aind_behavior_services.calibration package¶
Submodules¶
aind_behavior_services.calibration.aind_manipulator module¶
- pydantic model aind_behavior_services.calibration.aind_manipulator.AindManipulatorCalibration[source]¶
Bases:
CalibrationAind manipulator calibration class
Show JSON schema
{ "title": "AindManipulatorCalibration", "description": "Aind manipulator calibration class", "type": "object", "properties": { "device_name": { "default": "AindManipulator", "description": "Must match a device name in rig/instrument", "title": "Device name", "type": "string" }, "input": { "$ref": "#/$defs/AindManipulatorCalibrationInput", "title": "Input of the calibration" }, "output": { "$ref": "#/$defs/AindManipulatorCalibrationOutput", "title": "Output of the calibration." }, "date": { "anyOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "default": null, "title": "Date" }, "description": { "const": "Calibration of the load cells system", "default": "Calibration of the load cells system", "title": "Description", "type": "string" }, "notes": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Notes" } }, "$defs": { "AindManipulatorCalibrationInput": { "properties": { "full_step_to_mm": { "$ref": "#/$defs/ManipulatorPosition", "default": { "x": 0.01, "y1": 0.01, "y2": 0.01, "z": 0.01 }, "title": "Full step to mm. Used to convert steps to SI Units" }, "axis_configuration": { "default": [ { "axis": 2, "step_acceleration_interval": 100, "step_interval": 100, "microstep_resolution": 0, "maximum_step_interval": 2000, "motor_operation_mode": 0, "max_limit": 25.0, "min_limit": -0.01 }, { "axis": 3, "step_acceleration_interval": 100, "step_interval": 100, "microstep_resolution": 0, "maximum_step_interval": 2000, "motor_operation_mode": 0, "max_limit": 25.0, "min_limit": -0.01 }, { "axis": 1, "step_acceleration_interval": 100, "step_interval": 100, "microstep_resolution": 0, "maximum_step_interval": 2000, "motor_operation_mode": 0, "max_limit": 25.0, "min_limit": -0.01 }, { "axis": 4, "step_acceleration_interval": 100, "step_interval": 100, "microstep_resolution": 0, "maximum_step_interval": 2000, "motor_operation_mode": 0, "max_limit": 25.0, "min_limit": -0.01 } ], "items": { "$ref": "#/$defs/AxisConfiguration" }, "title": "Axes configuration. Only the axes that are configured will be enabled.", "type": "array" }, "homing_order": { "default": [ 2, 3, 1, 4 ], "items": { "$ref": "#/$defs/Axis" }, "title": "Homing order", "type": "array" }, "initial_position": { "$ref": "#/$defs/ManipulatorPosition", "default": { "x": 0.0, "y1": 0.0, "y2": 0.0, "z": 0.0 } } }, "title": "AindManipulatorCalibrationInput", "type": "object" }, "AindManipulatorCalibrationOutput": { "properties": {}, "title": "AindManipulatorCalibrationOutput", "type": "object" }, "Axis": { "description": "Motor axis available", "enum": [ 0, 1, 2, 3, 4 ], "title": "Axis", "type": "integer" }, "AxisConfiguration": { "description": "Axis configuration", "properties": { "axis": { "$ref": "#/$defs/Axis", "title": "Axis to be configured" }, "step_acceleration_interval": { "default": 100, "description": "Acceleration of the step interval in microseconds", "maximum": 2000, "minimum": 2, "title": "Acceleration", "type": "integer" }, "step_interval": { "default": 100, "description": "Step interval in microseconds.", "maximum": 20000, "minimum": 100, "title": "Step interval", "type": "integer" }, "microstep_resolution": { "$ref": "#/$defs/MicrostepResolution", "default": 0, "title": "Microstep resolution" }, "maximum_step_interval": { "default": 2000, "maximum": 20000, "minimum": 100, "title": "Configures the time between step motor pulses (us) used when starting or stopping a movement", "type": "integer" }, "motor_operation_mode": { "$ref": "#/$defs/MotorOperationMode", "default": 0, "title": "Motor operation mode" }, "max_limit": { "default": 25, "title": "Maximum limit in SI units. A value of 0 disables this limit.", "type": "number" }, "min_limit": { "default": -0.01, "title": "Minimum limit in SI units. A value of 0 disables this limit.", "type": "number" } }, "required": [ "axis" ], "title": "AxisConfiguration", "type": "object" }, "ManipulatorPosition": { "properties": { "x": { "title": "X coordinate", "type": "number" }, "y1": { "title": "Y1 coordinate", "type": "number" }, "y2": { "title": "Y2 coordinate", "type": "number" }, "z": { "title": "Z coordinate", "type": "number" } }, "required": [ "x", "y1", "y2", "z" ], "title": "ManipulatorPosition", "type": "object" }, "MicrostepResolution": { "enum": [ 0, 1, 2, 3 ], "title": "MicrostepResolution", "type": "integer" }, "MotorOperationMode": { "enum": [ 0, 1 ], "title": "MotorOperationMode", "type": "integer" } }, "required": [ "input", "output" ] }
- Fields:
- field description: Literal['Calibration of the load cells system'] = 'Calibration of the load cells system'[source]¶
- field input: AindManipulatorCalibrationInput [Required][source]¶
- field output: AindManipulatorCalibrationOutput [Required][source]¶
- pydantic model aind_behavior_services.calibration.aind_manipulator.AindManipulatorCalibrationInput[source]¶
Bases:
BaseModelShow JSON schema
{ "title": "AindManipulatorCalibrationInput", "type": "object", "properties": { "full_step_to_mm": { "$ref": "#/$defs/ManipulatorPosition", "default": { "x": 0.01, "y1": 0.01, "y2": 0.01, "z": 0.01 }, "title": "Full step to mm. Used to convert steps to SI Units" }, "axis_configuration": { "default": [ { "axis": 2, "step_acceleration_interval": 100, "step_interval": 100, "microstep_resolution": 0, "maximum_step_interval": 2000, "motor_operation_mode": 0, "max_limit": 25.0, "min_limit": -0.01 }, { "axis": 3, "step_acceleration_interval": 100, "step_interval": 100, "microstep_resolution": 0, "maximum_step_interval": 2000, "motor_operation_mode": 0, "max_limit": 25.0, "min_limit": -0.01 }, { "axis": 1, "step_acceleration_interval": 100, "step_interval": 100, "microstep_resolution": 0, "maximum_step_interval": 2000, "motor_operation_mode": 0, "max_limit": 25.0, "min_limit": -0.01 }, { "axis": 4, "step_acceleration_interval": 100, "step_interval": 100, "microstep_resolution": 0, "maximum_step_interval": 2000, "motor_operation_mode": 0, "max_limit": 25.0, "min_limit": -0.01 } ], "items": { "$ref": "#/$defs/AxisConfiguration" }, "title": "Axes configuration. Only the axes that are configured will be enabled.", "type": "array" }, "homing_order": { "default": [ 2, 3, 1, 4 ], "items": { "$ref": "#/$defs/Axis" }, "title": "Homing order", "type": "array" }, "initial_position": { "$ref": "#/$defs/ManipulatorPosition", "default": { "x": 0.0, "y1": 0.0, "y2": 0.0, "z": 0.0 } } }, "$defs": { "Axis": { "description": "Motor axis available", "enum": [ 0, 1, 2, 3, 4 ], "title": "Axis", "type": "integer" }, "AxisConfiguration": { "description": "Axis configuration", "properties": { "axis": { "$ref": "#/$defs/Axis", "title": "Axis to be configured" }, "step_acceleration_interval": { "default": 100, "description": "Acceleration of the step interval in microseconds", "maximum": 2000, "minimum": 2, "title": "Acceleration", "type": "integer" }, "step_interval": { "default": 100, "description": "Step interval in microseconds.", "maximum": 20000, "minimum": 100, "title": "Step interval", "type": "integer" }, "microstep_resolution": { "$ref": "#/$defs/MicrostepResolution", "default": 0, "title": "Microstep resolution" }, "maximum_step_interval": { "default": 2000, "maximum": 20000, "minimum": 100, "title": "Configures the time between step motor pulses (us) used when starting or stopping a movement", "type": "integer" }, "motor_operation_mode": { "$ref": "#/$defs/MotorOperationMode", "default": 0, "title": "Motor operation mode" }, "max_limit": { "default": 25, "title": "Maximum limit in SI units. A value of 0 disables this limit.", "type": "number" }, "min_limit": { "default": -0.01, "title": "Minimum limit in SI units. A value of 0 disables this limit.", "type": "number" } }, "required": [ "axis" ], "title": "AxisConfiguration", "type": "object" }, "ManipulatorPosition": { "properties": { "x": { "title": "X coordinate", "type": "number" }, "y1": { "title": "Y1 coordinate", "type": "number" }, "y2": { "title": "Y2 coordinate", "type": "number" }, "z": { "title": "Z coordinate", "type": "number" } }, "required": [ "x", "y1", "y2", "z" ], "title": "ManipulatorPosition", "type": "object" }, "MicrostepResolution": { "enum": [ 0, 1, 2, 3 ], "title": "MicrostepResolution", "type": "integer" }, "MotorOperationMode": { "enum": [ 0, 1 ], "title": "MotorOperationMode", "type": "integer" } } }
- Fields:
axis_configuration (List[aind_behavior_services.calibration.aind_manipulator.AxisConfiguration])full_step_to_mm (aind_behavior_services.calibration.aind_manipulator.ManipulatorPosition)homing_order (List[aind_behavior_services.calibration.aind_manipulator.Axis])initial_position (aind_behavior_services.calibration.aind_manipulator.ManipulatorPosition)
