feat(engine, api): alternate tip drop location for addressable area trash bins #14196

jbleon95 · 2023-12-13T22:32:01Z

Overview

This PR adds tip drop alternation back into the Protocol Engine, for both OT-2 and Flex, for both column 1 and column 3 trashes. A new moveToAddressableAreaForDropTip command was added to encapsulate the logic in protocol engine for cycling between a right bias and a left bias.

In order to make the deck points the pipette critical points move to accurate, the boundingBox and offsetFromCutoutFixture values needed to be changed for the trash bin addressable areas. The previous equation for a right mount moving to the left bias for a column 1 trash needed to be adjusted since the current logic was moving it too far to the right.

Test Plan

Extensively tested all combinations of columns, mounts, and 96 channel both with full configuration and partial tip configuration (only column in A12) to ensure that they go to the correct place, do no collide with anything, and cycle accurately through the locations. Most of this was done in postman, but this protocol was run for the partial tip drop test.

from opentrons.protocol_api import COLUMN


metadata = {
    'protocolName': '96 Channel Partial Tip Alternation',
}

requirements = {
    "robotType": "Flex",
    "apiLevel": "2.16"
}


def run(context):
    tiprack = context.load_labware('opentrons_flex_96_tiprack_1000ul', 'C2')

    pipette = context.load_instrument('flex_96channel_1000', 'left')
    pipette.configure_nozzle_layout(style=COLUMN, start="A12")

    trash_b3 = context.load_trash_bin('B3')
    trash_d1 = context.load_trash_bin('D1')

    pipette.pick_up_tip(tiprack.wells()[0])
    pipette.drop_tip(trash_b3)
    context.pause()
    pipette.reset_tipracks()

    pipette.pick_up_tip(tiprack.wells()[0])
    pipette.drop_tip(trash_b3)
    context.pause()
    pipette.reset_tipracks()

    pipette.pick_up_tip(tiprack.wells()[0])
    pipette.drop_tip(trash_b3)
    context.pause()
    pipette.reset_tipracks()

    pipette.pick_up_tip(tiprack.wells()[0])
    pipette.drop_tip(trash_d1)
    context.pause()
    pipette.reset_tipracks()

    pipette.pick_up_tip(tiprack.wells()[0])
    pipette.drop_tip(trash_d1)
    context.pause()
    pipette.reset_tipracks()

    pipette.pick_up_tip(tiprack.wells()[0])
    pipette.drop_tip(trash_d1)
    context.pause()
    pipette.reset_tipracks()

Changelog

added moveToAddressableAreaForDropTip PE command
hooked up PAPI drop tip for trash bins to use the new command
modified boundingBoxandoffsetFromCutoutFixture` values for trash bins in V4 deck definitions
modified the equation for a right mount single/multi channel pipette accessing the left tip drop location of a column 1 trash bin to be less conservative in its leftward offset.

Review requests

Risk assessment

Medium.

…entrons into alternate_tip_drop_for_addressable_areas

codecov · 2023-12-13T22:32:42Z

Codecov Report

Merging #14196 (3e44446) into chore_release-7.1.0 (fcbe7f5) will decrease coverage by 0.02%.
Report is 3 commits behind head on chore_release-7.1.0.
The diff coverage is n/a.

Additional details and impacted files

@@                   Coverage Diff                   @@
##           chore_release-7.1.0   #14196      +/-   ##
=======================================================
- Coverage                70.43%   70.42%   -0.02%     
=======================================================
  Files                     2512     1636     -876     
  Lines                    71272    54504   -16768     
  Branches                  8999     4028    -4971     
=======================================================
- Hits                     50203    38382   -11821     
+ Misses                   18860    15421    -3439     
+ Partials                  2209      701    -1508

Flag	Coverage Δ
app	`38.71% <ø> (-28.93%)`	⬇️
g-code-testing	`96.44% <ø> (ø)`
notify-server	`89.13% <ø> (ø)`
protocol-designer	`44.99% <ø> (ø)`
shared-data	`75.10% <ø> (ø)`
step-generation	`86.84% <ø> (ø)`

Flags with carried forward coverage won't be shown. Click here to find out more.

Files	Coverage Δ
...c/opentrons/protocol_engine/clients/sync_client.py	`100.00% <ø> (ø)`
...src/opentrons/protocol_engine/commands/__init__.py	`100.00% <ø> (ø)`
...entrons/protocol_engine/commands/command_unions.py	`100.00% <ø> (ø)`
...pi/src/opentrons/protocol_engine/state/geometry.py	`100.00% <ø> (ø)`
...pi/src/opentrons/protocol_engine/state/pipettes.py	`100.00% <ø> (ø)`

... and 877 files with indirect coverage changes

jerader

lgtm!

