Merge pull request #25 from AllenNeuralDynamics/rel-0.7.0

Release 0.7.0

README.md

@@ -24,7 +24,8 @@ These should only need to be installed once on a fresh new system, and are not r
 - [FTDI CDM Driver 2.12.28](https://www.ftdichip.com/Drivers/CDM/CDM21228_Setup.zip) (serial port drivers for HARP devices)
 - [Spinnaker SDK 1.29.0.5](https://www.flir.co.uk/support/products/spinnaker-sdk/#Downloads) (device drivers for FLIR cameras)
   - On FLIR website: `Download > archive > 1.29.0.5 > SpinnakerSDK_FULL_1.29.0.5_x64.exe`
-
+- [ffmpeg 7.0](https://www.gyan.dev/ffmpeg/builds/) (necessary to run GPU-accelerated video encoding)
+  - run `winget install ffmpeg -v 7.0` to install.
 ---
 
 ## Generating valid JSON input files

docs/conf.py

@@ -17,9 +17,9 @@
 SOURCE_ROOT = "https://github.com/AllenNeuralDynamics/Aind.Behavior.Services/tree/main/src/DataSchemas/"
 
 
-project = 'AIND Behavior Services'
+project = "AIND Behavior Services"
 copyright = "2024, Allen Institute for Neural Dynamics"
-author = 'Bruno Cruz'
+author = "Bruno Cruz"
 release = __version__
 
 
@@ -53,13 +53,12 @@
     json_file_name = os.path.basename(json_file)
     root_template += f"   json-schemas/{json_file_name.replace('.json', '')}\n"
     with open(os.path.join(rst_target_path, f"{json_file_name.replace('.json', '')}.rst"), "w") as f:
-        f.write(leaf_template.format(json_file_name=json_file_name.replace('.json', '')))
+        f.write(leaf_template.format(json_file_name=json_file_name.replace(".json", "")))
 
 with open("json-schemas.rst", "w") as f:
     f.write(root_template)
 
 
-
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
 
@@ -75,8 +74,8 @@
     "myst_parser",
     "sphinxcontrib.autodoc_pydantic",
 ]
-templates_path = ['_templates']
-exclude_patterns = ['_build', 'Thumbs.db', '.DS_Store']
+templates_path = ["_templates"]
+exclude_patterns = ["_build", "Thumbs.db", ".DS_Store"]
 
 autosummary_generate = True
 
@@ -103,13 +102,11 @@
 
 # -- Options for linkcode extension ---------------------------------------
 
+
 def linkcode_resolve(domain, info):
     if domain != "py":
         return None
     if not info["module"]:
         return None
     filename = info["module"].replace(".", "/")
     return f"{SOURCE_ROOT}/{filename}.py"
-
-
-

examples/aind_manipulator.py

@@ -21,7 +21,7 @@
     calibration_date=datetime.datetime.now(),
 )
 
-calibration_logic = m.CalibrationLogic()
+calibration_logic = m.CalibrationLogic(task_parameters=m.CalibrationParameters())
 
 
 calibration_session = AindBehaviorSessionModel(

examples/load_cells.py

@@ -21,7 +21,9 @@
     calibration_date=datetime.datetime.now(),
 )
 
-calibration_logic = lc.CalibrationLogic(channels=[0, 1], offset_buffer_size=10)
+calibration_logic = lc.CalibrationLogic(
+    task_parameters=lc.CalibrationParameters(channels=[0, 1], offset_buffer_size=10)
+)
 
 calibration_session = AindBehaviorSessionModel(
     root_path="C:\\Data",

examples/olfactometer.py

@@ -4,45 +4,45 @@
 from aind_behavior_services.calibration import olfactometer as olf
 from aind_behavior_services.session import AindBehaviorSessionModel
 
-channels_config = [
-    olf.OlfactometerChannelConfig(
+channels_config = {
+    olf.OlfactometerChannel.Channel0: olf.OlfactometerChannelConfig(
         channel_index=olf.OlfactometerChannel.Channel0,
         channel_type=olf.OlfactometerChannelType.ODOR,
         flow_rate=100,
         odorant="Banana",
         odorant_dilution=0.1,
     ),
-    olf.OlfactometerChannelConfig(
+    olf.OlfactometerChannel.Channel1: olf.OlfactometerChannelConfig(
         channel_index=olf.OlfactometerChannel.Channel1,
         channel_type=olf.OlfactometerChannelType.ODOR,
         flow_rate=100,
         odorant="Strawberry",
         odorant_dilution=0.1,
     ),
-    olf.OlfactometerChannelConfig(
+    olf.OlfactometerChannel.Channel2: olf.OlfactometerChannelConfig(
         channel_index=olf.OlfactometerChannel.Channel2,
         channel_type=olf.OlfactometerChannelType.ODOR,
         flow_rate=100,
         odorant="Apple",
         odorant_dilution=0.1,
     ),
-    olf.OlfactometerChannelConfig(
+    olf.OlfactometerChannel.Channel3: olf.OlfactometerChannelConfig(
         channel_index=olf.OlfactometerChannel.Channel3, channel_type=olf.OlfactometerChannelType.CARRIER, odorant="Air"
-    ),
-]
-
-channels_config = {channel.channel_index: channel for channel in channels_config}
+    )
+}
 