- field axis_configuration: List[AxisConfiguration] = [AxisConfiguration(axis=<Axis.Y1: 2>, step_acceleration_interval=100, step_interval=100, microstep_resolution=<MicrostepResolution.MICROSTEP8: 0>, maximum_step_interval=2000, motor_operation_mode=<MotorOperationMode.QUIET: 0>, max_limit=25, min_limit=-0.01), AxisConfiguration(axis=<Axis.Y2: 3>, step_acceleration_interval=100, step_interval=100, microstep_resolution=<MicrostepResolution.MICROSTEP8: 0>, maximum_step_interval=2000, motor_operation_mode=<MotorOperationMode.QUIET: 0>, max_limit=25, min_limit=-0.01), AxisConfiguration(axis=<Axis.X: 1>, step_acceleration_interval=100, step_interval=100, microstep_resolution=<MicrostepResolution.MICROSTEP8: 0>, maximum_step_interval=2000, motor_operation_mode=<MotorOperationMode.QUIET: 0>, max_limit=25, min_limit=-0.01), AxisConfiguration(axis=<Axis.Z: 4>, step_acceleration_interval=100, step_interval=100, microstep_resolution=<MicrostepResolution.MICROSTEP8: 0>, maximum_step_interval=2000, motor_operation_mode=<MotorOperationMode.QUIET: 0>, max_limit=25, min_limit=-0.01)][source]¶
- field full_step_to_mm: ManipulatorPosition = ManipulatorPosition(x=0.01, y1=0.01, y2=0.01, z=0.01)[source]¶
- field initial_position: ManipulatorPosition = ManipulatorPosition(x=0.0, y1=0.0, y2=0.0, z=0.0)[source]¶
- pydantic model aind_behavior_services.calibration.aind_manipulator.AindManipulatorCalibrationOutput[source]¶
Bases:
BaseModelShow JSON schema
{ "title": "AindManipulatorCalibrationOutput", "type": "object", "properties": {} }
- pydantic model aind_behavior_services.calibration.aind_manipulator.AindManipulatorDevice[source]¶
Bases:
HarpStepperDriverShow JSON schema
{ "title": "AindManipulatorDevice", "type": "object", "properties": { "device_type": { "const": "StepperDriver", "default": "StepperDriver", "title": "Device Type", "type": "string" }, "device_name": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "description": "Device name", "title": "Device Name" }, "additional_settings": { "anyOf": [ { "$ref": "#/$defs/BaseModel" }, { "type": "null" } ], "default": null, "description": "Additional settings" }, "calibration": { "anyOf": [ { "$ref": "#/$defs/AindManipulatorCalibration" }, { "type": "null" } ], "default": null, "title": "Calibration of the manipulator" }, "who_am_i": { "const": 1130, "default": 1130, "title": "Who Am I", "type": "integer" }, "serial_number": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "description": "Device serial number", "title": "Serial Number" }, "port_name": { "description": "Device port name", "title": "Port Name", "type": "string" } }, "$defs": { "AindManipulatorCalibration": { "description": "Aind manipulator calibration class", "properties": { "device_name": { "default": "AindManipulator", "description": "Must match a device name in rig/instrument", "title": "Device name", "type": "string" }, "input": { "$ref": "#/$defs/AindManipulatorCalibrationInput", "title": "Input of the calibration" }, "output": { "$ref": "#/$defs/AindManipulatorCalibrationOutput", "title": "Output of the calibration." }, "date": { "anyOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "default": null, "title": "Date" }, "description": { "const": "Calibration of the load cells system", "default": "Calibration of the load cells system", "title": "Description", "type": "string" }, "notes": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Notes" } }, "required": [ "input", "output" ], "title": "AindManipulatorCalibration", "type": "object" }, "AindManipulatorCalibrationInput": { "properties": { "full_step_to_mm": { "$ref": "#/$defs/ManipulatorPosition", "default": { "x": 0.01, "y1": 0.01, "y2": 0.01, "z": 0.01 }, "title": "Full step to mm. Used to convert steps to SI Units" }, "axis_configuration": { "default": [ { "axis": 2, "step_acceleration_interval": 100, "step_interval": 100, "microstep_resolution": 0, "maximum_step_interval": 2000, "motor_operation_mode": 0, "max_limit": 25.0, "min_limit": -0.01 }, { "axis": 3, "step_acceleration_interval": 100, "step_interval": 100, "microstep_resolution": 0, "maximum_step_interval": 2000, "motor_operation_mode": 0, "max_limit": 25.0, "min_limit": -0.01 }, { "axis": 1, "step_acceleration_interval": 100, "step_interval": 100, "microstep_resolution": 0, "maximum_step_interval": 2000, "motor_operation_mode": 0, "max_limit": 25.0, "min_limit": -0.01 }, { "axis": 4, "step_acceleration_interval": 100, "step_interval": 100, "microstep_resolution": 0, "maximum_step_interval": 2000, "motor_operation_mode": 0, "max_limit": 25.0, "min_limit": -0.01 } ], "items": { "$ref": "#/$defs/AxisConfiguration" }, "title": "Axes configuration. Only the axes that are configured will be enabled.", "type": "array" }, "homing_order": { "default": [ 2, 3, 1, 4 ], "items": { "$ref": "#/$defs/Axis" }, "title": "Homing order", "type": "array" }, "initial_position": { "$ref": "#/$defs/ManipulatorPosition", "default": { "x": 0.0, "y1": 0.0, "y2": 0.0, "z": 0.0 } } }, "title": "AindManipulatorCalibrationInput", "type": "object" }, "AindManipulatorCalibrationOutput": { "properties": {}, "title": "AindManipulatorCalibrationOutput", "type": "object" }, "Axis": { "description": "Motor axis available", "enum": [ 0, 1, 2, 3, 4 ], "title": "Axis", "type": "integer" }, "AxisConfiguration": { "description": "Axis configuration", "properties": { "axis": { "$ref": "#/$defs/Axis", "title": "Axis to be configured" }, "step_acceleration_interval": { "default": 100, "description": "Acceleration of the step interval in microseconds", "maximum": 2000, "minimum": 2, "title": "Acceleration", "type": "integer" }, "step_interval": { "default": 100, "description": "Step interval in microseconds.", "maximum": 20000, "minimum": 100, "title": "Step interval", "type": "integer" }, "microstep_resolution": { "$ref": "#/$defs/MicrostepResolution", "default": 0, "title": "Microstep resolution" }, "maximum_step_interval": { "default": 2000, "maximum": 20000, "minimum": 100, "title": "Configures the time between step motor pulses (us) used when starting or stopping a movement", "type": "integer" }, "motor_operation_mode": { "$ref": "#/$defs/MotorOperationMode", "default": 0, "title": "Motor operation mode" }, "max_limit": { "default": 25, "title": "Maximum limit in SI units. A value of 0 disables this limit.", "type": "number" }, "min_limit": { "default": -0.01, "title": "Minimum limit in SI units. A value of 0 disables this limit.", "type": "number" } }, "required": [ "axis" ], "title": "AxisConfiguration", "type": "object" }, "BaseModel": { "properties": {}, "title": "BaseModel", "type": "object" }, "ManipulatorPosition": { "properties": { "x": { "title": "X coordinate", "type": "number" }, "y1": { "title": "Y1 coordinate", "type": "number" }, "y2": { "title": "Y2 coordinate", "type": "number" }, "z": { "title": "Z coordinate", "type": "number" } }, "required": [ "x", "y1", "y2", "z" ], "title": "ManipulatorPosition", "type": "object" }, "MicrostepResolution": { "enum": [ 0, 1, 2, 3 ], "title": "MicrostepResolution", "type": "integer" }, "MotorOperationMode": { "enum": [ 0, 1 ], "title": "MotorOperationMode", "type": "integer" } }, "required": [ "port_name" ] }
- Fields:
- Validators:
- field calibration: AindManipulatorCalibration | None = None[source]¶
- Validated by:
_set_name
- class aind_behavior_services.calibration.aind_manipulator.Axis(value)[source]¶
Bases:
IntEnumMotor axis available
- pydantic model aind_behavior_services.calibration.aind_manipulator.AxisConfiguration[source]¶
Bases:
BaseModelAxis configuration
Show JSON schema
{ "title": "AxisConfiguration", "description": "Axis configuration", "type": "object", "properties": { "axis": { "$ref": "#/$defs/Axis", "title": "Axis to be configured" }, "step_acceleration_interval": { "default": 100, "description": "Acceleration of the step interval in microseconds", "maximum": 2000, "minimum": 2, "title": "Acceleration", "type": "integer" }, "step_interval": { "default": 100, "description": "Step interval in microseconds.", "maximum": 20000, "minimum": 100, "title": "Step interval", "type": "integer" }, "microstep_resolution": { "$ref": "#/$defs/MicrostepResolution", "default": 0, "title": "Microstep resolution" }, "maximum_step_interval": { "default": 2000, "maximum": 20000, "minimum": 100, "title": "Configures the time between step motor pulses (us) used when starting or stopping a movement", "type": "integer" }, "motor_operation_mode": { "$ref": "#/$defs/MotorOperationMode", "default": 0, "title": "Motor operation mode" }, "max_limit": { "default": 25, "title": "Maximum limit in SI units. A value of 0 disables this limit.", "type": "number" }, "min_limit": { "default": -0.01, "title": "Minimum limit in SI units. A value of 0 disables this limit.", "type": "number" } }, "$defs": { "Axis": { "description": "Motor axis available", "enum": [ 0, 1, 2, 3, 4 ], "title": "Axis", "type": "integer" }, "MicrostepResolution": { "enum": [ 0, 1, 2, 3 ], "title": "MicrostepResolution", "type": "integer" }, "MotorOperationMode": { "enum": [ 0, 1 ], "title": "MotorOperationMode", "type": "integer" } }, "required": [ "axis" ] }
