From 49455853a938852f15d7a492c855e95984b4fa1b Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Mon, 3 Mar 2025 15:32:25 +0100 Subject: [PATCH 01/84] tmp: prototype tps surface for splitting segments --- .../javascripts/oxalis/controller/renderer.ts | 2 + .../oxalis/controller/scene_controller.ts | 357 +++++++++++++++++- .../controller/segment_mesh_controller.ts | 71 ++-- .../oxalis/model/sagas/root_saga.ts | 2 + .../oxalis/shaders/main_data_shaders.glsl.ts | 2 + .../javascripts/oxalis/view/plane_view.ts | 2 +- 6 files changed, 398 insertions(+), 38 deletions(-) diff --git a/frontend/javascripts/oxalis/controller/renderer.ts b/frontend/javascripts/oxalis/controller/renderer.ts index b300afb0a8e..3ebd0cf42fa 100644 --- a/frontend/javascripts/oxalis/controller/renderer.ts +++ b/frontend/javascripts/oxalis/controller/renderer.ts @@ -40,6 +40,8 @@ function getRenderer(): THREE.WebGLRenderer { : {} ) as THREE.WebGLRenderer; + renderer.physicallyCorrectLights = true; + return renderer; } diff --git a/frontend/javascripts/oxalis/controller/scene_controller.ts b/frontend/javascripts/oxalis/controller/scene_controller.ts index a116be378c2..80a555ca52a 100644 --- a/frontend/javascripts/oxalis/controller/scene_controller.ts +++ b/frontend/javascripts/oxalis/controller/scene_controller.ts @@ -1,9 +1,11 @@ import app from "app"; import type Maybe from "data.maybe"; import { V3 } from "libs/mjs"; +import Toast from "libs/toast"; import * as Utils from "libs/utils"; import window from "libs/window"; import _ from "lodash"; + import type { BoundingBoxType, OrthoView, @@ -45,12 +47,296 @@ import { getVoxelPerUnit } from "oxalis/model/scaleinfo"; import { Model } from "oxalis/singletons"; import type { OxalisState, SkeletonTracing, UserBoundingBox } from "oxalis/store"; import Store from "oxalis/store"; +import PCA from "pca-js"; import * as THREE from "three"; import SegmentMeshController from "./segment_mesh_controller"; const CUBE_COLOR = 0x999999; const LAYER_CUBE_COLOR = 0xffff99; +// import Delaunator from "delaunator"; +import TPS3D from "libs/thin_plate_spline"; + +type EigenData = { eigenvalue: number; vector: number[] }; + +function createPointCloud(points: Vector3[], color: string) { + // Convert points to Three.js geometry + const geometry = new THREE.BufferGeometry(); + const vertices = new Float32Array(_.flatten(points)); + geometry.setAttribute("position", new THREE.BufferAttribute(vertices, 3)); + + // Create point material and add to objects list + const material = new THREE.PointsMaterial({ color, size: 5 }); + + const pointCloud = new THREE.Points(geometry, material); + return pointCloud; +} + +const rows = 100; +const cols = 100; +function computeBentSurface(points: Vector3[]): THREE.Object3D[] { + const eigenData: EigenData[] = PCA.getEigenVectors(points); + const objects: THREE.Object3D[] = []; + + const adData = PCA.computeAdjustedData(points, eigenData[0], eigenData[1]); + const compressed = adData.formattedAdjustedData; + const uncompressed = PCA.computeOriginalData(compressed, adData.selectedVectors, adData.avgData); + console.log("uncompressed", uncompressed); + + const projectedPoints: Vector3[] = uncompressed.originalData; + + // objects.push(createPointCloud(points, "red")); + // objects.push(createPointCloud(projectedPoints, "blue")); + + // todop: adapt scale + const scale = [1, 1, 1] as Vector3; + const tps = new TPS3D(projectedPoints, points, scale); + + // Align the plane with the principal components + const normal = new THREE.Vector3(...eigenData[2].vector); + const quaternion = new THREE.Quaternion().setFromUnitVectors(new THREE.Vector3(0, 0, 1), normal); + const quaternionInv = quaternion.clone().invert(); + + // Transform projectedPoints into the plane’s local coordinate system + const projectedLocalPoints = projectedPoints.map((p) => { + const worldPoint = new THREE.Vector3(...p); + return worldPoint.applyQuaternion(quaternionInv); // Move to local plane space + }); + + const mean = points.reduce( + (acc, p) => acc.add(new THREE.Vector3(...p).divideScalar(points.length)), + new THREE.Vector3(0, 0, 0), + ); + const projectedMean = mean.clone().applyQuaternion(quaternionInv); + + // Compute min/max bounds in local plane space + let minX = Number.POSITIVE_INFINITY, + maxX = Number.NEGATIVE_INFINITY, + minY = Number.POSITIVE_INFINITY, + maxY = Number.NEGATIVE_INFINITY; + projectedLocalPoints.forEach((p) => { + minX = Math.min(minX, p.x); + maxX = Math.max(maxX, p.x); + minY = Math.min(minY, p.y); + maxY = Math.max(maxY, p.y); + }); + + // Compute exact plane size based on bounds + const planeSizeX = 2 * Math.max(maxX - projectedMean.x, projectedMean.x - minX); + const planeSizeY = 2 * Math.max(maxY - projectedMean.y, projectedMean.y - minY); + + // Define the plane using the first two principal components + // const planeSizeX = Math.sqrt(eigenData[0].eigenvalue) * 10; + // const planeSizeY = Math.sqrt(eigenData[1].eigenvalue) * 10; + + const planeGeometry = new THREE.PlaneGeometry(planeSizeX, planeSizeY); + const planeMaterial = new THREE.MeshBasicMaterial({ + color: 0x00ff00, + side: THREE.DoubleSide, + opacity: 0.5, + transparent: true, + }); + const plane = new THREE.Mesh(planeGeometry, planeMaterial); + + plane.setRotationFromQuaternion(quaternion); + + // const centerLocal = new THREE.Vector3((minX + maxX) / 2, (minY + maxY) / 2, 0); + // centerLocal.applyMatrix4(plane.matrixWorld); + plane.position.copy(mean); + + plane.updateMatrixWorld(); + + // objects.push(plane); + + const gridPoints = generatePlanePoints(plane); + const bentSurfacePoints = gridPoints.map((point) => tps.transform(...point)); + + // objects.push(createPointCloud(gridPoints, "purple")); + // objects.push(createPointCloud(bentSurfacePoints, "orange")); + + const bentMesh = createBentSurfaceGeometry(bentSurfacePoints, rows, cols); + objects.push(bentMesh); + + // const light = new THREE.DirectionalLight(0xffffff, 1); + // light.position.set(100, 150, 100); // Above and slightly in front of the points + // light.lookAt(60, 60, 75); // Aim at the center of the point set + // light.updateMatrixWorld(); + + // const lightHelper = new THREE.DirectionalLightHelper(light, 10, 0xff0000); // The size of the helper + + // const arrowHelper = new THREE.ArrowHelper( + // light.position + // .clone() + // .normalize(), // Direction + // new THREE.Vector3(60, 60, 75), // Start position (light target) + // 20, // Arrow length + // 0xff0000, // Color (red) + // ); + + // light.castShadow = true; + + // objects.push(light, lightHelper, arrowHelper); + + // createNormalsVisualization(bentMesh.geometry, objects); + + return objects; +} + +// function createNormalsVisualization(geometry: THREE.BufferGeometry, objects: THREE.Object3D[]) { +// const positions = geometry.attributes.position.array; +// const normals = geometry.attributes.normal.array; +// const normalLines: number[] = []; + +// for (let i = 0; i < positions.length; i += 3) { +// const v = new THREE.Vector3(positions[i], positions[i + 1], positions[i + 2]); +// const n = new THREE.Vector3(normals[i], normals[i + 1], normals[i + 2]); + +// const vEnd = v.clone().add(n.multiplyScalar(5)); // Scale normals for visibility + +// normalLines.push(v.x, v.y, v.z, vEnd.x, vEnd.y, vEnd.z); +// } + +// const normalGeometry = new THREE.BufferGeometry(); +// normalGeometry.setAttribute("position", new THREE.Float32BufferAttribute(normalLines, 3)); + +// const normalMaterial = new THREE.LineBasicMaterial({ color: 0xff0000 }); // Red for visibility +// const normalLinesMesh = new THREE.LineSegments(normalGeometry, normalMaterial); + +// objects.push(normalLinesMesh); // Add to objects list instead of scene.add() +// } + +function generatePlanePoints(planeMesh: THREE.Mesh): Vector3[] { + const points: THREE.Vector3[] = []; + const width = planeMesh.geometry.parameters.width; + const height = planeMesh.geometry.parameters.height; + + // Use the full transformation matrix of the plane + const planeMatrix = planeMesh.matrixWorld.clone(); + + for (let i = 0; i < rows; i++) { + for (let j = 0; j < cols; j++) { + const x = (i / (rows - 1) - 0.5) * width; + const y = (j / (cols - 1) - 0.5) * height; + let point = new THREE.Vector3(x, y, 0); + + point = point.applyMatrix4(planeMatrix); + points.push(point); + } + } + return points.map((vec) => [vec.x, vec.y, vec.z]); +} + +function createBentSurfaceGeometry(points: Vector3[], rows: number, cols: number): THREE.Mesh { + const geometry = new THREE.BufferGeometry(); + + // Flattened position array + const positions = new Float32Array(points.length * 3); + points.forEach((p, i) => { + positions[i * 3] = p[0]; + positions[i * 3 + 1] = p[1]; + positions[i * 3 + 2] = p[2]; + }); + + // Create indices for two triangles per quad + const indices: number[] = []; + for (let i = 0; i < rows - 1; i++) { + for (let j = 0; j < cols - 1; j++) { + const a = i * cols + j; + const b = i * cols + (j + 1); + const c = (i + 1) * cols + j; + const d = (i + 1) * cols + (j + 1); + + // Two triangles per quad + indices.push(a, b, d); + indices.push(a, d, c); + } + } + + // Apply to geometry + geometry.setAttribute("position", new THREE.BufferAttribute(positions, 3)); + geometry.setIndex(indices); + geometry.computeVertexNormals(); // Generate normals for lighting + + const material = new THREE.MeshStandardMaterial({ + color: 0x0077ff, // A soft blue color + metalness: 0.5, // Slight metallic effect + roughness: 1, // Some surface roughness for a natural look + side: THREE.DoubleSide, // Render both sides + flatShading: false, // Ensures smooth shading with computed normals + }); + + // const material = new THREE.MeshLambertMaterial({ + // color: "blue", + // emissive: "green", + // side: THREE.DoubleSide, + // transparent: true, + // }); + + // const material = new THREE.MeshPhysicalMaterial({ + // color: 0x0077ff, + // metalness: 0.3, + // roughness: 0.5, + // clearcoat: 0.5, // Adds extra reflection + // side: THREE.DoubleSide, + // }); + + // const material = new THREE.MeshNormalMaterial({ side: THREE.DoubleSide }); + + // material.transparent = true; + const mesh = new THREE.Mesh(geometry, material); + mesh.receiveShadow = true; + mesh.castShadow = true; + return mesh; +} + +function generateTPSMesh(points, scale, resolution = 20) { + if (points.length < 3) { + throw new Error("At least 3 points are needed to define a surface."); + } + + const sourcePoints = points.map(projectToPlane); + const targetPoints = points.map((p) => [p[0], p[1], p[2]]); + + // Step 3: Create the TPS transformation + const tps = new TPS3D(sourcePoints, targetPoints, scale); + + // Step 4: Generate a grid of points in the base plane + const minX = Math.min(...sourcePoints.map((p) => p[0])); + const maxX = Math.max(...sourcePoints.map((p) => p[0])); + const minY = Math.min(...sourcePoints.map((p) => p[1])); + const maxY = Math.max(...sourcePoints.map((p) => p[1])); + + const gridPoints = []; + for (let i = 0; i <= resolution; i++) { + for (let j = 0; j <= resolution; j++) { + const x = minX + (i / resolution) * (maxX - minX); + const y = minY + (j / resolution) * (maxY - minY); + const transformed = tps.transform(x, y, 0); + gridPoints.push(new THREE.Vector3(transformed[0], transformed[1], transformed[2])); + } + } + + // Step 5: Perform Delaunay triangulation to create faces + const delaunay = Delaunator.from(gridPoints.map((p) => [p.x, p.y])); + const indices = delaunay.triangles; + + // Step 6: Convert data into THREE.BufferGeometry + const geometry = new THREE.BufferGeometry(); + const positions = new Float32Array(gridPoints.length * 3); + + gridPoints.forEach((p, i) => { + positions[i * 3] = p.x; + positions[i * 3 + 1] = p.y; + positions[i * 3 + 2] = p.z; + }); + + geometry.setAttribute("position", new THREE.BufferAttribute(positions, 3)); + geometry.setIndex(new