opentrons 8.2.0a4__py2.py3-none-any.whl → 8.3.0a1__py2.py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- opentrons/calibration_storage/deck_configuration.py +3 -3
- opentrons/calibration_storage/file_operators.py +3 -3
- opentrons/calibration_storage/helpers.py +3 -1
- opentrons/calibration_storage/ot2/models/v1.py +16 -29
- opentrons/calibration_storage/ot2/tip_length.py +7 -4
- opentrons/calibration_storage/ot3/models/v1.py +14 -23
- opentrons/cli/analyze.py +18 -6
- opentrons/config/defaults_ot3.py +1 -0
- opentrons/drivers/asyncio/communication/__init__.py +2 -0
- opentrons/drivers/asyncio/communication/errors.py +16 -3
- opentrons/drivers/asyncio/communication/serial_connection.py +24 -9
- opentrons/drivers/command_builder.py +2 -2
- opentrons/drivers/flex_stacker/__init__.py +9 -0
- opentrons/drivers/flex_stacker/abstract.py +89 -0
- opentrons/drivers/flex_stacker/driver.py +260 -0
- opentrons/drivers/flex_stacker/simulator.py +109 -0
- opentrons/drivers/flex_stacker/types.py +138 -0
- opentrons/drivers/heater_shaker/driver.py +18 -3
- opentrons/drivers/temp_deck/driver.py +13 -3
- opentrons/drivers/thermocycler/driver.py +17 -3
- opentrons/execute.py +3 -1
- opentrons/hardware_control/__init__.py +1 -2
- opentrons/hardware_control/api.py +28 -20
- opentrons/hardware_control/backends/flex_protocol.py +17 -7
- opentrons/hardware_control/backends/ot3controller.py +213 -63
- opentrons/hardware_control/backends/ot3simulator.py +18 -9
- opentrons/hardware_control/backends/ot3utils.py +43 -15
- opentrons/hardware_control/dev_types.py +4 -0
- opentrons/hardware_control/emulation/heater_shaker.py +4 -0
- opentrons/hardware_control/emulation/module_server/client.py +1 -1
- opentrons/hardware_control/emulation/module_server/server.py +5 -3
- opentrons/hardware_control/emulation/settings.py +3 -4
- opentrons/hardware_control/instruments/ot2/instrument_calibration.py +2 -1
- opentrons/hardware_control/instruments/ot2/pipette.py +15 -22
- opentrons/hardware_control/instruments/ot2/pipette_handler.py +8 -1
- opentrons/hardware_control/instruments/ot3/gripper.py +2 -2
- opentrons/hardware_control/instruments/ot3/pipette.py +23 -22
- opentrons/hardware_control/instruments/ot3/pipette_handler.py +10 -1
- opentrons/hardware_control/modules/mod_abc.py +2 -2
- opentrons/hardware_control/motion_utilities.py +68 -0
- opentrons/hardware_control/nozzle_manager.py +39 -41
- opentrons/hardware_control/ot3_calibration.py +1 -1
- opentrons/hardware_control/ot3api.py +60 -23
- opentrons/hardware_control/protocols/gripper_controller.py +3 -0
- opentrons/hardware_control/protocols/hardware_manager.py +5 -1
- opentrons/hardware_control/protocols/liquid_handler.py +18 -0
- opentrons/hardware_control/protocols/motion_controller.py +6 -0
- opentrons/hardware_control/robot_calibration.py +1 -1
- opentrons/hardware_control/types.py +61 -0
- opentrons/protocol_api/__init__.py +20 -1
- opentrons/protocol_api/_liquid.py +24 -49
- opentrons/protocol_api/_liquid_properties.py +754 -0
- opentrons/protocol_api/_types.py +24 -0
- opentrons/protocol_api/core/common.py +2 -0
- opentrons/protocol_api/core/engine/instrument.py +82 -10
- opentrons/protocol_api/core/engine/labware.py +29 -7
- opentrons/protocol_api/core/engine/protocol.py +130 -5
- opentrons/protocol_api/core/engine/robot.py +139 -0
- opentrons/protocol_api/core/engine/well.py +4 -1
- opentrons/protocol_api/core/instrument.py +46 -4
- opentrons/protocol_api/core/labware.py +13 -4
- opentrons/protocol_api/core/legacy/legacy_instrument_core.py +37 -3
- opentrons/protocol_api/core/legacy/legacy_labware_core.py +13 -4
- opentrons/protocol_api/core/legacy/legacy_protocol_core.py +32 -1
- opentrons/protocol_api/core/legacy/legacy_robot_core.py +0 -0
- opentrons/protocol_api/core/legacy_simulator/legacy_instrument_core.py +37 -3
- opentrons/protocol_api/core/protocol.py +34 -1
- opentrons/protocol_api/core/robot.py +51 -0
- opentrons/protocol_api/instrument_context.py +158 -44
- opentrons/protocol_api/labware.py +231 -7
- opentrons/protocol_api/module_contexts.py +21 -17
- opentrons/protocol_api/protocol_context.py +125 -4
- opentrons/protocol_api/robot_context.py +204 -32
- opentrons/protocol_api/validation.py +262 -3
- opentrons/protocol_engine/__init__.py +4 -0
- opentrons/protocol_engine/actions/actions.py +2 -3
- opentrons/protocol_engine/clients/sync_client.py +18 -0
- opentrons/protocol_engine/commands/__init__.py +81 -0
- opentrons/protocol_engine/commands/absorbance_reader/close_lid.py +0 -2
- opentrons/protocol_engine/commands/absorbance_reader/initialize.py +19 -5
- opentrons/protocol_engine/commands/absorbance_reader/open_lid.py +0 -1
- opentrons/protocol_engine/commands/absorbance_reader/read.py +32 -9
- opentrons/protocol_engine/commands/air_gap_in_place.py +160 -0
- opentrons/protocol_engine/commands/aspirate.py +103 -53
- opentrons/protocol_engine/commands/aspirate_in_place.py +55 -51
- opentrons/protocol_engine/commands/blow_out.py +44 -39
