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Automate manipulator initialization logic #81

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Merged
bruno-f-cruz merged 6 commits into from
May 18, 2026
Merged

Automate manipulator initialization logic #81

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1480a7d
Add animal_offset to manipulator
bruno-f-cruz May 4, 2026
1cc3b56
Add automatic homing and initial position to initialization
bruno-f-cruz May 4, 2026
e323df8
Remove unused log
bruno-f-cruz May 4, 2026
48520ce
Ensure sequence never ends when homing motor
bruno-f-cruz May 13, 2026
f454b97
regenerates
micahwoodard May 18, 2026
55f8453
updates rig example
micahwoodard May 18, 2026
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10 changes: 7 additions & 3 deletions examples/rig.py
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,6 @@

from aind_behavior_services.rig import cameras
from aind_behavior_services.rig.aind_manipulator import (
AindManipulator,
AindManipulatorCalibration,
Axis,
AxisConfiguration,
Expand All @@ -15,7 +14,12 @@
)
from aind_behavior_services.rig.water_valve import Measurement, calibrate_water_valves

from aind_behavior_dynamic_foraging.rig import AindDynamicForagingRig, DynamicForagingSoundCard, RigCalibration
from aind_behavior_dynamic_foraging.rig import (
AindDynamicForagingRig,
DynamicForagingAindManipulator,
DynamicForagingSoundCard,
RigCalibration,
)