 calibration = olf.OlfactometerCalibration(
     input=olf.OlfactometerCalibrationInput(), output=olf.OlfactometerCalibrationOutput()
 )
 
 calibration_logic = olf.CalibrationLogic(
-    channel_config=channels_config,
-    full_flow_rate=1000,
-    n_repeats_per_stimulus=10,
-    time_on=1,
-    time_off=1,
+    task_parameters=olf.CalibrationParameters(
+        channel_config=channels_config,
+        full_flow_rate=1000,
+        n_repeats_per_stimulus=10,
+        time_on=1,
+        time_off=1,
+    )
 )
 
 calibration_session = AindBehaviorSessionModel(

examples/water_valve.py

@@ -37,7 +37,9 @@ def linear_model(time, slope, offset):
     calibration_date=datetime.datetime.now(),
 )
 
-calibration_logic = wv.CalibrationLogic(valve_open_time=_delta_times, valve_open_interval=0.5, repeat_count=200)
+calibration_logic = wv.CalibrationLogic(
+    task_parameters=wv.CalibrationParameters(valve_open_time=_delta_times, valve_open_interval=0.5, repeat_count=200)
+)
 
 calibration_session = AindBehaviorSessionModel(
     root_path="C:\\Data",

pyproject.toml

@@ -17,12 +17,15 @@ dependencies = [
     'harp-python>=0.2',
     'gitpython>=3.1, <4.0',
     'scikit-learn',
-    'semver'
+    'semver',
+    'aind-behavior-curriculum@git+https://github.com/AllenNeuralDynamics/[email protected]',
+
 ]
 
 [project.optional-dependencies]
-dev = [
-    'aind_behavior_services[linters]'
+
+aind-data-schema-mapper = [
+    'aind-data-schema==0.33.9'
 ]
 
 linters = [

scripts/install_dependencies.ps1

@@ -0,0 +1,32 @@
+Write-Host "Installing dependencies..." -ForegroundColor White
+$autoaccept = @("--accept-package-agreements", "--accept-source-agreements")
+
+winget install -e --id 7zip.7zip @autoaccept
+winget install ffmpeg -v 7.0 @autoaccept
+winget install -e --id Git.Git @autoaccept
+winget install -e --id Python.Python.3.11 --scope user @autoaccept
+winget install -e --id Microsoft.VisualStudioCode --scope user @autoaccept --override '/SILENT /mergetasks="!runcode,addcontextmenufiles,addcontextmenufolders"'
+winget install -e --id Microsoft.DotNet.Framework.DeveloperPack_4 @autoaccept
+Winget install "Microsoft Visual C++ 2012 Redistributable (x64)" --force @autoaccept
+winget install -e --id Nvidia.GeForceExperience -v 3.26.0.160 @autoaccept
+winget install -e --id Notepad++.Notepad++ @autoaccept
+winget install -e --id dotPDNLLC.paintdotnet @autoaccept
+
+## Install vscode extensions
+$extensions =
+    "eamodio.gitlens",
+    "donjayamanne.python-extension-pack"
+    "redhat.vscode-yaml"
+
+$cmd = "code --list-extensions"
+Invoke-Expression $cmd -OutVariable output | Out-Null
+$installed = $output -split "\s"
+
+foreach ($ext in $extensions) {
+    if ($installed.Contains($ext)) {
+        Write-Host $ext "already installed." -ForegroundColor Gray
+    } else {
+        Write-Host "Installing" $ext "..." -ForegroundColor White
+        code --install-extension $ext
+    }
+}

setup.py

@@ -1,4 +1,4 @@
 from setuptools import setup
 
 if __name__ == "__main__":
-    setup()
+    setup()

src/DataSchemas/aind_behavior_services/__init__.py

@@ -1,4 +1,4 @@
-__version__ = "0.6.1"
+__version__ = "0.7.0"
 
 from .rig import AindBehaviorRigModel
 from .session import AindBehaviorSessionModel

src/DataSchemas/aind_behavior_services/aind_data_schema_mapper/__init__.py

@@ -0,0 +1,7 @@
+try:
+    import aind_data_schema
+except ImportError as e:
+    e.add_note(
+        "The 'aind-data-schema' package is required to use this module. Install the optional dependencies defined in `project.toml' by running `pip install .[aind-data-schema-mapper]`"
+    )
+    raise