- Fields:
- field microstep_resolution: MicrostepResolution = MicrostepResolution.MICROSTEP8[source]¶
- field motor_operation_mode: MotorOperationMode = MotorOperationMode.QUIET[source]¶
- pydantic model aind_behavior_services.calibration.aind_manipulator.CalibrationLogic[source]¶
Bases:
AindBehaviorTaskLogicModelShow JSON schema
{ "title": "CalibrationLogic", "type": "object", "properties": { "name": { "default": "AindManipulatorCalibrationLogic", "title": "Task name", "type": "string" }, "description": { "default": "", "description": "Description of the task.", "title": "Description", "type": "string" }, "task_parameters": { "$ref": "#/$defs/CalibrationParameters", "title": "Task parameters" }, "version": { "const": "0.2.0", "default": "0.2.0", "title": "Version", "type": "string" }, "stage_name": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "description": "Optional stage name the `Task` object instance represents.", "title": "Stage Name" } }, "$defs": { "CalibrationParameters": { "additionalProperties": true, "properties": { "rng_seed": { "anyOf": [ { "type": "number" }, { "type": "null" } ], "default": null, "description": "Seed of the random number generator", "title": "Rng Seed" }, "aind_behavior_services_pkg_version": { "const": "0.11.0", "default": "0.11.0", "title": "aind_behavior_services package version", "type": "string" } }, "title": "CalibrationParameters", "type": "object" } }, "additionalProperties": false, "required": [ "task_parameters" ] }
- Config:
extra: str = forbid
validate_assignment: bool = True
validate_default: bool = True
strict: bool = True
str_strip_whitespace: bool = True
- Fields:
- Validators:
- field task_parameters: CalibrationParameters [Required][source]¶
- pydantic model aind_behavior_services.calibration.aind_manipulator.CalibrationParameters[source]¶
Bases:
TaskParametersShow JSON schema
{ "title": "CalibrationParameters", "type": "object", "properties": { "rng_seed": { "anyOf": [ { "type": "number" }, { "type": "null" } ], "default": null, "description": "Seed of the random number generator", "title": "Rng Seed" }, "aind_behavior_services_pkg_version": { "const": "0.11.0", "default": "0.11.0", "title": "aind_behavior_services package version", "type": "string" } }, "additionalProperties": true }
- Config:
extra: str = allow
validate_assignment: bool = True
validate_default: bool = True
strict: bool = True
str_strip_whitespace: bool = True
- Fields:
- Validators:
- pydantic model aind_behavior_services.calibration.aind_manipulator.CalibrationRig[source]¶
Bases:
AindBehaviorRigModelShow JSON schema
{ "title": "CalibrationRig", "type": "object", "properties": { "aind_behavior_services_pkg_version": { "const": "0.11.0", "default": "0.11.0", "title": "aind_behavior_services package version", "type": "string" }, "version": { "const": "0.1.0", "default": "0.1.0", "title": "Version", "type": "string" }, "computer_name": { "description": "Computer name", "title": "Computer Name", "type": "string" }, "rig_name": { "description": "Rig name", "title": "Rig Name", "type": "string" }, "manipulator": { "$ref": "#/$defs/AindManipulatorDevice", "default": null, "title": "Manipulator device" } }, "$defs": { "AindManipulatorCalibration": { "description": "Aind manipulator calibration class", "properties": { "device_name": { "default": "AindManipulator", "description": "Must match a device name in rig/instrument", "title": "Device name", "type": "string" }, "input": { "$ref": "#/$defs/AindManipulatorCalibrationInput", "title": "Input of the calibration" }, "output": { "$ref": "#/$defs/AindManipulatorCalibrationOutput", "title": "Output of the calibration." }, "date": { "anyOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "default": null, "title": "Date" }, "description": { "const": "Calibration of the load cells system", "default": "Calibration of the load cells system", "title": "Description", "type": "string" }, "notes": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Notes" } }, "required": [ "input", "output" ], "title": "AindManipulatorCalibration", "type": "object" }, "AindManipulatorCalibrationInput": { "properties": { "full_step_to_mm": { "$ref": "#/$defs/ManipulatorPosition", "default": { "x": 0.01, "y1": 0.01, "y2": 0.01, "z": 0.01 }, "title": "Full step to mm. Used to convert steps to SI Units" }, "axis_configuration": { "default": [ { "axis": 2, "step_acceleration_interval": 100, "step_interval": 100, "microstep_resolution": 0, "maximum_step_interval": 2000, "motor_operation_mode": 0, "max_limit": 25.0, "min_limit": -0.01 }, { "axis": 3, "step_acceleration_interval": 100, "step_interval": 100, "microstep_resolution": 0, "maximum_step_interval": 2000, "motor_operation_mode": 0, "max_limit": 25.0, "min_limit": -0.01 }, { "axis": 1, "step_acceleration_interval": 100, "step_interval": 100, "microstep_resolution": 0, "maximum_step_interval": 2000, "motor_operation_mode": 0, "max_limit": 25.0, "min_limit": -0.01 }, { "axis": 4, "step_acceleration_interval": 100, "step_interval": 100, "microstep_resolution": 0, "maximum_step_interval": 2000, "motor_operation_mode": 0, "max_limit": 25.0, "min_limit": -0.01 } ], "items": { "$ref": "#/$defs/AxisConfiguration" }, "title": "Axes configuration. Only the axes that are configured will be enabled.", "type": "array" }, "homing_order": { "default": [ 2, 3, 1, 4 ], "items": { "$ref": "#/$defs/Axis" }, "title": "Homing order", "type": "array" }, "initial_position": { "$ref": "#/$defs/ManipulatorPosition", "default": { "x": 0.0, "y1": 0.0, "y2": 0.0, "z": 0.0 } } }, "title": "AindManipulatorCalibrationInput", "type": "object" }, "AindManipulatorCalibrationOutput": { "properties": {}, "title": "AindManipulatorCalibrationOutput", "type": "object" }, "AindManipulatorDevice": { "properties": { "device_type": { "const": "StepperDriver", "default": "StepperDriver", "title": "Device Type", "type": "string" }, "device_name": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "description": "Device name", "title": "Device Name" }, "additional_settings": { "anyOf": [ { "$ref": "#/$defs/BaseModel" }, { "type": "null" } ], "default": null, "description": "Additional settings" }, "calibration": { "anyOf": [ { "$ref": "#/$defs/AindManipulatorCalibration" }, { "type": "null" } ], "default": null, "title": "Calibration of the manipulator" }, "who_am_i": { "const": 1130, "default": 1130, "title": "Who Am I", "type": "integer" }, "serial_number": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "description": "Device serial number", "title": "Serial Number" }, "port_name": { "description": "Device port name", "title": "Port Name", "type": "string" } }, "required": [ "port_name" ], "title": "AindManipulatorDevice", "type": "object" }, "Axis": { "description": "Motor axis available", "enum": [ 0, 1, 2, 3, 4 ], "title": "Axis", "type": "integer" }, "AxisConfiguration": { "description": "Axis configuration", "properties": { "axis": { "$ref": "#/$defs/Axis", "title": "Axis to be configured" }, "step_acceleration_interval": { "default": 100, "description": "Acceleration of the step interval in microseconds", "maximum": 2000, "minimum": 2, "title": "Acceleration", "type": "integer" }, "step_interval": { "default": 100, "description": "Step interval in microseconds.", "maximum": 20000, "minimum": 100, "title": "Step interval", "type": "integer" }, "microstep_resolution": { "$ref": "#/$defs/MicrostepResolution", "default": 0, "title": "Microstep resolution" }, "maximum_step_interval": { "default": 2000, "maximum": 20000, "minimum": 100, "title": "Configures the time between step motor pulses (us) used when starting or stopping a movement", "type": "integer" }, "motor_operation_mode": { "$ref": "#/$defs/MotorOperationMode", "default": 0, "title": "Motor operation mode" }, "max_limit": { "default": 25, "title": "Maximum limit in SI units. A value of 0 disables this limit.", "type": "number" }, "min_limit": { "default": -0.01, "title": "Minimum limit in SI units. A value of 0 disables this limit.", "type": "number" } }, "required": [ "axis" ], "title": "AxisConfiguration", "type": "object" }, "BaseModel": { "properties": {}, "title": "BaseModel", "type": "object" }, "ManipulatorPosition": { "properties": { "x": { "title": "X coordinate", "type": "number" }, "y1": { "title": "Y1 coordinate", "type": "number" }, "y2": { "title": "Y2 coordinate", "type": "number" }, "z": { "title": "Z coordinate", "type": "number" } }, "required": [ "x", "y1", "y2", "z" ], "title": "ManipulatorPosition", "type": "object" }, "MicrostepResolution": { "enum": [ 0, 1, 2, 3 ], "title": "MicrostepResolution", "type": "integer" }, "MotorOperationMode": { "enum": [ 0, 1 ], "title": "MotorOperationMode", "type": "integer" } }, "required": [ "rig_name" ] }
