chore: 730 naming consistency bregma and zero coordinate to reference coordinate

Assets/Scripts/Pinpoint/Probes/ManipulatorBehaviorController/ManipulatorBehaviorController.cs

@@ -41,19 +41,19 @@ public partial class ManipulatorBehaviorController : MonoBehaviour
         ///     Getter and setter or the zero coordinate offset of the manipulator.
         ///     If passed a NaN value, the previous value is kept.
         /// </summary>
-        public Vector4 ZeroCoordinateOffset
+        public Vector4 ReferenceCoordinateOffset
         {
-            get => _zeroCoordinateOffset;
+            get => _referenceCoordinateOffset;
             set
             {
-                _zeroCoordinateOffset = new Vector4(
-                    float.IsNaN(value.x) ? _zeroCoordinateOffset.x : value.x,
-                    float.IsNaN(value.y) ? _zeroCoordinateOffset.y : value.y,
-                    float.IsNaN(value.z) ? _zeroCoordinateOffset.z : value.z,
-                    float.IsNaN(value.w) ? _zeroCoordinateOffset.w : value.w
+                _referenceCoordinateOffset = new Vector4(
+                    float.IsNaN(value.x) ? _referenceCoordinateOffset.x : value.x,
+                    float.IsNaN(value.y) ? _referenceCoordinateOffset.y : value.y,
+                    float.IsNaN(value.z) ? _referenceCoordinateOffset.z : value.z,
+                    float.IsNaN(value.w) ? _referenceCoordinateOffset.w : value.w
                 );
 
-                ZeroCoordinateOffsetChangedEvent.Invoke(_zeroCoordinateOffset);
+                ZeroCoordinateOffsetChangedEvent.Invoke(_referenceCoordinateOffset);
             }
         }
 
@@ -89,7 +89,7 @@ public bool IsRightHanded
         #region Private internal fields
 
         private Vector4 _lastLoggedManipulatorPosition = Vector4.zero;
-        private Vector4 _zeroCoordinateOffset = Vector4.zero;
+        private Vector4 _referenceCoordinateOffset = Vector4.zero;
         private float _brainSurfaceOffset;
         private bool _isRightHanded;
         private float _lastLoggedTime;
@@ -124,7 +124,7 @@ private void Awake()
         private void OnDisable()
         {
             ManipulatorID = null;
-            _zeroCoordinateOffset = Vector4.zero;
+            _referenceCoordinateOffset = Vector4.zero;
             _brainSurfaceOffset = 0;
         }
 
@@ -210,7 +210,7 @@ public Vector4 ConvertInsertionAPMLDVToManipulatorPosition(Vector3 insertionAPML
             posInManipulatorTransform.w -= float.IsNaN(BrainSurfaceOffset) ? 0 : BrainSurfaceOffset;
 
             // Apply coordinate offsets and return result
-            return posInManipulatorTransform + ZeroCoordinateOffset;
+            return posInManipulatorTransform + ReferenceCoordinateOffset;
         }
 
         /// <summary>
@@ -327,7 +327,7 @@ public async Awaitable<bool> MoveBackToZeroCoordinate()
             var setPositionResponse = await CommunicationManager.Instance.SetPosition(
                 new SetPositionRequest(
                     ManipulatorID,
-                    ZeroCoordinateOffset,
+                    ReferenceCoordinateOffset,
                     AUTOMATIC_MOVEMENT_SPEED
                 )
             );
@@ -362,7 +362,7 @@ private async Awaitable UpdateProbePositionFromManipulator()
 
             // Apply zero coordinate offset.
             var zeroCoordinateAdjustedManipulatorPosition =
-                positionResponse.Position - ZeroCoordinateOffset;
+                positionResponse.Position - ReferenceCoordinateOffset;
 
             // Convert to coordinate space.
             var manipulatorSpacePosition = CoordinateTransform.T2U(

Assets/Scripts/Pinpoint/Probes/ManipulatorBehaviorController/ManipulatorBehaviorController_Automation_Insertion.cs

@@ -380,7 +380,7 @@ private Vector3 GetOffsetAdjustedTargetCoordinate(ProbeManager targetInsertionPr
             var offsetAdjustedTargetCoordinateWorldT =
                 targetWorldT + offsetAdjustedRelativeTargetPositionWorldT;
 
-            // Converting worldT to AtlasT (to capture new Bregma offset when there is scaling)
+            // Converting worldT to AtlasT (to capture new reference coordinate offset when there is scaling)
             // then switch axes to get APMLDV.
             var offsetAdjustedTargetCoordinateAtlasT =
                 BrainAtlasManager.ActiveReferenceAtlas.World2Atlas(