jerader · 2023-12-13T22:43:58Z

shared-data/command/schemas/8.json

@@ -1996,6 +1999,90 @@
      },
      "required": ["params"]
    },
+    "MoveToAddressableAreaForDropTipParams": {
+      "title": "MoveToAddressableAreaForDropTipParams",
+      "description": "Payload required to move a pipette to a specific addressable area.\n\nAn *addressable area* is a space in the robot that may or may not be usable depending on how\nthe robot's deck is configured. For example, if a Flex is configured with a waste chute, it will\nhave additional addressable areas representing the opening of the waste chute, where tips and\nlabware can be dropped.\n\nThis moves the pipette so all of its nozzles are centered over the addressable area.\nIf the pipette is currently configured with a partial tip layout, this centering is over all\nthe pipette's physical nozzles, not just the nozzles that are active.\n\nThe z-position will be chosen to put the bottom of the tips---or the bottom of the nozzles,\nif there are no tips---level with the top of the addressable area.\n\nWhen this command is executed, Protocol Engine will make sure the robot's deck is configured\nsuch that the requested addressable area actually exists. For example, if you request\nthe addressable area B4, it will make sure the robot is set up with a B3/B4 staging area slot.\nIf that's not the case, the command will fail.",


this example with the waste chute is a bit confusing to me since this command is for trash bins and not waste chute right?

Yeah, I need to fix this up, but I can do that in a quick doc follow up tomorrow

api/src/opentrons/protocol_api/core/engine/instrument.py

CaseyBatten

This looks good with the noted change that _move_to_dispoal_locations needs to only alternate tip drops for a drop trip action and should ignore that for things like blowout/dispense/etc. We should take a look at how this relates to the transfer behaviors automatic drop tip behavior at the end of a given transfer. AKA:
If you have two transfers in a row, does it drop the tip in the same location twice?

Otherwise everything looks good to me.

SyntaxColoring

Reviewed on a call. Looks great, thanks!

SyntaxColoring · 2023-12-13T22:58:33Z

api/src/opentrons/protocol_engine/commands/move_to_addressable_area_for_drop_tip.py

+
+
+class MoveToAddressableAreaForDropTipParams(PipetteIdMixin, MovementMixin):
+    """Payload required to move a pipette to a specific addressable area.


We could probably nuke this docstring and say something like "this is like moveToAddressableArea except it has tip alternation.

SyntaxColoring · 2023-12-13T23:07:16Z

api/src/opentrons/protocol_engine/state/geometry.py

-                    well_x_dim / 2 - SLOT_WIDTH + drop_location_margin_from_labware_edge
+                    -well_x_dim / 2 + drop_location_margin_from_labware_edge * 2


Yeah this makes sense if the intent is to double the margin from the left edge.

I think this is another really good opportunity for motion planning based on high-fidelity pipette dimensions and deck limits. ("Go as far left as you can without bumping into the frame.")

jbleon95 added 8 commits December 13, 2023 09:44

new move to addressable area for drop tip

de60861

update command schema

55c1bfb

unit tests

dd77c01

update deck point and current addressable area

e08be5c

bounding box and math changes for corectness

c85fe95

Merge branch 'chore_release-7.1.0' of https://github.com/Opentrons/op…

fac4e6d

…entrons into alternate_tip_drop_for_addressable_areas

hook up tip alternation to PAPI

1587ceb

update ot2 fixed trash dimensions

918863a

jbleon95 requested review from brenthagen, jerader and a team December 13, 2023 22:32

jbleon95 requested review from a team as code owners December 13, 2023 22:32

jerader approved these changes Dec 13, 2023

View reviewed changes

SyntaxColoring reviewed Dec 13, 2023

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api/src/opentrons/protocol_api/core/engine/instrument.py Outdated Show resolved Hide resolved

only alternate for drop tip

3e44446

CaseyBatten approved these changes Dec 13, 2023

View reviewed changes

SyntaxColoring approved these changes Dec 13, 2023

View reviewed changes

jbleon95 merged commit 0e024a8 into chore_release-7.1.0 Dec 13, 2023
44 checks passed

jbleon95 deleted the alternate_tip_drop_for_addressable_areas branch December 13, 2023 23:07

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feat(engine, api): alternate tip drop location for addressable area trash bins #14196

feat(engine, api): alternate tip drop location for addressable area trash bins #14196

jbleon95 commented Dec 13, 2023

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SyntaxColoring Dec 13, 2023



		class MoveToAddressableAreaForDropTipParams(PipetteIdMixin, MovementMixin):
		"""Payload required to move a pipette to a specific addressable area.

		well_x_dim / 2 - SLOT_WIDTH + drop_location_margin_from_labware_edge
		-well_x_dim / 2 + drop_location_margin_from_labware_edge * 2

feat(engine, api): alternate tip drop location for addressable area trash bins #14196

feat(engine, api): alternate tip drop location for addressable area trash bins #14196

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jbleon95 commented Dec 13, 2023

Overview

Test Plan

Changelog

Review requests

Risk assessment

codecov bot commented Dec 13, 2023 • edited Loading

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