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Corrects metadata #154

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Merged
micahwoodard merged 7 commits into from
Aug 24, 2026
Merged

Corrects metadata #154

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06cfd65
fix: update instrument metadata mapper per issue DF-Refactoring#173
micahwoodard Aug 20, 2026
a1d9385
fix: update acquisition mapper per issue DF-Refactoring#172
micahwoodard Aug 20, 2026
6fdc731
adds additional metadata
micahwoodard Aug 20, 2026
17cdda5
fix: add required notes for LickSpout with Other manufacturer
micahwoodard Aug 20, 2026
6e442d4
adds note for other manufacturer
micahwoodard Aug 20, 2026
9f8358f
use task_logic.name for acquisition_type and adds camera note
micahwoodard Aug 21, 2026
03178fd
improves camera note
micahwoodard Aug 21, 2026
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7 changes: 5 additions & 2 deletions ...oraging_metadata_mapper/src/aind_behavior_dynamic_foraging_metadata_mapper/acquisition.py
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Original file line number Diff line number Diff line change
Expand Up @@ -161,6 +161,8 @@ def _map(self) -> Acquisition:
output_parameters=metrics.model_dump(),
)

curriculum_status = str(trainer_state.stage.name) if trainer_state.stage is not None else None

stimulus_epoch = StimulusEpoch(
stimulus_start_time=session_model.date,
stimulus_end_time=acquisition_end_time,
Expand All @@ -169,6 +171,7 @@ def _map(self) -> Acquisition:
stimulus_modalities=[StimulusModality.AUDITORY],
performance_metrics=performance_metrics,
training_protocol_name=str(trainer_state.curriculum.name),
curriculum_status=curriculum_status,
)

# Construct aind-data-schema session
Expand All @@ -179,7 +182,7 @@ def _map(self) -> Acquisition:
acquisition_end_time=acquisition_end_time,
acquisition_start_time=session_model.date,
experimenters=session_model.experimenter,
acquisition_type=session_model.experiment or task_logic_model.name,
acquisition_type=task_logic_model.name,
coordinate_system=None,
data_streams=data_streams,
stimulus_epochs=[stimulus_epoch],
Expand All @@ -189,7 +192,7 @@ def _map(self) -> Acquisition:
def _get_subject_details(data_path: os.PathLike) -> AcquisitionSubjectDetails:
water = calculate_consumed_water(data_path)
return AcquisitionSubjectDetails(
mouse_platform_name="tube",
mouse_platform_name="mouse_tube_foraging",
reward_consumed_total=None if not water else Decimal(str(water)),
reward_consumed_unit=units.VolumeUnit.ML,
)
Expand Down
115 changes: 92 additions & 23 deletions ...foraging_metadata_mapper/src/aind_behavior_dynamic_foraging_metadata_mapper/instrument.py
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Original file line number Diff line number Diff line change
Expand Up @@ -10,7 +10,7 @@
from aind_behavior_services.rig import water_valve as abs_water_valve
from aind_behavior_services.utils import get_fields_of_type, utcnow
from aind_data_schema.components.connections import Connection
from aind_data_schema.components.coordinates import Axis, AxisName, CoordinateSystem, Direction, Origin
from aind_data_schema.components.coordinates import Axis, AxisName, CoordinateSystem, Direction, Origin, Scale
from aind_data_schema.components.devices import (
AnatomicalRelative,
Camera,
Expand All @@ -20,11 +20,17 @@
Cooling,
DataInterface,
Device,
Enclosure,
HarpDevice,
HarpDeviceType,
Lens,
LickSensorType,
LickSpout,
LickSpoutAssembly,
LightEmittingDiode,
MotorizedStage,
SizeUnit,
Tube,
)
from aind_data_schema.components.measurements import CalibrationFit, FitType, GenericModel, VolumeCalibration
from aind_data_schema.core.acquisition import CALIBRATIONS
Expand Down Expand Up @@ -140,6 +146,13 @@ def _map(self) -> Instrument:
controller = rig.triggered_camera_controller
fps = float(controller.frame_rate) if controller.frame_rate else float("nan")
for name, cam in rig.triggered_camera_controller.cameras.items():
additional_settings = cam.model_dump()
additional_settings["note"] = (
"The additional_settings values are the input parameters used to initialize the camera. Model found at https://github.com/AllenNeuralDynamics/Aind.Behavior.Services/blob/a6c0f539275f73af87da82a8ea0101836389f1b3/src/aind_behavior_services/rig/cameras.py#L226. Enum clarifications: adc_bit_depth is an "
"Spinnaker SDK enum-coded value (0=ADC8BIT, 1=ADC10BIT, 2=ADC12BIT), and pixel_format "
"is also enum-coded (for this configuration, 0=MONO8)."
)

