From d50df5655ab175b3d0da17eea300631c664861ab Mon Sep 17 00:00:00 2001 From: Kenneth Yang <82800265+kjy5@users.noreply.github.com> Date: Thu, 5 Sep 2024 12:42:43 -0700 Subject: [PATCH 1/9] feat: Automation pipeline UI (#720) * Basic UI components * Hide and show side panels * Upgrade to Unity 6 * Create UI prefab, Switched to using prebuilt tab menu * Start to attach scripting * Build for Linux and WebGL (need to update Urchin) * Bind left side panel state, needs converter for bool to DisplayStyle * State based left side panel hide/show * RSP heading based on mode * Automation stack and initial styling * Inspector stack, color names (might remove) * Probe color buttons * Inspector stack visibility update based on mode * Create automation stack, add state to right side panel * Enable/disable automation stack based on probe's connection * Inspector selector probe * Add inspector state * Reset Bregma from UI, fixed inspector probe label binding * Prepare to use list instead of dropdown to pick insertion * Foundation for target list view * Removed styling * Generate options for target insertions * Separated automation stages, list not working, trying radio button group * Try with radio button group, not sure * List targetable in radio button group * Remove panel background when hidden * WIP color insertion options (worked then stopped) * Fixed options caching, colors work * Refactor MBC to prep for automation functions * Draw trajectory lines * Drive to entry coordinate. Lines seem to be regenerated unnecessarily * Fixed removal, inefficient redraw every frame * It'll continue to redraw * Implement probe state * Comments * Unified left/right panel state and handler * Bregma calibration text fields * Dura calibration, bad resume on entry coordinate * WIP Ensure trajectory is not recomputed unnecessarily * Fixed recompute after complete * Bindings for insertion section * Add stop and exit buttons, hyphened some names, need to fix probe switch * Update Unity, fixed exception on probe switch * Rollback commited main scene changes * Added new states to automation * Prepare for drive, change Bregma calibration to monitor depth * Compute depth based drive coordinate and navigate there * Drop to Dura via depth * Drive button visibility * WIP drive pipeline * WIP drive down, incorrect offsetting * Fixed offset * Drive and pause * Drive cycle * Enable Click through on panel --- .../.idea/projectSettingsUpdater.xml | 2 +- .../AddressableAssetSettings.asset | 84 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UpdateSchemas() { var webClient = new WebClient(); - - webClient.DownloadFile( - "https://raw.githubusercontent.com/VirtualBrainLab/vbl-aquarium/main/models/csharp/EphysLinkModels.cs", - "Assets/Scripts/EphysLink/EphysLinkModels.cs"); - + + EditorCoroutineUtility.StartCoroutineOwnerless( + DownloadFile( + "https://raw.githubusercontent.com/VirtualBrainLab/vbl-aquarium/main/models/csharp/EphysLinkModels.cs", + "Assets/Scripts/EphysLink/EphysLinkModels.cs" + ) + ); + Debug.Log("Schemas updated successfully!"); } private static void GetSchemas(string srcURL, string outFile) { + if (!Directory.Exists(outFile)) Directory.CreateDirectory(outFile); - if (!Directory.Exists(outFile)) - { - Directory.CreateDirectory(outFile); - } + var files = Directory.GetFiles(srcURL, "*.cs"); - string[] files = Directory.GetFiles(srcURL, "*.cs"); - - foreach (string file in files) + foreach (var file in files) { - string fileName = Path.GetFileName(file); - string destFilePath = Path.Combine(outFile, fileName); + var fileName = Path.GetFileName(file); + var destFilePath = Path.Combine(outFile, fileName); File.Copy(file, destFilePath, true); } AssetDatabase.Refresh(); } + + private static IEnumerator DownloadFile(string url, string outputPath) + { + using var request = UnityWebRequest.Get(url); + yield return request.SendWebRequest(); + + if ( + request.result + is UnityWebRequest.Result.ConnectionError + or UnityWebRequest.Result.ProtocolError + ) + { + Debug.LogError(request.error); + } + else + { + File.WriteAllBytes(outputPath, request.downloadHandler.data); + Debug.Log("File downloaded successfully!"); + } + } } } \ No newline at end of file diff --git a/Assets/InputSystem/ProbeControlInputActions.cs b/Assets/InputSystem/ProbeControlInputActions.cs index 9e4f3182..684ba9f7 100644 --- a/Assets/InputSystem/ProbeControlInputActions.cs +++ b/Assets/InputSystem/ProbeControlInputActions.cs @@ -1,7 +1,7 @@ //------------------------------------------------------------------------------ // // This code was auto-generated by com.unity.inputsystem:InputActionCodeGenerator -// version 1.7.0 +// version 1.9.0 // from Assets/InputSystem/ProbeControlInputActions.inputactions // // Changes to this file may cause incorrect behavior and will be lost if @@ -14,6 +14,7 @@ using System.Collections.Generic; using UnityEngine.InputSystem; using UnityEngine.InputSystem.Utilities; +using UnityEngine; public partial class @ProbeControlInputActions: IInputActionCollection2, IDisposable { @@ -592,6 +593,11 @@ public @ProbeControlInputActions() m_ProbeControl_InputControl = m_ProbeControl.FindAction("InputControl", throwIfNotFound: true); } + ~@ProbeControlInputActions() + { + Debug.Assert(!m_ProbeControl.enabled, "This will cause a leak and performance issues, ProbeControlInputActions.ProbeControl.Disable() has not been called."); + } + public void Dispose() { UnityEngine.Object.Destroy(asset); diff --git a/Assets/InputSystem/ProbeMetaControls.cs b/Assets/InputSystem/ProbeMetaControls.cs index 535269b1..60696cc9 100644 --- a/Assets/InputSystem/ProbeMetaControls.cs +++ b/Assets/InputSystem/ProbeMetaControls.cs @@ -1,7 +1,7 @@ //------------------------------------------------------------------------------ // // This code was auto-generated by com.unity.inputsystem:InputActionCodeGenerator -// version 1.7.0 +// version 1.9.0 // from Assets/InputSystem/ProbeMetaControls.inputactions // // Changes to this file may cause incorrect behavior and will be lost if @@ -14,6 +14,7 @@ using System.Collections.Generic; using UnityEngine.InputSystem; using UnityEngine.InputSystem.Utilities; +using UnityEngine; public partial class @ProbeMetaControls: IInputActionCollection2, IDisposable { @@ -134,6 +135,11 @@ public @ProbeMetaControls() m_ProbeMetaControl_SwitchAxisMode = m_ProbeMetaControl.FindAction("SwitchAxisMode", throwIfNotFound: true); } + ~@ProbeMetaControls() + { + Debug.Assert(!m_ProbeMetaControl.enabled, "This will cause a leak and performance issues, ProbeMetaControls.ProbeMetaControl.Disable() has not been called."); + } + public void Dispose() { UnityEngine.Object.Destroy(asset); diff --git a/Assets/Materials/BrainRegion/BrainRegionOpaqueLit.mat b/Assets/Materials/BrainRegion/BrainRegionOpaqueLit.mat index 60f82caf..a34cc45b 100644 --- a/Assets/Materials/BrainRegion/BrainRegionOpaqueLit.mat +++ b/Assets/Materials/BrainRegion/BrainRegionOpaqueLit.mat @@ -18,7 +18,8 @@ Material: m_DoubleSidedGI: 0 m_CustomRenderQueue: -1 stringTagMap: {} - disabledShaderPasses: [] + disabledShaderPasses: + - MOTIONVECTORS m_LockedProperties: m_SavedProperties: serializedVersion: 3 @@ -120,6 +121,7 @@ Material: - _MLClip: {r: 0, g: 11.4, b: 0, a: 0} - _SpecColor: {r: 0.2, g: 0.2, b: 0.2, a: 1} m_BuildTextureStacks: [] + m_AllowLocking: 1 --- !u!114 &7950688029384146499 MonoBehaviour: m_ObjectHideFlags: 11 @@ -132,4 +134,4 @@ MonoBehaviour: m_Script: {fileID: 11500000, guid: d0353a89b1f911e48b9e16bdc9f2e058, type: 3} m_Name: m_EditorClassIdentifier: - version: 7 + version: 9 diff --git a/Assets/Materials/BrainRegion/BrainRegionOpaqueUnlit.mat b/Assets/Materials/BrainRegion/BrainRegionOpaqueUnlit.mat index ada06e3a..dcfd40ec 100644 --- a/Assets/Materials/BrainRegion/BrainRegionOpaqueUnlit.mat +++ b/Assets/Materials/BrainRegion/BrainRegionOpaqueUnlit.mat @@ -12,7 +12,7 @@ MonoBehaviour: m_Script: {fileID: 11500000, guid: d0353a89b1f911e48b9e16bdc9f2e058, type: 3} m_Name: m_EditorClassIdentifier: - version: 7 + version: 9 --- !u!21 &2100000 Material: serializedVersion: 8 @@ -31,7 +31,8 @@ Material: m_DoubleSidedGI: 0 m_CustomRenderQueue: -1 stringTagMap: {} - disabledShaderPasses: [] + disabledShaderPasses: + - MOTIONVECTORS m_LockedProperties: m_SavedProperties: serializedVersion: 3 @@ -127,3 +128,4 @@ Material: - _EmissionColor: {r: 0, g: 0, b: 0, a: 1} - _SpecColor: {r: 0.2, g: 0.2, b: 0.2, a: 1} m_BuildTextureStacks: [] + m_AllowLocking: 1 diff --git a/Assets/Materials/BrainRegion/BrainRegionTransparentLit.mat b/Assets/Materials/BrainRegion/BrainRegionTransparentLit.mat index 2b7b47d0..d83f19c0 100644 --- a/Assets/Materials/BrainRegion/BrainRegionTransparentLit.mat +++ b/Assets/Materials/BrainRegion/BrainRegionTransparentLit.mat @@ -18,7 +18,8 @@ Material: m_DoubleSidedGI: 0 m_CustomRenderQueue: -1 stringTagMap: {} - disabledShaderPasses: [] + disabledShaderPasses: + - MOTIONVECTORS m_LockedProperties: m_SavedProperties: serializedVersion: 3 @@ -117,6 +118,7 @@ Material: - _MLClip: {r: 0, g: 11.4, b: 0, a: 0} - _SpecColor: {r: 0.2, g: 0.2, b: 0.2, a: 1} m_BuildTextureStacks: [] + m_AllowLocking: 1 --- !u!114 &1531999738427662394 MonoBehaviour: m_ObjectHideFlags: 11 @@ -129,4 +131,4 @@ MonoBehaviour: m_Script: {fileID: 11500000, guid: d0353a89b1f911e48b9e16bdc9f2e058, type: 3} m_Name: m_EditorClassIdentifier: - version: 7 + version: 9 diff --git a/Assets/Materials/BrainRegion/BrainRegionTransparentUnlit.mat b/Assets/Materials/BrainRegion/BrainRegionTransparentUnlit.mat index 1eb713ba..0b0bfa8f 100644 --- a/Assets/Materials/BrainRegion/BrainRegionTransparentUnlit.mat +++ b/Assets/Materials/BrainRegion/BrainRegionTransparentUnlit.mat @@ -18,7 +18,8 @@ Material: m_DoubleSidedGI: 0 m_CustomRenderQueue: -1 stringTagMap: {} - disabledShaderPasses: [] + disabledShaderPasses: + - MOTIONVECTORS m_LockedProperties: m_SavedProperties: serializedVersion: 3 @@ -117,6 +118,7 @@ Material: - _MLClip: {r: 0, g: 11.4, b: 0, a: 0} - _SpecColor: {r: 0.2, g: 0.2, b: 0.2, a: 1} m_BuildTextureStacks: [] + m_AllowLocking: 1 --- !u!114 &1531999738427662394 MonoBehaviour: m_ObjectHideFlags: 11 @@ -129,4 +131,4 @@ MonoBehaviour: m_Script: {fileID: 11500000, guid: d0353a89b1f911e48b9e16bdc9f2e058, type: 3} m_Name: m_EditorClassIdentifier: - version: 7 + version: 9 diff --git a/Assets/Materials/CraniotomyMaterial.mat