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feat: MPM and automation support #711

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Merged
kjy5 merged 5 commits into from
Jul 31, 2024
Merged

feat: MPM and automation support #711

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746e81d
Removed MPM exception
kjy5 Jul 30, 2024
daa0e8b
Re-enable copilot
kjy5 Jul 31, 2024
649680b
Removed references to Pathfinder probe and axis count
kjy5 Jul 31, 2024
25664b7
Fix 3lhm brain surface offset
kjy5 Jul 31, 2024
837ffce
Cleanup
kjy5 Jul 31, 2024
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2 changes: 1 addition & 1 deletion Assets/Prefabs/UI/SettingsMenu/Menus/EphysLinkMenu.prefab
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Original file line number Diff line number Diff line change
Expand Up @@ -4330,7 +4330,7 @@ MonoBehaviour:
m_PressedTrigger: Pressed
m_SelectedTrigger: Selected
m_DisabledTrigger: Disabled
m_Interactable: 0
m_Interactable: 1
m_TargetGraphic: {fileID: 6487466997665187127}
toggleTransition: 1
graphic: {fileID: 2477337667047670143}
Expand Down
37 changes: 0 additions & 37 deletions Assets/Scripts/Pinpoint/CoordinateSystems/PathfinderSpace.cs
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11 changes: 0 additions & 11 deletions Assets/Scripts/Pinpoint/CoordinateSystems/PathfinderSpace.cs.meta
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160 changes: 36 additions & 124 deletions Assets/Scripts/Pinpoint/Probes/ManipulatorBehaviorController.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -156,16 +156,16 @@ private void OnDisable()

public void Initialize(string manipulatorID, bool calibrated)
{
CommunicationManager.Instance.GetManipulators(reponse =>
CommunicationManager.Instance.GetManipulators(response =>
{
// Shortcut exit if we have an invalid manipulator ID
if (!reponse.Manipulators.Contains(manipulatorID))
if (!response.Manipulators.Contains(manipulatorID))
return;

// Set manipulator ID, number of axes, and dimensions
ManipulatorID = manipulatorID;
NumAxes = reponse.NumAxes;
Dimensions = reponse.Dimensions;
NumAxes = response.NumAxes;
Dimensions = response.Dimensions;

// Update transform and space
UpdateSpaceAndTransform();
Expand All @@ -191,20 +191,9 @@ void StartEchoing()
});
}

public void Deinitialize()
{
// Destroy Pathfinder probe.
if (NumAxes == -1)
DestroyThisProbe.Invoke();
}

private void UpdateSpaceAndTransform()
{
CoordinateSpace = NumAxes switch
{
-1 => new PathfinderSpace(),
_ => new ManipulatorSpace(Dimensions)
};
CoordinateSpace = new ManipulatorSpace(Dimensions);
CoordinateTransform = NumAxes switch
{
4
Expand Down Expand Up @@ -339,6 +328,7 @@ public void MoveByWorldSpaceDelta(
),
newPos =>
{
print("New pos: " + newPos + "; Setting depth...");
// Process depth movement
var targetDepth = newPos.w + manipulatorSpaceDepth;
// Move the manipulator
Expand Down Expand Up @@ -391,143 +381,66 @@ Action<string> onErrorCallBack

private void EchoPosition(Vector4 pos)
{
// Exit if disabled and there is no probe controller.
if (!enabled && _probeController == null)
return;

// Check for special Pathfinder mode
if (NumAxes == -1)
{
// Check if probe type changed
CommunicationManager.Instance.GetShankCount(
ManipulatorID,
shankCount =>
{
// Use 2.4 if 4 shank, otherwise default to 1
var probeType =
shankCount == 4
? ProbeProperties.ProbeType.Neuropixels24
: ProbeProperties.ProbeType.Neuropixels1;

// print("Read type: " + probeType + "; Current type: " + _probeManager.ProbeType);
// Check if change is needed
if (probeType != _probeManager.ProbeType)
{
// Unregister manipulator
_probeManager.SetIsEphysLinkControlled(
false,
ManipulatorID,
true,
() =>
{
// Create new probe
CreatePathfinderProbe.Invoke(probeType);

// Destroy current probe
DestroyThisProbe.Invoke();
},
Debug.LogError
);

// Exit early as this probe no longer exists
return;
}

// Otherwise, update probe angles
CommunicationManager.Instance.GetAngles(
ManipulatorID,
angles =>
{
_probeController.SetProbeAngles(
new Vector3(angles.x, 90 - angles.y, angles.z)
);

// If only the DV axis moved, then we drop on DV. Otherwise, we drop on depth.
if (Math.Abs(pos.z - _lastManipulatorPosition.z) > 0.0001)
IsSetToDropToSurfaceWithDepth =
Math.Abs(pos.x - _lastManipulatorPosition.x) > 0.0001
|| Math.Abs(pos.y - _lastManipulatorPosition.y) > 0.0001;

// Copy in new 3-axis position into saved 4-axis position
_lastManipulatorPosition = new Vector4(
pos.x,
pos.y,
pos.z,
_lastManipulatorPosition.w
);

// Apply brain surface offset on correct axis
var brainSurfaceAdjustment = float.IsNaN(BrainSurfaceOffset)
? 0
: BrainSurfaceOffset;
if (IsSetToDropToSurfaceWithDepth)
_lastManipulatorPosition.w -= brainSurfaceAdjustment;
else
_lastManipulatorPosition.z -= brainSurfaceAdjustment;

