feat(hardware): add csv file logging capability to capacitive_probe m…

…ethod (#14785)

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# Overview

This PR, along with Opentrons/ot3-firmware#768,
adds csv file logging capability to the capacitive_probe ot3api method.
This work utilizes the work that adds the same capability to the
liquid_probe process. The MoveGroupSingleAxisStep,
AddSensorLinearMoveRequest, and SendAccumulatedSensorDataRequest classes
were modified to include a sensor_type data field. The
capacitive_probe_ot3_tunable script was added for testing.

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# Test Plan

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Example Test Plan (HTTP API Change)

- Verified that new optional argument `dance-party` causes the robot to
flash its lights, move the pipettes,
then home.
- Verified that when you omit the `dance-party` option the robot homes
normally
- Added protocol that uses `dance-party` argument to G-Code Testing
Suite
- Ran protocol that did not use `dance-party` argument and everything
was successful
- Added unit tests to validate that changes to pydantic model are
correct

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- [x] Ran script without csv logging and detected saltwater liquid
height
 - [x] Ran script with csv loffing and detected saltwater liquid height

# Changelog

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- Fixed app crash when trying to calibrate an illegal pipette
- Added state to API to track pipette usage
- Updated API docs to mention only two pipettes are supported

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# Risk assessment

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.gitignore

@@ -160,4 +160,5 @@ opentrons-robot-app.tar.gz
 # asdf versions file
 .tool-versions
 mock_dir
+.npm-cache/
 .eslintcache

api/src/opentrons/config/defaults_ot3.py

@@ -40,6 +40,7 @@
  max_overrun_distance_mm=5.0,
  speed_mm_per_s=1.0,
  sensor_threshold_pf=3.0,
+ output_option=OutputOptions.sync_only,
  ),
  ),
  edge_sense=EdgeSenseSettings(
@@ -50,6 +51,7 @@
  max_overrun_distance_mm=0.5,
  speed_mm_per_s=1,
  sensor_threshold_pf=3.0,
+ output_option=OutputOptions.sync_only,
  ),
  search_initial_tolerance_mm=12.0,
  search_iteration_limit=8,
@@ -311,6 +313,7 @@ def _build_default_cap_pass(
  sensor_threshold_pf=from_conf.get(
  "sensor_threshold_pf", default.sensor_threshold_pf
  ),
+ output_option=from_conf.get("output_option", default.output_option),
  )
 
 

api/src/opentrons/config/types.py

@@ -103,29 +103,32 @@ def by_gantry_load(
  )
 
 
+class OutputOptions(int, Enum):
+ """Specifies where we should report sensor data to during a sensor pass."""
+
+ stream_to_csv = 0x1 # compile sensor data stream into a csv file, in addition to can_bus_only behavior
+ sync_buffer_to_csv = 0x2 # collect sensor data on pipette mcu, then stream to robot server and compile into a csv file, in addition to can_bus_only behavior
+ can_bus_only = (
+ 0x4 # stream sensor data over CAN bus, in addition to sync_only behavior
+ )
+ sync_only = 0x8 # trigger pipette sync line upon sensor's detection of something
+
+
 @dataclass(frozen=True)
 class CapacitivePassSettings:
  prep_distance_mm: float
  max_overrun_distance_mm: float
  speed_mm_per_s: float
  sensor_threshold_pf: float
+ output_option: OutputOptions
+ data_files: Optional[Dict[InstrumentProbeType, str]] = None
 
 
 @dataclass(frozen=True)
 class ZSenseSettings:
  pass_settings: CapacitivePassSettings
 
 
-# str enum so it can be json serializable
-class OutputOptions(int, Enum):
- """Specifies where we should report sensor data to during a sensor pass."""
-
- stream_to_csv = 0x1
- sync_buffer_to_csv = 0x2
- can_bus_only = 0x4
- sync_only = 0x8
-
-
 @dataclass
 class LiquidProbeSettings:
  starting_mount_height: float

api/src/opentrons/hardware_control/backends/flex_protocol.py

@@ -363,7 +363,9 @@ async def capacitive_probe(
  distance_mm: float,
  speed_mm_per_s: float,
  sensor_threshold_pf: float,
- probe: InstrumentProbeType,
+ probe: InstrumentProbeType = InstrumentProbeType.PRIMARY,
+ output_format: OutputOptions = OutputOptions.sync_only,
+ data_files: Optional[Dict[InstrumentProbeType, str]] = None,
  ) -> bool:
  ...
 