THREE.BufferAttribute(new Uint16Array(indices), 1)); + geometry.computeVertexNormals(); // Smooth shading + + return geometry; +} + class SceneController { skeletons: Record = {}; current: number; @@ -74,7 +360,7 @@ class SceneController { scene!: THREE.Scene; rootGroup!: THREE.Object3D; // Group for all meshes including a light. - meshesRootGroup!: THREE.Object3D; + // meshesRootGroup!: THREE.Object3D; segmentMeshController: SegmentMeshController; storePropertyUnsubscribers: Array<() => void>; @@ -94,6 +380,7 @@ class SceneController { } initialize() { + // this.meshesRootGroup = new THREE.Group(); this.renderer = getRenderer(); this.createMeshes(); this.bindToEvents(); @@ -106,7 +393,6 @@ class SceneController { this.rootGroup = new THREE.Object3D(); this.rootGroup.add(this.getRootNode()); - this.meshesRootGroup = new THREE.Group(); this.highlightedBBoxId = null; // The dimension(s) with the highest mag will not be distorted this.rootGroup.scale.copy( @@ -115,8 +401,36 @@ class SceneController { // Add scene to the group, all Geometries are then added to group this.scene.add(this.rootGroup); this.scene.add(this.segmentMeshController.meshesLODRootGroup); - this.scene.add(this.meshesRootGroup); - this.rootGroup.add(new THREE.DirectionalLight()); + // this.scene.add(this.meshesRootGroup); + + /* Scene + * - rootGroup + * - DirectionalLight + * - surfaceGroup + * - meshesLODRootGroup + * - DirectionalLight + */ + + const dir1 = new THREE.DirectionalLight(undefined, 3 * 0.25); + dir1.position.set(1, 1, 1); + // const dir2 = new THREE.DirectionalLight(undefined, 3 * 0.25); + // dir2.position.set(-1, -1, -1); + const dir3 = new THREE.AmbientLight(undefined, 3 * 0.25); + + this.rootGroup.add(dir1); + // this.rootGroup.add(dir2); + this.rootGroup.add(dir3); + + const dir4 = new THREE.DirectionalLight(undefined, 3 * 0.25); + dir4.position.set(1, 1, 1); + // const dir5 = new THREE.DirectionalLight(undefined, 10); + // dir5.position.set(-1, -1, -1); + const dir6 = new THREE.AmbientLight(undefined, 3 * 0.25); + + this.segmentMeshController.meshesLODRootGroup.add(dir4); + // this.segmentMeshController.meshesLODRootGroup.add(dir5); + this.segmentMeshController.meshesLODRootGroup.add(dir6); + this.rootGroup.add(new THREE.AmbientLight(2105376, 3 * 10)); this.setupDebuggingMethods(); } @@ -257,6 +571,40 @@ class SceneController { this.stopPlaneMode(); } + addBentSurface(points: Vector3[]) { + // const meshGeometry = generateTPSMesh(points, [1, 1, 1], 30); + // // const material = new THREE.MeshStandardMaterial({ color: 0x88ccff, wireframe: true }); + // const material = new THREE.MeshLambertMaterial({ + // color: "green", + // wireframe: true, + // }); + // material.side = THREE.FrontSide; + // // material.transparent = true; + // const surfaceMesh = new THREE.Mesh(meshGeometry, material); + // this.rootNode.add(surfaceMesh); + + let objs; + try { + objs = computeBentSurface(points); + } catch (exc) { + console.error(exc); + Toast.error("Could not compute surface"); + return () => {}; + } + + const surfaceGroup = new THREE.Group(); + for (const obj of objs) { + surfaceGroup.add(obj); + } + + this.rootGroup.add(surfaceGroup); + // surfaceGroup.scale.copy(new THREE.Vector3(...Store.getState().dataset.dataSource.scale.factor)); + + return () => { + this.rootGroup.remove(surfaceGroup); + }; + } + addSkeleton( skeletonTracingSelector: (arg0: OxalisState) => Maybe, supportsPicking: boolean, @@ -322,6 +670,7 @@ class SceneController { this.taskBoundingBox?.updateForCam(id); this.segmentMeshController.meshesLODRootGroup.visible = id === OrthoViews.TDView; + // this.segmentMeshController.meshesLODRootGroup.visible = false; this.annotationToolsGeometryGroup.visible = id !== OrthoViews.TDView; this.lineMeasurementGeometry.updateForCam(id); diff --git a/frontend/javascripts/oxalis/controller/segment_mesh_controller.ts b/frontend/javascripts/oxalis/controller/segment_mesh_controller.ts index 25839e7b136..8ab600593fe 100644 --- a/frontend/javascripts/oxalis/controller/segment_mesh_controller.ts +++ b/frontend/javascripts/oxalis/controller/segment_mesh_controller.ts @@ -84,7 +84,7 @@ export default class SegmentMeshController { bufferGeometry.setAttribute("position", new THREE.BufferAttribute(vertices, 3)); bufferGeometry = mergeVertices(bufferGeometry); - bufferGeometry.computeVertexNormals(); + // bufferGeometry.computeVertexNormals(); this.addMeshFromGeometry( bufferGeometry as BufferGeometryWithInfo, @@ -103,10 +103,19 @@ export default class SegmentMeshController { geometry: BufferGeometryWithInfo, ): MeshSceneNode { const color = this.getColorObjectForSegment(segmentId, layerName); - const meshMaterial = new THREE.MeshLambertMaterial({ - color, + // const meshMaterial = new THREE.MeshLambertMaterial({ + // color, + // }); + + const meshMaterial = new THREE.MeshStandardMaterial({ + color, // A soft blue color + metalness: 0.5, // Slight metallic effect + roughness: 1, // Some surface roughness for a natural look + side: THREE.DoubleSide, // Render both sides + flatShading: false, // Ensures smooth shading with computed normals }); - meshMaterial.side = THREE.FrontSide; + + // meshMaterial.side = THREE.FrontSide; meshMaterial.transparent = true; // mesh.parent is still null at this moment, but when the mesh is @@ -114,8 +123,8 @@ export default class SegmentMeshController { // this detail for now via the casting. const mesh = new THREE.Mesh(geometry, meshMaterial) as any as MeshSceneNode; - mesh.castShadow = true; - mesh.receiveShadow = true; + // mesh.castShadow = true; + // mesh.receiveShadow = true; const tweenAnimation = new TWEEN.Tween({ opacity: 0, }); @@ -180,6 +189,7 @@ export default class SegmentMeshController { meshChunk.translateY(offset[1]); meshChunk.translateZ(offset[2]); } + geometry.computeVertexNormals(); return meshChunk; }); const group = new THREE.Group() as SceneGroupForMeshes; @@ -301,33 +311,28 @@ export default class SegmentMeshController { addLights(): void { // Note that the PlaneView also attaches a directional light directly to the TD camera, // so that the light moves along the cam. - const AMBIENT_INTENSITY = 30; - const DIRECTIONAL_INTENSITY = 5; - const POINT_INTENSITY = 5; - - const ambientLight = new THREE.AmbientLight(2105376, AMBIENT_INTENSITY); - - const directionalLight = new THREE.DirectionalLight(16777215, DIRECTIONAL_INTENSITY); - directionalLight.position.x = 1; - directionalLight.position.y = 1; - directionalLight.position.z = 1; - directionalLight.position.normalize(); - - const directionalLight2 = new THREE.DirectionalLight(16777215, DIRECTIONAL_INTENSITY); - directionalLight2.position.x = -1; - directionalLight2.position.y = -1; - directionalLight2.position.z = -1; - directionalLight2.position.normalize(); - - const pointLight = new THREE.PointLight(16777215, POINT_INTENSITY); - pointLight.position.x = 0; - pointLight.position.y = -25; - pointLight.position.z = 10; - - this.meshesLODRootGroup.add(ambientLight); - this.meshesLODRootGroup.add(directionalLight); - this.meshesLODRootGroup.add(directionalLight2); - this.meshesLODRootGroup.add(pointLight); + // const AMBIENT_INTENSITY = 3; + // const DIRECTIONAL_INTENSITY = 5; + // const POINT_INTENSITY = 5; + // const ambientLight = new THREE.AmbientLight(2105376, AMBIENT_INTENSITY); + // const directionalLight = new THREE.DirectionalLight(16777215, DIRECTIONAL_INTENSITY); + // directionalLight.position.x = 1; + // directionalLight.position.y = 1; + // directionalLight.position.z = 1; + // directionalLight.position.normalize(); + // const directionalLight2 = new THREE.DirectionalLight(16777215, DIRECTIONAL_INTENSITY); + // directionalLight2.position.x = -1; + // directionalLight2.position.y = -1; + // directionalLight2.position.z = -1; + // directionalLight2.position.normalize(); + // const pointLight = new THREE.PointLight(16777215, POINT_INTENSITY); + // pointLight.position.x = 0; + // pointLight.position.y = -25; + // pointLight.position.z = 10; + // this.meshesLODRootGroup.add(ambientLight); + // this.meshesLODRootGroup.add(directionalLight); + // this.meshesLODRootGroup.add(directionalLight2); + // this.meshesLODRootGroup.add(pointLight); } getMeshGroupsByLOD( diff --git a/frontend/javascripts/oxalis/model/sagas/root_saga.ts b/frontend/javascripts/oxalis/model/sagas/root_saga.ts index f71ee81d0a4..f163ca7b8c9 100644 --- a/frontend/javascripts/oxalis/model/sagas/root_saga.ts +++ b/frontend/javascripts/oxalis/model/sagas/root_saga.ts @@ -21,6 +21,7 @@ import { race } from "redux-saga/effects"; import { all, call, cancel, fork, put, take, takeEvery } from "typed-redux-saga"; import type { EscalateErrorAction } from "../actions/actions"; import { setIsWkReadyAction } from "../actions/ui_actions"; +import bentSurfaceSaga from "./bent_surface_saga"; import maintainMaximumZoomForAllMagsSaga from "./flycam_info_cache_saga"; import { warnIfEmailIsUnverified } from "./user_saga"; @@ -82,6 +83,7 @@ function* restartableSaga(): Saga { call(handleAdditionalCoordinateUpdate), call(maintainMaximumZoomForAllMagsSaga), ...DatasetSagas.map((saga) => call(saga)), + call(bentSurfaceSaga), ]); } catch (err) { rootSagaCrashed = true; diff --git a/frontend/javascripts/oxalis/shaders/main_data_shaders.glsl.ts b/frontend/javascripts/oxalis/shaders/main_data_shaders.glsl.ts index d6e481c282f..b98399e4c39 100644 --- a/frontend/javascripts/oxalis/shaders/main_data_shaders.glsl.ts +++ b/frontend/javascripts/oxalis/shaders/main_data_shaders.glsl.ts @@ -158,6 +158,7 @@ const float bucketSize = <%= bucketSize %>; export default function getMainFragmentShader(params: Params) { const hasSegmentation = params.segmentationLayerNames.length > 0; + // return ""; return _.template(` precision highp float; @@ -414,6 +415,7 @@ void main() { export function getMainVertexShader(params: Params) { const hasSegmentation = params.segmentationLayerNames.length > 0; + // return ""; return _.template(` precision highp float; diff --git a/frontend/javascripts/oxalis/view/plane_view.ts b/frontend/javascripts/oxalis/view/plane_view.ts index 998bc464da4..ec69635eb6d 100644 --- a/frontend/javascripts/oxalis/view/plane_view.ts +++ b/frontend/javascripts/oxalis/view/plane_view.ts @@ -70,7 +70,7 @@ class PlaneView { } this.cameras = cameras; - createDirLight([10, 10, 10], [0, 0, 10], 5, this.cameras[OrthoViews.TDView]); + // createDirLight([10, 10, 10], [0, 0, 10], 5, this.cameras[OrthoViews.TDView]); this.cameras[OrthoViews.PLANE_XY].position.z = -1; this.cameras[OrthoViews.PLANE_YZ].position.x = 1; this.cameras[OrthoViews.PLANE_XZ].position.y = 1; From dcfa9ed343e5e26518970d7bee6e5ac62e9a755f Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Mon, 3 Mar 2025 15:32:59 +0100 Subject: [PATCH 02/84] temporarily disable some CI checks --- .circleci/not-on-master.sh | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.circleci/not-on-master.sh b/.circleci/not-on-master.sh index 581393ebead..e3078cdb9ce 100755 --- a/.circleci/not-on-master.sh +++ b/.circleci/not-on-master.sh @@ -1,8 +1,8 @@ #!