- opentrons/protocol_engine/commands/blow_out_in_place.py +21 -32
- opentrons/protocol_engine/commands/calibration/calibrate_gripper.py +13 -6
- opentrons/protocol_engine/commands/calibration/calibrate_module.py +1 -1
- opentrons/protocol_engine/commands/calibration/calibrate_pipette.py +3 -3
- opentrons/protocol_engine/commands/calibration/move_to_maintenance_position.py +1 -1
- opentrons/protocol_engine/commands/command.py +73 -66
- opentrons/protocol_engine/commands/command_unions.py +101 -1
- opentrons/protocol_engine/commands/comment.py +1 -1
- opentrons/protocol_engine/commands/configure_for_volume.py +10 -3
- opentrons/protocol_engine/commands/configure_nozzle_layout.py +6 -4
- opentrons/protocol_engine/commands/custom.py +6 -12
- opentrons/protocol_engine/commands/dispense.py +82 -48
- opentrons/protocol_engine/commands/dispense_in_place.py +71 -51
- opentrons/protocol_engine/commands/drop_tip.py +52 -31
- opentrons/protocol_engine/commands/drop_tip_in_place.py +13 -3
- opentrons/protocol_engine/commands/generate_command_schema.py +4 -11
- opentrons/protocol_engine/commands/get_next_tip.py +134 -0
- opentrons/protocol_engine/commands/get_tip_presence.py +1 -1
- opentrons/protocol_engine/commands/heater_shaker/close_labware_latch.py +1 -1
- opentrons/protocol_engine/commands/heater_shaker/deactivate_heater.py +1 -1
- opentrons/protocol_engine/commands/heater_shaker/deactivate_shaker.py +1 -1
- opentrons/protocol_engine/commands/heater_shaker/open_labware_latch.py +1 -1
- opentrons/protocol_engine/commands/heater_shaker/set_and_wait_for_shake_speed.py +1 -1
- opentrons/protocol_engine/commands/heater_shaker/set_target_temperature.py +1 -1
- opentrons/protocol_engine/commands/heater_shaker/wait_for_temperature.py +10 -4
- opentrons/protocol_engine/commands/home.py +13 -4
- opentrons/protocol_engine/commands/liquid_probe.py +67 -24
- opentrons/protocol_engine/commands/load_labware.py +29 -7
- opentrons/protocol_engine/commands/load_lid.py +146 -0
- opentrons/protocol_engine/commands/load_lid_stack.py +189 -0
- opentrons/protocol_engine/commands/load_liquid.py +12 -4
- opentrons/protocol_engine/commands/load_liquid_class.py +144 -0
- opentrons/protocol_engine/commands/load_module.py +31 -10
- opentrons/protocol_engine/commands/load_pipette.py +19 -8
- opentrons/protocol_engine/commands/magnetic_module/disengage.py +1 -1
- opentrons/protocol_engine/commands/magnetic_module/engage.py +1 -1
- opentrons/protocol_engine/commands/move_labware.py +19 -6
- opentrons/protocol_engine/commands/move_relative.py +35 -25
- opentrons/protocol_engine/commands/move_to_addressable_area.py +40 -27
- opentrons/protocol_engine/commands/move_to_addressable_area_for_drop_tip.py +53 -32
- opentrons/protocol_engine/commands/move_to_coordinates.py +36 -22
- opentrons/protocol_engine/commands/move_to_well.py +40 -24
- opentrons/protocol_engine/commands/movement_common.py +338 -0
- opentrons/protocol_engine/commands/pick_up_tip.py +49 -27
- opentrons/protocol_engine/commands/pipetting_common.py +169 -87
- opentrons/protocol_engine/commands/prepare_to_aspirate.py +24 -33
- opentrons/protocol_engine/commands/reload_labware.py +1 -1
- opentrons/protocol_engine/commands/retract_axis.py +1 -1
- opentrons/protocol_engine/commands/robot/__init__.py +69 -0
- opentrons/protocol_engine/commands/robot/close_gripper_jaw.py +86 -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 +77 -0
- opentrons/protocol_engine/commands/save_position.py +14 -5
- opentrons/protocol_engine/commands/set_rail_lights.py +1 -1
- opentrons/protocol_engine/commands/set_status_bar.py +1 -1
- opentrons/protocol_engine/commands/temperature_module/deactivate.py +1 -1
- opentrons/protocol_engine/commands/temperature_module/set_target_temperature.py +1 -1
- opentrons/protocol_engine/commands/temperature_module/wait_for_temperature.py +10 -4
- opentrons/protocol_engine/commands/thermocycler/close_lid.py +1 -1
- opentrons/protocol_engine/commands/thermocycler/deactivate_block.py +1 -1
- opentrons/protocol_engine/commands/thermocycler/deactivate_lid.py +1 -1
- opentrons/protocol_engine/commands/thermocycler/open_lid.py +1 -1
- opentrons/protocol_engine/commands/thermocycler/run_extended_profile.py +8 -2
- opentrons/protocol_engine/commands/thermocycler/run_profile.py +9 -3
- opentrons/protocol_engine/commands/thermocycler/set_target_block_temperature.py +11 -4
- opentrons/protocol_engine/commands/thermocycler/set_target_lid_temperature.py +1 -1
- opentrons/protocol_engine/commands/thermocycler/wait_for_block_temperature.py +1 -1
- opentrons/protocol_engine/commands/thermocycler/wait_for_lid_temperature.py +1 -1
- opentrons/protocol_engine/commands/touch_tip.py +65 -16
- opentrons/protocol_engine/commands/unsafe/unsafe_blow_out_in_place.py +4 -1
- opentrons/protocol_engine/commands/unsafe/unsafe_drop_tip_in_place.py +12 -3
- opentrons/protocol_engine/commands/unsafe/unsafe_engage_axes.py +1 -4
