into account for the actual gripper movement:
|
|
1550
|
+
#
|
|
1551
|
+
# * The pickup offset in the definition of the parent of the gripped labware.
|
|
1552
|
+
# * The "additional offset" or "user offset", e.g. the `pickUpOffset` and `dropOffset`
|
|
1553
|
+
# params in the `moveLabware` command.
|
|
1554
|
+
#
|
|
1555
|
+
# For robustness, we should combine this with `get_gripper_labware_movement_waypoints()`.
|
|
1556
|
+
#
|
|
1557
|
+
# We should also be more explicit about which offsets act to move the gripper paddles
|
|
1558
|
+
# relative to the gripped labware, and which offsets act to change how the gripped
|
|
1559
|
+
# labware sits atop its parent. Those have different effects on how far the gripped
|
|
1560
|
+
# labware juts beyond the paddles while it's in transit.
|
|
1561
|
+
def check_gripper_labware_tip_collision(
|
|
1562
|
+
self,
|
|
1563
|
+
gripper_homed_position_z: float,
|
|
1564
|
+
labware_id: str,
|
|
1565
|
+
# todo(mm, 2025-07-31): arg unused, investigate or remove.
|
|
1566
|
+
current_location: OnDeckLabwareLocation,
|
|
1567
|
+
) -> None:
|
|
1568
|
+
"""Check for potential collision of tips against labware to be lifted."""
|
|
1569
|
+
labware_definition = self._labware.get_definition(labware_id)
|
|
1570
|
+
pipettes = self._pipettes.get_all()
|
|
1571
|
+
for pipette in pipettes:
|
|
1572
|
+
# TODO(cb, 2024-01-22): Remove the 1 and 8 channel special case once we are doing X axis validation
|
|
1573
|
+
if self._pipettes.get_channels(pipette.id) in [1, 8]:
|
|
1574
|
+
return
|
|
1575
|
+
|
|
1576
|
+
tip = self._pipettes.get_attached_tip(pipette.id)
|
|
1577
|
+
if not tip:
|
|
1578
|
+
continue
|
|
1579
|
+
|
|
1580
|
+
labware_origin_to_grip_point = self._labware.get_grip_z(labware_definition)
|
|
1581
|
+
grip_point_to_labware_origin = -labware_origin_to_grip_point
|
|
1582
|
+
height_above_labware_origin = self._labware.get_extents_around_lw_origin(
|
|
1583
|
+
labware_definition
|
|
1584
|
+
).max_z
|
|
1585
|
+
labware_top_z_when_gripped = (
|
|
1586
|
+
gripper_homed_position_z
|
|
1587
|
+
+ grip_point_to_labware_origin
|
|
1588
|
+
+ height_above_labware_origin
|
|
1589
|
+
)
|
|
1590
|
+
|
|
1591
|
+
# TODO(cb, 2024-01-18): Utilizing the nozzle map and labware X coordinates,
|
|
1592
|
+
# verify if collisions will occur on the X axis (analysis will use hard coded data
|
|
1593
|
+
# to measure from the gripper critical point to the pipette mount)
|
|
1594
|
+
if (_PIPETTE_HOMED_POSITION_Z - tip.length) < labware_top_z_when_gripped:
|
|
1595
|
+
raise LabwareMovementNotAllowedError(
|
|
1596
|
+
f"Cannot move labware '{labware_definition.parameters.loadName}' when {int(tip.volume)} µL tips are attached."
|
|
1597
|
+
)
|
|
1598
|
+
|
|
1599
|
+
def _nominal_gripper_offsets_for_location(
|
|
1600
|
+
self, location: OnDeckLabwareLocation
|
|
1601
|
+
) -> LabwareMovementOffsetData:
|
|
1602
|
+
"""Provide the default gripper offset data for the given location type."""
|
|
1603
|
+
if isinstance(location, (DeckSlotLocation, AddressableAreaLocation)):
|
|
1604
|
+
# TODO we might need a separate type of gripper offset for addressable areas but that also might just
|
|
1605
|
+
# be covered by the drop labware offset/location
|
|
1606
|
+
offsets = self._labware.get_deck_default_gripper_offsets()
|
|
1607
|
+
elif isinstance(location, ModuleLocation):
|
|
1608
|
+
offsets = self._modules.get_default_gripper_offsets(location.moduleId)
|
|
1609
|
+
else:
|
|
1610
|
+
# Labware is on a labware/adapter
|
|
1611
|
+
offsets = self._labware_gripper_offsets(location.labwareId)
|
|
1612
|
+
return offsets or LabwareMovementOffsetData(
|
|
1613
|
+
pickUpOffset=LabwareOffsetVector(x=0, y=0, z=0),
|
|
1614
|
+
dropOffset=LabwareOffsetVector(x=0, y=0, z=0),
|
|
1615
|
+
)
|
|
1616
|
+
|
|
1617
|
+
def _labware_gripper_offsets(
|
|
1618
|
+
self, labware_id: str
|
|
1619
|
+
) -> Optional[LabwareMovementOffsetData]:
|
|
1620
|
+
"""Provide the most appropriate gripper offset data for the specified labware.
|
|
1621
|
+
|
|
1622
|
+
We check the types of gripper offsets available for the labware ("default" or slot-based)
|
|
1623
|
+
and return the most appropriate one for the overall location of the labware.
|
|
1624
|
+
Currently, only module adapters (specifically, the H/S universal flat adapter)
|
|
1625
|
+
have non-default offsets that are specific to location of the module on deck,
|
|
1626
|
+
so, this code only checks for the presence of those known offsets.
|
|
1627
|
+
"""
|
|
1628
|
+
parent_location = self._labware.get_parent_location(labware_id)
|
|
1629
|
+
assert isinstance(
|
|
1630
|
+
parent_location,
|
|
1631
|
+
(
|
|
1632
|
+
DeckSlotLocation,
|
|
1633
|
+
ModuleLocation,
|
|
1634
|
+
AddressableAreaLocation,
|
|
1635
|
+
OnLabwareLocation,
|
|
1636
|
+
),
|
|
1637
|
+
), "No gripper offsets for off-deck labware"
|
|
1638
|
+
|
|
1639
|
+
if isinstance(parent_location, DeckSlotLocation):
|
|
1640
|
+
slot_name = parent_location.slotName
|
|
1641
|
+
elif isinstance(parent_location, AddressableAreaLocation):
|
|
1642
|
+
slot_name = self._addressable_areas.get_addressable_area_base_slot(
|
|
1643
|
+
parent_location.addressableAreaName
|
|
1644
|
+
)
|
|
1645
|
+
else:
|
|
1646
|
+
module_loc = self._modules.get_location(parent_location.moduleId)
|
|
1647
|
+
slot_name = module_loc.slotName
|
|
1648
|
+
|
|
1649
|
+
slot_based_offset = self._labware.get_child_gripper_offsets(
|
|
1650
|
+
labware_id=labware_id, slot_name=slot_name.to_ot3_equivalent()
|
|
1651
|
+
)
|
|
1652
|
+
|
|
1653
|
+
return slot_based_offset or self._labware.get_child_gripper_offsets(
|
|
1654
|
+
labware_id=labware_id, slot_name=None
|
|
1655
|
+
)
|
|
1656
|
+
|
|
1657
|
+
def get_location_sequence(self, labware_id: str) -> LabwareLocationSequence:
|
|
1658
|
+
"""Provide the LocationSequence specifying the current position of the labware.