/usr/bin/env bash set -Eeuo pipefail -if [ "${CIRCLE_BRANCH}" == "master" ]; then +# if [ "${CIRCLE_BRANCH}" == "master" ]; then echo "Skipping this step on master..." -else - exec "$@" -fi +# else +# exec "$@" +# fi From b5c4d428593f9e4cdb5b2a6f67f5b02a6b33cede Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Tue, 4 Mar 2025 11:24:54 +0100 Subject: [PATCH 03/84] also implement delauny and splines approach --- frontend/javascripts/oxalis/api/wk_dev.ts | 1 + .../oxalis/controller/scene_controller.ts | 175 ++++++++++++++++-- package.json | 4 + yarn.lock | 73 +++++++- 4 files changed, 235 insertions(+), 18 deletions(-) diff --git a/frontend/javascripts/oxalis/api/wk_dev.ts b/frontend/javascripts/oxalis/api/wk_dev.ts index 0e94cac317d..4bfcc076622 100644 --- a/frontend/javascripts/oxalis/api/wk_dev.ts +++ b/frontend/javascripts/oxalis/api/wk_dev.ts @@ -32,6 +32,7 @@ export const WkDevFlags = { datasetComposition: { allowThinPlateSplines: false, }, + splittingStrategy: "tps", }; export default class WkDev { diff --git a/frontend/javascripts/oxalis/controller/scene_controller.ts b/frontend/javascripts/oxalis/controller/scene_controller.ts index 80a555ca52a..2158039620a 100644 --- a/frontend/javascripts/oxalis/controller/scene_controller.ts +++ b/frontend/javascripts/oxalis/controller/scene_controller.ts @@ -54,8 +54,9 @@ import SegmentMeshController from "./segment_mesh_controller"; const CUBE_COLOR = 0x999999; const LAYER_CUBE_COLOR = 0xffff99; -// import Delaunator from "delaunator"; +import Delaunator from "delaunator"; import TPS3D from "libs/thin_plate_spline"; +import { WkDevFlags } from "oxalis/api/wk_dev"; type EigenData = { eigenvalue: number; vector: number[] }; @@ -74,9 +75,39 @@ function createPointCloud(points: Vector3[], color: string) { const rows = 100; const cols = 100; -function computeBentSurface(points: Vector3[]): THREE.Object3D[] { - const eigenData: EigenData[] = PCA.getEigenVectors(points); + +function computeBentSurfaceDelauny(points3D: Vector3[]): THREE.Object3D[] { const objects: THREE.Object3D[] = []; + // Your precomputed 2D projection (same order as points3D) + + const { projectedLocalPoints } = projectPoints(points3D); + + // Compute Delaunay triangulation on the projected 2D points + const delaunay = Delaunator.from(projectedLocalPoints.map((vec) => [vec.x, vec.y])); + const indices = delaunay.triangles; // Triangle indices + + // Flatten 3D vertex positions for BufferGeometry + const vertices = points3D.flat(); + + // Create BufferGeometry + const geometry = new THREE.BufferGeometry(); + geometry.setAttribute("position", new THREE.Float32BufferAttribute(vertices, 3)); + geometry.setIndex(Array.from(indices)); + geometry.computeVertexNormals(); // Compute normals for shading + + const material = new THREE.MeshLambertMaterial({ + color: "green", + wireframe: false, + }); + material.side = THREE.DoubleSide; + // material.transparent = true; + const surfaceMesh = new THREE.Mesh(geometry, material); + objects.push(surfaceMesh); + return objects; +} + +function projectPoints(points: Vector3[]) { + const eigenData: EigenData[] = PCA.getEigenVectors(points); const adData = PCA.computeAdjustedData(points, eigenData[0], eigenData[1]); const compressed = adData.formattedAdjustedData; @@ -85,6 +116,22 @@ function computeBentSurface(points: Vector3[]): THREE.Object3D[] { const projectedPoints: Vector3[] = uncompressed.originalData; + // Align the plane with the principal components + const normal = new THREE.Vector3(...eigenData[2].vector); + const quaternion = new THREE.Quaternion().setFromUnitVectors(new THREE.Vector3(0, 0, 1), normal); + const quaternionInv = quaternion.clone().invert(); + + // Transform projectedPoints into the plane’s local coordinate system + const projectedLocalPoints = projectedPoints.map((p) => { + const worldPoint = new THREE.Vector3(...p); + return worldPoint.applyQuaternion(quaternionInv); // Move to local plane space + }); + return { projectedPoints, projectedLocalPoints, eigenData }; +} + +function computeBentSurfaceTPS(points: Vector3[]): THREE.Object3D[] { + const objects: THREE.Object3D[] = []; + const { projectedPoints, projectedLocalPoints, eigenData } = projectPoints(points); // objects.push(createPointCloud(points, "red")); // objects.push(createPointCloud(projectedPoints, "blue")); @@ -97,12 +144,6 @@ function computeBentSurface(points: Vector3[]): THREE.Object3D[] { const quaternion = new THREE.Quaternion().setFromUnitVectors(new THREE.Vector3(0, 0, 1), normal); const quaternionInv = quaternion.clone().invert(); - // Transform projectedPoints into the plane’s local coordinate system - const projectedLocalPoints = projectedPoints.map((p) => { - const worldPoint = new THREE.Vector3(...p); - return worldPoint.applyQuaternion(quaternionInv); // Move to local plane space - }); - const mean = points.reduce( (acc, p) => acc.add(new THREE.Vector3(...p).divideScalar(points.length)), new THREE.Vector3(0, 0, 0), @@ -182,6 +223,105 @@ function computeBentSurface(points: Vector3[]): THREE.Object3D[] { return objects; } +function computeBentSurfaceSplines(points: Vector3[]): THREE.Object3D[] { + const objects: THREE.Object3D[] = []; + console.log("fresh!"); + + const pointsByZ = _.groupBy(points, (p) => p[2]); + + const zValues = Object.keys(pointsByZ) + .map((el) => Number(el)) + .sort(); + + const curves = _.compact( + zValues.map((zValue) => { + const points2D = pointsByZ[zValue].map((p) => new THREE.Vector3(p[0], p[1], p[2])); + + if (points2D.length < 2) { + return null; + } + + console.log("points2D", points2D); + + // Use CatmullRomCurve3 for a smooth 3D spline + const curve = new THREE.CatmullRomCurve3(points2D); + + const curvePoints = curve.getPoints(50); // Generate more points along the curve + const geometry = new THREE.BufferGeometry().setFromPoints(curvePoints); + + const material = new THREE.LineBasicMaterial({ color: 0xff0000 }); + + // Create the final object to add to the scene + const splineObject = new THREE.Line(geometry, material); + objects.push(splineObject); + return curve; + }), + ); + + // Number of points per curve + const numPoints = 50; + + // Generate grid of points + const gridPoints = curves.map((curve) => curve.getPoints(numPoints - 1)); + + // Flatten into a single array of vertices + const vertices: number[] = []; + const indices = []; + + gridPoints.forEach((row) => { + row.forEach((point) => { + vertices.push(point.x, point.y, point.z); // Store as flat array for BufferGeometry + }); + }); + + // Connect vertices with triangles + // console.group("Computing indices"); + for (let i = 0; i < curves.length - 1; i++) { + // console.group("Curve i=" + i); + for (let j = 0; j < numPoints - 1; j++) { + // console.group("Point j=" + j); + let current = i * numPoints + j; + let next = (i + 1) * numPoints + j; + + // const printFace = (x, y, z) => { + // return [vertices[3 * x], vertices[3 * y], vertices[3 * z]]; + // }; + + // console.log("Creating faces with", { current, next }); + // console.log("First face:", printFace(current, next, current + 1)); + // console.log("Second face:", printFace(next, next + 1, current + 1)); + // Two triangles per quad + indices.push(current, next, current + 1); + indices.push(next, next + 1, current + 1); + // console.groupEnd(); + } + // console.groupEnd(); + } + // console.groupEnd(); + + // Convert to Three.js BufferGeometry + const geometry = new THREE.BufferGeometry(); + geometry.setAttribute("position", new THREE.Float32BufferAttribute(vertices, 3)); + geometry.setIndex(indices); + geometry.computeVertexNormals(); // Smooth shading + + // Material and Mesh + const material = new THREE.MeshStandardMaterial({ + color: 0x0077ff, // A soft blue color + metalness: 0.5, // Slight metallic effect + roughness: 1, // Some surface roughness for a natural look + side: THREE.DoubleSide, // Render both sides + flatShading: false, // Ensures smooth shading with computed normals + opacity: 0.8, + transparent: true, + wireframe: false, + }); + const surfaceMesh = new THREE.Mesh(geometry, material); + + objects.push(surfaceMesh); + return objects; +} + // function createNormalsVisualization(geometry: THREE.BufferGeometry, objects: THREE.Object3D[]) { // const positions = geometry.attributes.position.array; // const normals = geometry.attributes.normal.array; @@ -583,9 +723,22 @@ class SceneController { // const surfaceMesh = new THREE.Mesh(meshGeometry, material); // this.rootNode.add(surfaceMesh); - let objs; + if (points.length === 0) { + return; + } + + let objs: THREE.Object3D[] = []; try { - objs = computeBentSurface(points); + if (WkDevFlags.splittingStrategy === "tps") { + objs = computeBentSurfaceTPS(points); + } else if (WkDevFlags.splittingStrategy === "splines") { + objs = computeBentSurfaceSplines(points); + } else if (WkDevFlags.splittingStrategy === "delauny") { + objs = computeBentSurfaceDelauny(points); + } else { + Toast.error("Unknown splitting strategy. Use tps or splines or delauny"); + return () => {}; + } } catch (exc) { console.error(exc); Toast.error("Could not compute surface"); diff --git a/package.json b/package.json index ed2170d2400..ca0be3175fe 100644 --- a/package.json +++ b/package.json @@ -15,6 +15,7 @@ "@types/color-hash": "^1.0.2", "@types/cwise": "^1.0.4", "@types/dagre": "^0.7.48", + "@types/delaunator": "^5", "@types/file-saver": "^2.0.5", "@types/lodash": "^4.17.4", "@types/lz-string": "^1.3.34", @@ -158,6 +159,7 @@ "dayjs": "^1.11.13", "deep-for-each": "^2.0.3", "deep-freeze": "0.0.1", + "delaunator": "^5.0.1", "dice-coefficient": "^2.1.0", "distance-transform": "^1.0.2", "esbuild-loader": "^4.1.0", @@ -183,6 +185,7 @@ "ndarray-moments": "^1.0.0", "ndarray-ops": "^1.2.2", "pako": "^2.1.0", + "pca-js": "^1.0.2", "pretty-bytes": "^5.1.0", "process": "^0.11.10", "protobufjs": "^6.11.4", @@ -211,6 +214,7 @@ "typed-redux-saga": "^1.4.0", "url": "^0.11.0", "url-join": "^4.0.0", + "verb-nurbs": "^3.0.2", "worker-loader": "^3.0.8" }, "ava": { diff --git a/yarn.lock b/yarn.lock index c59b62a1312..f486b1cc733 100644 --- a/yarn.lock +++ b/yarn.lock @@ -300,12 +300,21 @@ __metadata: languageName: node linkType: hard -"@babel/runtime@npm:^7.1.2, @babel/runtime@npm:^7.10.1, @babel/runtime@npm:^7.10.4, @babel/runtime@npm:^7.11.1, @babel/runtime@npm:^7.11.2, @babel/runtime@npm:^7.12.1, @babel/runtime@npm:^7.12.13, @babel/runtime@npm:^7.12.5, @babel/runtime@npm:^7.16.7, @babel/runtime@npm:^7.18.0, @babel/runtime@npm:^7.18.3, @babel/runtime@npm:^7.18.9, @babel/runtime@npm:^7.20.0, @babel/runtime@npm:^7.20.7, @babel/runtime@npm:^7.21.0, @babel/runtime@npm:^7.22.5, @babel/runtime@npm:^7.23.2, @babel/runtime@npm:^7.23.6, @babel/runtime@npm:^7.23.9, @babel/runtime@npm:^7.24.4, @babel/runtime@npm:^7.24.7, @babel/runtime@npm:^7.24.8, @babel/runtime@npm:^7.6.3, @babel/runtime@npm:^7.7.2, @babel/runtime@npm:^7.9.2": - version: 7.26.10 - resolution: "@babel/runtime@npm:7.26.10" +"@babel/runtime@npm:^7.1.2, @babel/runtime@npm:^7.10.1, @babel/runtime@npm:^7.10.4, @babel/runtime@npm:^7.11.1, @babel/runtime@npm:^7.11.2, @babel/runtime@npm:^7.12.1, @babel/runtime@npm:^7.12.13, @babel/runtime@npm:^7.12.5, @babel/runtime@npm:^7.16.7, @babel/runtime@npm:^7.18.0, @babel/runtime@npm:^7.18.3, @babel/runtime@npm:^7.18.9, @babel/runtime@npm:^7.20.0, @babel/runtime@npm:^7.20.7, @babel/runtime@npm:^7.21.0, @babel/runtime@npm:^7.22.5, @babel/runtime@npm:^7.23.2, @babel/runtime@npm:^7.23.6, @babel/runtime@npm:^7.23.9, @babel/runtime@npm:^7.24.4, @babel/runtime@npm:^7.24.8, @babel/runtime@npm:^7.6.3, @babel/runtime@npm:^7.7.2, @babel/runtime@npm:^7.9.2": + version: 7.25.6 + resolution: "@babel/runtime@npm:7.25.6" dependencies: regenerator-runtime: "npm:^0.14.0" - checksum: 10c0/6dc6d88c7908f505c4f7770fb4677dfa61f68f659b943c2be1f2a99cb6680343462867abf2d49822adc435932919b36c77ac60125793e719ea8745f2073d3745 + checksum: 10c0/d6143adf5aa1ce79ed374e33fdfd74fa975055a80bc6e479672ab1eadc4e4bfd7484444e17dd063a1d180e051f3ec62b357c7a2b817e7657687b47313158c3d2 + languageName: node + linkType: hard + +"@babel/runtime@npm:^7.24.7": + version: 7.26.0 + resolution: "@babel/runtime@npm:7.26.0" + dependencies: + regenerator-runtime: "npm:^0.14.0" + checksum: 10c0/12c01357e0345f89f4f7e8c0e81921f2a3e3e101f06e8eaa18a382b517376520cd2fa8c237726eb094dab25532855df28a7baaf1c26342b52782f6936b07c287 languageName: node linkType: hard @@ -2378,6 +2387,13 @@ __metadata: languageName: node linkType: hard +"@types/delaunator@npm:^5": + version: 5.0.3 + resolution: "@types/delaunator@npm:5.0.3" + checksum: 10c0/4d6a5be512a382f6b7185e372d0569635a4877e1d04b90c86ce48ad3270f04bf944e0edf4ea6810bf2e65aacc3c52ee836ab7c329bcad3f3478375c5ed0a3611 + languageName: node + linkType: hard + "@types/eslint-scope@npm:^3.7.3": version: 3.7.3 resolution: "@types/eslint-scope@npm:3.7.3" @@ -5272,6 +5288,15 @@ __metadata: languageName: node linkType: hard +"delaunator@npm:^5.0.1": + version: 5.0.1 + resolution: "delaunator@npm:5.0.1" + dependencies: + robust-predicates: "npm:^3.0.2" + checksum: 10c0/3d7ea4d964731c5849af33fec0a271bc6753487b331fd7d43ccb17d77834706e1c383e6ab8fda0032da955e7576d1083b9603cdaf9cbdfd6b3ebd1fb8bb675a5 + languageName: node + linkType: hard + "delayed-stream@npm:~1.0.0": version: 1.0.0 resolution: "delayed-stream@npm:1.0.0" @@ -10501,6 +10526,13 @@ __metadata: languageName: node linkType: hard +"pca-js@npm:^1.0.2": + version: 1.0.2 + resolution: "pca-js@npm:1.0.2" + checksum: 10c0/65daa653d338959e588890bef631ce313da593722bff0e9e16dcc0428fa37d181c59662d17893a75118535f90ddd61576533ad27794d6346e15049ffbdda77c4 + languageName: node + linkType: hard + "pend@npm:~1.2.0": version: 1.2.0 resolution: "pend@npm:1.2.0" @@ -12506,6 +12538,13 @@ __metadata: languageName: node linkType: hard +"robust-predicates@npm:^3.0.2": + version: 3.0.2 + resolution: "robust-predicates@npm:3.0.2" + checksum: 10c0/4ecd53649f1c2d49529c85518f2fa69ffb2f7a4453f7fd19c042421c7b4d76c3efb48bc1c740c8f7049346d7cb58cf08ee0c9adaae595cc23564d360adb1fde4 + languageName: node + linkType: hard + "rrweb-cssom@npm:^0.6.0": version: 0.6.0 resolution: "rrweb-cssom@npm:0.6.0" @@ -12774,11 +12813,11 @@ __metadata: linkType: hard "serialize-javascript@npm:^6.0.0": - version: 6.0.2 - resolution: "serialize-javascript@npm:6.0.2" + version: 6.0.0 + resolution: "serialize-javascript@npm:6.0.0" dependencies: randombytes: "npm:^2.1.0" - checksum: 10c0/2dd09ef4b65a1289ba24a788b1423a035581bef60817bea1f01eda8e3bda623f86357665fe7ac1b50f6d4f583f97db9615b3f07b2a2e8cbcb75033965f771dd2 + checksum: 10c0/73104922ef0a919064346eea21caab99de1a019a1f5fb54a7daa7fcabc39e83b387a2a363e52a889598c3b1bcf507c4b2a7b26df76e991a310657af20eea2e7c languageName: node linkType: hard @@ -14394,6 +14433,15 @@ __metadata: languageName: node linkType: hard +"verb-nurbs@npm:^3.0.2": + version: 3.0.2 + resolution: "verb-nurbs@npm:3.0.2" + dependencies: + web-worker: "npm:^1.3.0" + checksum: 10c0/1959e412ab128b3377a2d114b584393a09d9e2ee80d958d61c3cd2336aa81ddfc9fe20e3ddcd2bb5abb697a36c6f8903476c267422b0df680ed21f46a46b58d2 + languageName: node + linkType: hard + "verror@npm:1.10.0": version: 1.10.0 resolution: "verror@npm:1.10.0" @@ -14545,6 +14593,13 @@ __metadata: languageName: node linkType: hard +"web-worker@npm:^1.3.0": + version: 1.5.0 + resolution: "web-worker@npm:1.5.0" + checksum: 10c0/d42744757422803c73ca64fa51e1ce994354ace4b8438b3f740425a05afeb8df12dd5dadbf6b0839a08dbda56c470d7943c0383854c4fb1ae40ab874eb10427a + languageName: node + linkType: hard + "webidl-conversions@npm:^3.0.0": version: 3.0.1 resolution: "webidl-conversions@npm:3.0.1" @@ -14587,6 +14642,7 @@ __metadata: "@types/color-hash": "npm:^1.0.2" "@types/cwise": "npm:^1.0.4" "@types/dagre": "npm:^0.7.48" + "@types/delaunator": "npm:^5" "@types/file-saver": "npm:^2.0.5" "@types/lodash": "npm:^4.17.4" "@types/lz-string": "npm:^1.3.34" @@ -14628,6 +14684,7 @@ __metadata: dayjs: "npm:^1.11.13" deep-for-each: "npm:^2.0.3" deep-freeze: "npm:0.0.1" + delaunator: "npm:^5.0.1" dependency-cruiser: "npm:^16.10.0" dice-coefficient: "npm:^2.1.0" distance-transform: "npm:^1.0.2" @@ -14669,6 +14726,7 @@ __metadata: ndarray-ops: "npm:^1.2.2" node-fetch: "npm:^2.6.7" pako: "npm:^2.1.0" + pca-js: "npm:^1.0.2" pg: "npm:^7.4.1" pixelmatch: "npm:^5.2.0" pngjs: "npm:^3.3.3" @@ -14710,6 +14768,7 @@ __metadata: typescript-coverage-report: "npm:^0.8.0" url: "npm:^0.11.0" url-join: "npm:^4.0.0" + verb-nurbs: "npm:^3.0.2" webpack: "npm:^5.74.0" webpack-cli: "npm:^5.1.4" webpack-dev-server: "npm:^5.0.2" From ab08454b40a505ccb4998bfc927d0fad93091f96 Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Tue, 4 Mar 2025 11:33:38 +0100 Subject: [PATCH 04/84] add missing saga --- .../oxalis/model/sagas/bent_surface_saga.ts | 58 +++++++++++++++++++ 1 file changed, 58 insertions(+) create mode 100644 frontend/javascripts/oxalis/model/sagas/bent_surface_saga.ts diff --git a/frontend/javascripts/oxalis/model/sagas/bent_surface_saga.ts b/frontend/javascripts/oxalis/model/sagas/bent_surface_saga.ts new file mode 100644 index 00000000000..e258195a6a2 --- /dev/null +++ b/frontend/javascripts/oxalis/model/sagas/bent_surface_saga.ts @@ -0,0 +1,58 @@ +import getSceneController from "oxalis/controller/scene_controller_provider"; +import type { Saga } from "oxalis/model/sagas/effect-generators"; +import { select } from "oxalis/model/sagas/effect-generators"; +import { call, takeEvery } from "typed-redux-saga"; +import { getActiveTree } from "../accessors/skeletontracing_accessor"; +import { ensureWkReady } from "./ready_sagas"; +import { takeWithBatchActionSupport } from "./saga_helpers"; + +let cleanUpFn: (() => void) | null = null; + +function* createBentSurface() { + if (cleanUpFn != null) { + cleanUpFn(); + cleanUpFn = null; + } + + const sceneController = yield* call(() => getSceneController()); + + // const points: Vector3[] = [ + // [40, 50, 60], + // [50, 70, 60], + // [80, 70, 90], + // [50, 60, 80], + // ]; + + const activeTree = yield* select((state) => getActiveTree(state.tracing.skeleton)); + // biome-ignore lint/complexity/useOptionalChain: + if (activeTree != null && activeTree.isVisible) { + const nodes = Array.from(activeTree.nodes.values()); + const points = nodes.map((node) => node.untransformedPosition); + console.log("points", points); + if (points.length > 3) { + cleanUpFn = sceneController.addBentSurface(points); + } + } +} + +export function* bentSurfaceSaga(): Saga { + cleanUpFn = null; + yield* takeWithBatchActionSupport("INITIALIZE_SKELETONTRACING"); + yield* ensureWkReady(); + + // initial rendering + yield* call(createBentSurface); + yield* takeEvery( + [ + "SET_ACTIVE_TREE", + "SET_ACTIVE_TREE_BY_NAME", + "CREATE_NODE", + "DELETE_NODE", + "SET_TREE_VISIBILITY", + "TOGGLE_TREE", + ], + createBentSurface, + ); +} + +export default bentSurfaceSaga; From 667fa5eb13ef2e748073dc9ddc80da843c492c0c Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Tue, 4 Mar 2025 11:58:17 +0100 Subject: [PATCH 05/84] change default to splines --- frontend/javascripts/oxalis/api/wk_dev.ts | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/frontend/javascripts/oxalis/api/wk_dev.ts b/frontend/javascripts/oxalis/api/wk_dev.ts index 4bfcc076622..8ead784ad2a 100644 --- a/frontend/javascripts/oxalis/api/wk_dev.ts +++ b/frontend/javascripts/oxalis/api/wk_dev.ts @@ -32,7 +32,7 @@ export const WkDevFlags = { datasetComposition: { allowThinPlateSplines: false, }, - splittingStrategy: "tps", + splittingStrategy: "splines", }; export default class WkDev { From d1691eca6ec4cb36a14f02e22bc1772e943c3d4d Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Tue, 4 Mar 2025 17:08:50 +0100 Subject: [PATCH 06/84] experiment with automatic ordering of points and flipping --- .../oxalis/controller/scene_controller.ts | 15 ++- .../oxalis/controller/splitting_stuff.ts | 105 ++++++++++++++++++ .../oxalis/model/sagas/bent_surface_saga.ts | 1 + 3 files changed, 120 insertions(+), 1 deletion(-) create mode 100644 frontend/javascripts/oxalis/controller/splitting_stuff.ts diff --git a/frontend/javascripts/oxalis/controller/scene_controller.ts b/frontend/javascripts/oxalis/controller/scene_controller.ts index 2158039620a..6da84d1e3c7 100644 --- a/frontend/javascripts/oxalis/controller/scene_controller.ts +++ b/frontend/javascripts/oxalis/controller/scene_controller.ts @@ -57,6 +57,7 @@ const LAYER_CUBE_COLOR = 0xffff99; import Delaunator from "delaunator"; import TPS3D from "libs/thin_plate_spline"; import { WkDevFlags } from "oxalis/api/wk_dev"; +import { enforceConsistentDirection, orderPointsMST } from "./splitting_stuff"; type EigenData = { eigenvalue: number; vector: number[] }; @@ -264,6 +265,18 @@ function computeBentSurfaceSplines(points: Vector3[]): THREE.Object3D[] { // Generate grid of points const gridPoints = curves.map((curve) => curve.getPoints(numPoints - 1)); + for (let curveIdx = 1; curveIdx < gridPoints.length; curveIdx++) { + const currentCurvePoints = gridPoints[curveIdx]; + const prevCurvePoints = gridPoints[curveIdx - 1]; + const distActual = currentCurvePoints[0].distanceTo(prevCurvePoints[0]); + const distFlipped = currentCurvePoints.at(-1).distanceTo(prevCurvePoints[0]); + + const shouldFlip = distFlipped < distActual; + if (shouldFlip) { + gridPoints[curveIdx].reverse(); + } + } + // Flatten into a single array of vertices const vertices: number[] = []; const indices = []; @@ -724,7 +737,7 @@ class SceneController { // this.rootNode.add(surfaceMesh); if (points.length === 0) { - return; + return () => {}; } let objs: THREE.Object3D[] = []; diff --git a/frontend/javascripts/oxalis/controller/splitting_stuff.ts b/frontend/javascripts/oxalis/controller/splitting_stuff.ts new file mode 100644 index 00000000000..bd4d6fd2e6c --- /dev/null +++ b/frontend/javascripts/oxalis/controller/splitting_stuff.ts @@ -0,0 +1,105 @@ +class DisjointSet { + private parent: number[]; + private rank: number[]; + + constructor(n: number) { + this.parent = Array.from({ length: n }, (_, i) => i); + this.rank = Array(n).fill(0); + } + + find(i: number): number { + if (this.parent[i] !== i) this.parent[i] = this.find(this.parent[i]); + return this.parent[i]; + } + + union(i: number, j: number): void { + let rootI = this.find(i), + rootJ = this.find(j); + if (rootI !== rootJ) { + if (this.rank[rootI] > this.rank[rootJ]) this.parent[rootJ] = rootI; + else if (this.rank[rootI] < this.rank[rootJ]) this.parent[rootI] = rootJ; + else { + this.parent[rootJ] = rootI; + this.rank[rootI]++; + } + } + } +} + +interface Edge { + i: number; + j: number; + dist: number; +} + +function computeMST(points: THREE.Vector3[]): number[][] { + const edges: Edge[] = []; + const numPoints = points.length; + + // Create all possible edges with distances + for (let i = 0; i < numPoints; i++) { + for (let j = i + 1; j < numPoints; j++) { + const dist = points[i].distanceTo(points[j]); + edges.push({ i, j, dist }); + } + } + + // Sort edges by distance (Kruskal's Algorithm) + edges.sort((a, b) => a.dist - b.dist); + + // Compute MST using Kruskal’s Algorithm + const ds = new DisjointSet(numPoints); + const mst: number[][] = Array.from({ length: numPoints }, () => []); + + for (const { i, j } of edges) { + if (ds.find(i) !