- opentrons/protocol_engine/commands/unsafe/update_position_estimators.py +1 -4
- opentrons/protocol_engine/commands/verify_tip_presence.py +11 -4
- opentrons/protocol_engine/commands/wait_for_duration.py +10 -3
- opentrons/protocol_engine/commands/wait_for_resume.py +10 -3
- opentrons/protocol_engine/errors/__init__.py +8 -0
- opentrons/protocol_engine/errors/error_occurrence.py +19 -20
- opentrons/protocol_engine/errors/exceptions.py +50 -0
- opentrons/protocol_engine/execution/command_executor.py +1 -1
- opentrons/protocol_engine/execution/equipment.py +73 -5
- opentrons/protocol_engine/execution/gantry_mover.py +364 -8
- opentrons/protocol_engine/execution/movement.py +27 -0
- opentrons/protocol_engine/execution/pipetting.py +5 -1
- opentrons/protocol_engine/execution/tip_handler.py +4 -6
- opentrons/protocol_engine/notes/notes.py +1 -1
- opentrons/protocol_engine/protocol_engine.py +7 -6
- opentrons/protocol_engine/resources/labware_data_provider.py +1 -1
- opentrons/protocol_engine/resources/labware_validation.py +5 -0
- opentrons/protocol_engine/resources/module_data_provider.py +1 -1
- opentrons/protocol_engine/resources/pipette_data_provider.py +26 -0
- opentrons/protocol_engine/slot_standardization.py +9 -9
- opentrons/protocol_engine/state/_move_types.py +9 -5
- opentrons/protocol_engine/state/_well_math.py +193 -0
- opentrons/protocol_engine/state/addressable_areas.py +25 -61
- opentrons/protocol_engine/state/command_history.py +12 -0
- opentrons/protocol_engine/state/commands.py +17 -13
- opentrons/protocol_engine/state/files.py +10 -12
- opentrons/protocol_engine/state/fluid_stack.py +138 -0
- opentrons/protocol_engine/state/frustum_helpers.py +57 -32
- opentrons/protocol_engine/state/geometry.py +47 -1
- opentrons/protocol_engine/state/labware.py +79 -25
- opentrons/protocol_engine/state/liquid_classes.py +82 -0
- opentrons/protocol_engine/state/liquids.py +16 -4
- opentrons/protocol_engine/state/modules.py +52 -70
- opentrons/protocol_engine/state/motion.py +6 -1
- opentrons/protocol_engine/state/pipettes.py +144 -58
- opentrons/protocol_engine/state/state.py +21 -2
- opentrons/protocol_engine/state/state_summary.py +4 -2
- opentrons/protocol_engine/state/tips.py +11 -44
- opentrons/protocol_engine/state/update_types.py +343 -48
- opentrons/protocol_engine/state/wells.py +19 -11
- opentrons/protocol_engine/types.py +176 -28
- opentrons/protocol_reader/extract_labware_definitions.py +5 -2
- opentrons/protocol_reader/file_format_validator.py +5 -5
- opentrons/protocol_runner/json_file_reader.py +9 -3
- opentrons/protocol_runner/json_translator.py +51 -25
- opentrons/protocol_runner/legacy_command_mapper.py +66 -64
- opentrons/protocol_runner/protocol_runner.py +35 -4
- opentrons/protocol_runner/python_protocol_wrappers.py +1 -1
- opentrons/protocol_runner/run_orchestrator.py +13 -3
- opentrons/protocols/advanced_control/common.py +38 -0
- opentrons/protocols/advanced_control/mix.py +1 -1
- opentrons/protocols/advanced_control/transfers/__init__.py +0 -0
- opentrons/protocols/advanced_control/transfers/common.py +56 -0
- opentrons/protocols/advanced_control/{transfers.py → transfers/transfer.py} +10 -85
- opentrons/protocols/api_support/definitions.py +1 -1
- opentrons/protocols/api_support/instrument.py +1 -1
- opentrons/protocols/api_support/util.py +10 -0
- opentrons/protocols/labware.py +39 -6
- opentrons/protocols/models/json_protocol.py +5 -9
- opentrons/simulate.py +3 -1
- opentrons/types.py +162 -2
- opentrons/util/logging_config.py +1 -1
- {opentrons-8.2.0a4.dist-info → opentrons-8.3.0a1.dist-info}/METADATA +16 -15
- {opentrons-8.2.0a4.dist-info → opentrons-8.3.0a1.dist-info}/RECORD +229 -202
- {opentrons-8.2.0a4.dist-info → opentrons-8.3.0a1.dist-info}/WHEEL +1 -1
- {opentrons-8.2.0a4.dist-info → opentrons-8.3.0a1.dist-info}/LICENSE +0 -0
- {opentrons-8.2.0a4.dist-info → opentrons-8.3.0a1.dist-info}/entry_points.txt +0 -0
- {opentrons-8.2.0a4.dist-info → opentrons-8.3.0a1.dist-info}/top_level.txt +0 -0
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"""All command IDs, in insertion order."""
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"""All failed command IDs, in insertion order."""
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"""All command IDs besides fixit command intents, in insertion order."""
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-
class CommandView
|
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+
class CommandView:
|
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|
"""Read-only command state view."""
|
|
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584
|
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_state: CommandState
|
|
@@ -684,7 +679,7 @@ class CommandView(HasState[CommandState]):
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684
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|
finish_error = self._state.finish_error
|
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680
|