b/Assets/Materials/CraniotomyMaterial.mat index 812eb4bf..30c76e87 100644 --- a/Assets/Materials/CraniotomyMaterial.mat +++ b/Assets/Materials/CraniotomyMaterial.mat @@ -12,7 +12,7 @@ MonoBehaviour: m_Script: {fileID: 11500000, guid: d0353a89b1f911e48b9e16bdc9f2e058, type: 3} m_Name: m_EditorClassIdentifier: - version: 7 + version: 9 --- !u!21 &2100000 Material: serializedVersion: 8 @@ -36,6 +36,7 @@ Material: disabledShaderPasses: - SHADOWCASTER - DepthOnly + - MOTIONVECTORS m_LockedProperties: m_SavedProperties: serializedVersion: 3 @@ -134,3 +135,4 @@ Material: - _EmissionColor: {r: 0, g: 0, b: 0, a: 1} - _SpecColor: {r: 0.2, g: 0.2, b: 0.2, a: 1} m_BuildTextureStacks: [] + m_AllowLocking: 1 diff --git a/Assets/Materials/EphysAtlasLineMaterial.mat b/Assets/Materials/EphysAtlasLineMaterial.mat index 85ad055d..1aacc64f 100644 --- a/Assets/Materials/EphysAtlasLineMaterial.mat +++ b/Assets/Materials/EphysAtlasLineMaterial.mat @@ -12,7 +12,7 @@ MonoBehaviour: m_Script: {fileID: 11500000, guid: d0353a89b1f911e48b9e16bdc9f2e058, type: 3} m_Name: m_EditorClassIdentifier: - version: 7 + version: 9 --- !u!21 &2100000 Material: serializedVersion: 8 @@ -32,7 +32,8 @@ Material: m_CustomRenderQueue: 2000 stringTagMap: RenderType: Opaque - disabledShaderPasses: [] + disabledShaderPasses: + - MOTIONVECTORS m_LockedProperties: m_SavedProperties: serializedVersion: 3 @@ -132,3 +133,4 @@ Material: - _EmissionColor: {r: 0, g: 0, b: 0, a: 1} - _SpecColor: {r: 0.2, g: 0.2, b: 0.2, a: 1} m_BuildTextureStacks: [] + m_AllowLocking: 1 diff --git a/Assets/Materials/LitGrey.mat b/Assets/Materials/LitGrey.mat index d77a7d83..77016c03 100644 --- a/Assets/Materials/LitGrey.mat +++ b/Assets/Materials/LitGrey.mat @@ -19,7 +19,8 @@ Material: m_CustomRenderQueue: -1 stringTagMap: RenderType: Opaque - disabledShaderPasses: [] + disabledShaderPasses: + - MOTIONVECTORS m_LockedProperties: m_SavedProperties: serializedVersion: 3 @@ -118,6 +119,7 @@ Material: - _EmissionColor: {r: 0, g: 0, b: 0, a: 1} - _SpecColor: {r: 0.2, g: 0.2, b: 0.2, a: 1} m_BuildTextureStacks: [] + m_AllowLocking: 1 --- !u!114 &5545177365015435086 MonoBehaviour: m_ObjectHideFlags: 11 @@ -130,4 +132,4 @@ MonoBehaviour: m_Script: {fileID: 11500000, guid: d0353a89b1f911e48b9e16bdc9f2e058, type: 3} m_Name: m_EditorClassIdentifier: - version: 7 + version: 9 diff --git a/Assets/Materials/Probe/GoldConnectorCable.mat b/Assets/Materials/Probe/GoldConnectorCable.mat index 0eae63dc..364a8a18 100644 --- a/Assets/Materials/Probe/GoldConnectorCable.mat +++ b/Assets/Materials/Probe/GoldConnectorCable.mat @@ -12,7 +12,7 @@ MonoBehaviour: m_Script: {fileID: 11500000, guid: d0353a89b1f911e48b9e16bdc9f2e058, type: 3} m_Name: m_EditorClassIdentifier: - version: 7 + version: 9 --- !u!21 &2100000 Material: serializedVersion: 8 @@ -32,7 +32,8 @@ Material: m_CustomRenderQueue: 2000 stringTagMap: RenderType: Opaque - disabledShaderPasses: [] + disabledShaderPasses: + - MOTIONVECTORS m_LockedProperties: m_SavedProperties: serializedVersion: 3 @@ -131,3 +132,4 @@ Material: - _EmissionColor: {r: 0, g: 0, b: 0, a: 1} - _SpecColor: {r: 0.2, g: 0.2, b: 0.2, a: 1} m_BuildTextureStacks: [] + m_AllowLocking: 1 diff --git a/Assets/Materials/Probe/Green.mat b/Assets/Materials/Probe/Green.mat index 0b857a5a..987e0380 100644 --- a/Assets/Materials/Probe/Green.mat +++ b/Assets/Materials/Probe/Green.mat @@ -19,7 +19,8 @@ Material: m_CustomRenderQueue: 2000 stringTagMap: RenderType: Opaque - disabledShaderPasses: [] + disabledShaderPasses: + - MOTIONVECTORS m_LockedProperties: m_SavedProperties: serializedVersion: 3 @@ -118,6 +119,7 @@ Material: - _EmissionColor: {r: 0, g: 0, b: 0, a: 1} - _SpecColor: {r: 0.2, g: 0.2, b: 0.2, a: 1} m_BuildTextureStacks: [] + m_AllowLocking: 1 --- !u!114 &2484206933931674713 MonoBehaviour: m_ObjectHideFlags: 11 @@ -130,4 +132,4 @@ MonoBehaviour: m_Script: {fileID: 11500000, guid: d0353a89b1f911e48b9e16bdc9f2e058, type: 3} m_Name: m_EditorClassIdentifier: - version: 7 + version: 9 diff --git a/Assets/Materials/Probe/IBLProbeMaterial.mat b/Assets/Materials/Probe/IBLProbeMaterial.mat index 7fc4857e..4d29ecf1 100644 --- a/Assets/Materials/Probe/IBLProbeMaterial.mat +++ b/Assets/Materials/Probe/IBLProbeMaterial.mat @@ -20,7 +20,8 @@ Material: m_CustomRenderQueue: 2000 stringTagMap: RenderType: Opaque - disabledShaderPasses: [] + disabledShaderPasses: + - MOTIONVECTORS m_LockedProperties: m_SavedProperties: serializedVersion: 3 @@ -119,6 +120,7 @@ Material: - _EmissionColor: {r: 0, g: 0, b: 0, a: 1} - _SpecColor: {r: 0.2, g: 0.2, b: 0.2, a: 1} m_BuildTextureStacks: [] + m_AllowLocking: 1 --- !u!114 &8990643678099489018 MonoBehaviour: m_ObjectHideFlags: 11 @@ -131,4 +133,4 @@ MonoBehaviour: m_Script: {fileID: 11500000, guid: d0353a89b1f911e48b9e16bdc9f2e058, type: 3} m_Name: m_EditorClassIdentifier: - version: 7 + version: 9 diff --git a/Assets/Materials/Probe/LitBlackMaterial.mat b/Assets/Materials/Probe/LitBlackMaterial.mat index 52972597..d2023f9b 100644 --- a/Assets/Materials/Probe/LitBlackMaterial.mat +++ b/Assets/Materials/Probe/LitBlackMaterial.mat @@ -19,7 +19,8 @@ Material: m_CustomRenderQueue: 2000 stringTagMap: RenderType: Opaque - disabledShaderPasses: [] + disabledShaderPasses: + - MOTIONVECTORS m_LockedProperties: m_SavedProperties: serializedVersion: 3 @@ -118,6 +119,7 @@ Material: - _EmissionColor: {r: 0, g: 0, b: 0, a: 1} - _SpecColor: {r: 0.2, g: 0.2, b: 0.2, a: 1} m_BuildTextureStacks: [] + m_AllowLocking: 1 --- !u!114 &5791354437846213698 MonoBehaviour: m_ObjectHideFlags: 11 @@ -130,4 +132,4 @@ MonoBehaviour: m_Script: {fileID: 11500000, guid: d0353a89b1f911e48b9e16bdc9f2e058, type: 3} m_Name: m_EditorClassIdentifier: - version: 7 + version: 9 diff --git a/Assets/Materials/Probe/NeuronMaterial.mat b/Assets/Materials/Probe/NeuronMaterial.mat index b3f852bb..5b6403b5 100644 --- a/Assets/Materials/Probe/NeuronMaterial.mat +++ b/Assets/Materials/Probe/NeuronMaterial.mat @@ -18,7 +18,8 @@ Material: m_DoubleSidedGI: 0 m_CustomRenderQueue: -1 stringTagMap: {} - disabledShaderPasses: [] + disabledShaderPasses: + - MOTIONVECTORS m_LockedProperties: m_SavedProperties: serializedVersion: 3 @@ -115,6 +116,7 @@ Material: - _EmissionColor: {r: 0, g: 0, b: 0, a: 1} - _SpecColor: {r: 0.2, g: 0.2, b: 0.2, a: 1} m_BuildTextureStacks: [] + m_AllowLocking: 1 --- !u!114 &2666491075564505777 MonoBehaviour: m_ObjectHideFlags: 11 @@ -127,4 +129,4 @@ MonoBehaviour: m_Script: {fileID: 11500000, guid: d0353a89b1f911e48b9e16bdc9f2e058, type: 3} m_Name: m_EditorClassIdentifier: - version: 7 + version: 9 diff --git a/Assets/Materials/ProbeMaterial.mat b/Assets/Materials/ProbeMaterial.mat index f1cb3b87..3d15dd0b 100644 --- a/Assets/Materials/ProbeMaterial.mat +++ b/Assets/Materials/ProbeMaterial.mat @@ -12,7 +12,7 @@ MonoBehaviour: m_Script: {fileID: 11500000, guid: d0353a89b1f911e48b9e16bdc9f2e058, type: 3} m_Name: m_EditorClassIdentifier: - version: 7 + version: 9 --- !u!21 &2100000 Material: serializedVersion: 8 @@ -36,6 +36,7 @@ Material: disabledShaderPasses: - SHADOWCASTER - DepthOnly + - MOTIONVECTORS m_LockedProperties: m_SavedProperties: serializedVersion: 3 @@ -141,3 +142,4 @@ Material: - _EmissionColor: {r: 0, g: 0, b: 0, a: 1} - _SpecColor: {r: 0.2, g: 0.2, b: 0.2, a: 1} m_BuildTextureStacks: [] + m_AllowLocking: 1 diff --git a/Assets/Materials/ProbeTransparentMaterial.mat b/Assets/Materials/ProbeTransparentMaterial.mat index fc24d173..5c8d4d86 100644 --- a/Assets/Materials/ProbeTransparentMaterial.mat +++ b/Assets/Materials/ProbeTransparentMaterial.mat @@ -23,6 +23,7 @@ Material: disabledShaderPasses: - SHADOWCASTER - DepthOnly + - MOTIONVECTORS m_LockedProperties: m_SavedProperties: serializedVersion: 3 @@ -122,6 +123,7 @@ Material: - _EmissionColor: {r: 0, g: 0, b: 0, a: 1} - _SpecColor: {r: 0.2, g: 0.2, b: 0.2, a: 1} m_BuildTextureStacks: [] + m_AllowLocking: 1 --- !u!114 &8489137983973626414 MonoBehaviour: m_ObjectHideFlags: 11 @@ -134,4 +136,4 @@ MonoBehaviour: m_Script: {fileID: 11500000, guid: d0353a89b1f911e48b9e16bdc9f2e058, type: 3} m_Name: m_EditorClassIdentifier: - version: 7 + version: 9 diff --git a/Assets/Materials/SiteMaterial.mat b/Assets/Materials/SiteMaterial.mat index 6901fcce..763b1c9f 100644 --- a/Assets/Materials/SiteMaterial.mat +++ b/Assets/Materials/SiteMaterial.mat @@ -19,7 +19,8 @@ Material: m_CustomRenderQueue: 2000 stringTagMap: RenderType: Opaque - disabledShaderPasses: [] + disabledShaderPasses: + - MOTIONVECTORS m_LockedProperties: m_SavedProperties: serializedVersion: 3 @@ -120,6 +121,7 @@ Material: - _EmissionColor: {r: 0, g: 0, b: 0, a: 1} - _SpecColor: {r: 0.2, g: 0.2, b: 0.2, a: 1} m_BuildTextureStacks: [] + m_AllowLocking: 1 --- !u!114 &1523391536134859176 MonoBehaviour: m_ObjectHideFlags: 11 @@ -132,4 +134,4 @@ MonoBehaviour: m_Script: {fileID: 11500000, guid: d0353a89b1f911e48b9e16bdc9f2e058, type: 3} m_Name: m_EditorClassIdentifier: - version: 7 + version: 9 diff --git a/Assets/Materials/SkullMaterial.mat b/Assets/Materials/SkullMaterial.mat index d5ad3da1..5a4fd0e3 100644 --- a/Assets/Materials/SkullMaterial.mat +++ b/Assets/Materials/SkullMaterial.mat @@ -18,7 +18,8 @@ Material: m_DoubleSidedGI: 0 m_CustomRenderQueue: -1 stringTagMap: {} - disabledShaderPasses: [] + disabledShaderPasses: + - MOTIONVECTORS m_LockedProperties: m_SavedProperties: serializedVersion: 3 @@ -128,6 +129,7 @@ Material: - _EmissionColor: {r: 0, g: 0, b: 0, a: 1} - _SpecColor: {r: 0.2, g: 0.2, b: 0.2, a: 1} m_BuildTextureStacks: [] + m_AllowLocking: 1 --- !u!114 &1110752586801046589 MonoBehaviour: m_ObjectHideFlags: 11 @@ -140,4 +142,4 @@ MonoBehaviour: m_Script: {fileID: 11500000, guid: d0353a89b1f911e48b9e16bdc9f2e058, type: 3} m_Name: m_EditorClassIdentifier: - version: 7 + version: 9 diff --git a/Assets/Materials/SurfacePointMaterial.mat b/Assets/Materials/SurfacePointMaterial.mat index f023055d..4d724cf6 100644 --- a/Assets/Materials/SurfacePointMaterial.mat +++ b/Assets/Materials/SurfacePointMaterial.mat @@ -12,7 +12,7 @@ MonoBehaviour: m_Script: {fileID: 11500000, guid: d0353a89b1f911e48b9e16bdc9f2e058, type: 3} m_Name: m_EditorClassIdentifier: - version: 7 + version: 9 --- !u!21 &2100000 Material: serializedVersion: 8 @@ -34,7 +34,8 @@ Material: m_CustomRenderQueue: 2000 stringTagMap: RenderType: Opaque - disabledShaderPasses: [] + disabledShaderPasses: + - MOTIONVECTORS