Comment thread
micahwoodard marked this conversation as resolved.
camera = Camera(
name=name,
manufacturer=Organization.FLIR,
Expand All @@ -160,7 +173,7 @@ def _map(self) -> Instrument:
crop_width=cam.region_of_interest.width if cam.region_of_interest.width > 0 else None,
crop_height=cam.region_of_interest.height if cam.region_of_interest.height > 0 else None,
crop_unit=SizeUnit.PX,
additional_settings=GenericModel.model_validate(cam.model_dump()),
additional_settings=GenericModel.model_validate(additional_settings),
)
assembly = CameraAssembly(
name=f"{name}Assembly",
Expand Down Expand Up @@ -269,32 +282,90 @@ def _map(self) -> Instrument:
)
)

# manipulator\
# lick spout assembly
components.append(
MotorizedStage(
name="motorized_stage",
manufacturer=Organization.AIND,
model="328-300-00",
travel=Decimal("30"),
travel_unit=SizeUnit.CM,
notes="This stage is driven by the manipulator device.",
LickSpoutAssembly(
name="LickSpoutAssembly",
lick_spouts=[
LickSpout(
name="Left lick spout",
manufacturer=Organization.OTHER,
notes=" (v1v2 upgrade): 'manufacturer' field was missing, defaulting to 'Other'.",

@micahwoodard micahwoodard Aug 20, 2026

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Copied from https://data.allenneuraldynamics.org/record?name=behavior_868933_2026-08-18_12-42-42_processed_2026-08-19_04-11-37

spout_diameter=Decimal("1.2"),
spout_diameter_unit=SizeUnit.MM,
solenoid_valve=Device(
name="Solenoid Left",
manufacturer=Organization.THE_LEE_COMPANY,
model="LHDB1233518H",
),
lick_sensor=Device(
name="Lick Sensor Left",
manufacturer=Organization.JANELIA,
),
lick_sensor_type=LickSensorType.CAPACITIVE,
),
LickSpout(
name="Right lick spout",
manufacturer=Organization.OTHER,
notes="Lick spout manufacturer is unknown.",
spout_diameter=Decimal("1.2"),
spout_diameter_unit=SizeUnit.MM,
solenoid_valve=Device(
name="Solenoid Right",
manufacturer=Organization.THE_LEE_COMPANY,
model="LHDB1233518H",
),
lick_sensor=Device(
name="Lick Sensor Right",
manufacturer=Organization.JANELIA,
),
lick_sensor_type=LickSensorType.CAPACITIVE,
),
],
motorized_stage=MotorizedStage(
name="motorized_stage",
manufacturer=Organization.AIND,
model="328-300-00",
travel=Decimal("30"),
travel_unit=SizeUnit.MM,
notes="This stage is driven by the manipulator device.",
),
)
)

# solenoid
# mouse platform
components.append(
Device(
name="left_water_valve_solenoid",
manufacturer=Organization.THE_LEE_COMPANY,
model="LHDB1233518H",
Tube(
name="mouse_tube_foraging",
manufacturer=Organization.CUSTOM,
diameter=Decimal("3.0"),
diameter_unit=SizeUnit.CM,
)
)

# IR light source
components.append(
Device(
name="right_water_valve_solenoid",
manufacturer=Organization.THE_LEE_COMPANY,
model="LHDB1233518H",
LightEmittingDiode(
name="IR LED",
manufacturer=Organization.THORLABS,
model="M810L5",
wavelength=810,
)
)

# enclosure
components.append(
Enclosure(
name="Behavior enclosure",
manufacturer=Organization.AIND,
size=Scale(scale=[54, 54, 54]),
size_unit=SizeUnit.CM,
internal_material="",
external_material="",
grounded=False,
laser_interlock=False,
air_filtration=False,
notes=" (v1v2 upgrade): Scale is width/length/height",
)
)

Expand All @@ -317,14 +388,12 @@ def _map(self) -> Instrument:
connections.append(
Connection(
source_device="BehaviorBoard",
target_device="left_water_valve_solenoid",
target_device="Solenoid Left",
source_port="SupplyPort0",
)
)
connections.append(
Connection(
source_device="BehaviorBoard", target_device="right_water_valve_solenoid", source_port="SupplyPort1"
)
Connection(source_device="BehaviorBoard", target_device="Solenoid Right", source_port="SupplyPort1")
)

return Instrument(
Expand Down