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681
|
if run_error and finish_error:
|
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|
-
combined_error = ErrorOccurrence
|
|
682
|
+
combined_error = ErrorOccurrence(
|
|
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683
|
id=finish_error.id,
|
|
689
684
|
createdAt=finish_error.createdAt,
|
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errorType="RunAndFinishFailed",
|
|
@@ -706,7 +701,12 @@ class CommandView(HasState[CommandState]):
|
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701
|
|
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707
702
|
def get_all_errors(self) -> List[ErrorOccurrence]:
|
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|
"""Get the run's full error list, if there was none, returns an empty list."""
|
|
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|
-
|
|
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|
+
failed_commands = self._state.command_history.get_all_failed_commands()
|
|
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|
+
return [
|
|
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+
command_error.error
|
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|
+
for command_error in failed_commands
|
|
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|
+
if command_error.error is not None
|
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|
+
]
|
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def get_has_entered_recovery_mode(self) -> bool:
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"""Get whether the run has entered recovery mode."""
|
|
@@ -916,7 +916,7 @@ class CommandView(HasState[CommandState]):
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916
916
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fatal error of the overall run coming from anywhere in the Python script,
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|
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including in between commands.
|
|
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"""
|
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-
failed_command = self.
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919
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+
failed_command = self._state.failed_command
|
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if (
|
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921
921
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failed_command
|
|
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922
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and failed_command.command.error
|
|
@@ -932,12 +932,16 @@ class CommandView(HasState[CommandState]):
|
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932
932
|
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|
933
933
|
The command ID is assumed to point to a failed command.
|
|
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934
|
"""
|
|
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|
-
return self.
|
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+
return self._state.command_error_recovery_types[command_id]
|
|
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936
|
|
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937
|
def get_is_stopped(self) -> bool:
|
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"""Get whether an engine stop has completed."""
|
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|
return self._state.run_completed_at is not None
|
|
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940
|
|
|
941
|
+
def get_is_stopped_by_estop(self) -> bool:
|
|
942
|
+
"""Return whether the engine was stopped specifically by an E-stop."""
|
|
943
|
+
return self._state.stopped_by_estop
|
|
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|
+
|
|
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945
|
def has_been_played(self) -> bool:
|
|
942
946
|
"""Get whether engine has started."""
|
|
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947
|
return self._state.run_started_at is not None
|
|
@@ -2,12 +2,11 @@
|
|
|
2
2
|
from dataclasses import dataclass
|
|
3
3
|
from typing import List
|
|
4
4
|
|
|
5
|
+
from opentrons.protocol_engine.actions.get_state_update import get_state_updates
|
|
6
|
+
from opentrons.protocol_engine.state import update_types
|
|
7
|
+
|
|
5
8
|
from ._abstract_store import HasState, HandlesActions
|
|
6
|
-
from ..actions import Action
|
|
7
|
-
from ..commands import (
|
|
8
|
-
Command,
|
|
9
|
-
absorbance_reader,
|
|
10
|
-
)
|
|
9
|
+
from ..actions import Action
|
|
11
10
|
|
|
12
11
|
|
|
13
12
|
@dataclass
|
|
@@ -28,16 +27,15 @@ class FileStore(HasState[FileState], HandlesActions):
|
|
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28
27
|
|
|
29
28
|
def handle_action(self, action: Action) -> None:
|
|
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|
"""Modify state in reaction to an action."""
