Merge branch 'main' into update-launcher

Author: bruno-f-cruz

pyproject.toml

@@ -12,7 +12,7 @@ classifiers = [
     "Programming Language :: Python :: 3.11",
     "Operating System :: Microsoft :: Windows",
 ]
-version = "0.6.2rc1"
+version = "0.6.2rc3"
 readme = {file = "README.md", content-type = "text/markdown"}
 
 dependencies = [

src/DataSchemas/aind_behavior_vr_foraging.json

@@ -359,8 +359,8 @@
           "type": "string"
         },
         "version": {
-          "const": "0.6.2-rc1",
-          "default": "0.6.2-rc1",
+          "const": "0.6.2-rc3",
+          "default": "0.6.2-rc3",
           "title": "Version",
           "type": "string"
         },
@@ -568,8 +568,8 @@
           "description": "Parameters of the task logic"
         },
         "version": {
-          "const": "0.6.2-rc1",
-          "default": "0.6.2-rc1",
+          "const": "0.6.2-rc3",
+          "default": "0.6.2-rc3",
           "title": "Version",
           "type": "string"
         },

src/Extensions/AindBehaviorVrForaging.Generated.cs

@@ -954,8 +954,8 @@ public partial class AindVrForagingRig
 
         public AindVrForagingRig()
         {
-            _aindBehaviorServicesPkgVersion = "0.12.5";
-            _version = "0.6.2-rc1";
+            _aindBehaviorServicesPkgVersion = "0.12.3";
+            _version = "0.6.2-rc3";
             _triggeredCameraController = new CameraControllerSpinnakerCamera();
             _harpBehavior = new HarpBehavior();
             _harpOlfactometer = new Olfactometer();
@@ -1362,7 +1362,7 @@ public AindVrForagingTaskLogic()
             _name = "AindVrForaging";
             _description = "";
             _taskParameters = new AindVrForagingTaskParameters();
-            _version = "0.6.2-rc1";
+            _version = "0.6.2-rc3";
         }
 
         protected AindVrForagingTaskLogic(AindVrForagingTaskLogic other)

src/aind_behavior_vr_foraging/data_mappers/_rig.py

@@ -26,14 +26,11 @@
 class _DeviceNode:
     """Helper class to keep track of devices, their connections and spawned devices"""
 
+    device_name: str
     device: devices.Device
     connections_from: list[connections.Connection] = dataclasses.field(default_factory=list)
     spawned_devices: list[devices.Device] = dataclasses.field(default_factory=list)
 
-    @property
-    def device_name(self) -> str:
-        return self.device.name
-
     def get_spawned_device(self, name: str) -> devices.Device:
         for d in self.spawned_devices:
             if d.name == name:
@@ -165,7 +162,7 @@ def _get_calibrations(rig: AindVrForagingRig) -> list[measurements.Calibration]:
     @staticmethod
     def _get_harp_behavior_node(rig: AindVrForagingRig) -> _DeviceNode:
         _connections: list[connections.Connection] = []
-        source_device = rig.harp_behavior.name or "harp_behavior"
+        source_device = validate_name(rig, "harp_behavior")
 
         # Add triggered camera controller
         if rig.triggered_camera_controller:
@@ -239,14 +236,15 @@ def _get_harp_behavior_node(rig: AindVrForagingRig) -> _DeviceNode:
         )
 
         return _DeviceNode(
+            device_name=source_device,
             device=_harp_device,
             connections_from=_connections,
             spawned_devices=[speaker, photodiode, water_valve],
         )
 
     @staticmethod
     def _get_harp_treadmill_node(rig: AindVrForagingRig) -> _DeviceNode:
-        source_device = rig.harp_treadmill.name or "harp_treadmill"
+        source_device = validate_name(rig, "harp_treadmill")
 
         _connections = [
             connections.Connection(
@@ -293,12 +291,16 @@ def _get_harp_treadmill_node(rig: AindVrForagingRig) -> _DeviceNode:
         )
 
         return _DeviceNode(
-            device=_harp_device, connections_from=_connections, spawned_devices=[magnetic_brake, encoder, torque_sensor]
+            device_name=source_device,
+            device=_harp_device,
+            connections_from=_connections,
+            spawned_devices=[magnetic_brake, encoder, torque_sensor],
         )
 
     @staticmethod
     def _get_harp_clock_generate_node(rig: AindVrForagingRig, components: list[devices.Device]) -> _DeviceNode:
-        source_device = rig.harp_clock_generator.name or "harp_clock_generator"
+        source_device = validate_name(rig, "harp_clock_generator")
+
         harp_devices = [d for d in components if isinstance(d, devices.HarpDevice)]
         _connections = [
             connections.Connection(
@@ -321,7 +323,7 @@ def _get_harp_clock_generate_node(rig: AindVrForagingRig, components: list[devic
             ],
         )
 