== ds.find(j)) { + ds.union(i, j); + mst[i].push(j); + mst[j].push(i); + } + } + + return mst; +} + +function traverseMST_DFS(mst: number[][], startIdx = 0): number[] { + const visited = new Set(); + const orderedPoints: number[] = []; + + function dfs(node: number) { + if (visited.has(node)) return; + visited.add(node); + orderedPoints.push(node); + for (let neighbor of mst[node]) { + dfs(neighbor); + } + } + + dfs(startIdx); + return orderedPoints; +} + +export function orderPointsMST(points: THREE.Vector3[]): THREE.Vector3[] { + if (points.length === 0) return []; + const mst = computeMST(points); + const dfsOrder = traverseMST_DFS(mst); + return enforceConsistentDirection(dfsOrder.map((index) => points[index])); +} + +export function enforceConsistentDirection(points: THREE.Vector3[]): THREE.Vector3[] { + if (points.length < 2) return points; + + const first = points[0]; + const last = points[points.length - 1]; + + // Check if the curve follows top-left → bottom-right order + const dx = last.x - first.x; + const dy = last.y - first.y; + const maxDelta = Math.abs(dx) > Math.abs(dy) ? dx : dy; + + if (maxDelta < 0) { + // The curve is flipped (going bottom-right → top-left), so reverse it + return points.reverse(); + } + return points; +} diff --git a/frontend/javascripts/oxalis/model/sagas/bent_surface_saga.ts b/frontend/javascripts/oxalis/model/sagas/bent_surface_saga.ts index e258195a6a2..468fb0fa54f 100644 --- a/frontend/javascripts/oxalis/model/sagas/bent_surface_saga.ts +++ b/frontend/javascripts/oxalis/model/sagas/bent_surface_saga.ts @@ -50,6 +50,7 @@ export function* bentSurfaceSaga(): Saga { "DELETE_NODE", "SET_TREE_VISIBILITY", "TOGGLE_TREE", + "SET_NODE_POSITION", ], createBentSurface, ); From a60c90ff9f927dd38c4325ac50a986fa4cda777d Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Thu, 6 Mar 2025 16:14:17 +0100 Subject: [PATCH 07/84] fix typo --- frontend/javascripts/messages.tsx | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/frontend/javascripts/messages.tsx b/frontend/javascripts/messages.tsx index 0a707115c15..25493bea946 100644 --- a/frontend/javascripts/messages.tsx +++ b/frontend/javascripts/messages.tsx @@ -475,7 +475,7 @@ instead. Only enable this option if you understand its effect. All layers will n "<%- userName %> is about to become a dataset manager and will be able to access and edit all datasets within this organization.", ), "users.set_admin": _.template( - "<%- userName %> is about to become an admin for this organization with full read/write access to all datasets and management capbilities for all users, projects, and tasks.", + "<%- userName %> is about to become an admin for this organization with full read/write access to all datasets and management capabilities for all users, projects, and tasks.", ), "users.change_email_title": "Do you really want to change the email?", "users.change_email": _.template( From 6f960e070d736d3db907d9745951cff2cdf69254 Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Thu, 6 Mar 2025 16:15:34 +0100 Subject: [PATCH 08/84] show spline on each section; don't cross surface in floodfill --- .../oxalis/controller/scene_controller.ts | 124 ++++++++++++++---- .../oxalis/controller/splitting_stuff.ts | 25 +++- .../model/bucket_data_handling/data_cube.ts | 99 +++++++++++++- .../oxalis/model/volumetracing/volumelayer.ts | 42 +++--- .../trees_tab/skeleton_tab_view.tsx | 2 +- package.json | 3 +- yarn.lock | 20 ++- 7 files changed, 261 insertions(+), 54 deletions(-) diff --git a/frontend/javascripts/oxalis/controller/scene_controller.ts b/frontend/javascripts/oxalis/controller/scene_controller.ts index 6da84d1e3c7..7916550fc83 100644 --- a/frontend/javascripts/oxalis/controller/scene_controller.ts +++ b/frontend/javascripts/oxalis/controller/scene_controller.ts @@ -59,6 +59,23 @@ import TPS3D from "libs/thin_plate_spline"; import { WkDevFlags } from "oxalis/api/wk_dev"; import { enforceConsistentDirection, orderPointsMST } from "./splitting_stuff"; +import { + computeBoundsTree, + disposeBoundsTree, + computeBatchedBoundsTree, + disposeBatchedBoundsTree, + acceleratedRaycast, +} from "three-mesh-bvh"; + +// Add the extension functions +THREE.BufferGeometry.prototype.computeBoundsTree = computeBoundsTree; +THREE.BufferGeometry.prototype.disposeBoundsTree = disposeBoundsTree; +THREE.Mesh.prototype.raycast = acceleratedRaycast; + +THREE.BatchedMesh.prototype.computeBoundsTree = computeBatchedBoundsTree; +THREE.BatchedMesh.prototype.disposeBoundsTree = disposeBatchedBoundsTree; +THREE.BatchedMesh.prototype.raycast = acceleratedRaycast; + type EigenData = { eigenvalue: number; vector: number[] }; function createPointCloud(points: Vector3[], color: string) { @@ -228,33 +245,50 @@ function computeBentSurfaceSplines(points: Vector3[]): THREE.Object3D[] { const objects: THREE.Object3D[] = []; console.log("fresh!"); - const pointsByZ = _.groupBy(points, (p) => p[2]); + const unfilteredPointsByZ = _.groupBy(points, (p) => p[2]); + const pointsByZ = _.omitBy(unfilteredPointsByZ, (value) => value.length < 2); const zValues = Object.keys(pointsByZ) .map((el) => Number(el)) .sort(); + const minZ = Math.min(...zValues); + const maxZ = Math.max(...zValues); + + const curvesByZ: Record = {}; + + // Create curves for existing z-values const curves = _.compact( - zValues.map((zValue) => { - const points2D = pointsByZ[zValue].map((p) => new THREE.Vector3(p[0], p[1], p[2])); + zValues.map((zValue, curveIdx) => { + let adaptedZ = zValue; + if (zValue === minZ) { + adaptedZ -= 0.5; + } else if (zValue === maxZ) { + adaptedZ += 0.5; + } + const points2D = orderPointsMST( + pointsByZ[zValue].map((p) => new THREE.Vector3(p[0], p[1], adaptedZ)), + ); if (points2D.length < 2) { return null; } - console.log("points2D", points2D); - - // Use CatmullRomCurve3 for a smooth 3D spline - const curve = new THREE.CatmullRomCurve3(points2D); + if (curveIdx > 0) { + const currentCurvePoints = points2D; + const prevCurvePoints = curvesByZ[zValues[curveIdx - 1]].points; - const curvePoints = curve.getPoints(50); // Generate more points along the curve - const geometry = new THREE.BufferGeometry().setFromPoints(curvePoints); + const distActual = currentCurvePoints[0].distanceTo(prevCurvePoints[0]); + const distFlipped = currentCurvePoints.at(-1).distanceTo(prevCurvePoints[0]); - const material = new THREE.LineBasicMaterial({ color: 0xff0000 }); + const shouldFlip = distFlipped < distActual; + if (shouldFlip) { + points2D.reverse(); + } + } - // Create the final object to add to the scene - const splineObject = new THREE.Line(geometry, material); - objects.push(splineObject); + const curve = new THREE.CatmullRomCurve3(points2D); + curvesByZ[zValue] = curve; return curve; }), ); @@ -262,21 +296,54 @@ function computeBentSurfaceSplines(points: Vector3[]): THREE.Object3D[] { // Number of points per curve const numPoints = 50; - // Generate grid of points - const gridPoints = curves.map((curve) => curve.getPoints(numPoints - 1)); + // Sort z-values for interpolation + const sortedZValues = Object.keys(curvesByZ) + .map(Number) + .sort((a, b) => a - b); - for (let curveIdx = 1; curveIdx < gridPoints.length; curveIdx++) { - const currentCurvePoints = gridPoints[curveIdx]; - const prevCurvePoints = gridPoints[curveIdx - 1]; - const distActual = currentCurvePoints[0].distanceTo(prevCurvePoints[0]); - const distFlipped = currentCurvePoints.at(-1).distanceTo(prevCurvePoints[0]); + // Interpolate missing z-values + for (let z = minZ; z <= maxZ; z++) { + if (curvesByZ[z]) continue; // Skip if curve already exists - const shouldFlip = distFlipped < distActual; - if (shouldFlip) { - gridPoints[curveIdx].reverse(); - } + // Find nearest lower and upper z-values + const lowerZ = Math.max(...sortedZValues.filter((v) => v < z)); + const upperZ = Math.min(...sortedZValues.filter((v) => v > z)); + + if (lowerZ === Number.NEGATIVE_INFINITY || upperZ === Number.POSITIVE_INFINITY) continue; + + // Get the two adjacent curves and sample 50 points from each + const lowerCurvePoints = curvesByZ[lowerZ].getPoints(numPoints); + const upperCurvePoints = curvesByZ[upperZ].getPoints(numPoints); + + // Interpolate between corresponding points + const interpolatedPoints = lowerCurvePoints.map((lowerPoint, i) => { + const upperPoint = upperCurvePoints[i]; + const alpha = (z - lowerZ) / (upperZ - lowerZ); // Interpolation factor + + return new THREE.Vector3( + THREE.MathUtils.lerp(lowerPoint.x, upperPoint.x, alpha), + THREE.MathUtils.lerp(lowerPoint.y, upperPoint.y, alpha), + z, + ); + }); + + // Create the interpolated curve + const interpolatedCurve = new THREE.CatmullRomCurve3(interpolatedPoints); + curvesByZ[z] = interpolatedCurve; } + // Generate and display all curves + Object.values(curvesByZ).forEach((curve) => { + const curvePoints = curve.getPoints(50); + const geometry = new THREE.BufferGeometry().setFromPoints(curvePoints); + const material = new THREE.LineBasicMaterial({ color: 0xff0000 }); + const splineObject = new THREE.Line(geometry, material); + objects.push(splineObject); + }); + + // Generate grid of points + const gridPoints = curves.map((curve) => curve.getPoints(numPoints - 1)); + // Flatten into a single array of vertices const vertices: number[] = []; const indices = []; @@ -317,6 +384,9 @@ function computeBentSurfaceSplines(points: Vector3[]): THREE.Object3D[] { geometry.setAttribute("position", new THREE.Float32BufferAttribute(vertices, 3)); geometry.setIndex(indices); geometry.computeVertexNormals(); // Smooth shading + geometry.computeBoundsTree(); + + window.bentGeometry = geometry; // Material and Mesh const material = new THREE.MeshStandardMaterial({ @@ -330,6 +400,7 @@ function computeBentSurfaceSplines(points: Vector3[]): THREE.Object3D[] { wireframe: false, }); const surfaceMesh = new THREE.Mesh(geometry, material); + window.bentMesh = surfaceMesh; objects.push(surfaceMesh); return objects; @@ -544,6 +615,7 @@ class SceneController { // For some reason, all objects have to be put into a group object. Changing // scene.scale does not have an effect. this.rootGroup = new THREE.Object3D(); + window.rootGroup = this.rootGroup; this.rootGroup.add(this.getRootNode()); this.highlightedBBoxId = null; @@ -836,6 +908,10 @@ class SceneController { this.taskBoundingBox?.updateForCam(id); this.segmentMeshController.meshesLODRootGroup.visible = id === OrthoViews.TDView; + // todop + if (window.bentMesh != null) { + window.bentMesh.visible = id === OrthoViews.TDView; + } // this.segmentMeshController.meshesLODRootGroup.visible = false; this.annotationToolsGeometryGroup.visible = id !== OrthoViews.TDView; this.lineMeasurementGeometry.updateForCam(id); diff --git a/frontend/javascripts/oxalis/controller/splitting_stuff.ts b/frontend/javascripts/oxalis/controller/splitting_stuff.ts index bd4d6fd2e6c..ca553f3bf1f 100644 --- a/frontend/javascripts/oxalis/controller/splitting_stuff.ts +++ b/frontend/javascripts/oxalis/controller/splitting_stuff.ts @@ -79,11 +79,32 @@ function traverseMST_DFS(mst: number[][], startIdx = 0): number[] { return orderedPoints; } +function computePathLength(points: THREE.Vector3[], order: number[]): number { + let length = 0; + for (let i = 0; i < order.length - 1; i++) { + length += points[order[i]].distanceTo(points[order[i + 1]]); + } + return length; +} + export function orderPointsMST(points: THREE.Vector3[]): THREE.Vector3[] { if (points.length === 0) return []; + const mst = computeMST(points); - const dfsOrder = traverseMST_DFS(mst); - return enforceConsistentDirection(dfsOrder.map((index) => points[index])); + let bestOrder: number[] = []; + let minLength = Number.POSITIVE_INFINITY; + + for (let startIdx = 0; startIdx < points.length; startIdx++) { + const order = traverseMST_DFS(mst, startIdx); + const length = computePathLength(points, order); + + if (length < minLength) { + minLength = length; + bestOrder = order; + } + } + + return bestOrder.map((index) => points[index]); } export function enforceConsistentDirection(points: THREE.Vector3[]): THREE.Vector3[] { diff --git a/frontend/javascripts/oxalis/model/bucket_data_handling/data_cube.ts b/frontend/javascripts/oxalis/model/bucket_data_handling/data_cube.ts index e1bca92a507..f80a95e17f8 100644 --- a/frontend/javascripts/oxalis/model/bucket_data_handling/data_cube.ts +++ b/frontend/javascripts/oxalis/model/bucket_data_handling/data_cube.ts @@ -35,6 +35,7 @@ import Store from "oxalis/store"; import type { AdditionalAxis, BucketDataArray, ElementClass } from "types/api_flow_types"; import type { AdditionalCoordinate } from "types/api_flow_types"; import type { MagInfo } from "../helpers/mag_info"; +import * as THREE from "three"; const warnAboutTooManyAllocations = _.once(() => { const msg = @@ -700,7 +701,12 @@ class DataCube { // Iterating over all neighbours from the initialAddress. while (!neighbourVoxelStackUvw.isEmpty()) { - const neighbours = neighbourVoxelStackUvw.getVoxelAndGetNeighbors(); + const { origin, neighbors: neighbours } = neighbourVoxelStackUvw.getVoxelAndGetNeighbors(); + + const originGlobalPosition = V3.add( + currentGlobalBucketPosition, + V3.scale3(origin, currentMag), + ); for (let neighbourIndex = 0; neighbourIndex < neighbours.length; ++neighbourIndex) { const neighbourVoxelUvw = neighbours[neighbourIndex]; @@ -719,7 +725,23 @@ class DataCube { // Add the bucket to the list of buckets to flood fill. const neighbourBucket = this.getOrCreateBucket(neighbourBucketAddress); - if (neighbourBucket.type !