- Fields:
- Validators:
- field manipulator: AindManipulatorDevice = None[source]¶
- pydantic model aind_behavior_services.calibration.aind_manipulator.ManipulatorPosition[source]¶
Bases:
BaseModelShow JSON schema
{ "title": "ManipulatorPosition", "type": "object", "properties": { "x": { "title": "X coordinate", "type": "number" }, "y1": { "title": "Y1 coordinate", "type": "number" }, "y2": { "title": "Y2 coordinate", "type": "number" }, "z": { "title": "Z coordinate", "type": "number" } }, "required": [ "x", "y1", "y2", "z" ] }
- Fields:
aind_behavior_services.calibration.load_cells module¶
- pydantic model aind_behavior_services.calibration.load_cells.LoadCellCalibrationInput[source]¶
Bases:
BaseModelShow JSON schema
{ "title": "LoadCellCalibrationInput", "type": "object", "properties": { "channel": { "description": "Load cell channel number available", "maximum": 7, "minimum": 0, "title": "Load cell channel number", "type": "integer" }, "offset_measurement": { "default": [], "items": { "$ref": "#/$defs/MeasuredOffset" }, "title": "Load cell offset calibration data", "type": "array" }, "weight_measurement": { "default": [], "items": { "$ref": "#/$defs/MeasuredWeight" }, "title": "Load cell weight calibration data", "type": "array" } }, "$defs": { "MeasuredOffset": { "properties": { "offset": { "description": "The applied offset resistor value[-255, 255]", "maximum": 255, "minimum": -255, "title": "Offset", "type": "integer" }, "baseline": { "description": "The measured baseline value", "title": "Baseline", "type": "number" } }, "required": [ "offset", "baseline" ], "title": "MeasuredOffset", "type": "object" }, "MeasuredWeight": { "properties": { "weight": { "description": "The applied weight in grams", "title": "Weight", "type": "number" }, "baseline": { "description": "The measured baseline value", "title": "Baseline", "type": "number" } }, "required": [ "weight", "baseline" ], "title": "MeasuredWeight", "type": "object" } }, "required": [ "channel" ] }
- Fields:
- field channel: LoadCellChannel [Required][source]¶
Load cell channel number available
- Constraints:
ge = 0
le = 7
- field offset_measurement: List[MeasuredOffset] = [][source]¶
- field weight_measurement: List[MeasuredWeight] = [][source]¶
- pydantic model aind_behavior_services.calibration.load_cells.LoadCellCalibrationOutput[source]¶
Bases:
BaseModelShow JSON schema
{ "title": "LoadCellCalibrationOutput", "type": "object", "properties": { "channel": { "description": "Load cell channel number available", "maximum": 7, "minimum": 0, "title": "Channel", "type": "integer" }, "offset": { "default": 0, "description": "Load cell offset value [-255, 255]", "maximum": 255, "minimum": -255, "title": "Load cell offset applied to the wheatstone bridge circuit", "type": "integer" }, "baseline": { "default": 0.0, "title": "Load cell baseline that will be DSP subtracted to the raw adc output.", "type": "number" }, "slope": { "default": 1.0, "title": "Load cell slope that will be used to convert tared (- baseline) adc units to weight (g).", "type": "number" }, "weight_lookup": { "default": [], "items": { "$ref": "#/$defs/MeasuredWeight" }, "title": "Load cell weight lookup calibration table", "type": "array" } }, "$defs": { "MeasuredWeight": { "properties": { "weight": { "description": "The applied weight in grams", "title": "Weight", "type": "number" }, "baseline": { "description": "The measured baseline value", "title": "Baseline", "type": "number" } }, "required": [ "weight", "baseline" ], "title": "MeasuredWeight", "type": "object" } }, "required": [ "channel" ] }
- Fields:
- field channel: LoadCellChannel [Required][source]¶
Load cell channel number available
- Constraints:
ge = 0
le = 7
- field offset: LoadCellOffset = 0[source]¶
Load cell offset value [-255, 255]
- Constraints:
ge = -255
le = 255
- field weight_lookup: List[MeasuredWeight] = [][source]¶
- pydantic model aind_behavior_services.calibration.load_cells.LoadCells[source]¶
Bases:
HarpLoadCellsShow JSON schema
{ "title": "LoadCells", "type": "object", "properties": { "device_type": { "const": "LoadCells", "default": "LoadCells", "title": "Device Type", "type": "string" }, "device_name": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "description": "Device name", "title": "Device Name" }, "additional_settings": { "anyOf": [ { "$ref": "#/$defs/BaseModel" }, { "type": "null" } ], "default": null, "description": "Additional settings" }, "calibration": { "anyOf": [ { "$ref": "#/$defs/LoadCellsCalibration" }, { "type": "null" } ], "default": null, "title": "Calibration of the load cells" }, "who_am_i": { "const": 1232, "default": 1232, "title": "Who Am I", "type": "integer" }, "serial_number": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "description": "Device serial number", "title": "Serial Number" }, "port_name": { "description": "Device port name", "title": "Port Name", "type": "string" } }, "$defs": { "BaseModel": { "properties": {}, "title": "BaseModel", "type": "object" }, "LoadCellCalibrationInput": { "properties": { "channel": { "description": "Load cell channel number available", "maximum": 7, "minimum": 0, "title": "Load cell channel number", "type": "integer" }, "offset_measurement": { "default": [], "items": { "$ref": "#/$defs/MeasuredOffset" }, "title": "Load cell offset calibration data", "type": "array" }, "weight_measurement": { "default": [], "items": { "$ref": "#/$defs/MeasuredWeight" }, "title": "Load cell weight calibration data", "type": "array" } }, "required": [ "channel" ], "title": "LoadCellCalibrationInput", "type": "object" }, "LoadCellCalibrationOutput": { "properties": { "channel": { "description": "Load cell channel number available", "maximum": 7, "minimum": 0, "title": "Channel", "type": "integer" }, "offset": { "default": 0, "description": "Load cell offset value [-255, 255]", "maximum": 255, "minimum": -255, "title": "Load cell offset applied to the wheatstone bridge circuit", "type": "integer" }, "baseline": { "default": 0.0, "title": "Load cell baseline that will be DSP subtracted to the raw adc output.", "type": "number" }, "slope": { "default": 1.0, "title": "Load cell slope that will be used to convert tared (- baseline) adc units to weight (g).", "type": "number" }, "weight_lookup": { "default": [], "items": { "$ref": "#/$defs/MeasuredWeight" }, "title": "Load cell weight lookup calibration table", "type": "array" } }, "required": [ "channel" ], "title": "LoadCellCalibrationOutput", "type": "object" }, "LoadCellsCalibration": { "description": "Load cells calibration class", "properties": { "device_name": { "default": "LoadCells", "description": "Must match a device name in rig/instrument", "title": "Device name", "type": "string" }, "input": { "$ref": "#/$defs/LoadCellsCalibrationInput", "title": "Input of the calibration" }, "output": { "$ref": "#/$defs/LoadCellsCalibrationOutput", "title": "Output of the calibration." }, "date": { "anyOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "default": null, "title": "Date" }, "description": { "const": "Calibration of the load cells system", "default": "Calibration of the load cells system", "title": "Description", "type": "string" }, "notes": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Notes" } }, "required": [ "input", "output" ], "title": "LoadCellsCalibration", "type": "object" }, "LoadCellsCalibrationInput": { "properties": { "channels": { "default": [], "items": { "$ref": "#/$defs/LoadCellCalibrationInput" }, "title": "Load cells calibration data", "type": "array" } }, "title": "LoadCellsCalibrationInput", "type": "object" }, "LoadCellsCalibrationOutput": { "properties": { "channels": { "default": [], "items": { "$ref": "#/$defs/LoadCellCalibrationOutput" }, "title": "Load cells calibration output", "type": "array" } }, "title": "LoadCellsCalibrationOutput", "type": "object" }, "MeasuredOffset": { "properties": { "offset": { "description": "The applied offset resistor value[-255, 255]", "maximum": 255, "minimum": -255, "title": "Offset", "type": "integer" }, "baseline": { "description": "The measured baseline value", "title": "Baseline", "type": "number" } }, "required": [ "offset", "baseline" ], "title": "MeasuredOffset", "type": "object" }, "MeasuredWeight": { "properties": { "weight": { "description": "The applied weight in grams", "title": "Weight", "type": "number" }, "baseline": { "description": "The measured baseline value", "title": "Baseline", "type": "number" } }, "required": [ "weight", "baseline" ], "title": "MeasuredWeight", "type": "object" } }, "required": [ "port_name" ] }
- Fields:
- Validators:
- field calibration: LoadCellsCalibration | None = None[source]¶
- Validated by:
_set_name
