feat: re-enabling disabled ephys link code

Author: dbirman

Assets/Scripts/EphysLink/trajectoryplanner.ephyslink.asmdef

@@ -6,7 +6,8 @@
         "trajectoryplanner.core.utilities",
         "vbl.brainatlas.runtime",
         "vbl.brainatlas.atlas",
-        "vbl.brainatlas.coordsystems"
+        "vbl.brainatlas.coordsystems",
+        "vblcore.coordinates"
     ],
     "includePlatforms": [],
     "excludePlatforms": [],

Assets/Scripts/Pinpoint/Probes/ManipulatorBehaviorController.cs

@@ -6,6 +6,7 @@
 using EphysLink;
 using UnityEngine;
 using UnityEngine.Events;
+using Urchin.Utils;
 
 namespace TrajectoryPlanner.Probes
 {
@@ -272,20 +273,19 @@ void StartEchoing()
 
         public void UpdateSpaceAndTransform()
         {
-            throw new NotImplementedException();
-            //if (ManipulatorType == "sensapex")
-            //{
-            //    CoordinateSpace = new SensapexSpace();
-            //    Transform = IsRightHanded
-            //        ? new SensapexRightTransform(_probeController.Insertion.Yaw)
-            //        : new SensapexLeftTransform(_probeController.Insertion.Yaw);
-            //}
-            //else
-            //{
-            //    CoordinateSpace = new NewScaleSpace();
-            //    Transform = new NewScaleLeftTransform(_probeController.Insertion.Yaw,
-            //        _probeController.Insertion.Pitch);
-            //}
+            if (ManipulatorType == "sensapex")
+            {
+                ReferenceAtlas = new SensapexSpace();
+                AtlasTransform = IsRightHanded
+                    ? new SensapexRightTransform(_probeController.Insertion.Yaw)
+                    : new SensapexLeftTransform(_probeController.Insertion.Yaw);
+            }
+            else
+            {
+                ReferenceAtlas = new NewScaleSpace();
+                AtlasTransform = new NewScaleLeftTransform(_probeController.Insertion.Yaw,
+                    _probeController.Insertion.Pitch);
+            }
         }
 
         public Vector4 ConvertInsertionToManipulatorPosition(Vector3 insertionAPMLDV)
@@ -317,36 +317,35 @@ public Vector4 ConvertInsertionToManipulatorPosition(Vector3 insertionAPMLDV)
         /// </summary>
         public void ComputeBrainSurfaceOffset()
         {
-            throw new NotImplementedException();
-            //if (_probeManager.IsProbeInBrain())
-            //{
-            //    // Just calculate the distance from the probe tip position to the brain surface            
-            //    BrainSurfaceOffset -= _probeManager.GetSurfaceCoordinateT().depthT;
-            //}
-            //else
-            //{
-            //    // We need to calculate the surface coordinate ourselves
-            //    var tipExtensionDirection =
-            //        IsSetToDropToSurfaceWithDepth ? _probeController.GetTipWorldU().tipUpWorldU : Vector3.up;
-
-            //    var brainSurfaceCoordinate = _annotationDataset.FindSurfaceCoordinate(
-            //        _annotationDataset.CoordinateSpace.World2Space(_probeController.GetTipWorldU().tipCoordWorldU -
-            //                                                       tipExtensionDirection * 5),
-            //        _annotationDataset.CoordinateSpace.World2Space_Vector(tipExtensionDirection));
-
-            //    if (float.IsNaN(brainSurfaceCoordinate.x))
-            //    {
-            //        Debug.LogWarning("Could not find brain surface! Canceling set brain offset.");
-            //        return;
-            //    }
-
-            //    var brainSurfaceToTransformed =
-            //        _probeController.Insertion.World2Transformed(
-            //            _annotationDataset.CoordinateSpace.Space2World(brainSurfaceCoordinate));
-
-            //    BrainSurfaceOffset += Vector3.Distance(brainSurfaceToTransformed,
-            //        _probeController.Insertion.apmldv);
-            //}
+            if (_probeManager.IsProbeInBrain())
+            {
+                // Just calculate the distance from the probe tip position to the brain surface            
+                BrainSurfaceOffset -= _probeManager.GetSurfaceCoordinateT().depthT;
+            }
+            else
+            {
+                // We need to calculate the surface coordinate ourselves
+                var tipExtensionDirection =
+                    IsSetToDropToSurfaceWithDepth ? _probeController.GetTipWorldU().tipUpWorldU : Vector3.up;
+
+                var brainSurfaceIdxCoordU = _probeManager.FindSurfaceIdxCoordinate(
+                    BrainAtlasManager.ActiveReferenceAtlas.World2AtlasIdx(_probeController.GetTipWorldU().tipCoordWorldU -
+                                                                   tipExtensionDirection * 5),
+                    BrainAtlasManager.ActiveReferenceAtlas.World2Atlas_Vector(tipExtensionDirection));
+
+                if (float.IsNaN(brainSurfaceIdxCoordU.x))
+                {
+                    Debug.LogWarning("Could not find brain surface! Canceling set brain offset.");
+                    return;
+                }
+
+                var brainSurfaceToTransformed =
+                    _probeController.Insertion.World2T(
+                        BrainAtlasManager.ActiveReferenceAtlas.World2AtlasIdx(brainSurfaceIdxCoordU));
+
+                BrainSurfaceOffset += Vector3.Distance(brainSurfaceToTransformed,
+                    _probeController.Insertion.apmldv);
+            }
         }
 
         /// <summary>

Assets/Scripts/Pinpoint/TrajectoryPlannerManager.cs

@@ -180,9 +180,6 @@ public async void Startup()
             }
             Settings.ReferenceCoord = referenceAtlas.AtlasSpace.ReferenceCoord;
 
-            // Now that the scene is loaded we can also set the BLDistance values
-            SetBLUI();
-
             // there is only one default set right now, tbd if we want to add others (beryl/cosmos/etc)
             var nodeTask = _atlasManager.LoadDefaultAreas("");
 
@@ -202,6 +199,11 @@ public async void Startup()
                 _pinpointAtlasManager.DefaultNodes.Add(node);
             }
 
+            // Now that the areas are loaded we can also set the BLDistance values
+            SetBLUI();
+            if (Settings.BregmaLambdaDistance > 0f)
+                ChangeBLDistance(Settings.BregmaLambdaDistance);
+
             StartupEvent_RefAtlasLoaded.Invoke();
             StartupEvent_AnnotationTextureLoaded.Invoke(BrainAtlasManager.ActiveReferenceAtlas.AnnotationTexture);
 
@@ -1028,7 +1030,7 @@ public void SetBLUI()
         /// <param name="newBLDistance"></param>
         public void ChangeBLDistance(float newBLDistance)
         {
-            if (BrainAtlasManager.ActiveReferenceAtlas == null)
+            if (BrainAtlasManager.ActiveReferenceAtlas == null || newBLDistance == _blDistance.DefaultBLDistance)
                 return;
 
             float blRatio = newBLDistance / _blDistance.DefaultBLDistance;

Assets/Scripts/Pinpoint/Utilities/Settings.cs

@@ -341,7 +341,7 @@ public static string AtlasTransformName
         }
     }
 
-    private const float BREGMALAMBDA_DEFAULT = 4.15f;
+    private const float BREGMALAMBDA_DEFAULT = -1f;
     [SerializeField] private Slider _blSlider;
     public UnityEvent<float> BregmaLambdaChangedEvent;