== "null") { + let shouldSkip = false; + if (window.bentGeometry) { + const currentGlobalPosition = V3.add( + currentGlobalBucketPosition, + V3.scale3(neighbourVoxelXyz, currentMag), + ); + const intersects = checkLineIntersection( + window.bentGeometry, + originGlobalPosition, + currentGlobalPosition, + ); + + shouldSkip = intersects; + } + + // console.log("reached bucket border. early abort for debugging"); + if (!shouldSkip && neighbourBucket.type !== "null") { bucketsWithXyzSeedsToFill.push([neighbourBucket, adjustedNeighbourVoxelXyz]); } } else { @@ -735,7 +757,25 @@ class DataCube { max: V3.add(currentGlobalPosition, currentMag), }); - if (bucketData[neighbourVoxelIndex] === sourceSegmentId) { + let shouldSkip = false; + if (window.bentGeometry) { + // const target = {}; + // window.bentGeometry.boundsTree.closestPointToPoint( + // new THREE.Vector3(...currentGlobalPosition), + // target, + // ); + + const intersects = checkLineIntersection( + window.bentGeometry, + originGlobalPosition, + currentGlobalPosition, + ); + + // const { distance } = target; + shouldSkip = intersects; + } + + if (!shouldSkip && bucketData[neighbourVoxelIndex] === sourceSegmentId) { if (floodfillBoundingBox.intersectedWith(voxelBoundingBoxInMag1).getVolume() > 0) { bucketData[neighbourVoxelIndex] = segmentId; markUvwInSliceAsLabeled(neighbourVoxelUvw); @@ -996,3 +1036,56 @@ class DataCube { } export default DataCube; + +window.test = (point: Vector3) => { + const geometry = window.bentGeometry; + let target = {}; + const retVal = geometry.boundsTree.closestPointToPoint(new THREE.Vector3(...point), target); + + console.log("retVal", retVal); + console.log("target", target); + // closestPointToPoint( + // point : Vector3, + // target : Object = {}, + // minThreshold : Number = 0, + // maxThreshold : Number = Infinity + // ) +}; + +let rayHelper; +// Function to check intersection +function checkLineIntersection(geometry, _pointA: Vector3, _pointB: Vector3) { + // Create BVH from geometry if not already built + if (!geometry.boundsTree) { + geometry.computeBoundsTree(); + } + const mul = (vec) => [11.24 * vec[0], 11.24 * vec[1], 28 * vec[2]]; + // geometry.boundsTree = undefined; + const pointA = new THREE.Vector3(...mul(_pointA)); + const pointB = new THREE.Vector3(...mul(_pointB)); + + // Create a ray from A to B + const ray = new THREE.Ray(); + ray.origin.copy(pointA); + ray.direction.subVectors(pointB, pointA).normalize(); + + // Perform raycast + const raycaster = new THREE.Raycaster(); + raycaster.ray = ray; + raycaster.far = pointA.distanceTo(pointB); // Limit to segment length + raycaster.firstHitOnly = true; + + // if (rayHelper != null) { + // window.rootGroup.remove(rayHelper); + // } + + // rayHelper = new THREE.ArrowHelper(ray.direction, ray.origin, raycaster.far, 0xff0000); + // window.rootGroup.add(rayHelper); + + const intersects = raycaster.intersectObject(window.bentMesh, true); + const retval = intersects.length > 0; // Returns true if an intersection is found + + return retval; +} + +window.checkLineIntersection = checkLineIntersection; diff --git a/frontend/javascripts/oxalis/model/volumetracing/volumelayer.ts b/frontend/javascripts/oxalis/model/volumetracing/volumelayer.ts index 2d6d71a6153..ba64630a8b5 100644 --- a/frontend/javascripts/oxalis/model/volumetracing/volumelayer.ts +++ b/frontend/javascripts/oxalis/model/volumetracing/volumelayer.ts @@ -89,9 +89,9 @@ export class VoxelNeighborQueue3D { return this.queue.length === 0; } - getVoxelAndGetNeighbors(): Array { + getVoxelAndGetNeighbors(): { origin: Vector3; neighbors: Array } { if (this.isEmpty()) { - return []; + return { origin: [0, 0, 0], neighbors: [] }; } const currentVoxel = this.queue.shift(); @@ -102,20 +102,23 @@ export class VoxelNeighborQueue3D { } // 6-neighborhood in 3D - return [ - [currentVoxel[0] + 1, currentVoxel[1], currentVoxel[2]], - [currentVoxel[0] - 1, currentVoxel[1], currentVoxel[2]], - [currentVoxel[0], currentVoxel[1] + 1, currentVoxel[2]], - [currentVoxel[0], currentVoxel[1] - 1, currentVoxel[2]], - [currentVoxel[0], currentVoxel[1], currentVoxel[2] + 1], - [currentVoxel[0], currentVoxel[1], currentVoxel[2] - 1], - ]; + return { + origin: currentVoxel, + neighbors: [ + [currentVoxel[0] + 1, currentVoxel[1], currentVoxel[2]], + [currentVoxel[0] - 1, currentVoxel[1], currentVoxel[2]], + [currentVoxel[0], currentVoxel[1] + 1, currentVoxel[2]], + [currentVoxel[0], currentVoxel[1] - 1, currentVoxel[2]], + [currentVoxel[0], currentVoxel[1], currentVoxel[2] + 1], + [currentVoxel[0], currentVoxel[1], currentVoxel[2] - 1], + ], + }; } } export class VoxelNeighborQueue2D extends VoxelNeighborQueue3D { - getVoxelAndGetNeighbors(): Array { + getVoxelAndGetNeighbors(): { origin: Vector3; neighbors: Array } { if (this.isEmpty()) { - return []; + return { origin: [0, 0, 0], neighbors: [] }; } const currentVoxel = this.queue.shift(); @@ -126,12 +129,15 @@ export class VoxelNeighborQueue2D extends VoxelNeighborQueue3D { } // 4-neighborhood in 2D - return [ - [currentVoxel[0] + 1, currentVoxel[1], currentVoxel[2]], - [currentVoxel[0] - 1, currentVoxel[1], currentVoxel[2]], - [currentVoxel[0], currentVoxel[1] + 1, currentVoxel[2]], - [currentVoxel[0], currentVoxel[1] - 1, currentVoxel[2]], - ]; + return { + origin: currentVoxel, + neighbors: [ + [currentVoxel[0] + 1, currentVoxel[1], currentVoxel[2]], + [currentVoxel[0] - 1, currentVoxel[1], currentVoxel[2]], + [currentVoxel[0], currentVoxel[1] + 1, currentVoxel[2]], + [currentVoxel[0], currentVoxel[1] - 1, currentVoxel[2]], + ], + }; } } diff --git a/frontend/javascripts/oxalis/view/right-border-tabs/trees_tab/skeleton_tab_view.tsx b/frontend/javascripts/oxalis/view/right-border-tabs/trees_tab/skeleton_tab_view.tsx index 1a40c7944a3..bc2d504872d 100644 --- a/frontend/javascripts/oxalis/view/right-border-tabs/trees_tab/skeleton_tab_view.tsx +++ b/frontend/javascripts/oxalis/view/right-border-tabs/trees_tab/skeleton_tab_view.tsx @@ -486,7 +486,7 @@ class SkeletonTabView extends React.PureComponent { const { selectedTreeIds } = this.state; const selectedTreeCount = selectedTreeIds.length; - if (selectedTreeCount > 0) { + if (selectedTreeCount > 1) { const deleteAllSelectedTrees = () => { checkAndConfirmDeletingInitialNode(selectedTreeIds).then(() => { this.props.onDeleteTrees(selectedTreeIds); diff --git a/package.json b/package.json index ca0be3175fe..e58da816f4a 100644 --- a/package.json +++ b/package.json @@ -209,7 +209,8 @@ "redux-saga": "^1.3.0", "resumablejs": "^1.1.0", "saxophone": "^0.8.0", - "three": "^0.137.0", + "three": "^0.169.0", + "three-mesh-bvh": "^0.9.0", "tween.js": "^16.3.1", "typed-redux-saga": "^1.4.0", "url": "^0.11.0", diff --git a/yarn.lock b/yarn.lock index f486b1cc733..81036e5b6a6 100644 --- a/yarn.lock +++ b/yarn.lock @@ -13660,10 +13660,19 @@ __metadata: languageName: node linkType: hard -"three@npm:^0.137.0": - version: 0.137.5 - resolution: "three@npm:0.137.5" - checksum: 10c0/ce5392396c21bf4569c7f8f694fdc49c0237e61a41ec3cf7bc82cb3bfdeca7c977229fbc70da95972f51a61a87850854e17d0a1d179daa7c7295724ea8e7670c +"three-mesh-bvh@npm:^0.9.0": + version: 0.9.0 + resolution: "three-mesh-bvh@npm:0.9.0" + peerDependencies: + three: ">= 0.159.0" + checksum: 10c0/76629dd6264fe4af877745669b1947ce8f3d5cf45c613daef062c3a8964a2a61f29b9f26f004ab1a57e935307f0a6eafebd97a3e4af437f1c3429bc4b27e630e + languageName: node + linkType: hard + +"three@npm:^0.169.0": + version: 0.169.0 + resolution: "three@npm:0.169.0" + checksum: 10c0/be2e20f45eaa50489cd22d366c41fa14528f00b873078f52fc6ef37140fa8e541e9805630bbe696ab9b027530c74e5cd341705266eb268b5219402fb9fa78ed4 languageName: node linkType: hard @@ -14759,7 +14768,8 @@ __metadata: semaphore-promise: "npm:^1.4.2" shelljs: "npm:^0.8.5" sinon: "npm:^12.0.1" - three: "npm:^0.137.0" + three: "npm:^0.169.0" + three-mesh-bvh: "npm:^0.9.0" tmp: "npm:0.0.33" ts-loader: "npm:^9.4.1" tween.js: "npm:^16.3.1" From 00ab1b0804f02576675b1044d1066e54621f0894 Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Tue, 8 Apr 2025 14:54:36 +0200 Subject: [PATCH 09/84] fix some stuff --- .../oxalis/controller/scene_controller.ts | 2 +- .../oxalis/controller/splitting_stuff.ts | 2 + .../javascripts/oxalis/geometries/skeleton.ts | 7 --- .../oxalis/model/sagas/bent_surface_saga.ts | 2 +- package.json | 2 +- yarn.lock | 50 +++++++++++++++++-- 6 files changed, 50 insertions(+), 15 deletions(-) diff --git a/frontend/javascripts/oxalis/controller/scene_controller.ts b/frontend/javascripts/oxalis/controller/scene_controller.ts index 7916550fc83..9f1990b1ae6 100644 --- a/frontend/javascripts/oxalis/controller/scene_controller.ts +++ b/frontend/javascripts/oxalis/controller/scene_controller.ts @@ -57,7 +57,7 @@ const LAYER_CUBE_COLOR = 0xffff99; import Delaunator from "delaunator"; import TPS3D from "libs/thin_plate_spline"; import { WkDevFlags } from "oxalis/api/wk_dev"; -import { enforceConsistentDirection, orderPointsMST } from "./splitting_stuff"; +import { orderPointsMST } from "./splitting_stuff"; import { computeBoundsTree, diff --git a/frontend/javascripts/oxalis/controller/splitting_stuff.ts b/frontend/javascripts/oxalis/controller/splitting_stuff.ts index ca553f3bf1f..fb05fa73ef4 100644 --- a/frontend/javascripts/oxalis/controller/splitting_stuff.ts +++ b/frontend/javascripts/oxalis/controller/splitting_stuff.ts @@ -1,3 +1,5 @@ +import * as THREE from "three"; + class DisjointSet { private parent: number[]; private rank: number[]; diff --git a/frontend/javascripts/oxalis/geometries/skeleton.ts b/frontend/javascripts/oxalis/geometries/skeleton.ts index 7f9ed8c3d00..374978216e9 100644 --- a/frontend/javascripts/oxalis/geometries/skeleton.ts +++ b/frontend/javascripts/oxalis/geometries/skeleton.ts @@ -562,15 +562,11 @@ class Skeleton { attributeAdditionalCoordinates.set([node.additionalCoordinates[idx].value], index); } } - // @ts-expect-error ts-migrate(2542) FIXME: Index signature in type 'any[] | ArrayLike... Remove this comment to see the full error message attributes.radius.array[index] = node.radius; - // @ts-expect-error ts-migrate(2542) FIXME: Index signature in type 'any[] | ArrayLike... Remove this comment to see the full error message attributes.type.array[index] = NodeTypes.NORMAL; // @ts-expect-error ts-migrate(2542) FIXME: Index signature in type 'any[] | ArrayLike... Remove this comment to see the full error message attributes.isCommented.array[index] = false; - // @ts-expect-error ts-migrate(2542) FIXME: Index signature in type 'any[] | ArrayLike... Remove this comment to see the full error message attributes.nodeId.array[index] = node.id; - // @ts-expect-error ts-migrate(2542) FIXME: Index signature in type 'any[] | ArrayLike... Remove this comment to see the full error message attributes.treeId.array[index] = treeId; return _.values(attributes); }, @@ -584,7 +580,6 @@ class Skeleton { const id = this.combineIds(nodeId, treeId); this.delete(id, this.nodes, ({ buffer, index }) => { const attribute = buffer.geometry.attributes.type; - // @ts-expect-error ts-migrate(2542) FIXME: Index signature in type 'ArrayLike' only p... Remove this comment to see the full error message attribute.array[index] = NodeTypes.INVALID; return [attribute]; }); @@ -597,7 +592,6 @@ class Skeleton { const id = this.combineIds(nodeId, treeId); this.update(id, this.nodes, ({ buffer, index }) => { const attribute = buffer.geometry.attributes.radius; - // @ts-expect-error