|
|
1659
|
+
|
|
1660
|
+
Elements in this sequence contain instance IDs of things. The chain is valid only until the
|
|
1661
|
+
labware is moved.
|
|
1662
|
+
"""
|
|
1663
|
+
return self.get_predicted_location_sequence(
|
|
1664
|
+
self._labware.get_location(labware_id)
|
|
1665
|
+
)
|
|
1666
|
+
|
|
1667
|
+
def get_predicted_location_sequence(
|
|
1668
|
+
self,
|
|
1669
|
+
labware_location: LabwareLocation,
|
|
1670
|
+
labware_pending_load: dict[str, LoadedLabware] | None = None,
|
|
1671
|
+
) -> LabwareLocationSequence:
|
|
1672
|
+
"""Get the location sequence for this location. Useful for a labware that hasn't been loaded."""
|
|
1673
|
+
return self._recurse_labware_location(
|
|
1674
|
+
labware_location, [], labware_pending_load or {}
|
|
1675
|
+
)
|
|
1676
|
+
|
|
1677
|
+
def _cutout_fixture_location_sequence_from_addressable_area(
|
|
1678
|
+
self, addressable_area_name: str
|
|
1679
|
+
) -> OnCutoutFixtureLocationSequenceComponent:
|
|
1680
|
+
(
|
|
1681
|
+
cutout_id,
|
|
1682
|
+
potential_fixtures,
|
|
1683
|
+
) = self._addressable_areas.get_current_potential_cutout_fixtures_for_addressable_area(
|
|
1684
|
+
addressable_area_name
|
|
1685
|
+
)
|
|
1686
|
+
return OnCutoutFixtureLocationSequenceComponent(
|
|
1687
|
+
possibleCutoutFixtureIds=sorted(
|
|
1688
|
+
[fixture.cutout_fixture_id for fixture in potential_fixtures]
|
|
1689
|
+
),
|
|
1690
|
+
cutoutId=cutout_id,
|
|
1691
|
+
)
|
|
1692
|
+
|
|
1693
|
+
def _recurse_labware_location_from_aa_component(
|
|
1694
|
+
self,
|
|
1695
|
+
labware_location: AddressableAreaLocation,
|
|
1696
|
+
building: LabwareLocationSequence,
|
|
1697
|
+
) -> LabwareLocationSequence:
|
|
1698
|
+
cutout_location = self._cutout_fixture_location_sequence_from_addressable_area(
|
|
1699
|
+
labware_location.addressableAreaName
|
|
1700
|
+
)
|
|
1701
|
+
# If the labware is loaded on an AA that is a module, we want to respect the convention
|
|
1702
|
+
# of giving it an OnModuleLocation.
|
|
1703
|
+
possible_module = self._modules.get_by_addressable_area(
|
|
1704
|
+
labware_location.addressableAreaName
|
|
1705
|
+
)
|
|
1706
|
+
if possible_module is not None:
|
|
1707
|
+
return building + [
|
|
1708
|
+
OnAddressableAreaLocationSequenceComponent(
|
|
1709
|
+
addressableAreaName=labware_location.addressableAreaName
|
|
1710
|
+
),
|
|
1711
|
+
OnModuleLocationSequenceComponent(moduleId=possible_module.id),
|
|
1712
|
+
cutout_location,
|
|
1713
|
+
]
|
|
1714
|
+
else:
|
|
1715
|
+
return building + [
|
|
1716
|
+
OnAddressableAreaLocationSequenceComponent(
|
|
1717
|
+
addressableAreaName=labware_location.addressableAreaName,
|
|
1718
|
+
),
|
|
1719
|
+
cutout_location,
|
|
1720
|
+
]
|
|
1721
|
+
|
|
1722
|
+
def _recurse_labware_location_from_module_component(
|
|
1723
|
+
self, labware_location: ModuleLocation, building: LabwareLocationSequence
|
|
1724
|
+
) -> LabwareLocationSequence:
|
|
1725
|
+
module_id = labware_location.moduleId
|
|
1726
|
+
module_aa = self._modules.get_provided_addressable_area(module_id)
|
|
1727
|
+
base_location: (
|
|
1728
|
+
OnCutoutFixtureLocationSequenceComponent
|
|
1729
|
+
| NotOnDeckLocationSequenceComponent
|
|
1730
|
+
) = self._cutout_fixture_location_sequence_from_addressable_area(module_aa)
|
|
1731
|
+
|
|
1732
|
+
if self._modules.get_deck_supports_module_fixtures():
|
|
1733
|
+
# On a deck with modules as cutout fixtures, we want, in order,
|
|
1734
|
+
# - the addressable area of the module
|
|
1735
|
+
# - the module with its module id, which is what clients want
|
|
1736
|
+
# - the cutout
|
|
1737
|
+
loc = self._modules.get_location(module_id)
|
|
1738
|
+
model = self._modules.get_connected_model(module_id)
|
|
1739
|
+
module_aa = self._modules.ensure_and_convert_module_fixture_location(
|
|
1740
|
+
loc.slotName, model
|
|
1741
|
+
)
|
|
1742
|
+
return building + [
|
|
1743
|
+
OnAddressableAreaLocationSequenceComponent(
|
|
1744
|
+
addressableAreaName=module_aa
|
|
1745
|
+
),
|
|
1746
|
+
OnModuleLocationSequenceComponent(moduleId=module_id),
|
|
1747
|
+
base_location,
|
|
1748
|
+
]
|
|
1749
|
+
else:
|
|
1750
|
+
# If the module isn't a cutout fixture, then we want
|
|
1751
|
+
# - the module
|
|
1752
|
+
# - the addressable area the module is loaded on
|
|
1753
|
+
# - the cutout
|
|
1754
|
+
location = self._modules.get_location(module_id)
|
|
1755
|
+
return building + [
|
|
1756
|
+
