fix: fixing two confusing bugs with coordinates

Issue was that the reference coordinate was incorrectly not being applied, causing coordinates to shift over time, and then I had fixed code downstream of this which was masking the problem

Author: dbirman

Assets/Scenes/TrajectoryPlanner.unity

@@ -38,7 +38,7 @@ RenderSettings:
   m_ReflectionIntensity: 1
   m_CustomReflection: {fileID: 0}
   m_Sun: {fileID: 0}
-  m_IndirectSpecularColor: {r: 0.44912726, g: 0.49919963, b: 0.5757154, a: 1}
+  m_IndirectSpecularColor: {r: 0.44824904, g: 0.49827605, b: 0.5755831, a: 1}
   m_UseRadianceAmbientProbe: 0
 --- !u!157 &3
 LightmapSettings:
@@ -8481,7 +8481,7 @@ PrefabInstance:
       objectReference: {fileID: 2108153954}
     - target: {fileID: 1302158968166640874, guid: 734f6254569c01842b9d2e2ff1b1d7ae, type: 3}
       propertyPath: m_IsActive
-      value: 1
+      value: 0
       objectReference: {fileID: 0}
     - target: {fileID: 1302158968379378328, guid: 734f6254569c01842b9d2e2ff1b1d7ae, type: 3}
       propertyPath: m_LocalScale.x

Assets/Scripts/Pinpoint/Probes/Controllers/CartesianProbeController.cs

@@ -805,10 +805,12 @@ public override void SetProbeAngles(Vector3 angles)
     /// <returns></returns>
     public override (Vector3 tipCoordWorldU, Vector3 tipRightWorldU, Vector3 tipUpWorldU, Vector3 tipForwardWorldU) GetTipWorldU()
     {
-        Vector3 tipCoordWorldU = BrainAtlasManager.WorldT2WorldU(_probeTipT.position);
-        Vector3 tipRightWorldU = (BrainAtlasManager.WorldT2WorldU(_probeTipT.position + _probeTipT.right, false) - tipCoordWorldU).normalized;
-        Vector3 tipUpWorldU = (BrainAtlasManager.WorldT2WorldU(_probeTipT.position + _probeTipT.up, false) - tipCoordWorldU).normalized;
-        Vector3 tipForwardWorldU = (BrainAtlasManager.WorldT2WorldU(_probeTipT.position + _probeTipT.forward, false) - tipCoordWorldU).normalized;
+        // Note: we need to use the reference coordinates here so that the world positions resolve to (0,0,0) at Bregma,
+        // otherwise any rotations that get applied will be incorrect
+        Vector3 tipCoordWorldU = BrainAtlasManager.WorldT2WorldU(_probeTipT.position, true);
+        Vector3 tipRightWorldU = (BrainAtlasManager.WorldT2WorldU(_probeTipT.position + _probeTipT.right, true) - tipCoordWorldU).normalized;
+        Vector3 tipUpWorldU = (BrainAtlasManager.WorldT2WorldU(_probeTipT.position + _probeTipT.up, true) - tipCoordWorldU).normalized;
+        Vector3 tipForwardWorldU = (BrainAtlasManager.WorldT2WorldU(_probeTipT.position + _probeTipT.forward, true) - tipCoordWorldU).normalized;
 
         return (tipCoordWorldU, tipRightWorldU, tipUpWorldU, tipForwardWorldU);
     }

Assets/Scripts/Pinpoint/Probes/ProbeManager.cs

@@ -801,8 +801,7 @@ public void UpdateSurfacePosition()
             // get the surface coordinate in un-transformed world space
             _brainSurfaceWorldU = BrainAtlasManager.ActiveReferenceAtlas.AtlasIdx2World(entryCoordAtlasIdx);
             // go back into transformed space, only using the reference coordinate for the entry coordinate (not the transform coordinate)
-            _brainSurfaceWorldT = BrainAtlasManager.WorldU2WorldT(_brainSurfaceWorldU, false);
-
+            _brainSurfaceWorldT = BrainAtlasManager.WorldU2WorldT(_brainSurfaceWorldU, true);
             _brainSurfaceCoordT = BrainAtlasManager.ActiveAtlasTransform.U2T(
                 BrainAtlasManager.ActiveReferenceAtlas.World2Atlas(_brainSurfaceWorldU, true));
         }
@@ -829,7 +828,7 @@ public void UpdateSurfacePosition()
         Vector3 tipInBrain = tipAtlasIdxU;
 
         // Adjust the tip coordinate to put it into the brain
-        // This is kind of a dumb algorithm, we 
+        // This is kind of a dumb algorithm 
         if (!probeInBrain)
         {
             // Get which direction we need to go