|
|
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|
-
|
|
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|
-
self.
|
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30
|
+
for state_update in get_state_updates(action):
|
|
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|
+
self._handle_state_update(state_update)
|
|
33
32
|
|
|
34
|
-
def
|
|
35
|
-
if
|
|
36
|
-
|
|
37
|
-
self._state.file_ids.extend(command.result.fileIds)
|
|
33
|
+
def _handle_state_update(self, state_update: update_types.StateUpdate) -> None:
|
|
34
|
+
if state_update.files_added != update_types.NO_CHANGE:
|
|
35
|
+
self._state.file_ids.extend(state_update.files_added.file_ids)
|
|
38
36
|
|
|
39
37
|
|
|
40
|
-
class FileView
|
|
38
|
+
class FileView:
|
|
41
39
|
"""Read-only engine created file state view."""
|
|
42
40
|
|
|
43
41
|
_state: FileState
|
|
@@ -0,0 +1,138 @@
|
|
|
1
|
+
"""Implements fluid stack tracking for pipettes.
|
|
2
|
+
|
|
3
|
+
Inside a pipette's tip, there can be a mix of kinds of fluids - here, "fluid" means "liquid" (i.e. a protocol-relevant
|
|
4
|
+
working liquid that is aspirated or dispensed from wells) or "air" (i.e. because there was an air gap). Since sometimes
|
|
5
|
+
you want air gaps in different places - physically-below liquid to prevent dripping, physically-above liquid to provide
|
|
6
|
+
extra room to push the plunger - we need to support some notion of at least phsyical ordinal position of air and liquid,
|
|
7
|
+
and we do so as a logical stack because that's physically relevant.
|
|
8
|
+
"""
|
|
9
|
+
from logging import getLogger
|
|
10
|
+
from numpy import isclose
|
|
11
|
+
from ..types import AspiratedFluid, FluidKind
|
|
12
|
+
|
|
13
|
+
_LOG = getLogger(__name__)
|
|
14
|
+
|
|
15
|
+
|
|
16
|
+
class FluidStack:
|
|
17
|
+
"""A FluidStack data structure is a list of AspiratedFluids, with stack-style (last-in-first-out) ordering.
|
|
18
|
+
|
|
19
|
+
The front of the list is the physical-top of the liquid stack (logical-bottom of the stack data structure)
|
|
20
|
+
and the back of the list is the physical-bottom of the liquid stack (logical-top of the stack data structure).
|
|
21
|
+
The state is internal and the interaction surface is the methods. This is a mutating API.
|
|
22
|
+
"""
|
|
23
|
+
|
|
24
|
+
_FluidStack = list[AspiratedFluid]
|
|
25
|
+
|
|
26
|
+
_fluid_stack: _FluidStack
|
|
27
|
+
|
|
28
|
+
def __init__(self, _fluid_stack: _FluidStack | None = None) -> None:
|
|
29
|
+
"""Build a FluidStack.
|
|
30
|
+
|
|
31
|
+
The argument is provided for testing and shouldn't be generally used.
|
|
32
|
+
"""
|
|
33
|
+
self._fluid_stack = _fluid_stack or []
|
|
34
|
+
|
|
35
|
+
def add_fluid(self, new: AspiratedFluid) -> None:
|
|
36
|
+
"""Add fluid to a stack.
|
|
37
|
+
|
|
38
|
+
If the new fluid is of a different kind than what's on the physical-bottom of the stack, add a new record.
|
|
39
|
+
If the new fluid is of the same kind as what's on the physical-bottom of the stack, add the new volume to
|
|
40
|
+
the same record.
|
|
41
|
+
"""
|
|
42
|
+
if len(self._fluid_stack) == 0 or self._fluid_stack[-1].kind != new.kind:
|
|
43
|
+
# this is a new kind of fluid, append the record
|
|
44
|
+
self._fluid_stack.append(new)
|
|
45
|
+
else:
|
|
46
|
+
# this is more of the same kind of fluid, add the volumes
|
|
47
|
+
old_fluid = self._fluid_stack.pop(-1)
|
|
48
|
+
self._fluid_stack.append(
|
|
49
|
+
AspiratedFluid(kind=new.kind, volume=old_fluid.volume + new.volume)
|
|
50
|
+
)
|
|
51
|
+
|
|
52
|
+
def _alter_fluid_records(
|
|
53
|
+
self, remove: int, new_last: AspiratedFluid | None
|
|
54
|
+
) -> None:
|
|
55
|
+
if remove >= len(self._fluid_stack) or len(self._fluid_stack) == 0:
|
|
56
|
+
self._fluid_stack = []
|
|
57
|
+
return
|
|
58
|
+
if remove != 0:
|
|
59
|
+
removed = self._fluid_stack[:-remove]
|
|
60
|
+
else:
|
|
61
|
+
removed = self._fluid_stack
|
|
62
|
+
if new_last:
|
|
63
|
+
removed[-1] = new_last
|
|
64
|
+
self._fluid_stack = removed
|
|
65
|
+
|
|
66
|
+
def remove_fluid(self, volume: float) -> None:
|
|
67
|
+
"""Remove a specific amount of fluid from the physical-bottom of the stack.