OnModuleLocationSequenceComponent(moduleId=module_id),
|
|
1757
|
+
OnAddressableAreaLocationSequenceComponent(
|
|
1758
|
+
addressableAreaName=location.slotName.value
|
|
1759
|
+
),
|
|
1760
|
+
base_location,
|
|
1761
|
+
]
|
|
1762
|
+
|
|
1763
|
+
def _recurse_labware_location_from_stacker_hopper(
|
|
1764
|
+
self,
|
|
1765
|
+
labware_location: InStackerHopperLocation,
|
|
1766
|
+
building: LabwareLocationSequence,
|
|
1767
|
+
) -> LabwareLocationSequence:
|
|
1768
|
+
loc = self._modules.get_location(labware_location.moduleId)
|
|
1769
|
+
model = self._modules.get_connected_model(labware_location.moduleId)
|
|
1770
|
+
module_aa = self._modules.ensure_and_convert_module_fixture_location(
|
|
1771
|
+
loc.slotName, model
|
|
1772
|
+
)
|
|
1773
|
+
cutout_base = self._cutout_fixture_location_sequence_from_addressable_area(
|
|
1774
|
+
module_aa
|
|
1775
|
+
)
|
|
1776
|
+
return building + [labware_location, cutout_base]
|
|
1777
|
+
|
|
1778
|
+
def _recurse_labware_location(
|
|
1779
|
+
self,
|
|
1780
|
+
labware_location: LabwareLocation,
|
|
1781
|
+
building: LabwareLocationSequence,
|
|
1782
|
+
labware_pending_load: dict[str, LoadedLabware],
|
|
1783
|
+
) -> LabwareLocationSequence:
|
|
1784
|
+
if isinstance(labware_location, AddressableAreaLocation):
|
|
1785
|
+
return self._recurse_labware_location_from_aa_component(
|
|
1786
|
+
labware_location, building
|
|
1787
|
+
)
|
|
1788
|
+
elif labware_location_is_off_deck(
|
|
1789
|
+
labware_location
|
|
1790
|
+
) or labware_location_is_system(labware_location):
|
|
1791
|
+
return building + [
|
|
1792
|
+
NotOnDeckLocationSequenceComponent(logicalLocationName=labware_location)
|
|
1793
|
+
]
|
|
1794
|
+
|
|
1795
|
+
elif isinstance(labware_location, OnLabwareLocation):
|
|
1796
|
+
labware = self._get_or_default_labware(
|
|
1797
|
+
labware_location.labwareId, labware_pending_load
|
|
1798
|
+
)
|
|
1799
|
+
return self._recurse_labware_location(
|
|
1800
|
+
labware.location,
|
|
1801
|
+
building
|
|
1802
|
+
+ [
|
|
1803
|
+
OnLabwareLocationSequenceComponent(
|
|
1804
|
+
labwareId=labware_location.labwareId, lidId=labware.lid_id
|
|
1805
|
+
)
|
|
1806
|
+
],
|
|
1807
|
+
labware_pending_load,
|
|
1808
|
+
)
|
|
1809
|
+
elif isinstance(labware_location, ModuleLocation):
|
|
1810
|
+
return self._recurse_labware_location_from_module_component(
|
|
1811
|
+
labware_location, building
|
|
1812
|
+
)
|
|
1813
|
+
elif isinstance(labware_location, DeckSlotLocation):
|
|
1814
|
+
return building + [
|
|
1815
|
+
OnAddressableAreaLocationSequenceComponent(
|
|
1816
|
+
addressableAreaName=labware_location.slotName.value,
|
|
1817
|
+
),
|
|
1818
|
+
self._cutout_fixture_location_sequence_from_addressable_area(
|
|
1819
|
+
labware_location.slotName.value
|
|
1820
|
+
),
|
|
1821
|
+
]
|
|
1822
|
+
elif isinstance(labware_location, InStackerHopperLocation):
|
|
1823
|
+
return self._recurse_labware_location_from_stacker_hopper(
|
|
1824
|
+
labware_location, building
|
|
1825
|
+
)
|
|
1826
|
+
else:
|
|
1827
|
+
_LOG.warn(f"Unhandled labware location kind: {labware_location}")
|
|
1828
|
+
return building
|
|
1829
|
+
|
|
1830
|
+
def get_offset_location(
|
|
1831
|
+
self, labware_id: str
|
|
1832
|
+
) -> Optional[LabwareOffsetLocationSequence]:
|
|
1833
|
+
"""Provide the LegacyLabwareOffsetLocation specifying the current position of the labware.
|
|
1834
|
+
|
|
1835
|
+
If the labware is in a location that cannot be specified by a LabwareOffsetLocationSequence
|
|
1836
|
+
(for instance, OFF_DECK) then return None.
|
|
1837
|
+
"""
|
|
1838
|
+
parent_location = self._labware.get_location(labware_id)
|
|
1839
|
+
return self.get_projected_offset_location(parent_location)
|
|
1840
|
+
|
|
1841
|
+
def get_projected_offset_location(
|
|
1842
|
+
self,
|
|
1843
|
+
labware_location: LabwareLocation,
|
|
1844
|
+
labware_pending_load: dict[str, LoadedLabware] | None = None,
|
|
1845
|
+
) -> Optional[LabwareOffsetLocationSequence]:
|
|
1846
|
+
"""Get the offset location that a labware loaded into this location would match.
|
|
1847
|
+
|
|
1848
|
+
`None` indicates that the very concept of a labware offset would not make sense
|
|
1849
|
+
for the given location, such as if it's some kind of off-deck location. This
|
|
1850
|
+
is a difference from `get_predicted_location_sequence()`, where off-deck
|
|
1851
|
+
locations are still represented as lists, but with special final elements.