- pydantic model aind_behavior_services.calibration.load_cells.LoadCellsCalibration[source]¶
Bases:
CalibrationLoad cells calibration class
Show JSON schema
{ "title": "LoadCellsCalibration", "description": "Load cells calibration class", "type": "object", "properties": { "device_name": { "default": "LoadCells", "description": "Must match a device name in rig/instrument", "title": "Device name", "type": "string" }, "input": { "$ref": "#/$defs/LoadCellsCalibrationInput", "title": "Input of the calibration" }, "output": { "$ref": "#/$defs/LoadCellsCalibrationOutput", "title": "Output of the calibration." }, "date": { "anyOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "default": null, "title": "Date" }, "description": { "const": "Calibration of the load cells system", "default": "Calibration of the load cells system", "title": "Description", "type": "string" }, "notes": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Notes" } }, "$defs": { "LoadCellCalibrationInput": { "properties": { "channel": { "description": "Load cell channel number available", "maximum": 7, "minimum": 0, "title": "Load cell channel number", "type": "integer" }, "offset_measurement": { "default": [], "items": { "$ref": "#/$defs/MeasuredOffset" }, "title": "Load cell offset calibration data", "type": "array" }, "weight_measurement": { "default": [], "items": { "$ref": "#/$defs/MeasuredWeight" }, "title": "Load cell weight calibration data", "type": "array" } }, "required": [ "channel" ], "title": "LoadCellCalibrationInput", "type": "object" }, "LoadCellCalibrationOutput": { "properties": { "channel": { "description": "Load cell channel number available", "maximum": 7, "minimum": 0, "title": "Channel", "type": "integer" }, "offset": { "default": 0, "description": "Load cell offset value [-255, 255]", "maximum": 255, "minimum": -255, "title": "Load cell offset applied to the wheatstone bridge circuit", "type": "integer" }, "baseline": { "default": 0.0, "title": "Load cell baseline that will be DSP subtracted to the raw adc output.", "type": "number" }, "slope": { "default": 1.0, "title": "Load cell slope that will be used to convert tared (- baseline) adc units to weight (g).", "type": "number" }, "weight_lookup": { "default": [], "items": { "$ref": "#/$defs/MeasuredWeight" }, "title": "Load cell weight lookup calibration table", "type": "array" } }, "required": [ "channel" ], "title": "LoadCellCalibrationOutput", "type": "object" }, "LoadCellsCalibrationInput": { "properties": { "channels": { "default": [], "items": { "$ref": "#/$defs/LoadCellCalibrationInput" }, "title": "Load cells calibration data", "type": "array" } }, "title": "LoadCellsCalibrationInput", "type": "object" }, "LoadCellsCalibrationOutput": { "properties": { "channels": { "default": [], "items": { "$ref": "#/$defs/LoadCellCalibrationOutput" }, "title": "Load cells calibration output", "type": "array" } }, "title": "LoadCellsCalibrationOutput", "type": "object" }, "MeasuredOffset": { "properties": { "offset": { "description": "The applied offset resistor value[-255, 255]", "maximum": 255, "minimum": -255, "title": "Offset", "type": "integer" }, "baseline": { "description": "The measured baseline value", "title": "Baseline", "type": "number" } }, "required": [ "offset", "baseline" ], "title": "MeasuredOffset", "type": "object" }, "MeasuredWeight": { "properties": { "weight": { "description": "The applied weight in grams", "title": "Weight", "type": "number" }, "baseline": { "description": "The measured baseline value", "title": "Baseline", "type": "number" } }, "required": [ "weight", "baseline" ], "title": "MeasuredWeight", "type": "object" } }, "required": [ "input", "output" ] }
- Fields:
- field description: Literal['Calibration of the load cells system'] = 'Calibration of the load cells system'[source]¶
- field input: LoadCellsCalibrationInput [Required][source]¶
- field output: LoadCellsCalibrationOutput [Required][source]¶
- pydantic model aind_behavior_services.calibration.load_cells.LoadCellsCalibrationInput[source]¶
Bases:
BaseModelShow JSON schema
{ "title": "LoadCellsCalibrationInput", "type": "object", "properties": { "channels": { "default": [], "items": { "$ref": "#/$defs/LoadCellCalibrationInput" }, "title": "Load cells calibration data", "type": "array" } }, "$defs": { "LoadCellCalibrationInput": { "properties": { "channel": { "description": "Load cell channel number available", "maximum": 7, "minimum": 0, "title": "Load cell channel number", "type": "integer" }, "offset_measurement": { "default": [], "items": { "$ref": "#/$defs/MeasuredOffset" }, "title": "Load cell offset calibration data", "type": "array" }, "weight_measurement": { "default": [], "items": { "$ref": "#/$defs/MeasuredWeight" }, "title": "Load cell weight calibration data", "type": "array" } }, "required": [ "channel" ], "title": "LoadCellCalibrationInput", "type": "object" }, "MeasuredOffset": { "properties": { "offset": { "description": "The applied offset resistor value[-255, 255]", "maximum": 255, "minimum": -255, "title": "Offset", "type": "integer" }, "baseline": { "description": "The measured baseline value", "title": "Baseline", "type": "number" } }, "required": [ "offset", "baseline" ], "title": "MeasuredOffset", "type": "object" }, "MeasuredWeight": { "properties": { "weight": { "description": "The applied weight in grams", "title": "Weight", "type": "number" }, "baseline": { "description": "The measured baseline value", "title": "Baseline", "type": "number" } }, "required": [ "weight", "baseline" ], "title": "MeasuredWeight", "type": "object" } } }
- Fields:
- Validators:
- field channels: List[LoadCellCalibrationInput] = [][source]¶
- Validated by:
- classmethod calibrate_loadcell_output(value)[source]¶
- Parameters:
value (LoadCellCalibrationInput)
- Return type:
- validator ensure_unique_channels » channels[source]¶
- Parameters:
values (List[LoadCellCalibrationInput])
- Return type:
List[LoadCellCalibrationInput]
- static get_optimum_offset(value)[source]¶
- Parameters:
value (List[MeasuredOffset] | None)
- Return type:
Annotated[int, FieldInfo(annotation=NoneType, required=True, description=’Load cell offset value [-255, 255]’, metadata=[Ge(ge=-255), Le(le=255)])] | None
- pydantic model aind_behavior_services.calibration.load_cells.LoadCellsCalibrationOutput[source]¶
Bases:
BaseModelShow JSON schema
{ "title": "LoadCellsCalibrationOutput", "type": "object", "properties": { "channels": { "default": [], "items": { "$ref": "#/$defs/LoadCellCalibrationOutput" }, "title": "Load cells calibration output", "type": "array" } }, "$defs": { "LoadCellCalibrationOutput": { "properties": { "channel": { "description": "Load cell channel number available", "maximum": 7, "minimum": 0, "title": "Channel", "type": "integer" }, "offset": { "default": 0, "description": "Load cell offset value [-255, 255]", "maximum": 255, "minimum": -255, "title": "Load cell offset applied to the wheatstone bridge circuit", "type": "integer" }, "baseline": { "default": 0.0, "title": "Load cell baseline that will be DSP subtracted to the raw adc output.", "type": "number" }, "slope": { "default": 1.0, "title": "Load cell slope that will be used to convert tared (- baseline) adc units to weight (g).", "type": "number" }, "weight_lookup": { "default": [], "items": { "$ref": "#/$defs/MeasuredWeight" }, "title": "Load cell weight lookup calibration table", "type": "array" } }, "required": [ "channel" ], "title": "LoadCellCalibrationOutput", "type": "object" }, "MeasuredWeight": { "properties": { "weight": { "description": "The applied weight in grams", "title": "Weight", "type": "number" }, "baseline": { "description": "The measured baseline value", "title": "Baseline", "type": "number" } }, "required": [ "weight", "baseline" ], "title": "MeasuredWeight", "type": "object" } } }
- Fields:
- Validators:
- field channels: List[LoadCellCalibrationOutput] = [][source]¶
- Validated by:
- validator ensure_unique_channels » channels[source]¶
- Parameters:
values (List[LoadCellCalibrationOutput])
- Return type:
- pydantic model aind_behavior_services.calibration.load_cells.MeasuredOffset[source]¶
Bases:
BaseModelShow JSON schema
{ "title": "MeasuredOffset", "type": "object", "properties": { "offset": { "description": "The applied offset resistor value[-255, 255]", "maximum": 255, "minimum": -255, "title": "Offset", "type": "integer" }, "baseline": { "description": "The measured baseline value", "title": "Baseline", "type": "number" } }, "required": [ "offset", "baseline" ] }
- Fields:
- pydantic model aind_behavior_services.calibration.load_cells.MeasuredWeight[source]¶
Bases:
BaseModelShow JSON schema
{ "title": "MeasuredWeight", "type": "object", "properties": { "weight": { "description": "The applied weight in grams", "title": "Weight", "type": "number" }, "baseline": { "description": "The measured baseline value", "title": "Baseline", "type": "number" } }, "required": [ "weight", "baseline" ] }