|
|
68
|
+
|
|
69
|
+
This will consume records that are wholly included in the provided volume and alter the remaining
|
|
70
|
+
final records (if any) to decrement the amount of volume removed from it.
|
|
71
|
+
|
|
72
|
+
This function is designed to be used inside pipette store action handlers, which are generally not
|
|
73
|
+
exception-safe, and therefore swallows and logs errors.
|
|
74
|
+
"""
|
|
75
|
+
self._fluid_stack_iterator = reversed(self._fluid_stack)
|
|
76
|
+
removed_elements: list[AspiratedFluid] = []
|
|
77
|
+
while volume > 0:
|
|
78
|
+
try:
|
|
79
|
+
last_stack_element = next(self._fluid_stack_iterator)
|
|
80
|
+
except StopIteration:
|
|
81
|
+
_LOG.error(
|
|
82
|
+
f"Attempting to remove more fluid than present, {volume}uL left over"
|
|
83
|
+
)
|
|
84
|
+
self._alter_fluid_records(len(removed_elements), None)
|
|
85
|
+
return
|
|
86
|
+
if last_stack_element.volume < volume:
|
|
87
|
+
removed_elements.append(last_stack_element)
|
|
88
|
+
volume -= last_stack_element.volume
|
|
89
|
+
elif isclose(last_stack_element.volume, volume):
|
|
90
|
+
self._alter_fluid_records(len(removed_elements) + 1, None)
|
|
91
|
+
return
|
|
92
|
+
else:
|
|
93
|
+
self._alter_fluid_records(
|
|
94
|
+
len(removed_elements),
|
|
95
|
+
AspiratedFluid(
|
|
96
|
+
kind=last_stack_element.kind,
|
|
97
|
+
volume=last_stack_element.volume - volume,
|
|
98
|
+
),
|
|
99
|
+
)
|
|
100
|
+
return
|
|
101
|
+
|
|
102
|
+
_LOG.error(f"Failed to handle removing {volume}uL from {self._fluid_stack}")
|
|
103
|
+
|
|
104
|
+
def aspirated_volume(self, kind: FluidKind | None = None) -> float:
|
|
105
|
+
"""Measure the total amount of fluid (optionally filtered by kind) in the stack."""
|
|
106
|
+
volume = 0.0
|
|
107
|
+
for el in self._fluid_stack:
|
|
108
|
+
if kind is not None and el.kind != kind:
|
|
109
|
+
continue
|
|
110
|
+
volume += el.volume
|
|
111
|
+
return volume
|
|
112
|
+
|
|
113
|
+
def liquid_part_of_dispense_volume(self, volume: float) -> float:
|
|
114
|
+
"""Get the amount of liquid in the specified volume starting at the physical-bottom of the stack."""
|
|
115
|
+
liquid_volume = 0.0
|
|
116
|
+
for el in reversed(self._fluid_stack):
|
|
117
|
+
if el.kind == FluidKind.LIQUID:
|
|
118
|
+
liquid_volume += min(volume, el.volume)
|
|
119
|
+
volume -= min(el.volume, volume)
|
|
120
|
+
if isclose(volume, 0.0):
|
|
121
|
+
return liquid_volume
|
|
122
|
+
return liquid_volume
|
|
123
|
+
|
|
124
|
+
def __eq__(self, other: object) -> bool:
|
|
125
|
+
"""Equality."""
|
|
126
|
+
if isinstance(other, type(self)):
|
|
127
|
+
return other._fluid_stack == self._fluid_stack
|
|
128
|
+
return False
|
|
129
|
+
|
|
130
|
+
def __repr__(self) -> str:
|
|
131
|
+
"""String representation of a fluid stack."""