Assets/Scripts/Pinpoint/Probes/ManipulatorBehaviorController/ManipulatorBehaviorController_Automation_BregmaCalibration.cs → Assets/Scripts/Pinpoint/Probes/ManipulatorBehaviorController/ManipulatorBehaviorController_Automation_ReferenceCoordinate.cs

@@ -18,13 +18,13 @@ public partial class ManipulatorBehaviorController
         #endregion
 
         /// <summary>
-        ///     Reset zero coordinate of the manipulator
+        ///     Reset reference coordinate of the manipulator
         /// </summary>
         /// <remarks>
         ///     Alerts user of 4-axis manipulators if depth axis is not at 0 and 3-axis manipulators if depth is too far from
         ///     center.
         /// </remarks>
-        public async Awaitable<bool> ResetZeroCoordinate()
+        public async Awaitable<bool> ResetReferenceCoordinate()
         {
             // Query current position.
             var positionalResponse = await CommunicationManager.Instance.GetPosition(ManipulatorID);
@@ -70,18 +70,18 @@ when Mathf.Abs(Dimensions.z / 2f - positionalResponse.Position.w)
                 return false;
 
             // Complete reset.
-            ZeroCoordinateOffset = positionalResponse.Position;
+            ReferenceCoordinateOffset = positionalResponse.Position;
             BrainSurfaceOffset = 0;
 
             // Log event.
             OutputLog.Log(
                 new[]
                 {
-                    "Copilot",
+                    "Automation",
                     DateTime.Now.ToString(CultureInfo.InvariantCulture),
-                    "ResetZeroCoordinate",
+                    "ResetReferenceCoordinate",
                     ManipulatorID,
-                    ZeroCoordinateOffset.ToString()
+                    ReferenceCoordinateOffset.ToString()
                 }
             );
             return true;

Assets/Scripts/Pinpoint/Probes/ProbeAutomationState.cs

@@ -11,7 +11,7 @@ public enum ProbeAutomationState
         IsUncalibrated,
 
         /// <summary>
-        ///     Is calibrated to Bregma. Could be positioned anywhere.
+        ///     Is calibrated to the reference coordinate. Could be positioned anywhere.
         /// </summary>
         IsCalibrated,
 

Assets/Scripts/Pinpoint/Probes/ProbeManager.cs

@@ -1275,7 +1275,7 @@ public static ProbeManagerData ProbeManager2ProbeData(ProbeManager probeManager)
 
         data.NumAxes = probeManager.ManipulatorBehaviorController.NumAxes;
         data.ManipulatorID = probeManager.ManipulatorBehaviorController.ManipulatorID;
-        data.ZeroCoordOffset = probeManager.ManipulatorBehaviorController.ZeroCoordinateOffset;
+        data.ZeroCoordOffset = probeManager.ManipulatorBehaviorController.ReferenceCoordinateOffset;
         data.Dimensions = probeManager.ManipulatorBehaviorController.Dimensions;
         data.BrainSurfaceOffset = probeManager.ManipulatorBehaviorController.BrainSurfaceOffset;
         // data.Drop2SurfaceWithDepth = probeManager

Assets/Scripts/Pinpoint/TP_ProbeQuickSettings.cs

@@ -149,7 +149,7 @@ public void ResetZeroCoordinate()
             if (ProbeManager.ActiveProbeManager.IsEphysLinkControlled)
             {
                 _communicationManager.GetPosition(ProbeManager.ActiveProbeManager.ManipulatorBehaviorController.ManipulatorID,
-                    zeroCoordinate => ProbeManager.ActiveProbeManager.ManipulatorBehaviorController.ZeroCoordinateOffset = zeroCoordinate);
+                    zeroCoordinate => ProbeManager.ActiveProbeManager.ManipulatorBehaviorController.ReferenceCoordinateOffset = zeroCoordinate);
                 ProbeManager.ActiveProbeManager.ManipulatorBehaviorController.BrainSurfaceOffset = 0;
             }
             else

Assets/Scripts/Pinpoint/TrajectoryPlannerManager.cs

@@ -485,7 +485,7 @@ public ProbeManager AddNewProbe(ProbeProperties.ProbeType probeType, ProbeInsert
 
             // Repopulate Ephys Link information
             probeManager.ManipulatorBehaviorController.NumAxes = numAxes;
-            probeManager.ManipulatorBehaviorController.ZeroCoordinateOffset = zeroCoordinateOffset;
+            probeManager.ManipulatorBehaviorController.ReferenceCoordinateOffset = zeroCoordinateOffset;
             probeManager.ManipulatorBehaviorController.BrainSurfaceOffset = brainSurfaceOffset;
             // probeManager.ManipulatorBehaviorController.IsSetToDropToSurfaceWithDepth = dropToSurfaceWithDepth;
             // probeManager.ManipulatorBehaviorController.IsSetToDropToSurfaceWithDepth = dropToSurfaceWithDepth;