- Fields:
aind_behavior_services.calibration.olfactometer module¶
- pydantic model aind_behavior_services.calibration.olfactometer.Olfactometer[source]¶
Bases:
HarpOlfactometerShow JSON schema
{ "title": "Olfactometer", "type": "object", "properties": { "device_type": { "const": "Olfactometer", "default": "Olfactometer", "title": "Device Type", "type": "string" }, "device_name": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "description": "Device name", "title": "Device Name" }, "additional_settings": { "anyOf": [ { "$ref": "#/$defs/BaseModel" }, { "type": "null" } ], "default": null, "description": "Additional settings" }, "calibration": { "anyOf": [ { "$ref": "#/$defs/OlfactometerCalibration" }, { "type": "null" } ], "default": null, "title": "Calibration of the olfactometer" }, "who_am_i": { "const": 1140, "default": 1140, "title": "Who Am I", "type": "integer" }, "serial_number": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "description": "Device serial number", "title": "Serial Number" }, "port_name": { "description": "Device port name", "title": "Port Name", "type": "string" } }, "$defs": { "BaseModel": { "properties": {}, "title": "BaseModel", "type": "object" }, "OlfactometerCalibration": { "description": "Olfactometer calibration class", "properties": { "device_name": { "default": "Olfactometer", "description": "Name of the device being calibrated", "title": "Device name", "type": "string" }, "input": { "$ref": "#/$defs/OlfactometerCalibrationInput", "title": "Input of the calibration" }, "output": { "$ref": "#/$defs/OlfactometerCalibrationOutput", "title": "Output of the calibration" }, "date": { "anyOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "default": null, "title": "Date" }, "description": { "const": "Calibration of the harp olfactometer device", "default": "Calibration of the harp olfactometer device", "title": "Description", "type": "string" }, "notes": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Notes" } }, "required": [ "input", "output" ], "title": "OlfactometerCalibration", "type": "object" }, "OlfactometerCalibrationInput": { "properties": { "channel_config": { "additionalProperties": { "$ref": "#/$defs/OlfactometerChannelConfig" }, "default": {}, "description": "Configuration of olfactometer channels", "propertyNames": { "$ref": "#/$defs/OlfactometerChannel" }, "title": "Channel Config", "type": "object" } }, "title": "OlfactometerCalibrationInput", "type": "object" }, "OlfactometerCalibrationOutput": { "properties": {}, "title": "OlfactometerCalibrationOutput", "type": "object" }, "OlfactometerChannel": { "description": "Harp Olfactometer available channel", "enum": [ 0, 1, 2, 3 ], "title": "OlfactometerChannel", "type": "integer" }, "OlfactometerChannelConfig": { "properties": { "channel_index": { "title": "Channel index", "type": "integer" }, "channel_type": { "$ref": "#/$defs/OlfactometerChannelType", "default": "Odor", "title": "Channel type" }, "flow_rate_capacity": { "default": 100, "enum": [ 100, 1000 ], "title": "Flow capacity. mL/min", "type": "integer" }, "flow_rate": { "default": 100, "maximum": 100, "title": "Target flow rate. mL/min. If channel_type == CARRIER, this value is ignored.", "type": "number" }, "odorant": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Odorant name" }, "odorant_dilution": { "anyOf": [ { "type": "number" }, { "type": "null" } ], "default": null, "title": "Odorant dilution (%v/v)" } }, "required": [ "channel_index" ], "title": "OlfactometerChannelConfig", "type": "object" }, "OlfactometerChannelType": { "description": "Channel type", "enum": [ "Odor", "Carrier" ], "title": "OlfactometerChannelType", "type": "string" } }, "required": [ "port_name" ] }
- Fields:
- Validators:
- field calibration: OlfactometerCalibration | None = None[source]¶
- Validated by:
_set_name
- pydantic model aind_behavior_services.calibration.olfactometer.OlfactometerCalibration[source]¶
Bases:
CalibrationOlfactometer calibration class
Show JSON schema
{ "title": "OlfactometerCalibration", "description": "Olfactometer calibration class", "type": "object", "properties": { "device_name": { "default": "Olfactometer", "description": "Name of the device being calibrated", "title": "Device name", "type": "string" }, "input": { "$ref": "#/$defs/OlfactometerCalibrationInput", "title": "Input of the calibration" }, "output": { "$ref": "#/$defs/OlfactometerCalibrationOutput", "title": "Output of the calibration" }, "date": { "anyOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "default": null, "title": "Date" }, "description": { "const": "Calibration of the harp olfactometer device", "default": "Calibration of the harp olfactometer device", "title": "Description", "type": "string" }, "notes": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Notes" } }, "$defs": { "OlfactometerCalibrationInput": { "properties": { "channel_config": { "additionalProperties": { "$ref": "#/$defs/OlfactometerChannelConfig" }, "default": {}, "description": "Configuration of olfactometer channels", "propertyNames": { "$ref": "#/$defs/OlfactometerChannel" }, "title": "Channel Config", "type": "object" } }, "title": "OlfactometerCalibrationInput", "type": "object" }, "OlfactometerCalibrationOutput": { "properties": {}, "title": "OlfactometerCalibrationOutput", "type": "object" }, "OlfactometerChannel": { "description": "Harp Olfactometer available channel", "enum": [ 0, 1, 2, 3 ], "title": "OlfactometerChannel", "type": "integer" }, "OlfactometerChannelConfig": { "properties": { "channel_index": { "title": "Channel index", "type": "integer" }, "channel_type": { "$ref": "#/$defs/OlfactometerChannelType", "default": "Odor", "title": "Channel type" }, "flow_rate_capacity": { "default": 100, "enum": [ 100, 1000 ], "title": "Flow capacity. mL/min", "type": "integer" }, "flow_rate": { "default": 100, "maximum": 100, "title": "Target flow rate. mL/min. If channel_type == CARRIER, this value is ignored.", "type": "number" }, "odorant": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Odorant name" }, "odorant_dilution": { "anyOf": [ { "type": "number" }, { "type": "null" } ], "default": null, "title": "Odorant dilution (%v/v)" } }, "required": [ "channel_index" ], "title": "OlfactometerChannelConfig", "type": "object" }, "OlfactometerChannelType": { "description": "Channel type", "enum": [ "Odor", "Carrier" ], "title": "OlfactometerChannelType", "type": "string" } }, "required": [ "input", "output" ] }
- Fields:
- field description: Literal['Calibration of the harp olfactometer device'] = 'Calibration of the harp olfactometer device'[source]¶
- field input: OlfactometerCalibrationInput [Required][source]¶
- field output: OlfactometerCalibrationOutput [Required][source]¶
- pydantic model aind_behavior_services.calibration.olfactometer.OlfactometerCalibrationInput[source]¶
Bases:
BaseModelShow JSON schema
{ "title": "OlfactometerCalibrationInput", "type": "object", "properties": { "channel_config": { "additionalProperties": { "$ref": "#/$defs/OlfactometerChannelConfig" }, "default": {}, "description": "Configuration of olfactometer channels", "propertyNames": { "$ref": "#/$defs/OlfactometerChannel" }, "title": "Channel Config", "type": "object" } }, "$defs": { "OlfactometerChannel": { "description": "Harp Olfactometer available channel", "enum": [ 0, 1, 2, 3 ], "title": "OlfactometerChannel", "type": "integer" }, "OlfactometerChannelConfig": { "properties": { "channel_index": { "title": "Channel index", "type": "integer" }, "channel_type": { "$ref": "#/$defs/OlfactometerChannelType", "default": "Odor", "title": "Channel type" }, "flow_rate_capacity": { "default": 100, "enum": [ 100, 1000 ], "title": "Flow capacity. mL/min", "type": "integer" }, "flow_rate": { "default": 100, "maximum": 100, "title": "Target flow rate. mL/min. If channel_type == CARRIER, this value is ignored.", "type": "number" }, "odorant": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Odorant name" }, "odorant_dilution": { "anyOf": [ { "type": "number" }, { "type": "null" } ], "default": null, "title": "Odorant dilution (%v/v)" } }, "required": [ "channel_index" ], "title": "OlfactometerChannelConfig", "type": "object" }, "OlfactometerChannelType": { "description": "Channel type", "enum": [ "Odor", "Carrier" ], "title": "OlfactometerChannelType", "type": "string" } } }
- field channel_config: Dict[OlfactometerChannel, OlfactometerChannelConfig] = {}[source]¶
Configuration of olfactometer channels
- pydantic model aind_behavior_services.calibration.olfactometer.OlfactometerCalibrationOutput[source]¶
Bases:
BaseModelShow JSON schema
{ "title": "OlfactometerCalibrationOutput", "type": "object", "properties": {} }
- class aind_behavior_services.calibration.olfactometer.OlfactometerChannel(value)[source]¶
