From 1ec2223413ff291661b2fe90533abea65b771d47 Mon Sep 17 00:00:00 2001
From: Dan Birman <danbirman@gmail.com>
Date: Mon, 12 Feb 2024 14:31:45 -0800
Subject: [PATCH] fix: adding some docs and fixing a bug in slicerenderer

---
 Assets/Scripts/Pinpoint/Probes/ProbeManager.cs | 9 ++++++++-
 Assets/Scripts/Pinpoint/TP_SliceRenderer.cs    | 7 +++++--
 2 files changed, 13 insertions(+), 3 deletions(-)

diff --git a/Assets/Scripts/Pinpoint/Probes/ProbeManager.cs b/Assets/Scripts/Pinpoint/Probes/ProbeManager.cs
index 2d074358..590e7fc6 100644
--- a/Assets/Scripts/Pinpoint/Probes/ProbeManager.cs
+++ b/Assets/Scripts/Pinpoint/Probes/ProbeManager.cs
@@ -458,7 +458,12 @@ public List<string> GetProbeDepthIDs()
         }
         return depthIDs;
     }
-
+    
+    /// <summary>
+    /// Gets the probe anatomy in depth format (SpikeGLX)
+    /// </summary>
+    /// <param name="shank"></param>
+    /// <returns></returns>
     private string perShankDepthIDs(int shank)
     {
         // Create a list of range, acronym color
@@ -524,6 +529,8 @@ private string perShankDepthIDs(int shank)
 
     /// <summary>
     /// Get a serialized representation of the channel ID data
+    /// 
+    /// (OpenEphys format)
     /// </summary>
     /// <returns></returns>
     public string GetChannelAnnotationIDs(bool collapsed = true)
diff --git a/Assets/Scripts/Pinpoint/TP_SliceRenderer.cs b/Assets/Scripts/Pinpoint/TP_SliceRenderer.cs
index 10f88fad..f8da7c56 100644
--- a/Assets/Scripts/Pinpoint/TP_SliceRenderer.cs
+++ b/Assets/Scripts/Pinpoint/TP_SliceRenderer.cs
@@ -81,6 +81,7 @@ public void UpdateSlicePosition()
             if (ProbeManager.ActiveProbeManager != null)
                 (tipCoordWorld, _, _, _) = ProbeManager.ActiveProbeManager.ProbeController.GetTipWorldU();
 
+            Vector3 tipCoordWorldT = ProbeManager.ActiveProbeManager.ProbeController.ProbeTipT.position;
             // vertex order -x-y, +x-y, -x+y, +x+y
 
             // compute the world vertex positions from the raw coordinates
@@ -89,8 +90,10 @@ public void UpdateSlicePosition()
             Vector3[] newSagittalVerts = new Vector3[4];
             for (int i = 0; i < _coronalOrigWorldU.Length; i++)
             {
-                newCoronalVerts[i] = BrainAtlasManager.WorldU2WorldT(new Vector3(_coronalOrigWorldU[i].x, _coronalOrigWorldU[i].y, tipCoordWorld.z), false);
-                newSagittalVerts[i] = BrainAtlasManager.WorldU2WorldT(new Vector3(tipCoordWorld.x, _sagittalOrigWorldU[i].y, _sagittalOrigWorldU[i].z), false);
+                newCoronalVerts[i] = new Vector3(_coronalOrigWorldU[i].x, _coronalOrigWorldU[i].y, tipCoordWorldT.z);
+                newSagittalVerts[i] = new Vector3(tipCoordWorldT.x, _sagittalOrigWorldU[i].y, _sagittalOrigWorldU[i].z);
+                //newCoronalVerts[i] = BrainAtlasManager.WorldU2WorldT(new Vector3(_coronalOrigWorldU[i].x, _coronalOrigWorldU[i].y, tipCoordWorld.z), false);
+                //newSagittalVerts[i] = BrainAtlasManager.WorldU2WorldT(new Vector3(tipCoordWorld.x, _sagittalOrigWorldU[i].y, _sagittalOrigWorldU[i].z), false);
             }
 
             _coronalSliceGo.GetComponent<MeshFilter>().mesh.vertices = newCoronalVerts;