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feat(api): add execution of dispense steps for liquid class based transfer #17138

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feat(api): add execution of dispense steps for liquid class based transfer #17138

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c7ffe85
added dispense steps and refactored some components executors
sanni-t Dec 18, 2024
9b2de59
linter errors
sanni-t Dec 18, 2024
279a913
added tests
sanni-t Jan 2, 2025
bdfe17b
fixed validation test
sanni-t Jan 2, 2025
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137 changes: 118 additions & 19 deletions api/src/opentrons/protocol_api/core/engine/instrument.py
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Original file line number Diff line number Diff line change
Expand Up @@ -910,7 +910,7 @@ def transfer_liquid(
dest: List[Tuple[Location, WellCore]],
new_tip: TransferTipPolicyV2,
tiprack_uri: str,
tip_drop_location: Union[WellCore, Location, TrashBin, WasteChute],
trash_location: Union[Location, TrashBin, WasteChute],
) -> None:
"""Execute transfer using liquid class properties.

Expand Down Expand Up @@ -963,16 +963,16 @@ def transfer_liquid(
# TODO: add aspirate and dispense

if new_tip == TransferTipPolicyV2.ALWAYS:
if isinstance(tip_drop_location, (TrashBin, WasteChute)):
if isinstance(trash_location, (TrashBin, WasteChute)):
self.drop_tip_in_disposal_location(
disposal_location=tip_drop_location,
disposal_location=trash_location,
home_after=False,
alternate_tip_drop=True,
)
elif isinstance(tip_drop_location, Location):
elif isinstance(trash_location, Location):
self.drop_tip(
location=tip_drop_location,
well_core=tip_drop_location.labware.as_well()._core, # type: ignore[arg-type]
location=trash_location,
well_core=trash_location.labware.as_well()._core, # type: ignore[arg-type]
home_after=False,
alternate_drop_location=True,
)
Expand All @@ -982,7 +982,9 @@ def aspirate_liquid_class(
volume: float,
source: Tuple[Location, WellCore],
transfer_properties: TransferProperties,
) -> None:
transfer_type: tx_comps_executor.TransferType,
tip_contents: List[tx_comps_executor.LiquidAndAirGapPair],
) -> tx_comps_executor.LiquidAndAirGapPair:
"""Execute aspiration steps.

1. Submerge
Expand All @@ -991,6 +993,8 @@ def aspirate_liquid_class(
4. Aspirate
5. Delay- wait inside the liquid
6. Aspirate retract

Return: The last liquid and air gap pair in tip.
"""
aspirate_props = transfer_properties.aspirate
source_loc, source_well = source
Expand All @@ -1002,27 +1006,122 @@ def aspirate_liquid_class(
)
)
aspirate_location = Location(aspirate_point, labware=source_loc.labware)

components_executer = tx_comps_executor.TransferComponentsExecutor(
if len(tip_contents) > 0:
last_liquid_and_airgap_in_tip = tip_contents[-1]
else:
last_liquid_and_airgap_in_tip = tx_comps_executor.LiquidAndAirGapPair(
liquid=0,
air_gap=0,
)
components_executor = tx_comps_executor.TransferComponentsExecutor(
instrument_core=self,
transfer_properties=transfer_properties,
target_location=aspirate_location,
target_well=source_well,
transfer_type=transfer_type,
tip_state=tx_comps_executor.TipState(
last_liquid_and_air_gap_in_tip=last_liquid_and_airgap_in_tip
),
)
components_executer.submerge(
submerge_properties=aspirate_props.submerge,
# Assuming aspirate is not called with *liquid* in the tip
# TODO: evaluate if using the current volume to find air gap is not a good idea.
air_gap_volume=self.get_current_volume(),
)
components_executor.submerge(submerge_properties=aspirate_props.submerge)
# TODO: when aspirating for consolidation, do not perform mix
components_executer.mix(mix_properties=aspirate_props.mix)
components_executor.mix(
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Wait, when aspirating for liquid classes, you ALWAYS mix? Like, the user doesn't have an option to not mix?

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No, you don't always mix. The TransferComponentsExecutor.mix() checks whether mix is enabled or not and then performs the mix accordingly.

mix_properties=aspirate_props.mix, last_dispense_push_out=False
)
# TODO: when aspirating for consolidation, do not preform pre-wet
components_executer.pre_wet(
components_executor.pre_wet(
volume=volume,
)
components_executer.aspirate_and_wait(volume=volume)
components_executer.retract_after_aspiration(volume=volume)
components_executor.aspirate_and_wait(volume=volume)
components_executor.retract_after_aspiration(volume=volume)
return components_executor.tip_state.last_liquid_and_air_gap_in_tip
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To make sure I understand: You pass in a last_liquid_and_airgap_in_tip to the constructor when you make the components_executor. Then after you call submerge(), mix(), aspirate_and_wait(), etc., the components_executor will have a different last_liquid_and_air_gap_in_tip that you're reading back out here?