Bases:
IntEnumHarp Olfactometer available channel
- pydantic model aind_behavior_services.calibration.olfactometer.OlfactometerChannelConfig[source]¶
Bases:
BaseModelShow JSON schema
{ "title": "OlfactometerChannelConfig", "type": "object", "properties": { "channel_index": { "title": "Channel index", "type": "integer" }, "channel_type": { "$ref": "#/$defs/OlfactometerChannelType", "default": "Odor", "title": "Channel type" }, "flow_rate_capacity": { "default": 100, "enum": [ 100, 1000 ], "title": "Flow capacity. mL/min", "type": "integer" }, "flow_rate": { "default": 100, "maximum": 100, "title": "Target flow rate. mL/min. If channel_type == CARRIER, this value is ignored.", "type": "number" }, "odorant": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Odorant name" }, "odorant_dilution": { "anyOf": [ { "type": "number" }, { "type": "null" } ], "default": null, "title": "Odorant dilution (%v/v)" } }, "$defs": { "OlfactometerChannelType": { "description": "Channel type", "enum": [ "Odor", "Carrier" ], "title": "OlfactometerChannelType", "type": "string" } }, "required": [ "channel_index" ] }
- Fields:
- field channel_type: OlfactometerChannelType = OlfactometerChannelType.ODOR[source]¶
aind_behavior_services.calibration.treadmill module¶
- pydantic model aind_behavior_services.calibration.treadmill.Treadmill[source]¶
Bases:
HarpTreadmillShow JSON schema
{ "title": "Treadmill", "type": "object", "properties": { "device_type": { "const": "Treadmill", "default": "Treadmill", "title": "Device Type", "type": "string" }, "device_name": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "description": "Device name", "title": "Device Name" }, "additional_settings": { "anyOf": [ { "$ref": "#/$defs/BaseModel" }, { "type": "null" } ], "default": null, "description": "Additional settings" }, "calibration": { "anyOf": [ { "$ref": "#/$defs/TreadmillCalibration" }, { "type": "null" } ], "default": null, "title": "Calibration of the treadmill" }, "who_am_i": { "const": 1402, "default": 1402, "title": "Who Am I", "type": "integer" }, "serial_number": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "description": "Device serial number", "title": "Serial Number" }, "port_name": { "description": "Device port name", "title": "Port Name", "type": "string" } }, "$defs": { "BaseModel": { "properties": {}, "title": "BaseModel", "type": "object" }, "TreadmillCalibration": { "description": "Treadmill calibration class", "properties": { "device_name": { "default": "Treadmill", "description": "Must match a device name in rig/instrument", "title": "Device name", "type": "string" }, "input": { "$ref": "#/$defs/TreadmillCalibrationInput", "title": "Input of the calibration" }, "output": { "$ref": "#/$defs/TreadmillCalibrationOutput", "title": "Output of the calibration." }, "date": { "anyOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "default": null, "title": "Date" }, "description": { "const": "Calibration of the treadmill system", "default": "Calibration of the treadmill system", "title": "Description", "type": "string" }, "notes": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Notes" } }, "required": [ "input", "output" ], "title": "TreadmillCalibration", "type": "object" }, "TreadmillCalibrationInput": { "properties": {}, "title": "TreadmillCalibrationInput", "type": "object" }, "TreadmillCalibrationOutput": { "properties": { "wheel_diameter": { "default": 15, "description": "Wheel diameter", "minimum": 0, "title": "Wheel Diameter", "type": "number" }, "pulses_per_revolution": { "default": 28800, "description": "Pulses per revolution", "minimum": 1, "title": "Pulses Per Revolution", "type": "integer" }, "invert_direction": { "default": false, "description": "Invert direction", "title": "Invert Direction", "type": "boolean" }, "brake_lookup_calibration": { "description": "Brake lookup calibration. Each pair of values define (input [torque], output [brake set-point U16])", "items": { "items": { "type": "number" }, "maxItems": 2, "minItems": 2, "type": "array" }, "minItems": 2, "title": "Brake Lookup Calibration", "type": "array" } }, "required": [ "brake_lookup_calibration" ], "title": "TreadmillCalibrationOutput", "type": "object" } }, "required": [ "port_name" ] }
- Fields:
- Validators:
- field calibration: TreadmillCalibration | None = None[source]¶
- Validated by:
_set_name
- pydantic model aind_behavior_services.calibration.treadmill.TreadmillCalibration[source]¶
Bases:
CalibrationTreadmill calibration class
Show JSON schema
{ "title": "TreadmillCalibration", "description": "Treadmill calibration class", "type": "object", "properties": { "device_name": { "default": "Treadmill", "description": "Must match a device name in rig/instrument", "title": "Device name", "type": "string" }, "input": { "$ref": "#/$defs/TreadmillCalibrationInput", "title": "Input of the calibration" }, "output": { "$ref": "#/$defs/TreadmillCalibrationOutput", "title": "Output of the calibration." }, "date": { "anyOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "default": null, "title": "Date" }, "description": { "const": "Calibration of the treadmill system", "default": "Calibration of the treadmill system", "title": "Description", "type": "string" }, "notes": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Notes" } }, "$defs": { "TreadmillCalibrationInput": { "properties": {}, "title": "TreadmillCalibrationInput", "type": "object" }, "TreadmillCalibrationOutput": { "properties": { "wheel_diameter": { "default": 15, "description": "Wheel diameter", "minimum": 0, "title": "Wheel Diameter", "type": "number" }, "pulses_per_revolution": { "default": 28800, "description": "Pulses per revolution", "minimum": 1, "title": "Pulses Per Revolution", "type": "integer" }, "invert_direction": { "default": false, "description": "Invert direction", "title": "Invert Direction", "type": "boolean" }, "brake_lookup_calibration": { "description": "Brake lookup calibration. Each pair of values define (input [torque], output [brake set-point U16])", "items": { "items": { "type": "number" }, "maxItems": 2, "minItems": 2, "type": "array" }, "minItems": 2, "title": "Brake Lookup Calibration", "type": "array" } }, "required": [ "brake_lookup_calibration" ], "title": "TreadmillCalibrationOutput", "type": "object" } }, "required": [ "input", "output" ] }
- Fields:
- field description: Literal['Calibration of the treadmill system'] = 'Calibration of the treadmill system'[source]¶
- field input: TreadmillCalibrationInput [Required][source]¶
- field output: TreadmillCalibrationOutput [Required][source]¶
- pydantic model aind_behavior_services.calibration.treadmill.TreadmillCalibrationInput[source]¶
Bases:
BaseModelShow JSON schema
{ "title": "TreadmillCalibrationInput", "type": "object", "properties": {} }
- pydantic model aind_behavior_services.calibration.treadmill.TreadmillCalibrationOutput[source]¶
Bases:
BaseModelShow JSON schema
{ "title": "TreadmillCalibrationOutput", "type": "object", "properties": { "wheel_diameter": { "default": 15, "description": "Wheel diameter", "minimum": 0, "title": "Wheel Diameter", "type": "number" }, "pulses_per_revolution": { "default": 28800, "description": "Pulses per revolution", "minimum": 1, "title": "Pulses Per Revolution", "type": "integer" }, "invert_direction": { "default": false, "description": "Invert direction", "title": "Invert Direction", "type": "boolean" }, "brake_lookup_calibration": { "description": "Brake lookup calibration. Each pair of values define (input [torque], output [brake set-point U16])", "items": { "items": { "type": "number" }, "maxItems": 2, "minItems": 2, "type": "array" }, "minItems": 2, "title": "Brake Lookup Calibration", "type": "array" } }, "required": [ "brake_lookup_calibration" ] }
- Fields:
- Validators:
- field brake_lookup_calibration: List[Annotated[List[float], FieldInfo(annotation=NoneType, required=True, metadata=[MinLen(min_length=2), MaxLen(max_length=2)])]] [Required][source]¶
Brake lookup calibration. Each pair of values define (input [torque], output [brake set-point U16])
- Constraints:
min_length = 2
- Validated by:
- validator validate_brake_lookup_calibration » brake_lookup_calibration[source]¶
- Parameters:
value (List[Annotated[List[float], FieldInfo(annotation=NoneType, required=True, metadata=[MinLen(min_length=2), MaxLen(max_length=2)])]])
- Return type:
List[Annotated[List[float], FieldInfo(annotation=NoneType, required=True, metadata=[MinLen(min_length=2), MaxLen(max_length=2)])]]
aind_behavior_services.calibration.water_valve module¶
- pydantic model aind_behavior_services.calibration.water_valve.Measurement[source]¶
Bases:
BaseModelInput for water valve calibration class
Show JSON schema