m_LockedProperties: m_SavedProperties: serializedVersion: 3 @@ -133,3 +134,4 @@ Material: - _EmissionColor: {r: 0, g: 0, b: 0, a: 1} - _SpecColor: {r: 0.2, g: 0.2, b: 0.2, a: 1} m_BuildTextureStacks: [] + m_AllowLocking: 1 diff --git a/Assets/Materials/TrajectoryPlanner/CollisionMaterial.mat b/Assets/Materials/TrajectoryPlanner/CollisionMaterial.mat index 3111132b..1e602bbe 100644 --- a/Assets/Materials/TrajectoryPlanner/CollisionMaterial.mat +++ b/Assets/Materials/TrajectoryPlanner/CollisionMaterial.mat @@ -12,7 +12,7 @@ MonoBehaviour: m_Script: {fileID: 11500000, guid: d0353a89b1f911e48b9e16bdc9f2e058, type: 3} m_Name: m_EditorClassIdentifier: - version: 7 + version: 9 --- !u!21 &2100000 Material: serializedVersion: 8 @@ -32,7 +32,8 @@ Material: m_CustomRenderQueue: 2000 stringTagMap: RenderType: Opaque - disabledShaderPasses: [] + disabledShaderPasses: + - MOTIONVECTORS m_LockedProperties: m_SavedProperties: serializedVersion: 3 @@ -132,3 +133,4 @@ Material: - _EmissionColor: {r: 0, g: 0, b: 0, a: 1} - _SpecColor: {r: 0.2, g: 0.2, b: 0.2, a: 1} m_BuildTextureStacks: [] + m_AllowLocking: 1 diff --git a/Assets/Materials/TrajectoryPlanner/ProbeRecordingChunk.mat b/Assets/Materials/TrajectoryPlanner/ProbeRecordingChunk.mat index 79c51bef..040bfce9 100644 --- a/Assets/Materials/TrajectoryPlanner/ProbeRecordingChunk.mat +++ b/Assets/Materials/TrajectoryPlanner/ProbeRecordingChunk.mat @@ -19,7 +19,8 @@ Material: m_CustomRenderQueue: 2000 stringTagMap: RenderType: Opaque - disabledShaderPasses: [] + disabledShaderPasses: + - MOTIONVECTORS m_LockedProperties: m_SavedProperties: serializedVersion: 3 @@ -119,6 +120,7 @@ Material: - _EmissionColor: {r: 0, g: 0, b: 0, a: 1} - _SpecColor: {r: 0.2, g: 0.2, b: 0.2, a: 1} m_BuildTextureStacks: [] + m_AllowLocking: 1 --- !u!114 &7200608012259704473 MonoBehaviour: m_ObjectHideFlags: 11 @@ -131,4 +133,4 @@ MonoBehaviour: m_Script: {fileID: 11500000, guid: d0353a89b1f911e48b9e16bdc9f2e058, type: 3} m_Name: m_EditorClassIdentifier: - version: 7 + version: 9 diff --git a/Assets/Materials/TrajectoryPlanner/SensapexMetal.mat b/Assets/Materials/TrajectoryPlanner/SensapexMetal.mat index cbc15fb0..55a8abce 100644 --- a/Assets/Materials/TrajectoryPlanner/SensapexMetal.mat +++ b/Assets/Materials/TrajectoryPlanner/SensapexMetal.mat @@ -19,7 +19,8 @@ Material: m_CustomRenderQueue: 2000 stringTagMap: RenderType: Opaque - disabledShaderPasses: [] + disabledShaderPasses: + - MOTIONVECTORS m_LockedProperties: m_SavedProperties: serializedVersion: 3 @@ -118,6 +119,7 @@ Material: - _EmissionColor: {r: 0, g: 0, b: 0, a: 1} - _SpecColor: {r: 0.2, g: 0.2, b: 0.2, a: 1} m_BuildTextureStacks: [] + m_AllowLocking: 1 --- !u!114 &4492099221454130244 MonoBehaviour: m_ObjectHideFlags: 11 @@ -130,4 +132,4 @@ MonoBehaviour: m_Script: {fileID: 11500000, guid: d0353a89b1f911e48b9e16bdc9f2e058, type: 3} m_Name: m_EditorClassIdentifier: - version: 7 + version: 9 diff --git a/Assets/Materials/Volume/InPlaneSliceMaterial.mat b/Assets/Materials/Volume/InPlaneSliceMaterial.mat index 1c529c41..cbb159ca 100644 --- a/Assets/Materials/Volume/InPlaneSliceMaterial.mat +++ b/Assets/Materials/Volume/InPlaneSliceMaterial.mat @@ -12,7 +12,7 @@ MonoBehaviour: m_Script: {fileID: 11500000, guid: d0353a89b1f911e48b9e16bdc9f2e058, type: 3} m_Name: m_EditorClassIdentifier: - version: 7 + version: 9 --- !u!21 &2100000 Material: serializedVersion: 8 @@ -31,7 +31,8 @@ Material: m_DoubleSidedGI: 0 m_CustomRenderQueue: -1 stringTagMap: {} - disabledShaderPasses: [] + disabledShaderPasses: + - MOTIONVECTORS m_LockedProperties: m_SavedProperties: serializedVersion: 3 @@ -154,3 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[EditorBrowsable(EditorBrowsableState.Never)] + public class IsExternalInit { } +} diff --git a/Assets/Scripts/Core/Util/IsExternalInit.cs.meta b/Assets/Scripts/Core/Util/IsExternalInit.cs.meta new file mode 100644 index 00000000..08f96bf0 --- /dev/null +++ b/Assets/Scripts/Core/Util/IsExternalInit.cs.meta @@ -0,0 +1,2 @@ +fileFormatVersion: 2 +guid: c889421ec241fbf448a0105d64279cea \ No newline at end of file diff --git a/Assets/Scripts/Core/Util/ResettingScriptableObject.cs b/Assets/Scripts/Core/Util/ResettingScriptableObject.cs new file mode 100644 index 00000000..fc90ac4e --- /dev/null +++ b/Assets/Scripts/Core/Util/ResettingScriptableObject.cs @@ -0,0 +1,31 @@ +using UnityEngine; +#if UNITY_EDITOR +using UnityEditor; +#endif + +namespace Core.Util +{ + public abstract class ResettingScriptableObject : ScriptableObject + { +#if UNITY_EDITOR + private string _initialJson = string.Empty; + + private void OnEnable() + { + if (Application.isPlaying) + return; + EditorApplication.playModeStateChanged -= OnPlayModeStateChanged; + EditorApplication.playModeStateChanged += OnPlayModeStateChanged; + _initialJson = EditorJsonUtility.ToJson(this); + } + + private void OnPlayModeStateChanged(PlayModeStateChange state) + { + if (state != PlayModeStateChange.ExitingPlayMode) + return; + EditorApplication.playModeStateChanged -= OnPlayModeStateChanged; + EditorJsonUtility.FromJsonOverwrite(_initialJson, this); + } +#endif + } +} diff --git a/Assets/Scripts/Core/Util/ResettingScriptableObject.cs.meta b/Assets/Scripts/Core/Util/ResettingScriptableObject.cs.meta new file mode 100644 index 00000000..6cdda06f --- /dev/null +++ b/Assets/Scripts/Core/Util/ResettingScriptableObject.cs.meta @@ -0,0 +1,2 @@ +fileFormatVersion: 2 +guid: 22194e125c099d94da23503a00587831 \ No newline at end of file diff --git a/Assets/Scripts/EphysLink/EphysLinkModels.cs b/Assets/Scripts/EphysLink/EphysLinkModels.cs index 67e98139..039b30b5 100644 --- a/Assets/Scripts/EphysLink/EphysLinkModels.cs +++ b/Assets/Scripts/EphysLink/EphysLinkModels.cs @@ -125,7 +125,7 @@ public SetInsideBrainRequest(string manipulatorId, bool inside) } } -; + [Serializable] public struct SetPositionRequest { diff --git a/Assets/Scripts/Pinpoint/Probes/ManipulatorBehaviorController.meta b/Assets/Scripts/Pinpoint/Probes/ManipulatorBehaviorController.meta new file mode 100644 index 00000000..ecaf62e5 --- /dev/null +++ b/Assets/Scripts/Pinpoint/Probes/ManipulatorBehaviorController.meta @@ -0,0 +1,8 @@ +fileFormatVersion: 2 +guid: c2bc1aabdb00c0948831ca62cc76473f +folderAsset: yes +DefaultImporter: + externalObjects: {} + userData: + assetBundleName: + assetBundleVariant: diff --git a/Assets/Scripts/Pinpoint/Probes/ManipulatorBehaviorController.cs b/Assets/Scripts/Pinpoint/Probes/ManipulatorBehaviorController/ManipulatorBehaviorController.cs similarity index 81% rename from Assets/Scripts/Pinpoint/Probes/ManipulatorBehaviorController.cs rename to Assets/Scripts/Pinpoint/Probes/ManipulatorBehaviorController/ManipulatorBehaviorController.cs index 694351a7..83719bb9 100644 --- a/Assets/Scripts/Pinpoint/Probes/ManipulatorBehaviorController.cs +++ b/Assets/Scripts/Pinpoint/Probes/ManipulatorBehaviorController/ManipulatorBehaviorController.cs @@ -8,9 +8,9 @@ using UnityEngine; using UnityEngine.Events; -namespace Pinpoint.Probes +namespace Pinpoint.Probes.ManipulatorBehaviorController { - public class ManipulatorBehaviorController : MonoBehaviour + public partial class ManipulatorBehaviorController : MonoBehaviour { #region Constants @@ -37,10 +37,10 @@ public class ManipulatorBehaviorController : MonoBehaviour public Vector3 Dimensions { get; private set; } - /** - * Getter and setter or the zero coordinate offset of the manipulator. - * If passed a NaN value, the previous value is kept. - */ + /// + /// Getter and setter or the zero coordinate offset of the manipulator. + /// If passed a NaN value, the previous value is kept. + /// public Vector4 ZeroCoordinateOffset { get => _zeroCoordinateOffset; @@ -67,18 +67,6 @@ public float BrainSurfaceOffset } } - public bool IsSetToDropToSurfaceWithDepth - { - get => _isSetToDropToSurfaceWithDepth; - set - { - if (BrainSurfaceOffset != 0) - return; - _isSetToDropToSurfaceWithDepth = value; - IsSetToDropToSurfaceWithDepthChangedEvent.Invoke(value); - } - } - public CoordinateSpace CoordinateSpace { get; private set; } private CoordinateTransform CoordinateTransform { get; set; } @@ -92,17 +80,17 @@ public bool IsRightHanded } } + public readonly ProbeAutomationStateManager ProbeAutomationStateManager = new(); + // Helper functions to create and destroy a probe public Action CreatePathfinderProbe { private get; set; } public Action DestroyThisProbe { private get; set; } #region Private internal fields - private Vector4 _lastManipulatorPosition = Vector4.zero; private Vector4 _lastLoggedManipulatorPosition = Vector4.zero; private Vector4 _zeroCoordinateOffset = Vector4.zero; private float _brainSurfaceOffset; - private bool _isSetToDropToSurfaceWithDepth = true; private bool _isRightHanded; private float _lastLoggedTime; private bool _isSetToInsideBrain; @@ -122,26 +110,17 @@ public bool IsRightHanded #region Unity /// - /// Setup this instance + /// Setup this instance. /// private void Awake() { // Start off as disabled enabled = false; - - // Update manipulator inside brain state - // _probeController.MovedThisFrameEvent.AddListener(() => - // { - // if (_isSetToInsideBrain != _probeManager.IsProbeInBrain()) - // CommunicationManager.Instance.SetInsideBrain(ManipulatorID, _probeManager.IsProbeInBrain(), - // insideBrain => - // { - // _isSetToInsideBrain = insideBrain; - // _probeController.UnlockedDir = insideBrain ? new Vector4(0, 0, 0, 1) : Vector4.one; - // }); - // }); } + /// + /// Cleanup this instance. + /// private void OnDisable() { ManipulatorID = null; @@ -154,6 +133,12 @@ private void OnDisable() #region Public Methods + /// + /// Initialize the manipulator behavior controller with the given manipulator ID and calibration status.