manipulator_calibration = AindManipulatorCalibration(
full_step_to_mm=(ManipulatorPosition(x=0.010, y1=0.010, y2=0.010, z=0.010)),
Expand Down Expand Up @@ -60,7 +64,7 @@
harp_lickometer_left=None,
harp_lickometer_right=None,
harp_clock_generator=HarpWhiteRabbit(port_name="COM11"),
manipulator=AindManipulator(port_name="COM9", calibration=manipulator_calibration),
manipulator=DynamicForagingAindManipulator(port_name="COM9", calibration=manipulator_calibration),
calibration=RigCalibration(
water_valve_left=water_valve_calibration,
water_valve_right=water_valve_calibration,
Expand Down
227 changes: 118 additions & 109 deletions schema/aind_behavior_dynamic_foraging.json
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Original file line number Diff line number Diff line change
Expand Up @@ -107,7 +107,7 @@
]
},
"manipulator": {
"$ref": "#/$defs/AindManipulator",
"$ref": "#/$defs/DynamicForagingAindManipulator",
"description": "Manipulator"
},
"calibration": {
Expand Down Expand Up @@ -218,114 +218,6 @@
"title": "AindDynamicForagingTaskParameters",
"type": "object"
},
"AindManipulator": {
"description": "AindManipulator device definition",
"properties": {
"device_type": {
"const": "StepperDriver",
"default": "StepperDriver",
"title": "Device Type",
"type": "string"
},
"calibration": {
"$ref": "#/$defs/AindManipulatorCalibration",
"default": {
"description": "AindManipulator calibration and settings",
"full_step_to_mm": {
"x": 0.01,
"y1": 0.01,
"y2": 0.01,
"z": 0.01
},
"axis_configuration": [
{
"axis": 2,
"max_limit": 25.0,
"maximum_step_interval": 2000,
"microstep_resolution": 0,
"min_limit": -0.01,
"motor_operation_mode": 0,
"step_acceleration_interval": 100,
"step_interval": 100
},
{
"axis": 3,
"max_limit": 25.0,
"maximum_step_interval": 2000,
"microstep_resolution": 0,
"min_limit": -0.01,
"motor_operation_mode": 0,
"step_acceleration_interval": 100,
"step_interval": 100
},
{
"axis": 1,
"max_limit": 25.0,
"maximum_step_interval": 2000,
"microstep_resolution": 0,
"min_limit": -0.01,
"motor_operation_mode": 0,
"step_acceleration_interval": 100,
"step_interval": 100
},
{
"axis": 4,
"max_limit": 25.0,
"maximum_step_interval": 2000,
"microstep_resolution": 0,
"min_limit": -0.01,
"motor_operation_mode": 0,
"step_acceleration_interval": 100,
"step_interval": 100
}
],
"homing_order": [
2,
3,
1,
4
],
"initial_position": {
"x": 0.0,
"y1": 0.0,
"y2": 0.0,
"z": 0.0
}
},
"description": "Calibration for the device."
},
"who_am_i": {
"const": 1130,
"default": 1130,
"title": "Who Am I",
"type": "integer"
},
"serial_number": {
"default": null,
"description": "Device serial number",
"oneOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Serial Number"
},
"port_name": {
"description": "Device port name",
"title": "Port Name",
"type": "string"
}
},
"required": [
"port_name"
],
"title": "AindManipulator",
"type": "object",
"x-sgen-typename": "AllenNeuralDynamics.AindManipulator.AindManipulator"
},
"AindManipulatorCalibration": {
"description": "AindManipulator calibration class",
"properties": {
Expand Down Expand Up @@ -1470,6 +1362,123 @@
"title": "Distribution",
"x-sgen-typename": "AllenNeuralDynamics.AindBehaviorServices.Distributions.Distribution"
},
"DynamicForagingAindManipulator": {
"description": "A calibrated manipulator for the dynamic foraging rig. This is a subclass of the AindManipulator that includes an offset of the subject position relative to the initial position.",
"properties": {
"device_type": {
"const": "StepperDriver",
"default": "StepperDriver",
"title": "Device Type",
"type": "string"
},
"calibration": {
"$ref": "#/$defs/AindManipulatorCalibration",
"default": {
"description": "AindManipulator calibration and settings",
"full_step_to_mm": {
"x": 0.01,
"y1": 0.01,
"y2": 0.01,
"z": 0.01
},
"axis_configuration": [
{
"axis": 2,
"max_limit": 25.0,
"maximum_step_interval": 2000,
"microstep_resolution": 0,
"min_limit": -0.01,
"motor_operation_mode": 0,
"step_acceleration_interval": 100,
"step_interval": 100
},
{
"axis": 3,
"max_limit": 25.0,
"maximum_step_interval": 2000,
"microstep_resolution": 0,
"min_limit": -0.01,
"motor_operation_mode": 0,
"step_acceleration_interval": 100,
"step_interval": 100
},
{
"axis": 1,
"max_limit": 25.0,
"maximum_step_interval": 2000,
"microstep_resolution": 0,
"min_limit": -0.01,
"motor_operation_mode": 0,
"step_acceleration_interval": 100,
"step_interval": 100
},
{
"axis": 4,
"max_limit": 25.0,
"maximum_step_interval": 2000,
"microstep_resolution": 0,
"min_limit": -0.01,
"motor_operation_mode": 0,
"step_acceleration_interval": 100,
"step_interval": 100
}
],
"homing_order": [
2,
3,
1,
4
],
"initial_position": {
"x": 0.0,
"y1": 0.0,
"y2": 0.0,
"z": 0.0
}
},
"description": "Calibration for the device."
},
"who_am_i": {
"const": 1130,
"default": 1130,
"title": "Who Am I",
"type": "integer"
},
"serial_number": {
"default": null,
"description": "Device serial number",
"oneOf": [
{
"type": "string"
},
{
"type": "null"
}
],
"title": "Serial Number"
},
"port_name": {
"description": "Device port name",
"title": "Port Name",
"type": "string"
},
"subject_offset": {
"$ref": "#/$defs/ManipulatorPosition",
"default": {
"x": 0.0,
"y1": 0.0,
"y2": 0.0,
"z": 0.0
},
"description": "Offset of the subject position relative to the `initial_position` parameter"
}
},
"required": [
"port_name"
],
"title": "DynamicForagingAindManipulator",
"type": "object"
},
"DynamicForagingSoundCard": {
"description": "A calibrated sound card for the dynamic foraging rig. This is a subclass of the HarpSoundCard that includes the sound card calibration.",
"properties": {
Expand Down
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