{ "title": "Measurement", "description": "Input for water valve calibration class", "type": "object", "properties": { "valve_open_interval": { "description": "Time between two consecutive valve openings (s)", "exclusiveMinimum": 0, "title": "Valve open interval", "type": "number" }, "valve_open_time": { "description": "Valve open interval (s)", "exclusiveMinimum": 0, "title": "Valve open time", "type": "number" }, "water_weight": { "description": "Weight of water delivered (g)", "items": { "exclusiveMinimum": 0, "type": "number" }, "minItems": 1, "title": "Water weight", "type": "array" }, "repeat_count": { "description": "Number of times the valve opened.", "minimum": 0, "title": "Repeat count", "type": "integer" } }, "required": [ "valve_open_interval", "valve_open_time", "water_weight", "repeat_count" ] }
- Fields:
- pydantic model aind_behavior_services.calibration.water_valve.WaterValveCalibration[source]¶
Bases:
CalibrationWater valve calibration class
Show JSON schema
{ "title": "WaterValveCalibration", "description": "Water valve calibration class", "type": "object", "properties": { "device_name": { "default": "WaterValve", "description": "Name of the device being calibrated", "title": "Device name", "type": "string" }, "input": { "$ref": "#/$defs/WaterValveCalibrationInput", "title": "Input of the calibration" }, "output": { "$ref": "#/$defs/WaterValveCalibrationOutput", "title": "Output of the calibration." }, "date": { "anyOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "default": null, "title": "Date" }, "description": { "const": "Calibration of the water valve delivery system", "default": "Calibration of the water valve delivery system", "title": "Description", "type": "string" }, "notes": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Notes" } }, "$defs": { "Measurement": { "description": "Input for water valve calibration class", "properties": { "valve_open_interval": { "description": "Time between two consecutive valve openings (s)", "exclusiveMinimum": 0, "title": "Valve open interval", "type": "number" }, "valve_open_time": { "description": "Valve open interval (s)", "exclusiveMinimum": 0, "title": "Valve open time", "type": "number" }, "water_weight": { "description": "Weight of water delivered (g)", "items": { "exclusiveMinimum": 0, "type": "number" }, "minItems": 1, "title": "Water weight", "type": "array" }, "repeat_count": { "description": "Number of times the valve opened.", "minimum": 0, "title": "Repeat count", "type": "integer" } }, "required": [ "valve_open_interval", "valve_open_time", "water_weight", "repeat_count" ], "title": "Measurement", "type": "object" }, "WaterValveCalibrationInput": { "properties": { "measurements": { "default": [], "description": "List of measurements", "items": { "$ref": "#/$defs/Measurement" }, "title": "Measurements", "type": "array" } }, "title": "WaterValveCalibrationInput", "type": "object" }, "WaterValveCalibrationOutput": { "description": "Output for water valve calibration class", "properties": { "interval_average": { "anyOf": [ { "additionalProperties": { "exclusiveMinimum": 0, "type": "number" }, "type": "object" }, { "type": "null" } ], "default": null, "description": "Dictionary keyed by measured valve interval and corresponding average single event volume.", "title": "Interval average" }, "slope": { "description": "Slope of the linear regression : Volume(g) = Slope(g/s) * time(s) + offset(g)", "title": "Regression slope", "type": "number" }, "offset": { "description": "Offset of the linear regression : Volume(g) = Slope(g/s) * time(s) + offset(g)", "title": "Regression offset", "type": "number" }, "r2": { "anyOf": [ { "maximum": 1, "minimum": 0, "type": "number" }, { "type": "null" } ], "default": null, "description": "R2 metric from the linear model.", "title": "R2" }, "valid_domain": { "anyOf": [ { "items": { "exclusiveMinimum": 0, "type": "number" }, "minItems": 2, "type": "array" }, { "type": "null" } ], "default": null, "description": "The optional time-intervals the calibration curve was calculated on.", "title": "Valid domain" } }, "required": [ "slope", "offset" ], "title": "WaterValveCalibrationOutput", "type": "object" } }, "required": [ "input", "output" ] }
- Fields:
- field description: Literal['Calibration of the water valve delivery system'] = 'Calibration of the water valve delivery system'[source]¶
- field input: WaterValveCalibrationInput [Required][source]¶
- field output: WaterValveCalibrationOutput [Required][source]¶
- pydantic model aind_behavior_services.calibration.water_valve.WaterValveCalibrationInput[source]¶
Bases:
BaseModelShow JSON schema
{ "title": "WaterValveCalibrationInput", "type": "object", "properties": { "measurements": { "default": [], "description": "List of measurements", "items": { "$ref": "#/$defs/Measurement" }, "title": "Measurements", "type": "array" } }, "$defs": { "Measurement": { "description": "Input for water valve calibration class", "properties": { "valve_open_interval": { "description": "Time between two consecutive valve openings (s)", "exclusiveMinimum": 0, "title": "Valve open interval", "type": "number" }, "valve_open_time": { "description": "Valve open interval (s)", "exclusiveMinimum": 0, "title": "Valve open time", "type": "number" }, "water_weight": { "description": "Weight of water delivered (g)", "items": { "exclusiveMinimum": 0, "type": "number" }, "minItems": 1, "title": "Water weight", "type": "array" }, "repeat_count": { "description": "Number of times the valve opened.", "minimum": 0, "title": "Repeat count", "type": "integer" } }, "required": [ "valve_open_interval", "valve_open_time", "water_weight", "repeat_count" ], "title": "Measurement", "type": "object" } } }
- field measurements: List[Measurement] = [][source]¶
List of measurements
- calibrate_output(input=None)[source]¶
Calibrate the water valve delivery system by populating the output field
- Parameters:
input (WaterValveCalibrationInput | None)
- Return type:
- pydantic model aind_behavior_services.calibration.water_valve.WaterValveCalibrationOutput[source]¶
Bases:
BaseModelOutput for water valve calibration class
Show JSON schema
{ "title": "WaterValveCalibrationOutput", "description": "Output for water valve calibration class", "type": "object", "properties": { "interval_average": { "anyOf": [ { "additionalProperties": { "exclusiveMinimum": 0, "type": "number" }, "type": "object" }, { "type": "null" } ], "default": null, "description": "Dictionary keyed by measured valve interval and corresponding average single event volume.", "title": "Interval average" }, "slope": { "description": "Slope of the linear regression : Volume(g) = Slope(g/s) * time(s) + offset(g)", "title": "Regression slope", "type": "number" }, "offset": { "description": "Offset of the linear regression : Volume(g) = Slope(g/s) * time(s) + offset(g)", "title": "Regression offset", "type": "number" }, "r2": { "anyOf": [ { "maximum": 1, "minimum": 0, "type": "number" }, { "type": "null" } ], "default": null, "description": "R2 metric from the linear model.", "title": "R2" }, "valid_domain": { "anyOf": [ { "items": { "exclusiveMinimum": 0, "type": "number" }, "minItems": 2, "type": "array" }, { "type": "null" } ], "default": null, "description": "The optional time-intervals the calibration curve was calculated on.", "title": "Valid domain" } }, "required": [ "slope", "offset" ] }
- Fields:
- field interval_average: Dict[PositiveFloat, PositiveFloat] | None = None[source]¶
Dictionary keyed by measured valve interval and corresponding average single event volume.
- field offset: float [Required][source]¶
Offset of the linear regression : Volume(g) = Slope(g/s) * time(s) + offset(g)
Module contents¶
- pydantic model aind_behavior_services.calibration.Calibration[source]¶
Bases:
BaseModelBase class for all Calibration models. Stores calibration (meta)data.
Show JSON schema
{ "title": "Calibration", "description": "Base class for all Calibration models. Stores calibration (meta)data.", "type": "object", "properties": { "device_name": { "description": "Name of the device being calibrated", "title": "Device name", "type": "string" }, "input": { "anyOf": [ { "$ref": "#/$defs/BaseModel" }, { "type": "null" } ], "default": null, "title": "Input data" }, "output": { "anyOf": [ { "$ref": "#/$defs/BaseModel" }, { "type": "null" } ], "default": null, "title": "Output data" }, "date": { "anyOf": [ { "format": "date-time", "type": "string" }, { "type": "null" } ], "default": null, "title": "Date" }, "description": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Brief description of what is being calibrated" }, "notes": { "anyOf": [ { "type": "string" }, { "type": "null" } ], "default": null, "title": "Notes" } }, "$defs": { "BaseModel": { "properties": {}, "title": "BaseModel", "type": "object" } }, "required": [ "device_name" ] }
- Fields:
date (datetime.datetime | None)description (str | None)device_name (str)input (pydantic.main.BaseModel | None)notes (str | None)output (pydantic.main.BaseModel | None)