|
|
1852
|
+
"""
|
|
1853
|
+
return self._recurse_labware_offset_location(
|
|
1854
|
+
labware_location, [], labware_pending_load or {}
|
|
1855
|
+
)
|
|
1856
|
+
|
|
1857
|
+
def _recurse_labware_offset_location(
|
|
1858
|
+
self,
|
|
1859
|
+
labware_location: LabwareLocation,
|
|
1860
|
+
building: LabwareOffsetLocationSequence,
|
|
1861
|
+
labware_pending_load: dict[str, LoadedLabware],
|
|
1862
|
+
) -> LabwareOffsetLocationSequence | None:
|
|
1863
|
+
if isinstance(labware_location, DeckSlotLocation):
|
|
1864
|
+
return building + [
|
|
1865
|
+
OnAddressableAreaOffsetLocationSequenceComponent(
|
|
1866
|
+
addressableAreaName=labware_location.slotName.value
|
|
1867
|
+
)
|
|
1868
|
+
]
|
|
1869
|
+
|
|
1870
|
+
elif isinstance(labware_location, ModuleLocation):
|
|
1871
|
+
module_id = labware_location.moduleId
|
|
1872
|
+
# Allow ModuleNotLoadedError to propagate.
|
|
1873
|
+
# Note also that we match based on the module's requested model, not its
|
|
1874
|
+
# actual model, to implement robot-server's documented HTTP API semantics.
|
|
1875
|
+
module_model = self._modules.get_requested_model(module_id=module_id)
|
|
1876
|
+
|
|
1877
|
+
# If `module_model is None`, it probably means that this module was added by
|
|
1878
|
+
# `ProtocolEngine.use_attached_modules()`, instead of an explicit
|
|
1879
|
+
# `loadModule` command.
|
|
1880
|
+
#
|
|
1881
|
+
# This assert should never raise in practice because:
|
|
1882
|
+
# 1. `ProtocolEngine.use_attached_modules()` is only used by
|
|
1883
|
+
# robot-server's "stateless command" endpoints, under `/commands`.
|
|
1884
|
+
# 2. Those endpoints don't support loading labware, so this code will
|
|
1885
|
+
# never run.
|
|
1886
|
+
#
|
|
1887
|
+
# Nevertheless, if it does happen somehow, we do NOT want to pass the
|
|
1888
|
+
# `None` value along to `LabwareView.find_applicable_labware_offset()`.
|
|
1889
|
+
# `None` means something different there, which will cause us to return
|
|
1890
|
+
# wrong results.
|
|
1891
|
+
assert module_model is not None, (
|
|
1892
|
+
"Can't find offsets for labware"
|
|
1893
|
+
" that are loaded on modules"
|
|
1894
|
+
" that were loaded with ProtocolEngine.use_attached_modules()."
|
|
1895
|
+
)
|
|
1896
|
+
|
|
1897
|
+
module_location = self._modules.get_location(module_id=module_id)
|
|
1898
|
+
if self._modules.get_deck_supports_module_fixtures():
|
|
1899
|
+
module_aa = self._modules.ensure_and_convert_module_fixture_location(
|
|
1900
|
+
module_location.slotName, module_model
|
|
1901
|
+
)
|
|
1902
|
+
else:
|
|
1903
|
+
module_aa = module_location.slotName.value
|
|
1904
|
+
return building + [
|
|
1905
|
+
OnModuleOffsetLocationSequenceComponent(moduleModel=module_model),
|
|
1906
|
+
OnAddressableAreaOffsetLocationSequenceComponent(
|
|
1907
|
+
addressableAreaName=module_aa
|
|
1908
|
+
),
|
|
1909
|
+
]
|
|
1910
|
+
|
|
1911
|
+
elif isinstance(labware_location, OnLabwareLocation):
|
|
1912
|
+
parent_labware_id = labware_location.labwareId
|
|
1913
|
+
parent_labware = self._get_or_default_labware(
|
|
1914
|
+
parent_labware_id, labware_pending_load
|
|
1915
|
+
)
|
|
1916
|
+
parent_labware_uri = LabwareUri(parent_labware.definitionUri)
|
|
1917
|
+
base_location = parent_labware.location
|
|
1918
|
+
return self._recurse_labware_offset_location(
|
|
1919
|
+
base_location,
|
|
1920
|
+
building
|
|
1921
|
+
+ [
|
|
1922
|
+
OnLabwareOffsetLocationSequenceComponent(
|
|
1923
|
+
labwareUri=parent_labware_uri
|
|
1924
|
+
)
|
|
1925
|
+
],
|
|
1926
|
+
labware_pending_load,
|
|
1927
|
+
)
|
|
1928
|
+
|
|
1929
|
+
else: # Off deck
|
|
1930
|
+
return None
|
|
1931
|
+
|
|
1932
|
+
def get_liquid_handling_z_change(
|
|
1933
|
+
self,
|
|
1934
|
+
labware_id: str,
|
|
1935
|
+
well_name: str,
|
|
1936
|
+
pipette_id: str,
|
|
1937
|
+
operation_volume: float,
|
|
1938
|
+
) -> float:
|
|
1939
|
+
"""Get the change in height from a liquid handling operation."""
|
|
1940
|
+
initial_handling_height = self.get_meniscus_height(
|
|
1941
|
+
labware_id=labware_id, well_name=well_name
|
|
1942
|
+
)
|
|
1943
|
+
final_height = self.get_well_height_after_liquid_handling(
|
|
1944
|
+
labware_id=labware_id,
|
|
1945
|
+
well_name=well_name,
|
|
1946
|
+
pipette_id=pipette_id,
|
|
1947
|
+
initial_height=initial_handling_height,
|
|
1948
|
+
volume=operation_volume,
|
|
1949
|
+
)
|
|
1950
|
+
# this function is only called by
|
|
1951
|
+
# HardwarePipetteHandler::aspirate/dispense while_tracking, and shouldn't
|
|
1952
|
+
# be reached in the case of a simulated liquid_probe
|
|
1953
|
+
assert not isinstance(
|
|
1954
|
+
initial_handling_height, SimulatedProbeResult
|
|
1955
|
+
), "Initial handling height got SimulatedProbeResult"
|
|
1956
|
+
assert not isinstance(
|
|
1957
|
+
final_height, SimulatedProbeResult
|
|
1958
|
+
), "final height is SimulatedProbeResult"
|
|
1959
|
+
return final_height - initial_handling_height
|
|
1960
|
+
|
|
1961
|
+
def get_well_offset_adjustment(
|
|
1962
|
+
self,
|
|
1963
|
+
labware_id: str,
|
|
1964
|
+
well_name: str,
|
|
1965
|
+
well_location: WellLocationType,
|
|
1966
|
+
well_depth: float,
|
|
1967
|
+
pipette_id: Optional[str] = None,
|
|
1968
|
+
operation_volume: Optional[float] = None,
|
|
1969
|
+
) -> LiquidTrackingType:
|
|
1970
|
+
"""Return a z-axis distance that accounts for well handling height and operation volume.
|
|
1971
|
+
|
|
1972
|
+
Distance is with reference to the well bottom.