+ /// Starts to echo the manipulator position and locks the manipulator from manual control. + /// + /// ID of the manipulator to represent. + /// Whether this manipulator has been calibrated. public void Initialize(string manipulatorID, bool calibrated) { CommunicationManager.Instance.GetManipulators(response => @@ -191,6 +176,9 @@ void StartEchoing() }); } + /// + /// Configure this manipulator's coordinate space and transform based on its handedness, number of axes, and angles. + /// private void UpdateSpaceAndTransform() { CoordinateSpace = new ManipulatorSpace(Dimensions); @@ -213,11 +201,16 @@ private void UpdateSpaceAndTransform() }; } + /// + /// Convert insertion AP, ML, DV coordinates to manipulator translation stage position. + /// + /// AP, ML, DV coordinates from an insertion. + /// Computed manipulator translation stage positions to match this coordinate. public Vector4 ConvertInsertionAPMLDVToManipulatorPosition(Vector3 insertionAPMLDV) { // Convert apmldv to world coordinate - var convertToWorld = _probeManager.ProbeController.Insertion.T2World_Vector( - insertionAPMLDV + var convertToWorld = BrainAtlasManager.ActiveReferenceAtlas.Atlas2World_Vector( + BrainAtlasManager.ActiveAtlasTransform.T2U_Vector(insertionAPMLDV) ); // Convert to Manipulator space @@ -225,16 +218,28 @@ public Vector4 ConvertInsertionAPMLDVToManipulatorPosition(Vector3 insertionAPML Vector4 posInManipulatorTransform = CoordinateTransform.U2T(posInManipulatorSpace); // Apply brain surface offset - var brainSurfaceAdjustment = float.IsNaN(BrainSurfaceOffset) ? 0 : BrainSurfaceOffset; - if (_probeManager.ManipulatorBehaviorController.IsSetToDropToSurfaceWithDepth) - posInManipulatorTransform.w -= brainSurfaceAdjustment; - else - posInManipulatorTransform.z += brainSurfaceAdjustment; + posInManipulatorTransform.w -= float.IsNaN(BrainSurfaceOffset) ? 0 : BrainSurfaceOffset; // Apply coordinate offsets and return result return posInManipulatorTransform + ZeroCoordinateOffset; } + /// + /// Compute if a given AP, ML, DV coordinate is within the manipulator's reach. + /// + /// Coordinate to check. + /// True if the coordinates are within the bounds, false otherwise. + public bool IsAPMLDVWithinManipulatorBounds(Vector3 apmldv) + { + var manipulatorPosition = ConvertInsertionAPMLDVToManipulatorPosition(apmldv); + return !(manipulatorPosition.x < 0) + && !(manipulatorPosition.x > Dimensions.x) + && !(manipulatorPosition.y < 0) + && !(manipulatorPosition.y > Dimensions.y) + && !(manipulatorPosition.z < 0) + && !(manipulatorPosition.z > Dimensions.z); + } + /// /// Set manipulator space offset from brain surface as Depth from manipulator or probe coordinates. /// @@ -248,9 +253,7 @@ public void ComputeBrainSurfaceOffset() else { // We need to calculate the surface coordinate ourselves - var (brainSurfaceCoordinateIdx, _) = _probeManager.CalculateEntryCoordinate( - !IsSetToDropToSurfaceWithDepth - ); + var (brainSurfaceCoordinateIdx, _) = _probeManager.CalculateEntryCoordinate(); if (float.IsNaN(brainSurfaceCoordinateIdx.x)) { @@ -258,8 +261,12 @@ public void ComputeBrainSurfaceOffset() return; } - var brainSurfaceToTransformed = _probeController.Insertion.World2T( - BrainAtlasManager.ActiveReferenceAtlas.AtlasIdx2World(brainSurfaceCoordinateIdx) + var brainSurfaceToTransformed = BrainAtlasManager.ActiveAtlasTransform.U2T( + BrainAtlasManager.ActiveReferenceAtlas.World2Atlas( + BrainAtlasManager.ActiveReferenceAtlas.AtlasIdx2World( + brainSurfaceCoordinateIdx + ) + ) ); BrainSurfaceOffset += Vector3.Distance( @@ -379,19 +386,16 @@ Action onErrorCallBack #region Private Methods + /// + /// Given a manipulator position, set the probe position to match. + /// + /// Absolute manipulator translation stage position. private void EchoPosition(Vector4 pos) { // Exit if disabled and there is no probe controller. if (!enabled && _probeController == null) 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. var zeroCoordinateAdjustedManipulatorPosition = pos - ZeroCoordinateOffset; @@ -402,16 +406,9 @@ private void EchoPosition(Vector4 pos) // Brain surface adjustment. var brainSurfaceAdjustment = float.IsNaN(BrainSurfaceOffset) ? 0 : BrainSurfaceOffset; - if (IsSetToDropToSurfaceWithDepth) - { - // Apply depth adjustment to manipulator position for non-3 axis manipulators. - if (CoordinateTransform.Prefix != "3lhm") - zeroCoordinateAdjustedManipulatorPosition.w += brainSurfaceAdjustment; - } - else - { - manipulatorSpacePosition.y -= brainSurfaceAdjustment; - } + // Apply depth adjustment to manipulator position for non-3 axis manipulators. + if (CoordinateTransform.Prefix != "3lhm") + zeroCoordinateAdjustedManipulatorPosition.w += brainSurfaceAdjustment; // Convert to world space. var zeroCoordinateAdjustedWorldPosition = CoordinateSpace.Space2World( @@ -426,21 +423,15 @@ private void EchoPosition(Vector4 pos) // Set probe position. // For 3-axis manipulators, use depth to adjust brain offset if applying offset on depth. if (CoordinateTransform.Prefix == "3lhm") - { - if (IsSetToDropToSurfaceWithDepth) - _probeController.SetProbePosition( - new Vector4( - transformedApmldv.x, - transformedApmldv.y, - transformedApmldv.z, - brainSurfaceAdjustment - ) - ); - else - _probeController.SetProbePosition(transformedApmldv); - } + _probeController.SetProbePosition( + new Vector4( + transformedApmldv.x, + transformedApmldv.y, + transformedApmldv.z, + brainSurfaceAdjustment + ) + ); else - { _probeController.SetProbePosition( new Vector4( transformedApmldv.x, @@ -449,7 +440,6 @@ private void EchoPosition(Vector4 pos) zeroCoordinateAdjustedManipulatorPosition.w ) ); - } // Log and continue echoing LogAndContinue(); diff --git a/Assets/Scripts/Pinpoint/Probes/ManipulatorBehaviorController.cs.meta b/Assets/Scripts/Pinpoint/Probes/ManipulatorBehaviorController/ManipulatorBehaviorController.cs.meta similarity index 100% rename from Assets/Scripts/Pinpoint/Probes/ManipulatorBehaviorController.cs.meta rename to Assets/Scripts/Pinpoint/Probes/ManipulatorBehaviorController/ManipulatorBehaviorController.cs.meta diff --git a/Assets/Scripts/Pinpoint/Probes/ManipulatorBehaviorController/ManipulatorBehaviorController_Automation_BregmaCalibration.cs b/Assets/Scripts/Pinpoint/Probes/ManipulatorBehaviorController/ManipulatorBehaviorController_Automation_BregmaCalibration.cs new file mode 100644 index 00000000..ab28beca --- /dev/null +++ b/Assets/Scripts/Pinpoint/Probes/ManipulatorBehaviorController/ManipulatorBehaviorController_Automation_BregmaCalibration.cs @@ -0,0 +1,79 @@ +using System; +using System.Globalization; +using EphysLink; +using UnityEngine; + +namespace Pinpoint.Probes.ManipulatorBehaviorController +{ + public partial class ManipulatorBehaviorController + { + #region Constants + + /// + /// How far the depth axis can be off center of its range before the user is warned. + /// + /// Applies to 3-axis manipulators when calibrating. + private const float CENTER_DEVIATION_FACTOR = 0.125f; + + #endregion + + /// + /// Reset zero coordinate of the manipulator + /// + /// + /// Alerts user of 4-axis manipulators if depth axis is not at 0 and 3-axis manipulators if depth is too far from + /// center. + /// + public void ResetZeroCoordinate() + { + CommunicationManager.Instance.GetPosition( + ManipulatorID, + zeroCoordinate => + { + // Setup alert affirmative callback (continue with reset). + QuestionDialogue.Instance.YesCallback = DoReset; + + // Check depth position and alert. + switch (NumAxes) + { + case 3 + when Mathf.Abs(Dimensions.z / 2f - zeroCoordinate.w) + > CENTER_DEVIATION_FACTOR * Dimensions.z: + QuestionDialogue.Instance.NewQuestion( + "The depth axis is too far from the center of its range and may not have enough space to reach the target. Are you sure you want to continue?" + ); + break; + case 4 when Mathf.Approximately(zeroCoordinate.w, 0f): + QuestionDialogue.Instance.NewQuestion( + "The depth axis is not at 0 and may not have enough space to reach the target. Are you sure you want to continue?" + ); + break; + default: + DoReset(); + break; + } + + return; + + void DoReset() + { + ZeroCoordinateOffset = zeroCoordinate; + BrainSurfaceOffset = 0; + + // Log event. + OutputLog.Log( + new[] + { + "Copilot", + DateTime.Now.ToString(CultureInfo.InvariantCulture), + "ResetZeroCoordinate", + ManipulatorID, + ZeroCoordinateOffset.ToString() + } + ); + } + } + ); + } + } +} diff --git a/Assets/Scripts/Pinpoint/Probes/ManipulatorBehaviorController/ManipulatorBehaviorController_Automation_BregmaCalibration.cs.meta b/Assets/Scripts/Pinpoint/Probes/ManipulatorBehaviorController/ManipulatorBehaviorController_Automation_BregmaCalibration.cs.meta new file mode 100644 index 00000000..a0c24d89 --- /dev/null +++ b/Assets/Scripts/Pinpoint/Probes/ManipulatorBehaviorController/ManipulatorBehaviorController_Automation_BregmaCalibration.cs.meta @@ -0,0 +1,2 @@ +fileFormatVersion: 2 +guid: 2f99a30517f49f04fa41d8524a7c4357 \ No newline at end of file diff --git a/Assets/Scripts/Pinpoint/Probes/ManipulatorBehaviorController/ManipulatorBehaviorController_Automation_DuraCalibration.cs b/Assets/Scripts/Pinpoint/Probes/ManipulatorBehaviorController/ManipulatorBehaviorController_Automation_DuraCalibration.cs new file mode 100644 index 00000000..934caa08 --- /dev/null +++ b/Assets/Scripts/Pinpoint/Probes/ManipulatorBehaviorController/ManipulatorBehaviorController_Automation_DuraCalibration.cs @@ -0,0 +1,58 @@ +using System; +using System.Globalization; +using EphysLink; +using UnityEngine; + +namespace Pinpoint.Probes.ManipulatorBehaviorController +{ + /// + /// Manage the Dura calibration of the manipulator. + /// + public partial class ManipulatorBehaviorController + { + #region Properties + + /// + /// Record of the manipulator's depth coordinate at the Dura. + /// + private float _duraDepth; + + /// + /// Record of the probe's coordinate at the Dura. + /// + private Vector3 _duraCoordinate; + + #endregion + + /// + /// Reset the dura offset of the probe and enable the next step + /// + public void ResetDuraOffset() + { + // Reset dura offset. + ComputeBrainSurfaceOffset(); + + // Record the dura depth. + CommunicationManager.Instance.GetPosition( + ManipulatorID, + pos => + { + _duraDepth = pos.w; + _duraCoordinate = _probeController.Insertion.APMLDV; + } + ); + + // Log the event. + OutputLog.Log( + new[] + { + "Automation", + DateTime.Now.ToString(CultureInfo.InvariantCulture), + "ResetDuraOffset", + ManipulatorID, + BrainSurfaceOffset.ToString(CultureInfo.InvariantCulture) + } + ); + } + } +} diff --git a/Assets/Scripts/Pinpoint/Probes/ManipulatorBehaviorController/ManipulatorBehaviorController_Automation_DuraCalibration.cs.meta b/Assets/Scripts/Pinpoint/Probes/ManipulatorBehaviorController/ManipulatorBehaviorController_Automation_DuraCalibration.cs.meta new file mode 100644 index 00000000..9368860b --- /dev/null +++ b/Assets/Scripts/Pinpoint/Probes/ManipulatorBehaviorController/ManipulatorBehaviorController_Automation_DuraCalibration.cs.meta @@ -0,0 +1,2 @@ +fileFormatVersion: 2 +guid: 0609c7d3d307feb4cb539412cc7669ec diff --git a/Assets/Scripts/Pinpoint/Probes/ManipulatorBehaviorController/ManipulatorBehaviorController_Automation_Insertion.cs b/Assets/Scripts/Pinpoint/Probes/ManipulatorBehaviorController/ManipulatorBehaviorController_Automation_Insertion.cs new file mode 100644 index 00000000..24cea222 --- /dev/null +++ b/Assets/Scripts/Pinpoint/Probes/ManipulatorBehaviorController/ManipulatorBehaviorController_Automation_Insertion.cs @@ -0,0 +1,471 @@ +using System; +using System.Globalization; +using BrainAtlas; +using EphysLink; +using UnityEngine; + +namespace Pinpoint.Probes.ManipulatorBehaviorController +{ + public partial class ManipulatorBehaviorController + { + #region Constants + + #region Relative distances + + /// + /// Extra safety margin for the Dura to outside to ensure probe is fully retracted (mm). + /// + private const float DURA_MARGIN_DISTANCE = 0.2f; + + /// + /// Distance from target to start slowing down probe (mm). + /// + private const float NEAR_TARGET_DISTANCE = 1f; + + #endregion + + #region Speed multipliers + + /// + /// Slowdown factor for the probe when it is near the target. + /// + private const float NEAR_TARGET_SPEED_MULTIPLIER = 2f / 3f; + + /// + /// Extra speed multiplier for the probe when it is exiting. + /// + private const int EXIT_DRIVE_SPEED_MULTIPLIER = 6; + + /// + /// Speed multiplier of the probe once outside the brain. + /// + private const int OUTSIDE_DRIVE_SPEED_MULTIPLIER = 50; + + #endregion + + #endregion + + #region Properties + + /// + /// Is the probe driving in the insertion cycle? + /// + /// Used to identify which buttons should be made available. + public bool IsMoving { get; private set; } + + #region Caches + + private Vector3 _cachedTargetCoordinate = Vector3.negativeInfinity; + private Vector3 _cachedOffsetAdjustedTargetCoordinate = Vector3.negativeInfinity; + + #endregion + + #endregion + + #region Drive Functions + + /// + /// Start or resume inserting the probe to the target insertion. + /// + /// Probe manager for the target insertion. + /// Base driving speed in mm/s. + /// Distance to drive past target in mm. + /// Probe is not in a drivable state. + /// Unhandled probe drive state. + public void Drive( + ProbeManager targetInsertionProbeManager, + float baseSpeed, + float drivePastDistance + ) + { + // Throw exception if invariant is violated. + if (!ProbeAutomationStateManager.IsInsertable()) + throw new InvalidOperationException( + "Cannot drive to target insertion if the probe is not in a drivable state." + ); + + // Get target depth. + var targetDepth = GetTargetDepth(targetInsertionProbeManager); + + // Set state to driving state (if needed). + ProbeAutomationStateManager.SetToInsertionDrivingState(); + + // Log set to driving state. + LogDrive(targetDepth, baseSpeed, drivePastDistance); + + // Set probe to be moving. + IsMoving = true; + + // Handle driving state. + switch (ProbeAutomationStateManager.ProbeAutomationState) + { + case ProbeAutomationState.DrivingToNearTarget: + // Drive to near target if not already there. + if ( + GetCurrentDistanceToTarget(targetInsertionProbeManager) + > NEAR_TARGET_DISTANCE + ) + CommunicationManager.Instance.SetDepth( + new SetDepthRequest( + ManipulatorID, + targetDepth - NEAR_TARGET_DISTANCE, + baseSpeed + ), + _ => CompleteDriveStep(), + Debug.LogError + ); + // Skip to next step if already through near target. + else + CompleteDriveStep(); + break; + case ProbeAutomationState.DrivingToPastTarget: + // Drive to past target. + CommunicationManager.Instance.SetDepth( + new SetDepthRequest( + ManipulatorID, + targetDepth + drivePastDistance, + baseSpeed * NEAR_TARGET_SPEED_MULTIPLIER + ), + _ => CompleteDriveStep(), + Debug.LogError + ); + break; + case ProbeAutomationState.ReturningToTarget: + // Drive up to target. + CommunicationManager.Instance.SetDepth( + new SetDepthRequest( + ManipulatorID, + targetDepth, + baseSpeed * NEAR_TARGET_SPEED_MULTIPLIER + ), + _ => CompleteDriveStep(), + Debug.LogError + ); + break; + case ProbeAutomationState.IsUncalibrated: + case ProbeAutomationState.IsCalibrated: + case ProbeAutomationState.DrivingToTargetEntryCoordinate: + case ProbeAutomationState.AtEntryCoordinate: + case ProbeAutomationState.AtDuraInsert: + case ProbeAutomationState.AtNearTargetInsert: + case ProbeAutomationState.AtPastTarget: + case ProbeAutomationState.AtTarget: + case ProbeAutomationState.ExitingToNearTarget: + case ProbeAutomationState.AtNearTargetExit: + case ProbeAutomationState.ExitingToDura: + case ProbeAutomationState.AtDuraExit: + case ProbeAutomationState.ExitingToMargin: + case ProbeAutomationState.AtExitMargin: + case ProbeAutomationState.ExitingToTargetEntryCoordinate: + case ProbeAutomationState.DrivingToBregma: + throw new InvalidOperationException( + $"Not a valid driving state: {ProbeAutomationStateManager.ProbeAutomationState}" + ); + default: + throw new ArgumentOutOfRangeException( + $"Unhandled probe drive state: {ProbeAutomationStateManager.ProbeAutomationState}" + ); + } + + return; + + // Increment the state in the insertion cycle and call drive if not at target yet. + void CompleteDriveStep() + { + // Increment cycle state. + ProbeAutomationStateManager.IncrementInsertionCycleState(); + + // Log the event. + LogDrive(targetDepth, baseSpeed, drivePastDistance); + + // Call drive if not at target yet. + if ( + ProbeAutomationStateManager.ProbeAutomationState + != ProbeAutomationState.AtTarget + ) + Drive(targetInsertionProbeManager, baseSpeed, drivePastDistance); + // Set probe to be done moving. + else + IsMoving = false; + } + } + + /// + /// Stop the probe's movement. + /// + public void Stop() + { + CommunicationManager.Instance.Stop( + ManipulatorID, + () => + { + // Set probe to be not moving. + IsMoving = false; + + // Log stop event. + OutputLog.Log( + new[] + { + "Automation", + DateTime.Now.ToString(CultureInfo.InvariantCulture), + "Drive", + ManipulatorID, + "Stop" + } + ); + }, + Debug.LogError + ); + } + + /// + /// Start or resume exiting the probe to the target insertion. + /// + /// Probe manager for the target insertion. + /// Base driving speed in mm/s. + /// Probe is not in an exitable state. + /// Unhandled probe exit state. + public void Exit(ProbeManager targetInsertionProbeManager, float baseSpeed) + { + // Throw exception if state is not valid. + if (!ProbeAutomationStateManager.IsExitable()) + throw new InvalidOperationException( + "Cannot exit to target insertion if the probe is not in a state that can exit." + ); + + // Get target depth. + var targetDepth = GetTargetDepth(targetInsertionProbeManager); + + // Set state to exiting state (if needed). + ProbeAutomationStateManager.SetToExitingDrivingState(); + + // Log set to exiting state. + LogDrive(targetDepth, baseSpeed); + + // Set probe to be moving. + IsMoving = true; + + // Handle exiting state. + switch (ProbeAutomationStateManager.ProbeAutomationState) + { + case ProbeAutomationState.ExitingToNearTarget: + // Exit to near target if not already there. + if ( + GetCurrentDistanceToTarget(targetInsertionProbeManager) + < NEAR_TARGET_DISTANCE + ) + CommunicationManager.Instance.SetDepth( + new SetDepthRequest( + ManipulatorID, + targetDepth - NEAR_TARGET_DISTANCE, + baseSpeed + * EXIT_DRIVE_SPEED_MULTIPLIER + * NEAR_TARGET_SPEED_MULTIPLIER + ), + _ => CompleteExitStep(), + Debug.LogError + ); + // Skip to next step if already above near target. + else + CompleteExitStep(); + break; + case ProbeAutomationState.ExitingToDura: + // Exit back up to the Dura. + CommunicationManager.Instance.SetDepth( + new SetDepthRequest( + ManipulatorID, + _duraDepth, + baseSpeed * EXIT_DRIVE_SPEED_MULTIPLIER + ), + _ => CompleteExitStep(), + Debug.LogError + ); + break; + case ProbeAutomationState.ExitingToMargin: + // Exit to the safe margin above the Dura. + CommunicationManager.Instance.SetDepth( + new SetDepthRequest( + ManipulatorID, + _duraDepth - DURA_MARGIN_DISTANCE, + baseSpeed * EXIT_DRIVE_SPEED_MULTIPLIER + ), + _ => CompleteExitStep(), + Debug.LogError + ); + break; + case ProbeAutomationState.ExitingToTargetEntryCoordinate: + // Drive to the target entry coordinate (same place before calibrating to the Dura). + CommunicationManager.Instance.SetPosition( + new SetPositionRequest( + ManipulatorID, + ConvertInsertionAPMLDVToManipulatorPosition( + _trajectoryCoordinates.third + ), + AUTOMATIC_MOVEMENT_SPEED + ), + _ => CompleteExitStep(), + Debug.LogError + ); + break; + case ProbeAutomationState.IsUncalibrated: + case ProbeAutomationState.IsCalibrated: + case ProbeAutomationState.DrivingToTargetEntryCoordinate: + case ProbeAutomationState.AtEntryCoordinate: + case ProbeAutomationState.AtDuraInsert: + case ProbeAutomationState.DrivingToNearTarget: + case ProbeAutomationState.AtNearTargetInsert: + case ProbeAutomationState.DrivingToPastTarget: + case ProbeAutomationState.AtPastTarget: + case ProbeAutomationState.ReturningToTarget: + case ProbeAutomationState.AtTarget: + case ProbeAutomationState.AtNearTargetExit: + case ProbeAutomationState.AtDuraExit: + case ProbeAutomationState.AtExitMargin: + case ProbeAutomationState.DrivingToBregma: + throw new InvalidOperationException( + $"Not a valid exit state: {ProbeAutomationStateManager.ProbeAutomationState}" + ); + default: + throw new ArgumentOutOfRangeException( + $"Unhandled probe exit state: {ProbeAutomationStateManager.ProbeAutomationState}" + ); + } + + return; + + // Increment the state in the insertion cycle and call exit if not at entry coordinate yet. + void CompleteExitStep() + { + // Increment cycle state. + ProbeAutomationStateManager.IncrementInsertionCycleState(); + + // Log the event. + LogDrive(targetDepth, baseSpeed); + + // Call exit if not back at entry coordinate yet. + if ( + ProbeAutomationStateManager.ProbeAutomationState + != ProbeAutomationState.AtEntryCoordinate + ) + { + Exit(targetInsertionProbeManager, baseSpeed); + } + // Set probe to be done moving and remove Dura offset. + else + { + IsMoving = false; + BrainSurfaceOffset = 0; + } + } + } + + #endregion + + #region Helper Functions + + /// + /// Log a drive event. + /// + /// Target depth of drive. + /// Base speed of drive. + /// Distance (mm) driven past the target. Only