Assets/Scripts/Pinpoint/UI/EphysCopilot/ResetZeroCoordinatePanelHandler.cs

@@ -30,7 +30,7 @@ public void ResetZeroCoordinate()
                 ProbeManager.ManipulatorBehaviorController.ManipulatorID,
                 zeroCoordinate =>
                 {
-                    ProbeManager.ManipulatorBehaviorController.ZeroCoordinateOffset =
+                    ProbeManager.ManipulatorBehaviorController.ReferenceCoordinateOffset =
                         zeroCoordinate;
                     ProbeManager.ManipulatorBehaviorController.BrainSurfaceOffset = 0;
                 }
@@ -44,7 +44,7 @@ public void ResetZeroCoordinate()
                     DateTime.Now.ToString(CultureInfo.InvariantCulture),
                     "ResetZeroCoordinate",
                     ProbeManager.ManipulatorBehaviorController.ManipulatorID,
-                    ProbeManager.ManipulatorBehaviorController.ZeroCoordinateOffset.ToString()
+                    ProbeManager.ManipulatorBehaviorController.ReferenceCoordinateOffset.ToString()
                 }
             );
         }

Assets/Scripts/Pinpoint/UI/EphysLinkSettings/ManipulatorConnectionPanel.cs

@@ -250,7 +250,7 @@ public void OnLinkedProbeSelectionChanged(int value)
         /// <param name="newValue">New offset X-axis value</param>
         public void UpdateZeroCoordinateOffsetX(string newValue)
         {
-            _attachedProbe.ManipulatorBehaviorController.ZeroCoordinateOffset = new Vector4(
+            _attachedProbe.ManipulatorBehaviorController.ReferenceCoordinateOffset = new Vector4(
                 float.Parse(newValue),
                 float.NaN,
                 float.NaN,
@@ -264,7 +264,7 @@ public void UpdateZeroCoordinateOffsetX(string newValue)
         /// <param name="newValue">New offset Y-axis value</param>
         public void UpdateZeroCoordinateOffsetY(string newValue)
         {
-            _attachedProbe.ManipulatorBehaviorController.ZeroCoordinateOffset = new Vector4(
+            _attachedProbe.ManipulatorBehaviorController.ReferenceCoordinateOffset = new Vector4(
                 float.NaN,
                 float.Parse(newValue),
                 float.NaN,
@@ -278,7 +278,7 @@ public void UpdateZeroCoordinateOffsetY(string newValue)
         /// <param name="newValue">New offset Z-axis value</param>
         public void UpdateZeroCoordinateOffsetZ(string newValue)
         {
-            _attachedProbe.ManipulatorBehaviorController.ZeroCoordinateOffset = new Vector4(
+            _attachedProbe.ManipulatorBehaviorController.ReferenceCoordinateOffset = new Vector4(
                 float.NaN,
                 float.NaN,
                 float.Parse(newValue),
@@ -292,7 +292,7 @@ public void UpdateZeroCoordinateOffsetZ(string newValue)
         /// <param name="newValue">New offset D-axis value</param>
         public void UpdateZeroCoordinateOffsetD(string newValue)
         {
-            _attachedProbe.ManipulatorBehaviorController.ZeroCoordinateOffset = new Vector4(
+            _attachedProbe.ManipulatorBehaviorController.ReferenceCoordinateOffset = new Vector4(
                 float.NaN,
                 float.NaN,
                 float.NaN,
@@ -402,7 +402,7 @@ private void UpdateProbePropertiesSectionState()
             {
                 _probePropertiesSection.SetActive(true);
                 UpdateZeroCoordinateOffsetInputFields(
-                    _attachedProbe.ManipulatorBehaviorController.ZeroCoordinateOffset
+                    _attachedProbe.ManipulatorBehaviorController.ReferenceCoordinateOffset
                 );
                 UpdateBrainSurfaceOffsetInputField(
                     _attachedProbe.ManipulatorBehaviorController.BrainSurfaceOffset

Assets/Scripts/UI/AutomationStack/AutomationStackHandler.cs

@@ -34,9 +34,9 @@ public partial class AutomationStackHandler : MonoBehaviour
         // Panels.
         private VisualElement _automationStackPanel;
 
-        #region Bregma Calibration
+        #region Reference Coordinate Calibration
 
-        private Button _resetBregmaCalibrationButton;
+        private Button _resetReferenceCoordinateButton;
 