|
|
1973
|
+
"""
|
|
1974
|
+
# TODO(pbm, 10-23-24): refactor to smartly reduce height/volume conversions
|
|
1975
|
+
|
|
1976
|
+
initial_handling_height = self.get_well_handling_height(
|
|
1977
|
+
labware_id=labware_id,
|
|
1978
|
+
well_name=well_name,
|
|
1979
|
+
well_location=well_location,
|
|
1980
|
+
well_depth=well_depth,
|
|
1981
|
+
)
|
|
1982
|
+
# if we're tracking a MENISCUS origin, and targeting either the beginning
|
|
1983
|
+
# position of the liquid or doing dynamic tracking, return the initial height
|
|
1984
|
+
if (
|
|
1985
|
+
well_location.origin == WellOrigin.MENISCUS
|
|
1986
|
+
and not well_location.volumeOffset
|
|
1987
|
+
):
|
|
1988
|
+
return initial_handling_height
|
|
1989
|
+
volume: Optional[float] = None
|
|
1990
|
+
if isinstance(well_location, PickUpTipWellLocation):
|
|
1991
|
+
volume = 0.0
|
|
1992
|
+
elif isinstance(well_location, LiquidHandlingWellLocation):
|
|
1993
|
+
if well_location.volumeOffset == "operationVolume":
|
|
1994
|
+
volume = operation_volume or 0.0
|
|
1995
|
+
else:
|
|
1996
|
+
if not isinstance(well_location.volumeOffset, float):
|
|
1997
|
+
raise ValueError("Invalid volume offset.")
|
|
1998
|
+
volume = well_location.volumeOffset
|
|
1999
|
+
|
|
2000
|
+
if volume:
|
|
2001
|
+
if pipette_id is None:
|
|
2002
|
+
raise ValueError(
|
|
2003
|
+
"cannot get liquid handling offset without pipette id."
|
|
2004
|
+
)
|
|
2005
|
+
liquid_height_after = self.get_well_height_after_liquid_handling(
|
|
2006
|
+
labware_id=labware_id,
|
|
2007
|
+
well_name=well_name,
|
|
2008
|
+
pipette_id=pipette_id,
|
|
2009
|
+
initial_height=initial_handling_height,
|
|
2010
|
+
volume=volume,
|
|
2011
|
+
)
|
|
2012
|
+
return liquid_height_after
|
|
2013
|
+
else:
|
|
2014
|
+
return initial_handling_height
|
|
2015
|
+
|
|
2016
|
+
def get_current_well_volume(
|
|
2017
|
+
self,
|
|
2018
|
+
labware_id: str,
|
|
2019
|
+
well_name: str,
|
|
2020
|
+
) -> LiquidTrackingType:
|
|
2021
|
+
"""Returns most recently updated volume in specified well."""
|
|
2022
|
+
last_updated = self._wells.get_last_liquid_update(labware_id, well_name)
|
|
2023
|
+
if last_updated is None:
|
|
2024
|
+
raise errors.LiquidHeightUnknownError(
|
|
2025
|
+
"Must LiquidProbe or LoadLiquid before specifying WellOrigin.MENISCUS."
|
|
2026
|
+
)
|
|
2027
|
+
|
|
2028
|
+
well_liquid = self._wells.get_well_liquid_info(
|
|
2029
|
+
labware_id=labware_id, well_name=well_name
|
|
2030
|
+
)
|
|
2031
|
+
if (
|
|
2032
|
+
well_liquid.probed_height is not None
|
|
2033
|
+
and well_liquid.probed_height.height is not None
|
|
2034
|
+
and well_liquid.probed_height.last_probed == last_updated
|
|
2035
|
+
):
|
|
2036
|
+
volume = self.get_well_volume_at_height(
|
|
2037
|
+
labware_id=labware_id,
|
|
2038
|
+
well_name=well_name,
|
|
2039
|
+
height=well_liquid.probed_height.height,
|
|
2040
|
+
)
|
|
2041
|
+
return volume
|
|
2042
|
+
elif (
|
|
2043
|
+
well_liquid.loaded_volume is not None
|
|
2044
|
+
and well_liquid.loaded_volume.volume is not None
|
|
2045
|
+
and well_liquid.loaded_volume.last_loaded == last_updated
|
|
2046
|
+
):
|
|
2047
|
+
return well_liquid.loaded_volume.volume
|
|
2048
|
+
elif (
|
|
2049
|
+
well_liquid.probed_volume is not None
|
|
2050
|
+
and well_liquid.probed_volume.volume is not None
|
|
2051
|
+
and well_liquid.probed_volume.last_probed == last_updated
|
|
2052
|
+
):
|
|
2053
|
+
return well_liquid.probed_volume.volume
|
|
2054
|
+
else:
|
|
2055
|
+
# This should not happen if there was an update but who knows
|
|
2056
|
+
raise errors.LiquidVolumeUnknownError(
|
|
2057
|
+
f"Unable to find liquid volume despite an update at {last_updated}."
|
|
2058
|
+
)
|
|
2059
|
+
|
|
2060
|
+
def get_meniscus_height(
|
|
2061
|
+
self,
|
|
2062
|
+
labware_id: str,
|
|
2063
|
+
well_name: str,
|
|
2064
|
+
) -> LiquidTrackingType:
|
|
2065
|
+
"""Returns stored meniscus height in specified well."""
|
|
2066
|
+
last_updated = self._wells.get_last_liquid_update(labware_id, well_name)
|
|
2067
|
+
if last_updated is None:
|
|
2068
|
+
raise errors.LiquidHeightUnknownError(
|
|
2069
|
+
"Must LiquidProbe or LoadLiquid before specifying WellOrigin.MENISCUS."
|
|
2070
|
+
)
|
|
2071
|
+
|
|
2072
|
+
well_liquid = self._wells.get_well_liquid_info(
|
|
2073
|
+
labware_id=labware_id, well_name=well_name
|
|
2074
|
+
)
|
|
2075
|
+
if (
|
|
2076
|
+
well_liquid.probed_height is not None
|
|
2077
|
+
and well_liquid.probed_height.height is not None
|
|
2078
|
+
and well_liquid.probed_height.last_probed == last_updated
|
|
2079
|
+
):
|
|
2080
|
+
return well_liquid.probed_height.height
|
|
2081
|
+
elif (
|
|
2082
|
+
well_liquid.loaded_volume is not None
|
|
2083
|
+
and well_liquid.loaded_volume.volume is not None
|
|
2084
|
+
and well_liquid.loaded_volume.last_loaded == last_updated
|
|
2085
|
+
):
|
|
2086
|
+
return self.get_well_height_at_volume(
|
|
2087
|
+
labware_id=labware_id,
|
|
2088
|
+
well_name=well_name,
|
|
2089
|
+
volume=well_liquid.loaded_volume.volume,
|
|
2090
|
+
)
|
|
2091
|
+
elif (
|
|
2092
|
+
well_liquid.probed_volume is not None
|
|
2093
|
+
and well_liquid.probed_volume.volume is not None
|
|
2094
|
+
and well_liquid.probed_volume.last_probed == last_updated
|
|
2095
|
+
):
|
|
2096
|
+
return self.get_well_height_at_volume(
|
|
2097
|
+
labware_id=labware_id,
|
|
2098
|
+
well_name=well_name,
|
|
2099
|
+
volume=well_liquid.probed_volume.volume,
|
|
2100
|
+
)
|
|
2101
|
+
else:
|
|
2102
|
+
# This should not happen if there was an update but who knows
|
|
2103
|
+
raise errors.LiquidHeightUnknownError(
|
|
2104
|
+
f"Unable to find liquid height despite an update at {last_updated}."
