deploy: e68cf5e

.buildinfo

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+# Sphinx build info version 1
+# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
+config: ffbcb2f1419685c2cae3d11f3e36c580
+tags: 645f666f9bcd5a90fca523b33c5a78b7

_sources/api.base.rst.txt

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+Base
+-------------
+
+.. toctree::
+   :maxdepth: 2
+
+   api.base/session
+   api.base/rig
+   api.base/task_logic

_sources/api.base/rig.rst.txt

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+AindBehaviorRigModel
+-------------------------
+
+.. autopydantic_model:: aind_behavior_services.AindBehaviorRigModel
+   :members:
+   :undoc-members:
+   :show-inheritance:

_sources/api.base/session.rst.txt

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+AindBehaviorSessionModel
+--------------------------
+
+.. image:: ../_static/AindBehaviorSessionModel.svg
+   :target: ../_static/AindBehaviorSessionModel.svg
+
+.. autopydantic_model:: aind_behavior_services.session.AindBehaviorSessionModel
+   :members:
+   :undoc-members:
+   :show-inheritance:

_sources/api.base/task_logic.rst.txt

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+AindBehaviorTaskLogicModel
+--------------------------------
+
+.. autopydantic_model:: aind_behavior_services.AindBehaviorTaskLogicModel
+   :members:
+   :undoc-members:
+   :show-inheritance:

_sources/api.calibration.rst.txt

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+Calibration
+-------------
+
+Calibration Module
+####################
+
+The calibration module of this library is used to generate the metadata necessary configure and run calibration workflows for different assets/devices.
+
+The metadata follows the general logic of the library by implementing the three core classes:
+   - :py:class:`~aind_behavior_services.session.AindBehaviorSessionModel`
+   - :py:class:`~aind_behavior_services.rig.AindBehaviorRigModel`
+   - :py:class:`~aind_behavior_services.task_logic.AindBehaviorTaskLogicModel`
+
+A fourth class :py:class:`~aind_behavior_services.calibration.Calibration`, 
+specific to the Calibration module, is also implemented to keep track of the calibration metrics.
+This class was written to be aligned to the Calibration class in `aind-data-schemas
+<https://github.com/AllenNeuralDynamics/aind-data-schema/blob/2fd0e403bf46f0f1a47e5922c4228517e68376a3/src/aind_data_schema/components/devices.py#L274>`_.
+An application example will be provided below.
+
+While we use the base :py:class:`~aind_behavior_services.session.AindBehaviorSessionModel` class to keep track of the session metadata,
+both :py:class:`~aind_behavior_services.rig.AindBehaviorRigModel` and :py:class:`~aind_behavior_services.task_logic.AindBehaviorTaskLogicModel` are
+expected to be sub-classed to specify the necessary dependencies of the calibration workflow.
+
+Sub-classing :py:class:`~aind_behavior_services.calibration.Calibration`
+##########################################################################
+
+Sub-classing :py:class:`~aind_behavior_services.calibration.Calibration` boils down to providing a subtype of the `input` and `output` fields.
+These fields are expected to be of a sub-type of `~pydantic.BaseModel` and define the structure of the calibration outcome.
+Conceptually, `input` is the pre-process data that resulted from the calibration workflow (i.e. the weight of delivered water),
+whereas `output` is used to represent a post-processed version of the calibration outcome (e.g. a linear model that relates valve-opening times to water volume).
+
+An example of a sub-class of `Calibration` is provided below:
+
+.. code-block:: python
+
+   from pydantic import BaseModel, Field
+   from typing import List, Literal
+   from aind_behavior_services.calibration import Calibration
+
+
+   class BarContainer(BaseModel):
+      baz: string = Field(..., description="Baz value")
+      bar: float = Field(..., description="Bar value")
+
+
+   class DeviceCalibrationInput(BaseModel):
+      measured_foo: List[int] = Field(..., description="Measurements of Foo")
+      bar_container: List[BarContainer] = Field(..., description="Bar container")
+
+
+   class DeviceCalibrationOutput(BaseModel):
+      param_a = float = Field(default=1, description="Parameter A")
+      param_b = float = Field(default=0, description="Parameter B")
+
+
+   class DeviceCalibration(Calibration):
+      device_name: Literal["MyDevice"] = "MyDevice"
+      description: Literal["Stores the calibration of a device"] = "Stores the calibration of a device"
+      input: DeviceCalibrationInput = Field(..., title="Input of the calibration")
+      output: DeviceCalibrationOutput = Field(..., title="Output of the calibration")
+
+Sub-classing :py:class:`~aind_behavior_services.rig.AindBehaviorRigModel`
+##########################################################################
+
+We adopt the following pattern to sub-class the :py:class:`~aind_behavior_services.rig.AindBehaviorRigModel` class:
+
+.. code-block:: python
+
+   from aind_behavior_services.rig import AindBehaviorRigModel, Device
+
+   RIG_VERSION = "1.0.0" # Use SemVer
+
+   class FooDevice(Device):
+      calibration: DeviceCalibration = Field(..., title="Calibration of the device foo")
+
+
+   class CalibrationRig(AindBehaviorRigModel):
+      version: Literal[RIG_VERSION] = RIG_VERSION
+      device_foo: FooDevice = Field(..., title="Device Foo")
+      device_bar: Device = Field(..., title="Device Bar")
+
+
+For an example see :py:class:`aind_behavior_services.calibration.olfactometer.CalibrationRig`.
+
+
+
+Sub-classing :py:class:`~aind_behavior_services.task_logic.AindBehaviorTaskLogicModel`
+################################################################################
+
+The same way a :py:class:`~aind_behavior_services.task_logic.AindBehaviorTaskLogicModel` is used to define
+the settings to run a behavior task, it is also used to define the settings to run a calibration workflow.
+It will thus fallow an identical sub-classing pattern:
+
+
+.. code-block:: python
+
+   from aind_behavior_services.task_logic import AindBehaviorTaskLogicModel, TaskParameters
+
+   TASK_LOGIC_VERSION = "0.1.0"
+
+   class CalibrationParameters(TaskParameters):
+      n_iterations: int = Field(default=10, description="Number of iterations to run the calibration")
+      channels_to_calibrate: List[Literal[1,2,3]] = Field(default=[1], description="List of channels to calibrate")
+
+   class CalibrationLogic(AindBehaviorTaskLogicModel):
+      name: Literal["CalibrationLogic"] = "CalibrationLogic
+      version: Literal[TASK_LOGIC_VERSION] = TASK_LOGIC_VERSION
+      task_parameters: CalibrationParameters = Field(default=CalibrationParameters(), title="Task parameters", validate_default=True)
+
+
+For an example see :py:class:`aind_behavior_services.calibration.olfactometer.CalibrationLogic`.
+
+
+
+.. toctree::
+   :maxdepth: 4
+
+   api.calibration/aind_manipulator
+   api.calibration/load_cells
+   api.calibration/olfactometer
+   api.calibration/water_valve
+
+