-        return _DeviceNode(device=harp_device, connections_from=_connections)
+        return _DeviceNode(device_name=source_device, device=harp_device, connections_from=_connections)
 
     @staticmethod
     def _get_wheel(
@@ -367,16 +369,25 @@ def _get_all_components_and_connections(
 
         # Get all other harp devices
         harp_lickometer = devices.HarpDevice(
-            name=rig.harp_lickometer.name or "harp_lickometer",
+            name=validate_name(rig, "harp_lickometer"),
             harp_device_type=devices.HarpDeviceType.LICKETYSPLIT,
             manufacturer=devices.Organization.AIND,
             is_clock_generator=False,
         )
 
+        harp_stepper_motor = devices.HarpDevice(
+            name=validate_name(rig, "manipulator"),
+            harp_device_type=devices.HarpDeviceType.STEPPERDRIVER,
+            manufacturer=devices.Organization.OEPS,
+            is_clock_generator=False,
+        )
+
+        _components.append(harp_stepper_motor)
+
         if rig.harp_sniff_detector is not None:
             _components.append(
                 devices.HarpDevice(
-                    name=rig.harp_sniff_detector.name or "harp_sniff_detector",
+                    name=validate_name(rig, "harp_sniff_detector"),
                     harp_device_type=devices.HarpDeviceType.SNIFFDETECTOR,
                     is_clock_generator=False,
                 )
@@ -385,7 +396,7 @@ def _get_all_components_and_connections(
         if rig.harp_environment_sensor is not None:
             _components.append(
                 devices.HarpDevice(
-                    name=rig.harp_environment_sensor.name or "harp_environment_sensor",
+                    name=validate_name(rig, "harp_environment_sensor"),
                     harp_device_type=devices.HarpDeviceType.ENVIRONMENTSENSOR,
                     is_clock_generator=False,
                 )
@@ -490,7 +501,7 @@ def _get_lickspout_assembly(
             model="328-300-00",
             travel=Decimal("30"),
             travel_unit=units.SizeUnit.CM,
-            notes="This stage is driven by the HarpStepperDriver device.",
+            notes="This stage is driven by the manipulator device.",
         )
 
         return devices.LickSpoutAssembly(
@@ -695,3 +706,10 @@ def _get_olfactometer_channel(
         channel_type=ch_type_to_ch_type[ch.channel_type],
         flow_capacity=ch.flow_rate_capacity,
     )
+
+
+def validate_name(obj: object, name: str) -> str:
+    if hasattr(obj, name):
+        return name
+    else:
+        raise ValueError(f"Model {obj.__class__.__name__} does not contain a field {name}.")

src/aind_behavior_vr_foraging/data_mappers/_session.py

@@ -3,7 +3,7 @@
 import os
 import sys
 from pathlib import Path
-from typing import List, Optional, Union
+from typing import List, Optional, Union, cast, get_args
 
 import aind_behavior_services.rig as AbsRig
 import git
@@ -114,23 +114,36 @@ def _get_calibrations(self) -> List[acquisition.CALIBRATIONS]:
         calibrations += _get_water_calibration(self.rig_model)
         return calibrations
 
+    @staticmethod
+    def _include_device(device: AbsRig.Device) -> bool:
+        if isinstance(device, AbsRig.visual_stimulation.Screen):
+            return False
+        if isinstance(device, AbsRig.cameras.CameraController):
+            return False
+        if isinstance(device, get_args(AbsRig.cameras.CameraTypes)):
+            return cast(AbsRig.cameras.CameraTypes, device).video_writer is not None
+        return True
+
     def _get_data_streams(self) -> List[acquisition.DataStream]:
         assert self.session_end_time is not None, "Session end time is not set."
 
         modalities: list[Modality] = [getattr(Modality, "BEHAVIOR")]
         if len(self._get_cameras_config()) > 0:
             modalities.append(getattr(Modality, "BEHAVIOR_VIDEOS"))
         modalities = list(set(modalities))
+
+        active_devices = [
+            _device[0]
+            for _device in get_fields_of_type(self.rig_model, AbsRig.Device, stop_recursion_on_type=False)
+            if _device[0] is not None and self._include_device(_device[1])
+        ]
+
         data_streams: list[acquisition.DataStream] = [
             acquisition.DataStream(
                 stream_start_time=self.session_model.date,
                 stream_end_time=self.session_end_time,
                 code=[self._get_bonsai_as_code(), self._get_python_as_code()],
-                active_devices=[
-                    _device[0]
-                    for _device in get_fields_of_type(self.rig_model, AbsRig.Device, stop_recursion_on_type=False)
-                    if _device[0] is not None
-                ],
+                active_devices=active_devices,
                 modalities=modalities,
                 configurations=self._get_cameras_config(),
                 notes=self.session_model.notes,