|
|
2105
|
+
)
|
|
2106
|
+
|
|
2107
|
+
def get_well_handling_height(
|
|
2108
|
+
self,
|
|
2109
|
+
labware_id: str,
|
|
2110
|
+
well_name: str,
|
|
2111
|
+
well_location: WellLocationType,
|
|
2112
|
+
well_depth: float,
|
|
2113
|
+
) -> LiquidTrackingType:
|
|
2114
|
+
"""Return the handling height for a labware well (with reference to the well bottom)."""
|
|
2115
|
+
handling_height: LiquidTrackingType = 0.0
|
|
2116
|
+
if well_location.origin == WellOrigin.TOP:
|
|
2117
|
+
handling_height = float(well_depth)
|
|
2118
|
+
elif well_location.origin == WellOrigin.CENTER:
|
|
2119
|
+
handling_height = float(well_depth / 2.0)
|
|
2120
|
+
elif well_location.origin == WellOrigin.MENISCUS:
|
|
2121
|
+
handling_height = self.get_meniscus_height(
|
|
2122
|
+
labware_id=labware_id, well_name=well_name
|
|
2123
|
+
)
|
|
2124
|
+
return handling_height
|
|
2125
|
+
|
|
2126
|
+
def find_volume_at_well_height(
|
|
2127
|
+
self,
|
|
2128
|
+
labware_id: str,
|
|
2129
|
+
well_name: str,
|
|
2130
|
+
target_height: LiquidTrackingType,
|
|
2131
|
+
) -> LiquidTrackingType:
|
|
2132
|
+
"""Call the correct volume from height function based on well geoemtry type."""
|
|
2133
|
+
well_geometry = self._labware.get_well_geometry(
|
|
2134
|
+
labware_id=labware_id, well_name=well_name
|
|
2135
|
+
)
|
|
2136
|
+
if isinstance(well_geometry, InnerWellGeometry):
|
|
2137
|
+
return find_volume_inner_well_geometry(
|
|
2138
|
+
target_height=target_height, well_geometry=well_geometry
|
|
2139
|
+
)
|
|
2140
|
+
else:
|
|
2141
|
+
return find_volume_user_defined_volumes(
|
|
2142
|
+
target_height=target_height, well_geometry=well_geometry
|
|
2143
|
+
)
|
|
2144
|
+
|
|
2145
|
+
def find_height_at_well_volume(
|
|
2146
|
+
self,
|
|
2147
|
+
labware_id: str,
|
|
2148
|
+
well_name: str,
|
|
2149
|
+
target_volume: LiquidTrackingType,
|
|
2150
|
+
) -> LiquidTrackingType:
|
|
2151
|
+
"""Call the correct height from volume function based on well geometry type."""
|
|
2152
|
+
well_geometry = self._labware.get_well_geometry(
|
|
2153
|
+
labware_id=labware_id, well_name=well_name
|
|
2154
|
+
)
|
|
2155
|
+
if isinstance(well_geometry, InnerWellGeometry):
|
|
2156
|
+
return find_height_inner_well_geometry(
|
|
2157
|
+
target_volume=target_volume, well_geometry=well_geometry
|
|
2158
|
+
)
|
|
2159
|
+
else:
|
|
2160
|
+
return find_height_user_defined_volumes(
|
|
2161
|
+
target_volume=target_volume, well_geometry=well_geometry
|
|
2162
|
+
)
|
|
2163
|
+
|
|
2164
|
+
def get_well_height_after_liquid_handling(
|
|
2165
|
+
self,
|
|
2166
|
+
labware_id: str,
|
|
2167
|
+
well_name: str,
|
|
2168
|
+
pipette_id: str,
|
|
2169
|
+
initial_height: LiquidTrackingType,
|
|
2170
|
+
volume: float,
|
|
2171
|
+
) -> LiquidTrackingType:
|
|
2172
|
+
"""Return the height of liquid in a labware well after a given volume has been handled.
|
|
2173
|
+
|
|
2174
|
+
This is given an initial handling height, with reference to the well bottom.
|
|
2175
|
+
"""
|
|
2176
|
+
well_def = self._labware.get_well_definition(labware_id, well_name)
|
|
2177
|
+
well_depth = well_def.depth
|
|
2178
|
+
|
|
2179
|
+
try:
|
|
2180
|
+
initial_volume = self.find_volume_at_well_height(
|
|
2181
|
+
labware_id=labware_id, well_name=well_name, target_height=initial_height
|
|
2182
|
+
)
|
|
2183
|
+
final_volume = initial_volume + (
|
|
2184
|
+
volume
|
|
2185
|
+
* self.get_nozzles_per_well(
|
|
2186
|
+
labware_id=labware_id,
|
|
2187
|
+
target_well_name=well_name,
|
|
2188
|
+
pipette_id=pipette_id,
|
|
2189
|
+
)
|
|
2190
|
+
)
|
|
2191
|
+
# NOTE(cm): if final_volume is outside the bounds of the well, it will get
|
|
2192
|
+
# adjusted inside find_height_at_well_volume to accomodate well the height
|
|
2193
|
+
# calculation.
|
|
2194
|
+
height_inside_well = self.find_height_at_well_volume(
|
|
2195
|
+
labware_id=labware_id, well_name=well_name, target_volume=final_volume
|
|
2196
|
+
)
|
|
2197
|
+
return self._validate_well_position(
|
|
2198
|
+
target_height=height_inside_well,
|
|
2199
|
+
well_max_height=well_depth,
|
|
2200
|
+
pipette_id=pipette_id,
|
|
2201
|
+
)
|
|
2202
|
+
except InvalidLiquidHeightFound as _exception:
|
|
2203
|
+
raise InvalidLiquidHeightFound(
|
|
2204
|
+
message=_exception.message
|
|
2205
|
+
+ f"for well {well_name} of {self._labware.get_display_name(labware_id)} on slot {self.get_ancestor_slot_name(labware_id)}"
|
|
2206
|
+
)
|
|
2207
|
+
|
|
2208
|
+
def get_well_height_at_volume(
|
|
2209
|
+
self, labware_id: str, well_name: str, volume: LiquidTrackingType
|
|
2210
|
+
) -> LiquidTrackingType:
|
|
2211
|
+
"""Convert well volume to height."""