_sources/api.calibration/aind_manipulator.rst.txt

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+aind_manipulator
+-----------------
+
+.. automodule:: aind_behavior_services.calibration.aind_manipulator
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Example
+##########
+
+.. literalinclude:: ../../examples/aind_manipulator.py
+      :language: python

_sources/api.calibration/load_cells.rst.txt

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+load_cells
+-------------
+
+.. automodule:: aind_behavior_services.calibration.load_cells
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Example
+########
+
+.. literalinclude:: ../../examples/load_cells.py
+      :language: python

_sources/api.calibration/olfactometer.rst.txt

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+olfactometer
+-------------
+
+.. automodule:: aind_behavior_services.calibration.olfactometer
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Example
+########
+
+.. literalinclude:: ../../examples/olfactometer.py
+      :language: python

_sources/api.calibration/water_valve.rst.txt

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+water_valve
+-------------
+
+.. automodule:: aind_behavior_services.calibration.water_valve
+   :members:
+   :undoc-members:
+   :show-inheritance:
+
+Example
+########
+
+.. literalinclude:: ../../examples/water_valve.py
+      :language: python

_sources/api.rst.txt

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+API
+-------------
+
+.. toctree::
+   :maxdepth: 2
+
+   api.base
+   api.calibration
+

_sources/index.rst.txt

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+.. Aind.Behavior.Services documentation master file, created by
+   sphinx-quickstart on Thu Apr 25 11:48:33 2024.
+   You can adapt this file completely to your liking, but it should at least
+   contain the root `toctree` directive.
+
+Welcome to AIND Behavior Services's documentation!
+==================================================
+
+.. include:: ../README.md
+   :parser: myst_parser.sphinx_
+
+.. toctree::
+   :maxdepth: 4
+   :caption: Contents:
+
+   self
+   api
+   json-schemas
+   GitHub Source Code <https://github.com/AllenNeuralDynamics/Aind.Behavior.Services>
+
+Indices and tables
+==================
+
+* :ref:`genindex`
+* :ref:`search`

_sources/json-schemas.rst.txt

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+
+JsonSchema
+-------------
+.. toctree::
+   :maxdepth: 4
+
+   json-schemas/aind_manipulator_calibration_rig
+   json-schemas/olfactometer_calibration_rig
+   json-schemas/load_cells_calibration_rig
+   json-schemas/water_valve_calibration_logic
+   json-schemas/water_valve_calibration_rig
+   json-schemas/aind_behavior_subject_database
+   json-schemas/aind_manipulator_calibration_logic
+   json-schemas/aind_behavior_session
+   json-schemas/olfactometer_calibration_logic
+   json-schemas/load_cells_calibration_logic

_sources/json-schemas/aind_behavior_session.rst.txt

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+
+aind_behavior_session
+----------------------------------------------------
+
+`Download Schema <https://raw.githubusercontent.com/AllenNeuralDynamics/Aind.Behavior.Services/main/src/DataSchemas/schemas/aind_behavior_session.json>`_
+
+.. jsonschema:: https://raw.githubusercontent.com/AllenNeuralDynamics/Aind.Behavior.Services/main/src/DataSchemas/schemas/aind_behavior_session.json
+   :lift_definitions:
+   :auto_reference:
+

_sources/json-schemas/aind_behavior_subject_database.rst.txt

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+
+aind_behavior_subject_database
+----------------------------------------------------
+
+`Download Schema <https://raw.githubusercontent.com/AllenNeuralDynamics/Aind.Behavior.Services/main/src/DataSchemas/schemas/aind_behavior_subject_database.json>`_
+
+.. jsonschema:: https://raw.githubusercontent.com/AllenNeuralDynamics/Aind.Behavior.Services/main/src/DataSchemas/schemas/aind_behavior_subject_database.json
+   :lift_definitions:
+   :auto_reference:
+

_sources/json-schemas/aind_manipulator_calibration_logic.rst.txt

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+
+aind_manipulator_calibration_logic
+----------------------------------------------------
+
+`Download Schema <https://raw.githubusercontent.com/AllenNeuralDynamics/Aind.Behavior.Services/main/src/DataSchemas/schemas/aind_manipulator_calibration_logic.json>`_
+
+.. jsonschema:: https://raw.githubusercontent.com/AllenNeuralDynamics/Aind.Behavior.Services/main/src/DataSchemas/schemas/aind_manipulator_calibration_logic.json
+   :lift_definitions:
+   :auto_reference:
+