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Yep


def dispense_liquid_class(
self,
volume: float,
dest: Tuple[Location, WellCore],
source: Optional[Tuple[Location, WellCore]],
transfer_properties: TransferProperties,
transfer_type: tx_comps_executor.TransferType,
tip_contents: List[tx_comps_executor.LiquidAndAirGapPair],
trash_location: Union[Location, TrashBin, WasteChute],
) -> tx_comps_executor.LiquidAndAirGapPair:
"""Execute single-dispense steps.
1. Move pipette to the ‘submerge’ position with normal speed.
- The pipette will move in an arc- move to max z height of labware
(if asp & disp are in same labware)
or max z height of all labware (if asp & disp are in separate labware)
2. Air gap removal:
- If dispense location is above the meniscus, DO NOT remove air gap
(it will be dispensed along with rest of the liquid later).
All other scenarios, remove the air gap by doing a dispense
- Flow rate = min(dispenseFlowRate, (airGapByVolume)/sec)
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Hm, I don't understand this expression. What is sec here?

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sec is seconds. Flow rate is measured in uL volume per second.

- Use the post-dispense delay
4. Move to the dispense position at the specified ‘submerge’ speed
(even if we might not be moving into the liquid)
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Can you explain how this differs from Step 1 where you move to the submerge position?

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Submerge position is more like a 'start position'. It's the position from which we start submerging into the liquid at the specified submerge speed.

- Do a delay (submerge delay)
6. Dispense:
- Dispense at the specified flow rate.
- Do a push out as specified ONLY IF there is no mix following the dispense AND the tip is empty.
Volume for push out is the volume being dispensed. So if we are dispensing 50uL, use pushOutByVolume[50] as push out volume.
7. Delay
8. Mix using the same flow rate and delays as specified for asp+disp,
with the volume and the number of repetitions specified. Use the delays in asp & disp.
- If the dispense position is outside the liquid, then raise error if mix is enabled.
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Heh, I think I'll need you to explain how all these positions relate to each other.

But (1) Where you do enforce raising an error if the dispense position is outside the liquid?

(2) I'm curious how you handle a situation like this:

Before dispense:

|     |
|  v  |  tip dispense position
|     |
|~~~~~|  liquid level
|     |
+-----+

After dispense:

|~~~~~|  liquid level
|  v  |  tip is now below liquid
|     |
|     |
|     |
+-----+

Would mix be allowed in this case?

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Ah, good catch. It's a bit outdated comment (although not wrong). The only way to correctly check for that condition is if liquid level detection is enabled for liquid classes transfer and liquid-meniscus-based positioning is used in these steps.
Without these, we can't reliably check if tip will be in the liquid after the dispense, so we will just allow the mix, assuming that the user has set the dispense correctly in order to perform a mix after.

- If the user wants to perform a mix then they should specify a dispense position that’s inside the liquid OR do mix() on the wells after transfer.
- Do push out at the last dispense.
9. Retract

Return:
The last liquid and air gap pair in tip.
"""
dispense_props = transfer_properties.dispense
dest_loc, dest_well = dest
dispense_point = (
tx_comps_executor.absolute_point_from_position_reference_and_offset(
well=dest_well,
position_reference=dispense_props.position_reference,
offset=dispense_props.offset,
)
)
dispense_location = Location(dispense_point, labware=dest_loc.labware)
if len(tip_contents) > 0:
last_liquid_and_airgap_in_tip = tip_contents[-1]
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I think I'm still a little confused about the division of labor between the TransferComponentsExecutor and the functions that use it. Like, the reason you have to keep passing last_liquid_and_airgap_in_tip around is because you create and destroy the TransferComponentsExecutor for each of the substeps?

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Talked about this in person. The reason last_liquid_and_airgap_in_tip is passed to each aspirate and dispense separate is because we will need this separation when implementing distribute & consolidate (transfers which don't have one aspirate and one dispense in repetition but rather one aspirate+many dispenses or many aspirates+one dispense combinations)

else:
last_liquid_and_airgap_in_tip = tx_comps_executor.LiquidAndAirGapPair(
liquid=0,
air_gap=0,
)
components_executor = tx_comps_executor.TransferComponentsExecutor(
instrument_core=self,
transfer_properties=transfer_properties,
target_location=dispense_location,
target_well=dest_well,
transfer_type=transfer_type,
tip_state=tx_comps_executor.TipState(
last_liquid_and_air_gap_in_tip=last_liquid_and_airgap_in_tip
),
)
components_executor.submerge(submerge_properties=dispense_props.submerge)
if dispense_props.mix.enabled:
push_out_vol = 0.0
else:
# TODO: if distributing, do a push out only at the last dispense
push_out_vol = dispense_props.push_out_by_volume.get_for_volume(volume)
components_executor.dispense_and_wait(
volume=volume,
push_out_override=push_out_vol,
)
components_executor.mix(
mix_properties=dispense_props.mix,
last_dispense_push_out=True,
)
components_executor.retract_after_dispensing(
trash_location=trash_location,
source_location=source[0] if source else None,
source_well=source[1] if source else None,
)
return components_executor.tip_state.last_liquid_and_air_gap_in_tip

def retract(self) -> None:
"""Retract this instrument to the top of the gantry."""
Expand Down
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