|
|
2212
|
+
try:
|
|
2213
|
+
return self.find_height_at_well_volume(
|
|
2214
|
+
labware_id=labware_id, well_name=well_name, target_volume=volume
|
|
2215
|
+
)
|
|
2216
|
+
except InvalidLiquidHeightFound as _exception:
|
|
2217
|
+
raise InvalidLiquidHeightFound(
|
|
2218
|
+
message=_exception.message
|
|
2219
|
+
+ f"for well {well_name} of {self._labware.get_display_name(labware_id)} on slot {self.get_ancestor_slot_name(labware_id)}"
|
|
2220
|
+
)
|
|
2221
|
+
|
|
2222
|
+
def get_well_volume_at_height(
|
|
2223
|
+
self,
|
|
2224
|
+
labware_id: str,
|
|
2225
|
+
well_name: str,
|
|
2226
|
+
height: LiquidTrackingType,
|
|
2227
|
+
) -> LiquidTrackingType:
|
|
2228
|
+
"""Convert well height to volume."""
|
|
2229
|
+
try:
|
|
2230
|
+
return self.find_volume_at_well_height(
|
|
2231
|
+
labware_id=labware_id, well_name=well_name, target_height=height
|
|
2232
|
+
)
|
|
2233
|
+
except InvalidLiquidHeightFound as _exception:
|
|
2234
|
+
raise InvalidLiquidHeightFound(
|
|
2235
|
+
message=_exception.message
|
|
2236
|
+
+ f"for well {well_name} of {self._labware.get_display_name(labware_id)} on slot {self.get_ancestor_slot_name(labware_id)}"
|
|
2237
|
+
)
|
|
2238
|
+
|
|
2239
|
+
def validate_dispense_volume_into_well(
|
|
2240
|
+
self,
|
|
2241
|
+
labware_id: str,
|
|
2242
|
+
well_name: str,
|
|
2243
|
+
well_location: WellLocationType,
|
|
2244
|
+
volume: float,
|
|
2245
|
+
) -> None:
|
|
2246
|
+
"""Raise InvalidDispenseVolumeError if planned dispense volume will overflow well."""
|
|
2247
|
+
well_def = self._labware.get_well_definition(labware_id, well_name)
|
|
2248
|
+
well_volumetric_capacity = float(well_def.totalLiquidVolume)
|
|
2249
|
+
if well_location.origin == WellOrigin.MENISCUS:
|
|
2250
|
+
# TODO(pbm, 10-23-24): refactor to smartly reduce height/volume conversions
|
|
2251
|
+
meniscus_height = self.get_meniscus_height(
|
|
2252
|
+
labware_id=labware_id, well_name=well_name
|
|
2253
|
+
)
|
|
2254
|
+
try:
|
|
2255
|
+
meniscus_volume = self.find_volume_at_well_height(
|
|
2256
|
+
labware_id=labware_id,
|
|
2257
|
+
well_name=well_name,
|
|
2258
|
+
target_height=meniscus_height,
|
|
2259
|
+
)
|
|
2260
|
+
except InvalidLiquidHeightFound as _exception:
|
|
2261
|
+
raise InvalidLiquidHeightFound(
|
|
2262
|
+
message=_exception.message
|
|
2263
|
+
+ f"for well {well_name} of {self._labware.get_display_name(labware_id)} on slot {self.get_ancestor_slot_name(labware_id)}"
|
|
2264
|
+
)
|
|
2265
|
+
# if meniscus volume is a simulated value, comparisons aren't meaningful
|
|
2266
|
+
if isinstance(meniscus_volume, SimulatedProbeResult):
|
|
2267
|
+
return
|
|
2268
|
+
remaining_volume = well_volumetric_capacity - meniscus_volume
|
|
2269
|
+
if volume > remaining_volume:
|
|
2270
|
+
raise errors.InvalidDispenseVolumeError(
|
|
2271
|
+
f"Attempting to dispense {volume}µL of liquid into a well that can currently only hold {remaining_volume}µL (well {well_name} in labware_id: {labware_id})"
|
|
2272
|
+
)
|
|
2273
|
+
else:
|
|
2274
|
+
# TODO(pbm, 10-08-24): factor in well (LabwareStore) state volume
|
|
2275
|
+
if volume > well_volumetric_capacity:
|
|
2276
|
+
raise errors.InvalidDispenseVolumeError(
|
|
2277
|
+
f"Attempting to dispense {volume}µL of liquid into a well that can only hold {well_volumetric_capacity}µL (well {well_name} in labware_id: {labware_id})"
|
|
2278
|
+
)
|
|
2279
|
+
|
|
2280
|
+
def get_wells_covered_by_pipette_with_active_well(
|
|
2281
|
+
self, labware_id: str, target_well_name: str, pipette_id: str
|
|
2282
|
+
) -> list[str]:
|
|
2283
|
+
"""Get a flat list of wells that are covered by a pipette when moved to a specified well.
|
|
2284
|
+
|
|
2285
|
+
When you move a pipette in a multichannel configuration to a specific well - the target well -
|
|
2286
|
+
the pipette will operate on other wells as well.
|
|
2287
|
+
|
|
2288
|
+
For instance, a pipette with a COLUMN configuration with well A1 of an SBS standard labware target
|
|
2289
|
+
will also "cover", under this definition, wells B1-H1. That same pipette, when C5 is the target well, will "cover"
|
|
2290
|
+
wells C5-H5.
|
|
2291
|
+
|
|
2292
|
+
This math only works, and may only be applied, if one of the following is true:
|
|
2293
|
+
- The pipette is in a SINGLE configuration
|
|
2294
|
+
- The pipette is in a non-SINGLE configuration, and the labware is an SBS-format 96 or 384 well plate (and is so
|
|
2295
|
+
marked in its definition's parameters.format key, as 96Standard or 384Standard)
|
|
2296
|
+
|
|
2297
|
+
If all of the following do not apply, regardless of the nozzle configuration of the pipette this function will
|
|
2298
|
+
return only the labware covered by the primary well.