api/src/opentrons/hardware_control/backends/ot3controller.py

@@ -1428,15 +1428,44 @@ async def capacitive_probe(
  distance_mm: float,
  speed_mm_per_s: float,
  sensor_threshold_pf: float,
- probe: InstrumentProbeType,
+ probe: InstrumentProbeType = InstrumentProbeType.PRIMARY,
+ output_option: OutputOptions = OutputOptions.sync_only,
+ data_files: Optional[Dict[InstrumentProbeType, str]] = None,
  ) -> bool:
+ if output_option == OutputOptions.sync_buffer_to_csv:
+ assert (
+ self._subsystem_manager.device_info[
+ SubSystem.of_mount(mount)
+ ].revision.tertiary
+ == "1"
+ )
+ csv_output = bool(output_option.value & OutputOptions.stream_to_csv.value)
+ sync_buffer_output = bool(
+ output_option.value & OutputOptions.sync_buffer_to_csv.value
+ )
+ can_bus_only_output = bool(
+ output_option.value & OutputOptions.can_bus_only.value
+ )
+ data_files_transposed = (
+ None
+ if data_files is None
+ else {
+ sensor_id_for_instrument(probe): data_files[probe]
+ for probe in data_files.keys()
+ }
+ )
  status = await capacitive_probe(
- self._messenger,
- sensor_node_for_mount(mount),
- axis_to_node(moving),
- distance_mm,
- speed_mm_per_s,
- sensor_id_for_instrument(probe),
+ messenger=self._messenger,
+ tool=sensor_node_for_mount(mount),
+ mover=axis_to_node(moving),
+ distance=distance_mm,
+ plunger_speed=speed_mm_per_s,
+ mount_speed=speed_mm_per_s,
+ csv_output=csv_output,
+ sync_buffer_output=sync_buffer_output,
+ can_bus_only_output=can_bus_only_output,
+ data_files=data_files_transposed,
+ sensor_id=sensor_id_for_instrument(probe),
  relative_threshold_pf=sensor_threshold_pf,
  )
 

api/src/opentrons/hardware_control/backends/ot3simulator.py

@@ -747,7 +747,9 @@ async def capacitive_probe(
  distance_mm: float,
  speed_mm_per_s: float,
  sensor_threshold_pf: float,
- probe: InstrumentProbeType,
+ probe: InstrumentProbeType = InstrumentProbeType.PRIMARY,
+ output_format: OutputOptions = OutputOptions.sync_only,
+ data_files: Optional[Dict[InstrumentProbeType, str]] = None,
  ) -> bool:
  self._position[moving] += distance_mm
  return True

api/src/opentrons/hardware_control/ot3api.py

@@ -2682,7 +2682,9 @@ async def capacitive_probe(
  machine_pass_distance,
  pass_settings.speed_mm_per_s,
  pass_settings.sensor_threshold_pf,
- probe=probe,
+ probe,
+ pass_settings.output_option,
+ pass_settings.data_files,
  )
  end_pos = await self.gantry_position(mount, refresh=True)
  if retract_after:

api/tests/opentrons/config/ot3_settings.py

@@ -134,6 +134,8 @@
  "max_overrun_distance_mm": 2,
  "speed_mm_per_s": 3,
  "sensor_threshold_pf": 4,
+ "output_option": OutputOptions.sync_only,
+ "data_files": None,
  },
  },
  "edge_sense": {
@@ -144,6 +146,8 @@
  "max_overrun_distance_mm": 5,
  "speed_mm_per_s": 6,
  "sensor_threshold_pf": 7,
+ "output_option": OutputOptions.sync_only,
+ "data_files": None,
  },
  "search_initial_tolerance_mm": 18,
  "search_iteration_limit": 3,

api/tests/opentrons/hardware_control/test_ot3_api.py

@@ -107,6 +107,7 @@ def fake_settings() -> CapacitivePassSettings:
  max_overrun_distance_mm=2,
  speed_mm_per_s=4,
  sensor_threshold_pf=1.0,
+ output_option=OutputOptions.sync_only,
  )
 
 
@@ -482,6 +483,8 @@ def _update_position(
  speed_mm_per_s: float,
  threshold_pf: float,
  probe: InstrumentProbeType,
+ output_option: OutputOptions = OutputOptions.sync_only,
+ data_file: Optional[str] = None,
  ) -> None:
  hardware_backend._position[moving] += distance_mm / 2
 