src/DataSchemas/aind_behavior_services/aind_data_schema_mapper/mapper.py

@@ -0,0 +1,129 @@
+import json
+import os
+from pathlib import Path
+from typing import Any, Dict, Optional, Type, TypeVar, Union
+
+from aind_behavior_services import AindBehaviorRigModel, AindBehaviorSessionModel, AindBehaviorTaskLogicModel
+from aind_data_schema.core.session import Modality, Session, Software, StimulusEpoch, Stream
+
+TSession = TypeVar("TSession", bound=AindBehaviorSessionModel)
+TRig = TypeVar("TRig", bound=AindBehaviorRigModel)
+TTaskLogic = TypeVar("TTaskLogic", bound=AindBehaviorTaskLogicModel)
+TSchema = TypeVar("TSchema", bound=Union[AindBehaviorSessionModel, AindBehaviorRigModel, AindBehaviorTaskLogicModel])
+
+
+def map_to_aind_data_schema(
+    session_root: Path,
+    session: Type[TSession] = AindBehaviorSessionModel,
+    rig: Type[TRig] = AindBehaviorRigModel,
+    task_logic: Optional[type[TTaskLogic]] = None,
+) -> Session:
+    """
+    Maps the input session found in `session_root` to the aind-data-schema Session object.
+
+    Args:
+        session_root (Path): The root path of the session.
+        session (Type[TSession]): The session class.
+        rig (Type[TRig]): The rig class.
+        task_logic (Type[TTaskLogic]): The task logic class.
+
+    Returns:
+        Session: The mapped aind-data-schema session object.
+    """
+
+    session_path = session_root / "Config" / "session_input.json"
+    task_logic_path = session_root / "Config" / "tasklogic_input.json"
+    rig_path = session_root / "Config" / "rig_input.json"
+
+    if task_logic is None:
+        return mapper(
+            model_from_json_file(session_path, session),
+            model_from_json_file(rig_path, rig),
+            json.loads((task_logic_path.read_text())),
+        )
+    else:
+        return mapper(
+            model_from_json_file(session_path, session),
+            model_from_json_file(rig_path, rig),
+            model_from_json_file(task_logic_path, task_logic),
+        )
+
+
+def mapper(
+    session: TSession,
+    rig: TRig,
+    task_logic: TTaskLogic | Dict[str, Any],
+) -> Session:
+    """
+    Maps the input session, rig, and task logic to an aind-data-schema Session object.
+
+    Args:
+        session (TSession): The input session object.
+        rig (TRig): The input rig object.
+        task_logic (TTaskLogic): The input task logic object.
+
+    Returns:
+        Session: The mapped aind-data-schema Session object.
+    """
+
+    if isinstance(task_logic, dict):
+        pass
+    elif isinstance(task_logic, AindBehaviorTaskLogicModel):
+        task_logic = task_logic.model_dump()
+    else:
+        raise ValueError("task_logic must be a dict or AindBehaviorTaskLogicModel")
+
+    ads_session = Session(
+        experimenter_full_name=session.experimenter,
+        session_start_time=session.date,
+        session_type=session.experiment,
+        rig_id=rig.rig_name,
+        subject_id=session.subject,
+        notes=session.notes,
+        data_streams=[
+            Stream(
+                stream_modalities=[Modality.BEHAVIOR, Modality.BEHAVIOR_VIDEOS],
+                stream_start_time=session.date,
+                stream_end_time=session.date,
+                camera_names=["NULL"],
+            ),
+        ],
+        mouse_platform_name="Mouse platform",
+        active_mouse_platform=True,
+        stimulus_epochs=[
+            StimulusEpoch(
+                stimulus_name="vr-foraging task",
+                stimulus_start_time=session.date,
+                stimulus_end_time=session.date,
+                stimulus_modalities=["None"],
+                software=[
+                    Software(
+                        name="Bonsai",
+                        version=session.commit_hash,
+                        url="https://github.com/AllenNeuralDynamics/Aind.Behavior.VrForaging/blob/{sha}/bonsai/Bonsai.config".format(
+                            sha=session.commit_hash
+                        ),
+                    )
+                ],
+                script=Software(
+                    name="vr-foraging.bonsai",
+                    version=session.commit_hash,
+                    url="https://github.com/AllenNeuralDynamics/Aind.Behavior.VrForaging/blob/{sha}/src/vr-foraging.bonsai".format(
+                        sha=session.commit_hash
+                    ),
+                    parameters=task_logic,
+                ),
+            )
+        ],
+    )
+    return ads_session
+
+
+def model_from_json_file(json_path: os.PathLike | str, model_class: Type[TSchema]) -> TSchema:
+    with open(json_path, encoding="utf-8") as f:
+        return model_class.model_validate_json(f.read())
+
+
+def model_to_json_file(json_path: os.PathLike | str, model: TSchema) -> None:
+    with open(json_path, "w", encoding="utf-8") as f:
+        f.write(model.model_dump_json(indent=4))