supplied in insertion drives. + private void LogDrive(float targetDepth, float baseSpeed, float drivePastDistance = 0) + { + OutputLog.Log( + new[] + { + "Automation", + DateTime.Now.ToString(CultureInfo.InvariantCulture), + "Drive", + ManipulatorID, + ProbeAutomationStateManager.ProbeAutomationState.ToString(), + targetDepth.ToString(CultureInfo.InvariantCulture), + baseSpeed.ToString(CultureInfo.InvariantCulture), + drivePastDistance.ToString(CultureInfo.InvariantCulture) + } + ); + } + + /// + /// Compute the target coordinate adjusted for the probe's actual position. + /// + /// + /// APMLDV coordinates of where the probe should actually go. + private Vector3 GetOffsetAdjustedTargetCoordinate(ProbeManager targetInsertionProbeManager) + { + // Extract target insertion. + var targetInsertion = targetInsertionProbeManager.ProbeController.Insertion; + + // Shortcut exit if already computed and targetInsertion did not change. + if ( + targetInsertion.APMLDV == _cachedTargetCoordinate + && !float.IsNegativeInfinity(_cachedOffsetAdjustedTargetCoordinate.x) + ) + return _cachedOffsetAdjustedTargetCoordinate; + + var targetWorldT = targetInsertion.PositionWorldT(); + var relativePositionWorldT = _probeController.Insertion.PositionWorldT() - targetWorldT; + var probeTipTForward = _probeController.ProbeTipT.forward; + var offsetAdjustedRelativeTargetPositionWorldT = Vector3.ProjectOnPlane( + relativePositionWorldT, + probeTipTForward + ); + var offsetAdjustedTargetCoordinateWorldT = + targetWorldT + offsetAdjustedRelativeTargetPositionWorldT; + + // Converting worldT to AtlasT (to capture new Bregma offset when there is scaling) + // then switch axes to get APMLDV. + var offsetAdjustedTargetCoordinateAtlasT = + BrainAtlasManager.ActiveReferenceAtlas.World2Atlas( + offsetAdjustedTargetCoordinateWorldT + ); + var offsetAdjustedTargetCoordinateT = BrainAtlasManager.ActiveAtlasTransform.U2T_Vector( + offsetAdjustedTargetCoordinateAtlasT + ); + + // Cache the computed values. + _cachedTargetCoordinate = targetInsertion.APMLDV; + _cachedOffsetAdjustedTargetCoordinate = offsetAdjustedTargetCoordinateT; + + return _cachedOffsetAdjustedTargetCoordinate; + } + + /// + /// Compute the absolute distance from the target insertion to the Dura. + /// + /// Target to computer distance to. + /// Distance in mm to the target from the Dura. + private float GetTargetDistanceToDura(ProbeManager targetInsertionProbeManager) + { + return Vector3.Distance( + GetOffsetAdjustedTargetCoordinate(targetInsertionProbeManager), + _duraCoordinate + ); + } + + /// + /// Compute the current distance to the target insertion. + /// + /// + /// Distance in mm to the target from the probe. + private float GetCurrentDistanceToTarget(ProbeManager targetInsertionProbeManager) + { + return Vector3.Distance( + _probeController.Insertion.APMLDV, + GetOffsetAdjustedTargetCoordinate(targetInsertionProbeManager) + ); + } + + /// + /// Compute the target depth for the probe to drive to. + /// + /// Target to drive (insert) to. + /// The depth the manipulator needs to drive to reach the target insertion. + private float GetTargetDepth(ProbeManager targetInsertionProbeManager) + { + return _duraDepth + GetTargetDistanceToDura(targetInsertionProbeManager); + } + + #endregion + } +} diff --git a/Assets/Scripts/Pinpoint/Probes/ManipulatorBehaviorController/ManipulatorBehaviorController_Automation_Insertion.cs.meta b/Assets/Scripts/Pinpoint/Probes/ManipulatorBehaviorController/ManipulatorBehaviorController_Automation_Insertion.cs.meta new file mode 100644 index 00000000..3bf4072a --- /dev/null +++ b/Assets/Scripts/Pinpoint/Probes/ManipulatorBehaviorController/ManipulatorBehaviorController_Automation_Insertion.cs.meta @@ -0,0 +1,2 @@ +fileFormatVersion: 2 +guid: bbc85cfb8bef2b54a8d4643231d64cf7 diff --git a/Assets/Scripts/Pinpoint/Probes/ManipulatorBehaviorController/ManipulatorBehaviorController_Automation_TargetInsertion.cs b/Assets/Scripts/Pinpoint/Probes/ManipulatorBehaviorController/ManipulatorBehaviorController_Automation_TargetInsertion.cs new file mode 100644 index 00000000..84c047f3 --- /dev/null +++ b/Assets/Scripts/Pinpoint/Probes/ManipulatorBehaviorController/ManipulatorBehaviorController_Automation_TargetInsertion.cs @@ -0,0 +1,360 @@ +using System; +using System.Globalization; +using BrainAtlas; +using EphysLink; +using UnityEngine; + +namespace Pinpoint.Probes.ManipulatorBehaviorController +{ + public partial class ManipulatorBehaviorController + { + #region Constants + + // Axes colors. + private static readonly Color AP_COLOR = new(1, 0.3215686f, 0.3215686f); + private static readonly Color ML_COLOR = new(0.2039216f, 0.6745098f, 0.8784314f); + private static readonly Color DV_COLOR = new(1, 0.854902f, 0.4745098f); + + // Trajectory line properties. + private const float LINE_WIDTH = 0.1f; + private const int NUM_SEGMENTS = 2; + + // Trajectory values. + public static readonly Vector3 PRE_DEPTH_DRIVE_DV_OFFSET = new(0, 3.5f, 0); + + /// + /// Distance from the entry coordinate to the Dura. This is considered a safe distance to put the probe. + /// + private const float ENTRY_COORDINATE_DURA_DISTANCE = 3.5f; + + #endregion + + #region Components + + private (GameObject ap, GameObject ml, GameObject dv) _trajectoryLineGameObjects; + private (LineRenderer ap, LineRenderer ml, LineRenderer dv) _trajectoryLineLineRenderers; + + #endregion + + #region Properties + + /// + /// Trajectory broken into 3 stages (for 3 axes of movement). + /// + /// Execution order: DV, AP, ML. Defaults to negative infinity when there is no trajectory. + private (Vector3 first, Vector3 second, Vector3 third) _trajectoryCoordinates = ( + Vector3.negativeInfinity, + Vector3.negativeInfinity, + Vector3.negativeInfinity + ); + + #endregion + + #region Public Functions + + /// + /// Compute the entry coordinate and trajectory for the target insertion. Also, draw the trajectory lines. + /// + /// Probe manager of the target insertion + /// + /// The computed entry coordinate in AP, ML, DV coordinates. Negative infinity if target is unset or already + /// there. + /// + public Vector3 ComputeEntryCoordinateTrajectory(ProbeManager targetInsertionProbeManager) + { + // If set to null or already past the entry coordinate, cleanup and remove insertion trajectory. + if ( + targetInsertionProbeManager == null + || ProbeAutomationStateManager.HasReachedTargetEntryCoordinate() + ) + { + RemoveTrajectoryLines(); + return Vector3.negativeInfinity; + } + + // Compute the trajectory. + ComputeTargetEntryCoordinateTrajectory(targetInsertionProbeManager); + + // Create trajectory lines. + CreateTrajectoryLines(); + + // Set trajectory lines. + UpdateTrajectoryLines(); + + // Return final entry coordinate (coordinate of the ML movement, the last in the trajectory). + return _trajectoryCoordinates.third; + } + + /// + /// Move the probe along the planned trajectory to the target entry coordinate.
+ /// + /// Callback action after movement is completed. + /// No trajectory planned for probe + /// Will log that movement has started and completed. + public void DriveToTargetEntryCoordinate(Action onDriveEnd) + { + // Throw exception if invariant is violated. + if (float.IsNegativeInfinity(_trajectoryCoordinates.first.x)) + throw new InvalidOperationException( + "No trajectory planned for probe " + _probeManager.name + ); + + // Convert insertions to manipulator positions. + var dvPosition = ConvertInsertionAPMLDVToManipulatorPosition(_trajectoryCoordinates.first); + var apPosition = ConvertInsertionAPMLDVToManipulatorPosition(_trajectoryCoordinates.second); + var mlPosition = ConvertInsertionAPMLDVToManipulatorPosition(_trajectoryCoordinates.third); + + // Log that movement is starting. + OutputLog.Log( + new[] + { + "Automation", + DateTime.Now.ToString(CultureInfo.InvariantCulture), + "DriveToTargetEntryCoordinate", + ManipulatorID, + "Start" + } + ); + + // Move. + CommunicationManager.Instance.SetPosition( + new SetPositionRequest(ManipulatorID, dvPosition, AUTOMATIC_MOVEMENT_SPEED), + _ => + { + CommunicationManager.Instance.SetPosition( + new SetPositionRequest(ManipulatorID, apPosition, AUTOMATIC_MOVEMENT_SPEED), + _ => + { + CommunicationManager.Instance.SetPosition( + new SetPositionRequest( + ManipulatorID, + mlPosition, + AUTOMATIC_MOVEMENT_SPEED + ), + _ => + { + // Remove trajectory lines. + RemoveTrajectoryLines(); + + // Conclude drive. + ConcludeDrive(); + }, + error => + { + Debug.LogError(error); + ConcludeDrive(); + } + ); + }, + error => + { + Debug.LogError(error); + ConcludeDrive(); + } + ); + }, + error => + { + Debug.LogError(error); + ConcludeDrive(); + } + ); + + return; + + void ConcludeDrive() + { + // Log drive finished. + OutputLog.Log( + new[] + { + "Automation", + DateTime.Now.ToString(CultureInfo.InvariantCulture), + "DriveToTargetEntryCoordinate", + ManipulatorID, + "Finish" + } + ); + + // Callback drive end. + onDriveEnd.Invoke(); + } + } + + /// + /// Stop the probe from moving to the target entry coordinate. + /// + /// Will log that movement has stopped. + /// Callback action after movement is stopped. + public void StopDriveToTargetEntryCoordinate(Action onStopped) + { + // Log that movement is stopping. + OutputLog.Log( + new[] + { + "Copilot", + DateTime.Now.ToString(CultureInfo.InvariantCulture), + "MoveToTargetInsertion", + ManipulatorID, + "Stop" + } + ); + + // Stop movement. + CommunicationManager.Instance.Stop(ManipulatorID, onStopped.Invoke, Debug.LogError); + } + + #endregion + + #region Internal Functions + + /// + /// Compute the trajectory to the target insertion entry coordinate. + /// + /// Probe manager of the target insertion to compute the entry coordinate for. + private void ComputeTargetEntryCoordinateTrajectory( + ProbeManager targetInsertionProbeManager + ) + { + // Compute entry coordinate in world space. + var entryCoordinateWorld = + targetInsertionProbeManager.GetSurfaceCoordinateWorldT() + - targetInsertionProbeManager.ProbeController.GetTipWorldU().tipForwardWorldU + * ENTRY_COORDINATE_DURA_DISTANCE; + + // Convert world space to transformed space. + var entryCoordinateAPMLDV = BrainAtlasManager.ActiveAtlasTransform.U2T( + BrainAtlasManager.ActiveReferenceAtlas.World2Atlas(entryCoordinateWorld) + ); + + // Get current probe coordinate. + var