@@ -881,7 +884,14 @@ async def test_capacitive_probe(
  # This is a negative probe because the current position is the home position
  # which is very large.
  mock_backend_capacitive_probe.assert_called_once_with(
- mount, moving, 3, 4, 1.0, InstrumentProbeType.PRIMARY
+ mount,
+ moving,
+ 3,
+ 4,
+ 1.0,
+ InstrumentProbeType.PRIMARY,
+ fake_settings.output_option,
+ fake_settings.data_files,
  )
 
  original = moving.set_in_point(here, 0)

hardware-testing/hardware_testing/examples/capacitive_probe_ot3.py

@@ -2,7 +2,7 @@
 import argparse
 import asyncio
 
-from opentrons.config.types import CapacitivePassSettings
+from opentrons.config.types import CapacitivePassSettings, OutputOptions
 from opentrons.hardware_control.ot3api import OT3API
 
 from hardware_testing.opentrons_api import types
@@ -44,12 +44,14 @@
  max_overrun_distance_mm=3,
  speed_mm_per_s=1,
  sensor_threshold_pf=STABLE_CAP_PF,
+ output_option=OutputOptions.sync_only,
 )
 PROBE_SETTINGS_XY_AXIS = CapacitivePassSettings(
  prep_distance_mm=CUTOUT_SIZE / 2,
  max_overrun_distance_mm=3,
  speed_mm_per_s=1,
  sensor_threshold_pf=STABLE_CAP_PF,
+ output_option=OutputOptions.sync_only,
 )
 
 

hardware-testing/hardware_testing/examples/capacitive_probe_ot3_tunable.py

@@ -0,0 +1,109 @@
+"""Capacitive probe OT3."""
+import argparse
+import asyncio
+
+from opentrons.config.types import CapacitivePassSettings, OutputOptions
+from opentrons.hardware_control.ot3api import OT3API
+from opentrons.hardware_control.types import InstrumentProbeType
+
+from hardware_testing.opentrons_api import types
+from hardware_testing.opentrons_api import helpers_ot3
+
+# distance added to the pipette shaft
+# when the calibration probe is attached
+PROBE_LENGTH = 34.5
+
+# the capacitive readings need to be stable <0.1
+# before probing anything
+STABLE_CAP_PF = 0.1
+
+# capacitance relative threshold in picofarads
+CAP_REL_THRESHOLD_PF = 10.0
+
+# ideally these values come from either:
+# 1) the API config file
+# 2) or, found through manually jogging
+# The Z is different from the XY probing location
+# because the pipette cannot reach the bottom of the
+# cutout, so we cannot probe the Z inside the cutout
+ASSUMED_Z_LOCATION = types.Point(x=228, y=150, z=80) # C2 slot center
+ASSUMED_XY_LOCATION = types.Point(x=228, y=150, z=ASSUMED_Z_LOCATION.z)
+
+# configure how the probing motion behaves
+# capacitive_probe will always automatically do the following:
+# 1) move to the "prep" distance away from the assumed location
+# 2) set the capacitive threshold
+# a) the value is sent over CAN to the pipette's MCU
+# b) the pipette will trigger the SYNC line when the threshold is reached
+# 3) move along the specified axis, at the specified speed
+# a) the max distance probed = prep + max_overrun
+# 4) movement will stop when (either/or):
+# a) the sensor is triggered
+# b) or, the max distance is reached
+# 5) move to the "prep" distance away from the assumed location
+PROBE_SETTINGS_Z_AXIS = CapacitivePassSettings(
+ prep_distance_mm=10,
+ max_overrun_distance_mm=3,
+ speed_mm_per_s=1,
+ sensor_threshold_pf=CAP_REL_THRESHOLD_PF,
+ output_option=OutputOptions.sync_only,
+)
+PROBE_SETTINGS_Z_AXIS_OUTPUT = CapacitivePassSettings(
+ prep_distance_mm=10,
+ max_overrun_distance_mm=3,
+ speed_mm_per_s=1,
+ sensor_threshold_pf=CAP_REL_THRESHOLD_PF,
+ output_option=OutputOptions.sync_buffer_to_csv,
+ data_files={InstrumentProbeType.PRIMARY: "/data/capacitive_sensor_data.csv"},
+)
+
+
+async def _probe_sequence(api: OT3API, mount: types.OT3Mount, stable: bool) -> float:
+ z_ax = types.Axis.by_mount(mount)
+
+ print("Align the XY axes above Z probe location...")
+ home_pos_z = helpers_ot3.get_endstop_position_ot3(api, mount)[z_ax]
+ await api.move_to(mount, ASSUMED_Z_LOCATION._replace(z=home_pos_z))
+
+ if stable:
+ await helpers_ot3.wait_for_stable_capacitance_ot3(
+ api, mount, threshold_pf=STABLE_CAP_PF, duration=1.0
+ )
+ found_z, _ = await api.capacitive_probe(
+ mount, z_ax, ASSUMED_Z_LOCATION.z, PROBE_SETTINGS_Z_AXIS
+ )
+ print(f"Found deck Z location = {found_z} mm")
+ return found_z
+
+
+async def _main(is_simulating: bool, cycles: int, stable: bool) -> None:
+ api = await helpers_ot3.build_async_ot3_hardware_api(
+ is_simulating=is_simulating, pipette_left="p1000_single_v3.3"
+ )
+ mount = types.OT3Mount.LEFT
+ if not api.hardware_pipettes[mount.to_mount()]:
+ raise RuntimeError("No pipette attached")
+
+ # add length to the pipette, to account for the attached probe
+ await api.add_tip(mount, PROBE_LENGTH)
+
+ await helpers_ot3.home_ot3(api)
+ for c in range(cycles):
+ print(f"Cycle {c + 1}/{cycles}")
+ await _probe_sequence(api, mount, stable)
+
+ # move up, "remove" the probe, then disengage the XY motors when done
+ z_ax = types.Axis.by_mount(mount)
+ top_z = helpers_ot3.get_endstop_position_ot3(api, mount)[z_ax]
+ await api.move_to(mount, ASSUMED_XY_LOCATION._replace(z=top_z))
+ await api.remove_tip(mount)
+ await api.disengage_axes([types.Axis.X, types.Axis.Y])
+
+
+if __name__ == "__main__":
+ parser = argparse.ArgumentParser()
+ parser.add_argument("--simulate", action="store_true")
+ parser.add_argument("--cycles", type=int, default=1)
+ parser.add_argument("--stable", type=bool, default=True)
+ args = parser.parse_args()
+ asyncio.run(_main(args.simulate, args.cycles, args.stable))