ts-migrate(2542) FIXME: Index signature in type 'ArrayLike' only p... Remove this comment to see the full error message attribute.array[index] = radius; return [attribute]; }); @@ -658,7 +652,6 @@ class Skeleton { const id = this.combineIds(nodeId, treeId); this.update(id, this.nodes, ({ buffer, index }) => { const attribute = buffer.geometry.attributes.type; - // @ts-expect-error ts-migrate(2542) FIXME: Index signature in type 'ArrayLike' only p... Remove this comment to see the full error message attribute.array[index] = type; return [attribute]; }); diff --git a/frontend/javascripts/oxalis/model/sagas/bent_surface_saga.ts b/frontend/javascripts/oxalis/model/sagas/bent_surface_saga.ts index 468fb0fa54f..10771e73243 100644 --- a/frontend/javascripts/oxalis/model/sagas/bent_surface_saga.ts +++ b/frontend/javascripts/oxalis/model/sagas/bent_surface_saga.ts @@ -23,7 +23,7 @@ function* createBentSurface() { // [50, 60, 80], // ]; - const activeTree = yield* select((state) => getActiveTree(state.tracing.skeleton)); + const activeTree = yield* select((state) => getActiveTree(state.annotation.skeleton)); // biome-ignore lint/complexity/useOptionalChain: if (activeTree != null && activeTree.isVisible) { const nodes = Array.from(activeTree.nodes.values()); diff --git a/package.json b/package.json index e58da816f4a..71c8bc1fa33 100644 --- a/package.json +++ b/package.json @@ -32,7 +32,7 @@ "@types/react-dom": "^18.3.0", "@types/react-router-dom": "^5.3.3", "@types/sinon": "^10.0.11", - "@types/three": "^0.142.0", + "@types/three": "^0.169.0", "@types/url-join": "^4.0.0", "abort-controller": "^3.0.0", "ava": "^6.1.3", diff --git a/yarn.lock b/yarn.lock index 81036e5b6a6..ebf2c3ddf1c 100644 --- a/yarn.lock +++ b/yarn.lock @@ -2020,6 +2020,13 @@ __metadata: languageName: node linkType: hard +"@tweenjs/tween.js@npm:~23.1.3": + version: 23.1.3 + resolution: "@tweenjs/tween.js@npm:23.1.3" + checksum: 10c0/811b30f5f0e7409fb41833401c501c2d6f600eb5f43039dd9067a7f70aff6dad5f5ce1233848e13f0b33a269a160d9c133f344d986cbff4f1f6b72ddecd06c89 + languageName: node + linkType: hard + "@types/body-parser@npm:*": version: 1.19.2 resolution: "@types/body-parser@npm:1.19.2" @@ -2837,6 +2844,13 @@ __metadata: languageName: node linkType: hard +"@types/stats.js@npm:*": + version: 0.17.3 + resolution: "@types/stats.js@npm:0.17.3" + checksum: 10c0/ccccc992c6dfe08fb85049aa3ce44ca7e428db8da4a3edd20298f1c8b72768021fa8bacdfbe8e9735a7552ee5d57f667c6f557050ad2d9a87b699b3566a6177a + languageName: node + linkType: hard + "@types/supports-color@npm:^8.0.0": version: 8.1.1 resolution: "@types/supports-color@npm:8.1.1" @@ -2844,12 +2858,17 @@ __metadata: languageName: node linkType: hard -"@types/three@npm:^0.142.0": - version: 0.142.0 - resolution: "@types/three@npm:0.142.0" +"@types/three@npm:^0.169.0": + version: 0.169.0 + resolution: "@types/three@npm:0.169.0" dependencies: + "@tweenjs/tween.js": "npm:~23.1.3" + "@types/stats.js": "npm:*" "@types/webxr": "npm:*" - checksum: 10c0/7616a571ed8df10265caca723f686f52a2a43d34412682547f6e4737763c14a1f975b1c56a903c14d27f2b76d47f28693ba6725dfe86f9e6fcb2c7e4352d2b63 + "@webgpu/types": "npm:*" + fflate: "npm:~0.8.2" + meshoptimizer: "npm:~0.18.1" + checksum: 10c0/d5f588dcc9df02875d46e5e6ea8ea6dc346cd1e4c0fbe7bcca4c8d9584f82ac39a951788a79fc2ffae3d5e232f99e66046adec8f93fdf51d30561a4a00c52b40 languageName: node linkType: hard @@ -3149,6 +3168,13 @@ __metadata: languageName: node linkType: hard +"@webgpu/types@npm:*": + version: 0.1.60 + resolution: "@webgpu/types@npm:0.1.60" + checksum: 10c0/6dcd28680637b41258287b241e6807160c78464cd67b008c1aaafdbe78e0f1eb1bdc4cace8c8628d2d088a449643e7af71804d33261865f00967557989b0e29b + languageName: node + linkType: hard + "@webpack-cli/configtest@npm:^2.1.1": version: 2.1.1 resolution: "@webpack-cli/configtest@npm:2.1.1" @@ -6422,6 +6448,13 @@ __metadata: languageName: node linkType: hard +"fflate@npm:~0.8.2": + version: 0.8.2 + resolution: "fflate@npm:0.8.2" + checksum: 10c0/03448d630c0a583abea594835a9fdb2aaf7d67787055a761515bf4ed862913cfd693b4c4ffd5c3f3b355a70cf1e19033e9ae5aedcca103188aaff91b8bd6e293 + languageName: node + linkType: hard + "figures@npm:^6.0.1": version: 6.1.0 resolution: "figures@npm:6.1.0" @@ -9131,6 +9164,13 @@ __metadata: languageName: node linkType: hard +"meshoptimizer@npm:~0.18.1": + version: 0.18.1 + resolution: "meshoptimizer@npm:0.18.1" + checksum: 10c0/8a825c58b20b65585e8d00788843929b60c66ba4297e89afaa49f7c51ab9a0f7b9130f90cc9ad1b9b48b3d1bee3beb1bc93608acba0d73e78995c3e6e5ca436b + languageName: node + linkType: hard + "methods@npm:~1.1.2": version: 1.1.2 resolution: "methods@npm:1.1.2" @@ -14668,7 +14708,7 @@ __metadata: "@types/react-dom": "npm:^18.3.0" "@types/react-router-dom": "npm:^5.3.3" "@types/sinon": "npm:^10.0.11" - "@types/three": "npm:^0.142.0" + "@types/three": "npm:^0.169.0" "@types/url-join": "npm:^4.0.0" "@zip.js/zip.js": "npm:^2.7.32" abort-controller: "npm:^3.0.0" From f2504bfa1d53bad132b21fd0aee81b1be425f77f Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Tue, 8 Apr 2025 15:26:03 +0200 Subject: [PATCH 10/84] allow to continously place skeleton nodes like in a draw tool --- .../controller/combinations/tool_controls.ts | 39 ++++++++++++++----- .../oxalis/controller/scene_controller.ts | 2 +- frontend/javascripts/oxalis/default_state.ts | 1 + .../model/bucket_data_handling/data_cube.ts | 15 ++----- .../oxalis/model/sagas/mesh_saga.ts | 2 +- frontend/javascripts/oxalis/store.ts | 1 + .../oxalis/view/action-bar/toolbar_view.tsx | 15 +++++++ 7 files changed, 52 insertions(+), 23 deletions(-) diff --git a/frontend/javascripts/oxalis/controller/combinations/tool_controls.ts b/frontend/javascripts/oxalis/controller/combinations/tool_controls.ts index 70cfa7e3d0b..cae8a4dfd5e 100644 --- a/frontend/javascripts/oxalis/controller/combinations/tool_controls.ts +++ b/frontend/javascripts/oxalis/controller/combinations/tool_controls.ts @@ -240,6 +240,7 @@ export class SkeletonTool { }; let draggingNodeId: number | null | undefined = null; + let lastContinouslyPlacedNodeTimestamp: number | null = null; let didDragNode: boolean = false; return { leftMouseDown: (pos: Point2, plane: OrthoView, _event: MouseEvent, isTouch: boolean) => { @@ -266,21 +267,39 @@ export class SkeletonTool { }, leftDownMove: ( delta: Point2, - _pos: Point2, - _id: string | null | undefined, + pos: Point2, + plane: string | null | undefined, event: MouseEvent, ) => { - const { annotation } = Store.getState(); + const { annotation, userConfiguration } = Store.getState(); const { useLegacyBindings } = Store.getState().userConfiguration; - if ( - annotation.skeleton != null && - (draggingNodeId != null || (useLegacyBindings && (event.ctrlKey || event.metaKey))) - ) { - didDragNode = true; - SkeletonHandlers.moveNode(delta.x, delta.y, draggingNodeId, true); + const { continuousNodeCreation } = userConfiguration; + + if (continuousNodeCreation) { + if ( + lastContinouslyPlacedNodeTimestamp && + Date.now() - lastContinouslyPlacedNodeTimestamp < 200 + ) { + return; + } + lastContinouslyPlacedNodeTimestamp = Date.now(); + + if (plane) { + const globalPosition = calculateGlobalPos(Store.getState(), pos); + // SkeletonHandlers.handleCreateNodeFromEvent(pos, false); + api.tracing.createNode(globalPosition, { center: false }); + } } else { - MoveHandlers.handleMovePlane(delta); + if ( + annotation.skeleton != null && + (draggingNodeId != null || (useLegacyBindings && (event.ctrlKey || event.metaKey))) + ) { + didDragNode = true; + SkeletonHandlers.moveNode(delta.x, delta.y, draggingNodeId, true); + } else { + MoveHandlers.handleMovePlane(delta); + } } }, leftClick: (pos: Point2, plane: OrthoView, event: MouseEvent, isTouch: boolean) => { diff --git a/frontend/javascripts/oxalis/controller/scene_controller.ts b/frontend/javascripts/oxalis/controller/scene_controller.ts index 9f1990b1ae6..d358cfe8615 100644 --- a/frontend/javascripts/oxalis/controller/scene_controller.ts +++ b/frontend/javascripts/oxalis/controller/scene_controller.ts @@ -78,7 +78,7 @@ THREE.BatchedMesh.prototype.raycast = acceleratedRaycast; type EigenData = { eigenvalue: number; vector: number[] }; -function createPointCloud(points: Vector3[], color: string) { +function _createPointCloud(points: Vector3[], color: string) { // Convert points to Three.js geometry const geometry = new THREE.BufferGeometry(); const vertices = new Float32Array(_.flatten(points)); diff --git a/frontend/javascripts/oxalis/default_state.ts b/frontend/javascripts/oxalis/default_state.ts index 578280510a6..4492e5fa365 100644 --- a/frontend/javascripts/oxalis/default_state.ts +++ b/frontend/javascripts/oxalis/default_state.ts @@ -71,6 +71,7 @@ const defaultState: OxalisState = { moveValue3d: 300, moveValue: 300, newNodeNewTree: false, + continuousNodeCreation: false, centerNewNode: true, overrideNodeRadius: true, particleSize: 5, diff --git a/frontend/javascripts/oxalis/model/bucket_data_handling/data_cube.ts b/frontend/javascripts/oxalis/model/bucket_data_handling/data_cube.ts index f80a95e17f8..e1d58b0ab3b 100644 --- a/frontend/javascripts/oxalis/model/bucket_data_handling/data_cube.ts +++ b/frontend/javascripts/oxalis/model/bucket_data_handling/data_cube.ts @@ -1052,14 +1052,14 @@ window.test = (point: Vector3) => { // ) }; -let rayHelper; // Function to check intersection -function checkLineIntersection(geometry, _pointA: Vector3, _pointB: Vector3) { +function checkLineIntersection(geometry: THREE.BufferGeometry, _pointA: Vector3, _pointB: Vector3) { // Create BVH from geometry if not already built if (!geometry.boundsTree) { geometry.computeBoundsTree(); } - const mul = (vec) => [11.24 * vec[0], 11.24 * vec[1], 28 * vec[2]]; + const scale = Store.getState().dataset.dataSource.scale.factor; + const mul = (vec: Vector3) => [scale[0] * vec[0], scale[1] * vec[1], scale[2] * vec[2]]; // geometry.boundsTree = undefined; const pointA = new THREE.Vector3(...mul(_pointA)); const pointB = new THREE.Vector3(...mul(_pointB)); @@ -1075,17 +1075,10 @@ function checkLineIntersection(geometry, _pointA: Vector3, _pointB: Vector3) { raycaster.far = pointA.distanceTo(pointB); // Limit to segment length raycaster.firstHitOnly = true; - // if (rayHelper != null) { - // window.rootGroup.remove(rayHelper); - // } - - // rayHelper = new THREE.ArrowHelper(ray.direction, ray.origin, raycaster.far, 0xff0000); - // window.rootGroup.add(rayHelper); - const intersects = raycaster.intersectObject(window.bentMesh, true); const retval = intersects.length > 0; // Returns true if an intersection is found return retval; } -window.checkLineIntersection = checkLineIntersection; +// window.checkLineIntersection = checkLineIntersection; diff --git a/frontend/javascripts/oxalis/model/sagas/mesh_saga.ts b/frontend/javascripts/oxalis/model/sagas/mesh_saga.ts index b8a25d93899..212772a2ecf 100644 --- a/frontend/javascripts/oxalis/model/sagas/mesh_saga.ts +++ b/frontend/javascripts/oxalis/model/sagas/mesh_saga.ts @@ -7,7 +7,7 @@ import { areVec3AlmostEqual, chunkDynamically, sleep } from "libs/utils"; import _ from "lodash"; import type { ActionPattern } from "redux-saga/effects"; import type { APIDataset, APIMeshFile, APISegmentationLayer } from "types/api_flow_types"; - +import type * as THREE from "three"; import { computeAdHocMesh, getBucketPositionsForAdHocMesh, diff --git a/frontend/javascripts/oxalis/store.ts b/frontend/javascripts/oxalis/store.ts index 7a32563b7ef..8ca512dad61 100644 --- a/frontend/javascripts/oxalis/store.ts +++ b/frontend/javascripts/oxalis/store.ts @@ -390,6 +390,7 @@ export type UserConfiguration = { readonly moveValue3d: number; readonly moveValue: number; readonly newNodeNewTree: boolean; + readonly continuousNodeCreation: boolean; readonly centerNewNode: boolean; readonly overrideNodeRadius: boolean; readonly