         #endregion
 
@@ -83,8 +83,8 @@ private void OnEnable()
         {
             // Get components.
             _automationStackPanel = _root.Q("automation-stack-panel");
-            _resetBregmaCalibrationButton = _automationStackPanel.Q<Button>(
-                "reset-bregma-calibration-button"
+            _resetReferenceCoordinateButton = _automationStackPanel.Q<Button>(
+                "reset-reference-coordinate-button"
             );
             _targetInsertionRadioButtonGroup = _automationStackPanel.Q<RadioButtonGroup>(
                 "target-insertion-radio-button-group"
@@ -102,7 +102,7 @@ private void OnEnable()
             _exitButton = _automationStackPanel.Q<Button>("exit-button");
 
             // Register callbacks.
-            _resetBregmaCalibrationButton.clicked += ResetBregmaCalibration;
+            _resetReferenceCoordinateButton.clicked += ResetReferenceCoordinate;
             _targetInsertionRadioButtonGroup.RegisterValueChangedCallback(
                 OnTargetInsertionSelectionChanged
             );
@@ -116,7 +116,7 @@ private void OnEnable()
         private void OnDisable()
         {
             // Unregister callbacks.
-            _resetBregmaCalibrationButton.clicked -= ResetBregmaCalibration;
+            _resetReferenceCoordinateButton.clicked -= ResetReferenceCoordinate;
             _targetInsertionRadioButtonGroup.UnregisterValueChangedCallback(
                 OnTargetInsertionSelectionChanged
             );
@@ -144,13 +144,13 @@ private void FixedUpdate()
 
         #region Stages
 
-        #region Bregma Calibration
+        #region Reference Coordinate Calibration
 
         /// <summary>
-        ///     Reset the Bregma calibration of the active probe.
+        ///     Reset the reference coordinate calibration of the active probe.
         /// </summary>
         /// <exception cref="InvalidOperationException">Probe is not selected/active and is not controlled by Ephys Link</exception>
-        private partial void ResetBregmaCalibration();
+        private partial void ResetReferenceCoordinate();
 
         #endregion
 
@@ -192,7 +192,7 @@ private void FixedUpdate()
         /// </remarks>
         /// <exception cref="InvalidOperationException">
         ///     Probe is not selected/active, is not controlled by Ephys Link, and is not
-        ///     calibrated to bregma.
+        ///     calibrated to reference coordinate.
         /// </exception>
         private partial void OnDriveToTargetEntryCoordinatePressed();
 

Assets/Scripts/UI/AutomationStack/AutomationStackHandler_Insertion.cs

@@ -4,7 +4,7 @@
 namespace UI.AutomationStack
 {
     /// <summary>
-    ///     Implements Bregma calibration in the Automation Stack.<br />
+    ///     Implements reference coordinate calibration in the Automation Stack.<br />
     /// </summary>
     public partial class AutomationStackHandler
     {

Assets/Scripts/UI/AutomationStack/AutomationStackHandler_BregmaCalibration.cs → Assets/Scripts/UI/AutomationStack/AutomationStackHandler_ReferenceCoordinate.cs

@@ -4,21 +4,21 @@
 namespace UI.AutomationStack
 {
     /// <summary>
-    ///     Implements Bregma calibration in the Automation Stack.<br />
+    ///     Implements reference coordinate calibration in the Automation Stack.<br />
     /// </summary>
     public partial class AutomationStackHandler
     {
-        private async partial void ResetBregmaCalibration()
+        private async partial void ResetReferenceCoordinate()
         {
             // Throw exception if invariant is violated.
             if (!AutomationStackState.IsEnabled)
                 throw new InvalidOperationException(
-                    "Cannot reset Bregma calibration if automation is not enabled on probe "
+                    "Cannot reset reference coordinate calibration if automation is not enabled on probe "
                         + ProbeManager.ActiveProbeManager.name
                 );
 
-            // Reset the Bregma calibration of the active probe manager.
-            if (await ActiveManipulatorBehaviorController.ResetZeroCoordinate())
+            // Reset the reference coordinate calibration of the active probe manager.
+            if (await ActiveManipulatorBehaviorController.ResetReferenceCoordinate())
                 // Set probe's automation state to be calibrated if it did happen.
                 ActiveProbeStateManager.SetCalibrated();
         }

Assets/Scripts/UI/AutomationStack/AutomationStackHandler_TargetInsertion.cs

@@ -178,7 +178,7 @@ private async partial void OnDriveToTargetEntryCoordinatePressed()
             // Throw exception if invariant is violated.
             if (!AutomationStackState.IsEnabled || !ActiveProbeStateManager.IsCalibrated())
                 throw new InvalidOperationException(
-                    $"Cannot drive {ProbeManager.ActiveProbeManager.name} to target insertion if not enabled and not calibrated to Bregma."
+                    $"Cannot drive {ProbeManager.ActiveProbeManager.name} to target insertion if not enabled and not calibrated to reference coordinate."
                 );
 
             // If the probe is moving, call stop.