|
|
132
|
+
if self._fluid_stack:
|
|
133
|
+
stringified_stack = (
|
|
134
|
+
f'(top) {", ".join([str(item) for item in self._fluid_stack])} (bottom)'
|
|
135
|
+
)
|
|
136
|
+
else:
|
|
137
|
+
stringified_stack = "empty"
|
|
138
|
+
return f"<{self.__class__.__name__}: {stringified_stack}>"
|
|
@@ -220,28 +220,40 @@ def _get_segment_capacity(segment: WellSegment) -> float:
|
|
|
220
220
|
section_height = segment.topHeight - segment.bottomHeight
|
|
221
221
|
match segment:
|
|
222
222
|
case SphericalSegment():
|
|
223
|
-
return
|
|
224
|
-
|
|
225
|
-
|
|
223
|
+
return (
|
|
224
|
+
_volume_from_height_spherical(
|
|
225
|
+
target_height=segment.topHeight,
|
|
226
|
+
radius_of_curvature=segment.radiusOfCurvature,
|
|
227
|
+
)
|
|
228
|
+
* segment.count
|
|
226
229
|
)
|
|
227
230
|
case CuboidalFrustum():
|
|
228
|
-
return
|
|
229
|
-
|
|
230
|
-
|
|
231
|
-
|
|
232
|
-
|
|
233
|
-
|
|
234
|
-
|
|
231
|
+
return (
|
|
232
|
+
_volume_from_height_rectangular(
|
|
233
|
+
target_height=section_height,
|
|
234
|
+
bottom_length=segment.bottomYDimension,
|
|
235
|
+
bottom_width=segment.bottomXDimension,
|
|
236
|
+
top_length=segment.topYDimension,
|
|
237
|
+
top_width=segment.topXDimension,
|
|
238
|
+
total_frustum_height=section_height,
|
|
239
|
+
)
|
|
240
|
+
* segment.count
|
|
235
241
|
)
|
|
236
242
|
case ConicalFrustum():
|
|
237
|
-
return
|
|
238
|
-
|
|
239
|
-
|
|
240
|
-
|
|
241
|
-
|
|
243
|
+
return (
|
|
244
|
+
_volume_from_height_circular(
|
|
245
|
+
target_height=section_height,
|
|
246
|
+
total_frustum_height=section_height,
|
|
247
|
+
bottom_radius=(segment.bottomDiameter / 2),
|
|
248
|
+
top_radius=(segment.topDiameter / 2),
|
|
249
|
+
)
|
|
250
|
+
* segment.count
|
|
242
251
|
)
|
|
243
252
|
case SquaredConeSegment():
|
|
244
|
-
return
|
|
253
|
+
return (
|
|
254
|
+
_volume_from_height_squared_cone(section_height, segment)
|
|
255
|
+
* segment.count
|
|
256
|
+
)
|
|
245
257
|
case _:
|
|
246
258
|
# TODO: implement volume calculations for truncated circular and rounded rectangular segments
|
|
247
259
|
raise NotImplementedError(
|
|
@@ -272,6 +284,7 @@ def height_at_volume_within_section(
|
|
|
272
284
|
section_height: float,
|
|
273
285
|
) -> float:
|
|
274
286
|
"""Calculate a height within a bounded section according to geometry."""
|
|
287
|
+
target_volume_relative = target_volume_relative / section.count
|
|
275
288
|
match section:
|
|
276
289
|
case SphericalSegment():
|
|
277
290
|
return _height_from_volume_spherical(
|
|
@@ -311,28 +324,40 @@ def volume_at_height_within_section(
|
|
|
311
324
|
"""Calculate a volume within a bounded section according to geometry."""
|
|
312
325
|
match section:
|
|
313
326
|
case SphericalSegment():
|
|
314
|
-
return
|
|
315
|
-
|
|
316
|
-
|
|
327
|
+
return (
|
|
328
|
+
_volume_from_height_spherical(
|
|
329
|
+
target_height=target_height_relative,
|
|
330
|
+
radius_of_curvature=section.radiusOfCurvature,
|
|
331
|
+
)
|
|
332
|
+
* section.count
|
|
317
333
|
)
|
|
318
334
|
case ConicalFrustum():
|
|
319
|
-
return
|
|
320
|
-
|
|
321
|
-
|
|
322
|
-
|
|
323
|
-
|
|
335
|
+
return (
|
|
336
|
+
_volume_from_height_circular(
|
|
337
|
+
target_height=target_height_relative,
|
|
338
|
+
total_frustum_height=section_height,
|
|
339
|
+
bottom_radius=(section.bottomDiameter / 2),
|
|
340
|
+
top_radius=(section.topDiameter / 2),
|
|
341
|
+
)
|
|
342
|
+
* section.count
|
|
324
343
|
)
|
|
325
344
|
case CuboidalFrustum():
|
|
326
|
-
return
|
|
327
|
-
|
|
328
|
-
|
|
329
|
-
|
|
330
|
-
|
|
331
|
-
|
|
332
|
-
|
|
345
|
+
return (
|
|
346
|
+
_volume_from_height_rectangular(
|
|
347
|
+
target_height=target_height_relative,
|
|
348
|
+
total_frustum_height=section_height,
|
|
349
|
+
bottom_width=section.bottomXDimension,
|
|
350
|
+
bottom_length=section.bottomYDimension,
|
|
351
|
+
top_width=section.topXDimension,
|
|
352
|
+
top_length=section.topYDimension,
|
|
353
|
+
)
|
|
354
|
+
* section.count
|
|
333
355
|
)
|
|
334
356
|
case SquaredConeSegment():
|
|
335
|
-
return
|
|
357
|
+
return (
|
|
358
|
+
_volume_from_height_squared_cone(target_height_relative, section)
|
|
359
|
+
* section.count
|
|
360
|
+
)
|
|
336
361
|
case _:
|
|
337
362
|
# TODO(cm): this would be the NEST-96 2uL wells referenced in EXEC-712
|
|
338
363
|
# we need to input the math attached to that issue
|
|
@@ -1,4 +1,5 @@
|
|
|
1
1
|
"""Geometry state getters."""