|
|
2299
|
+
"""
|
|
2300
|
+
pipette_nozzle_map = self._pipettes.get_nozzle_configuration(pipette_id)
|
|
2301
|
+
labware_columns = [
|
|
2302
|
+
column for column in self._labware.get_definition(labware_id).ordering
|
|
2303
|
+
]
|
|
2304
|
+
try:
|
|
2305
|
+
return list(
|
|
2306
|
+
wells_covered_by_pipette_configuration(
|
|
2307
|
+
pipette_nozzle_map, target_well_name, labware_columns
|
|
2308
|
+
)
|
|
2309
|
+
)
|
|
2310
|
+
except InvalidStoredData:
|
|
2311
|
+
return [target_well_name]
|
|
2312
|
+
|
|
2313
|
+
def get_nozzles_per_well(
|
|
2314
|
+
self, labware_id: str, target_well_name: str, pipette_id: str
|
|
2315
|
+
) -> int:
|
|
2316
|
+
"""Get the number of nozzles that will interact with each well."""
|
|
2317
|
+
return nozzles_per_well(
|
|
2318
|
+
self._pipettes.get_nozzle_configuration(pipette_id),
|
|
2319
|
+
target_well_name,
|
|
2320
|
+
self._labware.get_definition(labware_id).ordering,
|
|
2321
|
+
)
|
|
2322
|
+
|
|
2323
|
+
def get_height_of_labware_stack(
|
|
2324
|
+
self, definitions: list[LabwareDefinition]
|
|
2325
|
+
) -> float:
|
|
2326
|
+
"""Get the overall height of a stack of labware listed by definition in top-first order."""
|
|
2327
|
+
if len(definitions) == 0:
|
|
2328
|
+
return 0
|
|
2329
|
+
if len(definitions) == 1:
|
|
2330
|
+
return self._labware.get_dimensions(labware_definition=definitions[0]).z
|
|
2331
|
+
total_height = 0.0
|
|
2332
|
+
upper_def: LabwareDefinition = definitions[0]
|
|
2333
|
+
for lower_def in definitions[1:]:
|
|
2334
|
+
overlap = self._labware.get_labware_overlap_offsets(
|
|
2335
|
+
upper_def, lower_def.parameters.loadName
|
|
2336
|
+
).z
|
|
2337
|
+
total_height += (
|
|
2338
|
+
self._labware.get_dimensions(labware_definition=upper_def).z - overlap
|
|
2339
|
+
)
|
|
2340
|
+
upper_def = lower_def
|
|
2341
|
+
return (
|
|
2342
|
+
total_height + self._labware.get_dimensions(labware_definition=upper_def).z
|
|
2343
|
+
)
|
|
2344
|
+
return total_height + upper_def.dimensions.zDimension
|
|
2345
|
+
|
|
2346
|
+
def get_height_of_stacker_labware_pool(self, module_id: str) -> float:
|
|
2347
|
+
"""Get the overall height of a stack of labware in a Stacker module."""
|
|
2348
|
+
stacker = self._modules.get_flex_stacker_substate(module_id)
|
|
2349
|
+
pool_list = stacker.get_pool_definition_ordered_list()
|
|
2350
|
+
if not pool_list:
|
|
2351
|
+
return 0.0
|
|
2352
|
+
return self.get_height_of_labware_stack(pool_list)
|
|
2353
|
+
|
|
2354
|
+
def _get_or_default_labware(
|
|
2355
|
+
self, labware_id: str, pending_labware: dict[str, LoadedLabware]
|
|
2356
|
+
) -> LoadedLabware:
|
|
2357
|
+
try:
|
|
2358
|
+
return self._labware.get(labware_id)
|
|
2359
|
+
except LabwareNotLoadedError as lnle:
|
|
2360
|
+
try:
|
|
2361
|
+
return pending_labware[labware_id]
|
|
2362
|
+
except KeyError as ke:
|
|
2363
|
+
raise lnle from ke
|
|
2364
|
+
|
|
2365
|
+
def raise_if_labware_inaccessible_by_pipette( # noqa: C901
|
|
2366
|
+
self, labware_id: str
|
|
2367
|
+
) -> None:
|
|
2368
|
+
"""Raise an error if the specified location cannot be reached via a pipette."""
|
|
2369
|
+
labware = self._labware.get(labware_id)
|
|
2370
|
+
labware_location = labware.location
|
|
2371
|
+
if isinstance(labware_location, OnLabwareLocation):
|
|
2372
|
+
return self.raise_if_labware_inaccessible_by_pipette(
|
|
2373
|
+
labware_location.labwareId
|
|
2374
|
+
)
|
|
2375
|
+
elif labware.lid_id is not None:
|
|
2376
|
+
raise errors.LocationNotAccessibleByPipetteError(
|
|
2377
|
+
f"Cannot move pipette to {labware.loadName} "
|
|
2378
|
+
"because labware is currently covered by a lid."
|
|
2379
|
+
)
|
|
2380
|
+
elif isinstance(labware_location, AddressableAreaLocation):
|
|
2381
|
+
if fixture_validation.is_staging_slot(labware_location.addressableAreaName):
|
|
2382
|
+
raise errors.LocationNotAccessibleByPipetteError(
|
|
2383
|
+
f"Cannot move pipette to {labware.loadName},"
|
|
2384
|
+
f" labware is on staging slot {labware_location.addressableAreaName}"
|
|
2385
|
+
)
|
|
2386
|
+
elif fixture_validation.is_stacker_shuttle(
|
|
2387
|
+
labware_location.addressableAreaName
|
|
2388
|
+
):
|
|
2389
|
+
raise errors.LocationNotAccessibleByPipetteError(
|
|
2390
|
+
f"Cannot move pipette to {labware.loadName} because it is on a stacker shuttle"
|
|
2391
|
+
)
|
|
2392
|
+
elif (
|
|
2393
|
+
labware_location == OFF_DECK_LOCATION or labware_location == SYSTEM_LOCATION
|
|
2394
|
+
):
|
|
2395
|
+
raise errors.LocationNotAccessibleByPipetteError(
|
|
2396
|
+
f"Cannot move pipette to {labware.loadName}, labware is off-deck."
|
|
2397
|
+
)
|
|
2398
|
+
elif isinstance(labware_location, ModuleLocation):
|
|
2399
|
+
module = self._modules.get(labware_location.moduleId)
|
|
2400
|
+
if ModuleModel.is_flex_stacker(module.model):
|
|
2401
|
+
raise errors.LocationNotAccessibleByPipetteError(
|
|
2402
|
+
f"Cannot move pipette to {labware.loadName}, labware is on a stacker shuttle"
|
|
2403
|
+
)
|
|
2404
|
+
|
|
2405
|
+
elif isinstance(labware_location, InStackerHopperLocation):
|
|
2406
|
+
raise errors.LocationNotAccessibleByPipetteError(
|
|
2407
|
+
f"Cannot move pipette to {labware.loadName}, labware is in a stacker hopper"
|
|
2408
|
+
)
|