currentCoordinate = _probeManager.ProbeController.Insertion.APMLDV; + + // Set first movement (DV). + _trajectoryCoordinates.first = new Vector3( + currentCoordinate.x, + currentCoordinate.y, + entryCoordinateAPMLDV.z + ); + + // Set second movement (AP). + _trajectoryCoordinates.second = new Vector3( + entryCoordinateAPMLDV.x, + currentCoordinate.y, + entryCoordinateAPMLDV.z + ); + + // Set third movement (ML). + _trajectoryCoordinates.third = entryCoordinateAPMLDV; + } + + /// + /// Create the trajectory line game objects and line renderers (if needed). + /// + private void CreateTrajectoryLines() + { + // Shortcut exit if they already exist. + if (_trajectoryLineGameObjects.ap != null) + return; + + // Create the trajectory line game objects. + _trajectoryLineGameObjects = ( + new GameObject("APTrajectoryLine") { layer = 5 }, + new GameObject("MLTrajectoryLine") { layer = 5 }, + new GameObject("DVTrajectoryLine") { layer = 5 } + ); + + // Create the line renderers. + _trajectoryLineLineRenderers = ( + _trajectoryLineGameObjects.ap.AddComponent(), + _trajectoryLineGameObjects.ml.AddComponent(), + _trajectoryLineGameObjects.dv.AddComponent() + ); + + // Apply materials. + var defaultSpriteShader = Shader.Find("Sprites/Default"); + _trajectoryLineLineRenderers.ap.material = new Material(defaultSpriteShader) + { + color = AP_COLOR + }; + _trajectoryLineLineRenderers.ml.material = new Material(defaultSpriteShader) + { + color = ML_COLOR + }; + _trajectoryLineLineRenderers.dv.material = new Material(defaultSpriteShader) + { + color = DV_COLOR + }; + + // Set line widths. + _trajectoryLineLineRenderers.ap.startWidth = _trajectoryLineLineRenderers.ap.endWidth = + LINE_WIDTH; + _trajectoryLineLineRenderers.ml.startWidth = _trajectoryLineLineRenderers.ml.endWidth = + LINE_WIDTH; + _trajectoryLineLineRenderers.dv.startWidth = _trajectoryLineLineRenderers.dv.endWidth = + LINE_WIDTH; + + // Set segment counts. + _trajectoryLineLineRenderers.ap.positionCount = NUM_SEGMENTS; + _trajectoryLineLineRenderers.ml.positionCount = NUM_SEGMENTS; + _trajectoryLineLineRenderers.dv.positionCount = NUM_SEGMENTS; + } + + /// + /// Update the trajectory line positions. + /// + private void UpdateTrajectoryLines() + { + _trajectoryLineLineRenderers.dv.SetPosition(0, _probeController.ProbeTipT.position); + _trajectoryLineLineRenderers.dv.SetPosition( + 1, + BrainAtlasManager.ActiveReferenceAtlas.Atlas2World( + BrainAtlasManager.ActiveAtlasTransform.T2U_Vector(_trajectoryCoordinates.first) + ) + ); + + _trajectoryLineLineRenderers.ap.SetPosition( + 0, + BrainAtlasManager.ActiveReferenceAtlas.Atlas2World( + BrainAtlasManager.ActiveAtlasTransform.T2U_Vector(_trajectoryCoordinates.first) + ) + ); + _trajectoryLineLineRenderers.ap.SetPosition( + 1, + BrainAtlasManager.ActiveReferenceAtlas.Atlas2World( + BrainAtlasManager.ActiveAtlasTransform.T2U_Vector(_trajectoryCoordinates.second) + ) + ); + + _trajectoryLineLineRenderers.ml.SetPosition( + 0, + BrainAtlasManager.ActiveReferenceAtlas.Atlas2World( + BrainAtlasManager.ActiveAtlasTransform.T2U_Vector(_trajectoryCoordinates.second) + ) + ); + _trajectoryLineLineRenderers.ml.SetPosition( + 1, + BrainAtlasManager.ActiveReferenceAtlas.Atlas2World( + BrainAtlasManager.ActiveAtlasTransform.T2U_Vector(_trajectoryCoordinates.third) + ) + ); + } + + /// + /// Destroy the trajectory line game objects and line renderers. Also reset the references. + /// + private void RemoveTrajectoryLines() + { + // Destroy the objects. + Destroy(_trajectoryLineGameObjects.ap); + Destroy(_trajectoryLineGameObjects.ml); + Destroy(_trajectoryLineGameObjects.dv); + + // Reset the references. + _trajectoryLineGameObjects = (null, null, null); + _trajectoryLineLineRenderers = (null, null, null); + } + + #endregion + } +} diff --git a/Assets/Scripts/Pinpoint/Probes/ManipulatorBehaviorController/ManipulatorBehaviorController_Automation_TargetInsertion.cs.meta b/Assets/Scripts/Pinpoint/Probes/ManipulatorBehaviorController/ManipulatorBehaviorController_Automation_TargetInsertion.cs.meta new file mode 100644 index 00000000..afcacff3 --- /dev/null +++ b/Assets/Scripts/Pinpoint/Probes/ManipulatorBehaviorController/ManipulatorBehaviorController_Automation_TargetInsertion.cs.meta @@ -0,0 +1,2 @@ +fileFormatVersion: 2 +guid: 7ddaf4479f8b1b3479deb22865f7a5da diff --git a/Assets/Scripts/Pinpoint/Probes/ProbeAutomationState.cs b/Assets/Scripts/Pinpoint/Probes/ProbeAutomationState.cs new file mode 100644 index 00000000..4019a0de --- /dev/null +++ b/Assets/Scripts/Pinpoint/Probes/ProbeAutomationState.cs @@ -0,0 +1,103 @@ +namespace Pinpoint.Probes +{ + /// + /// Drive state in the automation cycle. + /// + public enum ProbeAutomationState + { + /// + /// Initial, uncalibrated state. + /// + IsUncalibrated, + + /// + /// Is calibrated to Bregma. Could be positioned anywhere. + /// + IsCalibrated, + + /// + /// Moving to the target entry coordinate. + /// + DrivingToTargetEntryCoordinate, + + /// + /// At the target entry coordinate. + /// + AtEntryCoordinate, + + /// + /// Calibrated to the Dura; ready for insertion drive. + /// + AtDuraInsert, + + /// + /// Driving to near target depth (insertion drive). + /// + DrivingToNearTarget, + + /// + /// At near target depth (insertion drive). Need to switch to 2/3 speed. + /// + AtNearTargetInsert, + + /// + /// Driving to past target depth (insertion drive). + /// + DrivingToPastTarget, + + /// + /// At past target depth (insertion drive). + /// + AtPastTarget, + + /// + /// Driving back up to target depth (insertion drive). + /// + ReturningToTarget, + + /// + /// At target depth (insertion drive). + /// + AtTarget, + + /// + /// Driving back up to near target depth (exit drive). + /// + ExitingToNearTarget, + + /// + /// At near target depth (exit drive). Can switch back to normal speed. + /// + AtNearTargetExit, + + /// + /// Driving back up to the Dura (exit drive). + /// + ExitingToDura, + + /// + /// At the Dura (exit drive). Should not re-insert. + /// + AtDuraExit, + + /// + /// Driving above the Dura by a safe margin (exit drive). + /// + ExitingToMargin, + + /// + /// At the safe margin above the Dura (exit drive). + /// + AtExitMargin, + + /// + /// Driving back up to the target entry coordinate (exit drive). + /// + ExitingToTargetEntryCoordinate, + + /// + /// Driving back to Bregma. + /// + DrivingToBregma + } +} diff --git a/Assets/Scripts/Pinpoint/Probes/ProbeAutomationState.cs.meta b/Assets/Scripts/Pinpoint/Probes/ProbeAutomationState.cs.meta new file mode 100644 index 00000000..4e2f2421 --- /dev/null +++ b/Assets/Scripts/Pinpoint/Probes/ProbeAutomationState.cs.meta @@ -0,0 +1,2 @@ +fileFormatVersion: 2 +guid: a883806dd4f7fd74d803c2bab7381b31 \ No newline at end of file diff --git a/Assets/Scripts/Pinpoint/Probes/ProbeAutomationStateManager.cs b/Assets/Scripts/Pinpoint/Probes/ProbeAutomationStateManager.cs new file mode 100644 index 00000000..a3bb8b0b --- /dev/null +++ b/Assets/Scripts/Pinpoint/Probes/ProbeAutomationStateManager.cs @@ -0,0 +1,225 @@ +using System; + +namespace Pinpoint.Probes +{ + /// + /// Define and manage the automation state of a probe. + /// + public class ProbeAutomationStateManager + { + #region Properties + + /// + /// The state of the probe. + /// + public ProbeAutomationState ProbeAutomationState { get; private set; } = + ProbeAutomationState.IsUncalibrated; + + #endregion + + #region Actions + + /// + /// Set the probe's state to be calibrated. + /// + /// This can be set from any state. This is the reset point. + public void SetCalibrated() + { + ProbeAutomationState = ProbeAutomationState.IsCalibrated; + } + + /// + /// Set the probe's state to be driving to the target entry coordinate. + /// + /// Probe is not calibrated or at entry coordinate. + public void SetDrivingToTargetEntryCoordinate() + { + if (!IsCalibrated() && ProbeAutomationState != ProbeAutomationState.AtEntryCoordinate) + throw new InvalidOperationException( + "Cannot set probe to driving to target entry coordinate if it is not calibrated." + ); + + ProbeAutomationState = ProbeAutomationState.DrivingToTargetEntryCoordinate; + } + + /// + /// Set the probe's state to be at the target entry coordinate. + /// + /// Probe is not driving there or exiting to there. + public void SetAtEntryCoordinate() + { + if ( + ProbeAutomationState != ProbeAutomationState.DrivingToTargetEntryCoordinate + && ProbeAutomationState != ProbeAutomationState.ExitingToTargetEntryCoordinate + ) + throw new InvalidOperationException( + "Cannot set probe to entry coordinate if it was not driving there or exiting to there." + ); + + ProbeAutomationState = ProbeAutomationState.AtEntryCoordinate; + } + + /// + /// Set the probe's state to be at the Dura for insertion. + /// + /// Probe is not at the entry coordinate or exiting to Dura. + public void SetAtDuraInsert() + { + if ( + ProbeAutomationState != ProbeAutomationState.AtEntryCoordinate + && ProbeAutomationState != ProbeAutomationState.ExitingToDura + ) + throw new InvalidOperationException( + "Cannot set probe to dura if it was not at the entry coordinate or exiting to Dura." + ); + ProbeAutomationState = ProbeAutomationState.AtDuraInsert; + } + + /// + /// Increment the state according to the normal loop for the insertion cycle. + /// + /// Probe is not in the insertion cycle. + public void IncrementInsertionCycleState() + { + switch (ProbeAutomationState) + { + // Throw exception if required state is not met. + case < ProbeAutomationState.AtDuraInsert + or > ProbeAutomationState.ExitingToTargetEntryCoordinate: + throw new InvalidOperationException( + "Cannot increment the insertion cycle state if the probe is not in the insertion cycle." + ); + + // If exiting to the target entry coordinate, set to the target entry coordinate (end of cycle). + case ProbeAutomationState.ExitingToTargetEntryCoordinate: + ProbeAutomationState = ProbeAutomationState.AtEntryCoordinate; + return; + + // Otherwise, increment state. + default: + ProbeAutomationState++; + break; + } + } + + /// + /// Set the probe's state to be in the next insertion driving state. + /// + /// Probe is not in a state that can go drive. + public void SetToInsertionDrivingState() + { + // Throw exception if required state is not met. + if (!IsInsertable()) + throw new InvalidOperationException( + "Cannot set probe to