hardware-testing/hardware_testing/production_qc/ninety_six_assembly_qc_ot3/test_capacitance.py

@@ -173,7 +173,8 @@ async def _probe(distance: float, speed: float) -> float:
  NodeId.pipette_left,
  NodeId.head_l,
  distance=distance,
- speed=speed,
+ plunger_speed=speed,
+ mount_speed=speed,
  sensor_id=sensor_id,
  relative_threshold_pf=default_probe_cfg.sensor_threshold_pf,
  )

hardware-testing/hardware_testing/production_qc/robot_assembly_qc_ot3/test_instruments.py

@@ -1,7 +1,7 @@
 """Test Instruments."""
 from typing import List, Tuple, Optional, Union
 
-from opentrons.config.types import CapacitivePassSettings
+from opentrons.config.types import CapacitivePassSettings, OutputOptions
 from opentrons.hardware_control.ot3api import OT3API
 
 from hardware_testing.data.csv_report import (
@@ -30,6 +30,7 @@
  max_overrun_distance_mm=0,
  speed_mm_per_s=Z_PROBE_DISTANCE_MM / Z_PROBE_TIME_SECONDS,
  sensor_threshold_pf=1.0,
+ output_option=OutputOptions.can_bus_only,
 )
 
 RELATIVE_MOVE_FROM_HOME_DELTA = Point(x=-500, y=-300)

hardware-testing/hardware_testing/scripts/gripper_ot3.py

@@ -4,7 +4,7 @@
 from dataclasses import dataclass
 from typing import Optional, List, Any, Dict
 
-from opentrons.config.defaults_ot3 import CapacitivePassSettings
+from opentrons.config.defaults_ot3 import CapacitivePassSettings, OutputOptions
 from opentrons.hardware_control.ot3api import OT3API
 
 from hardware_testing.opentrons_api import types
@@ -73,6 +73,7 @@
  max_overrun_distance_mm=1,
  speed_mm_per_s=1,
  sensor_threshold_pf=0.5,
+ output_option=OutputOptions.sync_only,
 )
 LABWARE_PROBE_CORNER_TOP_LEFT_XY = {
  "plate": Point(x=5, y=-5),

hardware/opentrons_hardware/firmware_bindings/constants.py

@@ -253,7 +253,7 @@ class MessageId(int, Enum):
  peripheral_status_request = 0x8C
  peripheral_status_response = 0x8D
  baseline_sensor_response = 0x8E
- send_accumulated_pressure_data = 0x8F
+ send_accumulated_sensor_data = 0x8F
 
  set_hepa_fan_state_request = 0x90
  get_hepa_fan_state_request = 0x91