|
|
2
|
+
|
|
2
3
|
import enum
|
|
3
4
|
from numpy import array, dot, double as npdouble
|
|
4
5
|
from numpy.typing import NDArray
|
|
@@ -8,6 +9,7 @@ from functools import cached_property
|
|
|
8
9
|
|
|
9
10
|
from opentrons.types import Point, DeckSlotName, StagingSlotName, MountType
|
|
10
11
|
|
|
12
|
+
from opentrons_shared_data.errors.exceptions import InvalidStoredData
|
|
11
13
|
from opentrons_shared_data.labware.constants import WELL_NAME_PATTERN
|
|
12
14
|
from opentrons_shared_data.deck.types import CutoutFixture
|
|
13
15
|
from opentrons_shared_data.pipette import PIPETTE_X_SPAN
|
|
@@ -61,6 +63,7 @@ from .frustum_helpers import (
|
|
|
61
63
|
find_volume_at_well_height,
|
|
62
64
|
find_height_at_well_volume,
|
|
63
65
|
)
|
|
66
|
+
from ._well_math import wells_covered_by_pipette_configuration, nozzles_per_well
|
|
64
67
|
|
|
65
68
|
|
|
66
69
|
SLOT_WIDTH = 128
|
|
@@ -486,7 +489,7 @@ class GeometryView:
|
|
|
486
489
|
well_depth=well_depth,
|
|
487
490
|
operation_volume=operation_volume,
|
|
488
491
|
)
|
|
489
|
-
offset = offset.
|
|
492
|
+
offset = offset.model_copy(update={"z": offset.z + offset_adjustment})
|
|
490
493
|
self.validate_well_position(
|
|
491
494
|
well_location=well_location, z_offset=offset.z, pipette_id=pipette_id
|
|
492
495
|
)
|
|
@@ -1559,3 +1562,46 @@ class GeometryView:
|
|
|
1559
1562
|
raise errors.InvalidDispenseVolumeError(
|
|
1560
1563
|
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})"
|
|
1561
1564
|
)
|
|
1565
|
+
|
|
1566
|
+
def get_wells_covered_by_pipette_with_active_well(
|
|
1567
|
+
self, labware_id: str, target_well_name: str, pipette_id: str
|
|
1568
|
+
) -> list[str]:
|
|
1569
|
+
"""Get a flat list of wells that are covered by a pipette when moved to a specified well.
|
|
1570
|
+
|
|
1571
|
+
When you move a pipette in a multichannel configuration to a specific well - the target well -
|
|
1572
|
+
the pipette will operate on other wells as well.
|
|
1573
|
+
|
|
1574
|
+
For instance, a pipette with a COLUMN configuration with well A1 of an SBS standard labware target
|
|
1575
|
+
will also "cover", under this definition, wells B1-H1. That same pipette, when C5 is the target well, will "cover"
|
|
1576
|
+
wells C5-H5.
|
|
1577
|
+
|
|
1578
|
+
This math only works, and may only be applied, if one of the following is true:
|
|
1579
|
+
- The pipette is in a SINGLE configuration
|
|
1580
|
+
- The pipette is in a non-SINGLE configuration, and the labware is an SBS-format 96 or 384 well plate (and is so
|
|
1581
|
+
marked in its definition's parameters.format key, as 96Standard or 384Standard)
|
|
1582
|
+
|
|
1583
|
+
If all of the following do not apply, regardless of the nozzle configuration of the pipette this function will
|
|
1584
|
+
return only the labware covered by the primary well.
|
|
1585
|
+
"""
|
|
1586
|
+
pipette_nozzle_map = self._pipettes.get_nozzle_configuration(pipette_id)
|
|
1587
|
+
labware_columns = [
|
|
1588
|
+
column for column in self._labware.get_definition(labware_id).ordering
|
|
1589
|
+
]
|
|
1590
|
+
try:
|
|
1591
|
+
return list(
|
|
1592
|
+
wells_covered_by_pipette_configuration(
|
|
1593
|
+
pipette_nozzle_map, target_well_name, labware_columns
|
|
1594
|
+
)
|
|
1595
|
+
)
|
|
1596
|
+
except InvalidStoredData:
|
|
1597
|
+
return [target_well_name]
|
|
1598
|
+
|
|
1599
|
+
def get_nozzles_per_well(
|
|
1600
|
+
self, labware_id: str, target_well_name: str, pipette_id: str
|
|
1601
|
+
) -> int:
|
|
1602
|
+
"""Get the number of nozzles that will interact with each well."""
|
|
1603
|
+
return nozzles_per_well(
|
|
1604
|
+
self._pipettes.get_nozzle_configuration(pipette_id),
|
|
1605
|
+
target_well_name,
|
|
1606
|
+
self._labware.get_definition(labware_id).ordering,
|
|
1607
|
+
)
|