insertion driving state if it is not at the Dura or inside the brain." + ); + + // Set state. + ProbeAutomationState = ProbeAutomationState switch + { + // States for driving to near target depth. + ProbeAutomationState.AtDuraInsert + or ProbeAutomationState.ExitingToDura + => ProbeAutomationState.DrivingToNearTarget, + + // States for driving to the target. + ProbeAutomationState.AtNearTargetInsert + or ProbeAutomationState.ExitingToNearTarget + or ProbeAutomationState.AtNearTargetExit + => ProbeAutomationState.DrivingToPastTarget, + + // States for returning to the target. + ProbeAutomationState.AtPastTarget + => ProbeAutomationState.ReturningToTarget, + + // Do nothing for driving states. + _ => ProbeAutomationState + }; + } + + /// + /// Set the probe's state to be in the next exit driving state. + /// + /// Probe is not in a state that can exit. + public void SetToExitingDrivingState() + { + // Throw exception if required state is not met. + if (!IsExitable()) + throw new InvalidOperationException( + "Cannot set probe to exit driving state if it is not past the Dura." + ); + + // Set state. + ProbeAutomationState = ProbeAutomationState switch + { + // States for Exiting to near target depth. + ProbeAutomationState.AtTarget + or ProbeAutomationState.ReturningToTarget + or ProbeAutomationState.DrivingToPastTarget + => ProbeAutomationState.ExitingToNearTarget, + + // States for Exiting to the Dura. + ProbeAutomationState.AtNearTargetExit + or ProbeAutomationState.AtNearTargetInsert + or ProbeAutomationState.DrivingToNearTarget + => ProbeAutomationState.ExitingToDura, + + // States for exiting to margin. + ProbeAutomationState.AtDuraExit + => ProbeAutomationState.ExitingToMargin, + + // States for exiting to target entry coordinate. + ProbeAutomationState.AtExitMargin + => ProbeAutomationState.ExitingToTargetEntryCoordinate, + + // Do nothing for driving states. + _ => ProbeAutomationState + }; + } + + #endregion + + #region Queries + + /// + /// Checks if the probe is past the calibration phase. + /// + /// True if the state is past the calibration phase, false otherwise. + public bool IsCalibrated() + { + return ProbeAutomationState >= ProbeAutomationState.IsCalibrated; + } + + /// + /// Checks if the probe has been to the target entry coordinate. + /// + /// True if the state is past reaching the target entry coordinate, false otherwise. + public bool HasReachedTargetEntryCoordinate() + { + return ProbeAutomationState >= ProbeAutomationState.AtEntryCoordinate; + } + + /// + /// Checks if the probe can be inserted (driven into the brain). + /// + /// Returns true if the probe is calibrated to the Dura and has not exited back out of the Dura. + public bool IsInsertable() + { + return ProbeAutomationState + is >= ProbeAutomationState.AtDuraInsert + and < ProbeAutomationState.AtDuraExit + && ProbeAutomationState != ProbeAutomationState.AtTarget; + } + + /// + /// Checks if the probe can be retracted (drive back out of the brain). + /// + /// Returns true if the probe has gone through/past the Dura. + public bool IsExitable() + { + return ProbeAutomationState > ProbeAutomationState.AtDuraInsert; + } + + #endregion + } +} diff --git a/Assets/Scripts/Pinpoint/Probes/ProbeAutomationStateManager.cs.meta b/Assets/Scripts/Pinpoint/Probes/ProbeAutomationStateManager.cs.meta new file mode 100644 index 00000000..d3d7177b --- /dev/null +++ b/Assets/Scripts/Pinpoint/Probes/ProbeAutomationStateManager.cs.meta @@ -0,0 +1,2 @@ +fileFormatVersion: 2 +guid: 9146e7c3759810d4ead53231e19eb641 \ No newline at end of file diff --git a/Assets/Scripts/Pinpoint/Probes/ProbeManager.cs b/Assets/Scripts/Pinpoint/Probes/ProbeManager.cs index ea4cde71..08a45bd9 100644 --- a/Assets/Scripts/Pinpoint/Probes/ProbeManager.cs +++ b/Assets/Scripts/Pinpoint/Probes/ProbeManager.cs @@ -6,6 +6,7 @@ using BrainAtlas; using EphysLink; using Pinpoint.Probes; +using Pinpoint.Probes.ManipulatorBehaviorController; using UnityEngine; using UnityEngine.Events; using UnityEngine.Serialization; @@ -229,7 +230,7 @@ public List GetProbeUIManagers() /// When true, this Probe will be saved and re-loaded in the scene the next time Pinpoint loads /// public bool Saved { get; set; } - + #endregion #region Unity @@ -906,10 +907,11 @@ public void UpdateSurfacePosition() } } + // TODO: Remove useDV and always use depth. /// /// Calculate the entry coordinate on the brain surface, returns coordIdx /// - /// + /// Whether the surface should be found along the DV axis or depth axis. /// (entryCoordAtlasIdx, probeInBrain) public (Vector3 entryCoordAtlasIdx, bool probeInBrain) CalculateEntryCoordinate( bool useDV = false @@ -1276,9 +1278,9 @@ public static ProbeManagerData ProbeManager2ProbeData(ProbeManager probeManager) data.ZeroCoordOffset = probeManager.ManipulatorBehaviorController.ZeroCoordinateOffset; data.Dimensions = probeManager.ManipulatorBehaviorController.Dimensions; data.BrainSurfaceOffset = probeManager.ManipulatorBehaviorController.BrainSurfaceOffset; - data.Drop2SurfaceWithDepth = probeManager - .ManipulatorBehaviorController - .IsSetToDropToSurfaceWithDepth; + // data.Drop2SurfaceWithDepth = probeManager + // .ManipulatorBehaviorController + // .IsSetToDropToSurfaceWithDepth; data.IsRightHanded = probeManager.ManipulatorBehaviorController.IsRightHanded; return data; diff --git a/Assets/Scripts/Pinpoint/TrajectoryPlannerManager.cs b/Assets/Scripts/Pinpoint/TrajectoryPlannerManager.cs index 6bd7e063..80ae13a2 100644 --- a/Assets/Scripts/Pinpoint/TrajectoryPlannerManager.cs +++ b/Assets/Scripts/Pinpoint/TrajectoryPlannerManager.cs @@ -487,8 +487,8 @@ public ProbeManager AddNewProbe(ProbeProperties.ProbeType probeType, ProbeInsert probeManager.ManipulatorBehaviorController.NumAxes = numAxes; probeManager.ManipulatorBehaviorController.ZeroCoordinateOffset = zeroCoordinateOffset; probeManager.ManipulatorBehaviorController.BrainSurfaceOffset = brainSurfaceOffset; - probeManager.ManipulatorBehaviorController.IsSetToDropToSurfaceWithDepth = dropToSurfaceWithDepth; - probeManager.ManipulatorBehaviorController.IsSetToDropToSurfaceWithDepth = dropToSurfaceWithDepth; + // probeManager.ManipulatorBehaviorController.IsSetToDropToSurfaceWithDepth = dropToSurfaceWithDepth; + // probeManager.ManipulatorBehaviorController.IsSetToDropToSurfaceWithDepth = dropToSurfaceWithDepth; probeManager.ManipulatorBehaviorController.IsRightHanded = isRightHanded; var communicationManager = GameObject.Find("EphysLink").GetComponent(); diff --git a/Assets/Scripts/Pinpoint/UI/EphysCopilot/InsertionSelectionPanelHandler.cs b/Assets/Scripts/Pinpoint/UI/EphysCopilot/InsertionSelectionPanelHandler.cs index 392c1e26..0dcb48a5 100644 --- a/Assets/Scripts/Pinpoint/UI/EphysCopilot/InsertionSelectionPanelHandler.cs +++ b/Assets/Scripts/Pinpoint/UI/EphysCopilot/InsertionSelectionPanelHandler.cs @@ -5,6 +5,7 @@ using BrainAtlas; using EphysLink; using Pinpoint.Probes; +using Pinpoint.Probes.ManipulatorBehaviorController; using TMPro; using UnityEngine; using UnityEngine.Events; diff --git a/Assets/Scripts/Pinpoint/UI/EphysLinkSettings/ManipulatorConnectionPanel.cs b/Assets/Scripts/Pinpoint/UI/EphysLinkSettings/ManipulatorConnectionPanel.cs index a88b5310..6eed14b8 100644 --- a/Assets/Scripts/Pinpoint/UI/EphysLinkSettings/ManipulatorConnectionPanel.cs +++ b/Assets/Scripts/Pinpoint/UI/EphysLinkSettings/ManipulatorConnectionPanel.cs @@ -303,9 +303,9 @@ public void UpdateZeroCoordinateOffsetD(string newValue) public void UpdateDuraDropDirection(int value) { // Set drop direction on attached probe if it exists - if (_attachedProbe) - _attachedProbe.ManipulatorBehaviorController.IsSetToDropToSurfaceWithDepth = - value == 1; + // if (_attachedProbe) + // _attachedProbe.ManipulatorBehaviorController.IsSetToDropToSurfaceWithDepth = + // value == 1; } private void SetDuraDropInteractable(bool interactable) diff --git a/Assets/Scripts/UI/AutomationStack.meta b/Assets/Scripts/UI/AutomationStack.meta new file mode 100644 index 00000000..246052d4 --- /dev/null +++ b/Assets/Scripts/UI/AutomationStack.meta @@ -0,0 +1,8 @@ +fileFormatVersion: 2 +guid: 4746c78f687d0a848a5c30aca67a9c44 +folderAsset: yes +DefaultImporter: + externalObjects: {} + userData: + assetBundleName: + assetBundleVariant: diff --git a/Assets/Scripts/UI/AutomationStack/AutomationStackHandler.cs b/Assets/Scripts/UI/AutomationStack/AutomationStackHandler.cs new file mode 100644 index 00000000..c91c9ca7 --- /dev/null +++ b/Assets/Scripts/UI/AutomationStack/AutomationStackHandler.cs @@ -0,0 +1,241 @@ +using System; +using Pinpoint.Probes; +using Pinpoint.Probes.ManipulatorBehaviorController; +using UI.States; +using UnityEngine; +using UnityEngine.UIElements; + +namespace UI.AutomationStack +{ + /// + /// Automation Stack UI origin class. + /// + /// + /// This script handles getting the components, running UI setup functions, and registering callbacks. + /// + public partial class AutomationStackHandler : MonoBehaviour + { + #region Components + + #region State + + [SerializeField] + private AutomationStackState _state; + + #endregion + + #region UI + + // Document. + [SerializeField] + private UIDocument _uiDocument; + private VisualElement _root => _uiDocument.rootVisualElement; + + // Panels. + private VisualElement _automationStackPanel; + + #region Bregma Calibration + + private Button _resetBregmaCalibrationButton; + + #endregion + + #region Target Insertion + + private RadioButtonGroup _targetInsertionRadioButtonGroup; + private Button _driveToTargetEntryCoordinateButton; + + #endregion + + #region Dura Calibration + + private Button _resetDuraCalibrationButton; + + #endregion + + #region Insertion + + private Button _driveToTargetInsertionButton; + private Button _stopButton; + private Button _exitButton; + + #endregion + + #endregion + + + #region Probes + + private static ManipulatorBehaviorController ActiveManipulatorBehaviorController => + ProbeManager.ActiveProbeManager.ManipulatorBehaviorController; + + private static ProbeAutomationStateManager ActiveProbeStateManager => + ActiveManipulatorBehaviorController.ProbeAutomationStateManager; + + #endregion + + #endregion + + + #region Unity + + private void OnEnable() + { + // Get components. + _automationStackPanel = _root.Q("automation-stack-panel"); + _resetBregmaCalibrationButton = _automationStackPanel.Q