// Convert Pathfinder space coordinates into active atlas space
var convertedPos = _probeController.Insertion.World2T_Vector(
CoordinateSpace.Space2World_Vector(_lastManipulatorPosition)
);

// Copy and add 4th axis back in
_probeController.SetProbePosition(
new Vector4(
convertedPos.x,
convertedPos.y,
convertedPos.z,
_lastManipulatorPosition.w
)
);

// Log and continue echoing
LogAndContinue();
},
Debug.LogError
);
},
Debug.LogError
);

// Exit early as we've handled Pathfinder
return;
}

// Calculate last used direction for dropping to brain surface (between depth and DV)
var dvDelta = Math.Abs(pos.z - _lastManipulatorPosition.z);
var depthDelta = Math.Abs(pos.w - _lastManipulatorPosition.w);
if (dvDelta > 0.0001 || depthDelta > 0.0001)
IsSetToDropToSurfaceWithDepth = depthDelta > dvDelta;
_lastManipulatorPosition = pos;

// Apply zero coordinate offset
// Apply zero coordinate offset.
var zeroCoordinateAdjustedManipulatorPosition = pos - ZeroCoordinateOffset;

// Convert to coordinate space
// Convert to coordinate space.
var manipulatorSpacePosition = CoordinateTransform.T2U(
zeroCoordinateAdjustedManipulatorPosition
);

// Brain surface adjustment
// Brain surface adjustment.
var brainSurfaceAdjustment = float.IsNaN(BrainSurfaceOffset) ? 0 : BrainSurfaceOffset;
if (IsSetToDropToSurfaceWithDepth)
zeroCoordinateAdjustedManipulatorPosition.w += brainSurfaceAdjustment;
{
// Apply depth adjustment to manipulator position for non-3 axis manipulators.
if (CoordinateTransform.Prefix != "3lhm")
zeroCoordinateAdjustedManipulatorPosition.w += brainSurfaceAdjustment;
}
else
{
manipulatorSpacePosition.y -= brainSurfaceAdjustment;
}

// Convert to world space
// Convert to world space.
var zeroCoordinateAdjustedWorldPosition = CoordinateSpace.Space2World(
manipulatorSpacePosition
);

// Set probe position (change axes to match probe)
// Set probe position (change axes to match probe).
var transformedApmldv = BrainAtlasManager.World2T_Vector(
zeroCoordinateAdjustedWorldPosition
);

// Split between 3 and 4 axis assignments
// Set probe position.
// For 3-axis manipulators, use depth to adjust brain offset if applying offset on depth.
if (CoordinateTransform.Prefix == "3lhm")
_probeController.SetProbePosition(transformedApmldv);
{
if (IsSetToDropToSurfaceWithDepth)
_probeController.SetProbePosition(
new Vector4(
transformedApmldv.x,
transformedApmldv.y,
transformedApmldv.z,
brainSurfaceAdjustment
)
);
else
_probeController.SetProbePosition(transformedApmldv);
}
else
{
_probeController.SetProbePosition(
new Vector4(
transformedApmldv.x,
Expand All @@ -536,6 +449,7 @@ private void EchoPosition(Vector4 pos)
zeroCoordinateAdjustedManipulatorPosition.w
)
);
}

// Log and continue echoing
LogAndContinue();
Expand All @@ -551,7 +465,6 @@ void LogAndContinue()
|| Mathf.Abs(positionDifference.z) > 0.0001
|| Mathf.Abs(positionDifference.w) > 0.0001
)
{
// Log every 4 hz
if (Time.time - _lastLoggedTime >= 0.25)
{
Expand Down Expand Up @@ -587,7 +500,6 @@ void LogAndContinue()
// Update last logged position
_lastLoggedManipulatorPosition = pos;
}
}

// Continue echoing position
CommunicationManager.Instance.GetPosition(ManipulatorID, EchoPosition);
Expand Down
1 change: 0 additions & 1 deletion Assets/Scripts/Pinpoint/Probes/ProbeManager.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -1068,7 +1068,6 @@ public void SetIsEphysLinkControlled(
}
else
{
ManipulatorBehaviorController.Deinitialize();
IsEphysLinkControlled = false;
onSuccess?.Invoke();
}
Expand Down
6 changes: 0 additions & 6 deletions Assets/Scripts/Pinpoint/UI/EphysLinkSettings/EphysLinkSettings.cs
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Original file line number Diff line number Diff line change
Expand Up @@ -392,9 +392,6 @@ public void ToggleCopilotPanel(bool isEnabled)
public void InvokeShouldUpdateProbesListEvent()
{
ShouldUpdateProbesListEvent.Invoke();

// Enable/Disable Copilot toggle based on if there are any probes that can be controlled by it.
_copilotToggle.interactable = LinkedProbes.Count > 0;
}

#endregion
Expand Down Expand Up @@ -436,9 +433,6 @@ var probeManager in ProbeManager.Instances.Where(probeManager =>
false,
probeManager.ManipulatorBehaviorController.ManipulatorID
);

// FIXME: This is done because of race condition with closing out server. Should be fixed with non-registration setup.
probeManager.ManipulatorBehaviorController.Deinitialize();
}

CommunicationManager.Instance.DisconnectFromServer(() =>
Expand Down
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