particleSize: number; diff --git a/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx b/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx index bf75400581b..5e7089828cd 100644 --- a/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx +++ b/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx @@ -391,6 +391,12 @@ function SkeletonSpecificButtons() { const isNewNodeNewTreeModeOn = useSelector( (state: OxalisState) => state.userConfiguration.newNodeNewTree, ); + const isContinuousNodeCreationEnabled = useSelector( + (state: OxalisState) => state.userConfiguration.continuousNodeCreation, + ); + const toggleContinuousNodeCreation = () => + dispatch(updateUserSettingAction("continuousNodeCreation", !isContinuousNodeCreationEnabled)); + const dataset = useSelector((state: OxalisState) => state.dataset); const isUserAdminOrManager = useIsActiveUserAdminOrManager(); @@ -455,6 +461,15 @@ function SkeletonSpecificButtons() { alt="Merger Mode" /> + + + + {isMergerModeEnabled && isMaterializeVolumeAnnotationEnabled && isUserAdminOrManager && ( Date: Wed, 9 Apr 2025 11:34:25 +0200 Subject: [PATCH 11/84] prototype workflow mode --- .../oxalis/view/action-bar/toolbar_view.tsx | 1 + .../view/action-bar/view_modes_view.tsx | 49 +++++++++++++++++-- 2 files changed, 45 insertions(+), 5 deletions(-) diff --git a/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx b/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx index 5e7089828cd..911f96347cf 100644 --- a/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx +++ b/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx @@ -7,6 +7,7 @@ import { } from "@ant-design/icons"; import { Badge, + Button, Col, Divider, Dropdown, diff --git a/frontend/javascripts/oxalis/view/action-bar/view_modes_view.tsx b/frontend/javascripts/oxalis/view/action-bar/view_modes_view.tsx index 4cf86d57530..fd6566c4bc4 100644 --- a/frontend/javascripts/oxalis/view/action-bar/view_modes_view.tsx +++ b/frontend/javascripts/oxalis/view/action-bar/view_modes_view.tsx @@ -85,14 +85,53 @@ class ViewModesView extends PureComponent { onClick: handleMenuClick, }; + const toolWorkspaceItems: MenuProps["items"] = [ + { + key: "1", + type: "group", + label: "Select Workflow", + children: [ + { + label: "All Tools", + key: "1", + }, + { + label: "View Only", + key: "2", + }, + { + label: "Volume Only", + key: "3", + }, + { + label: "Split Segments", + key: "4", + }, + ], + }, + ]; + + const toolWorkspaceMenuProps = { + items: toolWorkspaceItems, + onClick: () => {}, + }; + return ( // The outer div is necessary for proper spacing.
- - - + + + + + + + + +
); } From 573f1b76a2124917bbbd1ccc9de68ec52dd5fd70 Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Wed, 9 Apr 2025 14:42:27 +0200 Subject: [PATCH 12/84] start introducing tool workspaces --- .../oxalis/controller/scene_controller.ts | 1 - .../oxalis/model/accessors/tool_accessor.ts | 4 +- .../oxalis/model/actions/settings_actions.ts | 9 + .../model/bucket_data_handling/data_cube.ts | 17 - frontend/javascripts/oxalis/store.ts | 7 + .../oxalis/view/action-bar/toolbar_view.tsx | 687 +++++++++++------- .../view/action-bar/view_modes_view.tsx | 54 +- .../oxalis/view/action_bar_view.tsx | 46 +- .../javascripts/oxalis/view/plane_view.ts | 18 +- 9 files changed, 472 insertions(+), 371 deletions(-) diff --git a/frontend/javascripts/oxalis/controller/scene_controller.ts b/frontend/javascripts/oxalis/controller/scene_controller.ts index d358cfe8615..89f66985c88 100644 --- a/frontend/javascripts/oxalis/controller/scene_controller.ts +++ b/frontend/javascripts/oxalis/controller/scene_controller.ts @@ -615,7 +615,6 @@ class SceneController { // For some reason, all objects have to be put into a group object. Changing // scene.scale does not have an effect. this.rootGroup = new THREE.Object3D(); - window.rootGroup = this.rootGroup; this.rootGroup.add(this.getRootNode()); this.highlightedBBoxId = null; diff --git a/frontend/javascripts/oxalis/model/accessors/tool_accessor.ts b/frontend/javascripts/oxalis/model/accessors/tool_accessor.ts index b878148412d..49bc01a98e6 100644 --- a/frontend/javascripts/oxalis/model/accessors/tool_accessor.ts +++ b/frontend/javascripts/oxalis/model/accessors/tool_accessor.ts @@ -359,7 +359,9 @@ const _getDisabledInfoForTools = (state: OxalisState): Record; export type InitializeSettingsAction = ReturnType; type SetViewModeAction = ReturnType; +type SetToolWorkspaceAction = ReturnType; type SetHistogramDataForLayerAction = ReturnType; export type ReloadHistogramAction = ReturnType; export type ClipHistogramAction = ReturnType; @@ -40,6 +42,7 @@ export type SettingAction = | InitializeSettingsAction | UpdateLayerSettingAction | SetViewModeAction + | SetToolWorkspaceAction | SetFlightmodeRecordingAction | SetControlModeAction | SetMappingEnabledAction @@ -118,6 +121,12 @@ export const setViewModeAction = (viewMode: ViewMode) => viewMode, }) as const; +export const setToolWorkspaceAction = (toolWorkspace: ToolWorkspace) => + ({ + type: "SET_TOOL_WORKSPACE", + toolWorkspace, + }) as const; + export const setHistogramDataForLayerAction = ( layerName: string, histogramData: APIHistogramData | null | undefined, diff --git a/frontend/javascripts/oxalis/model/bucket_data_handling/data_cube.ts b/frontend/javascripts/oxalis/model/bucket_data_handling/data_cube.ts index e1d58b0ab3b..ff002e8430c 100644 --- a/frontend/javascripts/oxalis/model/bucket_data_handling/data_cube.ts +++ b/frontend/javascripts/oxalis/model/bucket_data_handling/data_cube.ts @@ -1037,21 +1037,6 @@ class DataCube { export default DataCube; -window.test = (point: Vector3) => { - const geometry = window.bentGeometry; - let target = {}; - const retVal = geometry.boundsTree.closestPointToPoint(new THREE.Vector3(...point), target); - - console.log("retVal", retVal); - console.log("target", target); - // closestPointToPoint( - // point : Vector3, - // target : Object = {}, - // minThreshold : Number = 0, - // maxThreshold : Number = Infinity - // ) -}; - // Function to check intersection function checkLineIntersection(geometry: THREE.BufferGeometry, _pointA: Vector3, _pointB: Vector3) { // Create BVH from geometry if not already built @@ -1080,5 +1065,3 @@ function checkLineIntersection(geometry: THREE.BufferGeometry, _pointA: Vector3, return retval; } - -// window.checkLineIntersection = checkLineIntersection; diff --git a/frontend/javascripts/oxalis/store.ts b/frontend/javascripts/oxalis/store.ts index 8ca512dad61..50cd3cab8be 100644 --- a/frontend/javascripts/oxalis/store.ts +++ b/frontend/javascripts/oxalis/store.ts @@ -372,6 +372,12 @@ export type QuickSelectConfig = { readonly dilateValue: number; }; +export type ToolWorkspace = + | "ALL_TOOLS" + | "READ_ONLY_TOOLS" + | "VOLUME_ANNOTATION" + | "SPLIT_SEGMENTS"; + export type UserConfiguration = { readonly autoSaveLayouts: boolean; readonly autoRenderMeshInProofreading: boolean; @@ -413,6 +419,7 @@ export type UserConfiguration = { readonly quickSelect: QuickSelectConfig; readonly renderWatermark: boolean; readonly antialiasRendering: boolean; + readonly toolWorkspace: ToolWorkspace; }; export type RecommendedConfiguration = Partial< UserConfiguration & diff --git a/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx b/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx index 911f96347cf..eb3e7e3d1b1 100644 --- a/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx +++ b/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx @@ -7,7 +7,6 @@ import { } from "@ant-design/icons"; import { Badge, - Button, Col, Divider, Dropdown, @@ -848,35 +847,15 @@ function calculateMediumBrushSize(maximumBrushSize: number) { return Math.ceil((maximumBrushSize - userSettings.brushSize.minimum) / 10) * 5; } -export default function ToolbarView({ isReadOnly }: { isReadOnly: boolean }) { - const dispatch = useDispatch(); +export default function ToolbarView() { const hasVolume = useSelector((state: OxalisState) => state.annotation?.volumes.length > 0); const hasSkeleton = useSelector((state: OxalisState) => state.annotation?.skeleton != null); - - const isAgglomerateMappingEnabled = useSelector(hasAgglomerateMapping); + const toolWorkspace = useSelector((state: OxalisState) => state.userConfiguration.toolWorkspace); const [lastForcefullyDisabledTool, setLastForcefullyDisabledTool] = useState(null); - const isVolumeModificationAllowed = - useSelector((state: OxalisState) => !hasEditableMapping(state)) && !isReadOnly; - const useLegacyBindings = useSelector( - (state: OxalisState) => state.userConfiguration.useLegacyBindings, - ); - const activeTool = useSelector((state: OxalisState) => state.uiInformation.activeTool); - const maybeMagWithZoomStep = useSelector(getRenderableMagForActiveSegmentationTracing); - const labeledMag = maybeMagWithZoomStep != null ? maybeMagWithZoomStep.mag : null; - const hasMagWithHigherDimension = (labeledMag || []).some((val) => val > 1); - const multiSliceAnnotationInfoIcon = hasMagWithHigherDimension ? ( - - - - ) : null; + const activeTool = useSelector((state: OxalisState) => state.uiInformation.activeTool); const disabledInfosForTools = useSelector(getDisabledInfoForTools); // Ensure that no volume-tool is selected when being in merger mode. @@ -920,254 +899,55 @@ export default function ToolbarView({ isReadOnly }: { isReadOnly: boolean }) { isControlOrMetaPressed, isAltPressed, ); - const areEditableMappingsEnabled = features().editableMappingsEnabled; - - const skeletonToolDescription = useLegacyBindings - ? "Use left-click to move around and right-click to create new skeleton nodes" - : "Use left-click to move around or to create/select/move nodes. Right-click opens a context menu with further options."; - const showEraseTraceTool = - adaptedActiveTool === AnnotationToolEnum.TRACE || - adaptedActiveTool === AnnotationToolEnum.ERASE_TRACE; - const showEraseBrushTool = !showEraseTraceTool; return ( <> - - - - - {hasSkeleton && !isReadOnly ? ( - - - + {toolWorkspace === "ALL_TOOLS" ? ( + <> + + + + + + + + + + + + + + ) : null} + {toolWorkspace === "READ_ONLY_TOOLS" ? ( + <> + + + + ) : null} - {hasVolume && isVolumeModificationAllowed ? ( - - - - {adaptedActiveTool === AnnotationToolEnum.BRUSH ? multiSliceAnnotationInfoIcon : null} - - - - - {adaptedActiveTool === AnnotationToolEnum.ERASE_BRUSH - ? multiSliceAnnotationInfoIcon - : null} - - - - Trace Tool Icon - {adaptedActiveTool === AnnotationToolEnum.TRACE ? multiSliceAnnotationInfoIcon : null} - - - - - {adaptedActiveTool === AnnotationToolEnum.ERASE_TRACE - ? multiSliceAnnotationInfoIcon - : null} - - - - - {adaptedActiveTool === AnnotationToolEnum.FILL_CELL - ? multiSliceAnnotationInfoIcon - : null} - - - - - - Quick Select Icon - - + {toolWorkspace === "VOLUME_ANNOTATION" ? ( + <> + + + + + + + + + ) : null} - {!isReadOnly && ( - - Bounding Box Icon - - )} - - {hasSkeleton && hasVolume && !isReadOnly ? ( - { - dispatch(ensureLayerMappingsAreLoadedAction()); - }} - > - - + {toolWorkspace === "SPLIT_SEGMENTS" ? ( + <> + + + + + + ) : null} - - - : null} {adaptedActiveTool === AnnotationToolEnum.PROOFREAD && areEditableMappingsEnabled ? ( - + ) : null} {MeasurementTools.includes(adaptedActiveTool) ? ( @@ -1427,7 +1207,7 @@ function FillModeSwitch() { ); } -function ProofReadingComponents() { +function ProofreadingComponents() { const dispatch = useDispatch(); const handleClearProofreading = () => dispatch(clearProofreadingByProducts()); const autoRenderMeshes = useSelector( @@ -1512,3 +1292,378 @@ function MeasurementToolSwitch({ activeTool }: { activeTool: AnnotationTool }) { ); } + +function MoveTool() { + return ( + + + + ); +} + +function SkeletonTool() { + const useLegacyBindings = useSelector( + (state: OxalisState) => state.userConfiguration.useLegacyBindings, + ); + const skeletonToolDescription = useLegacyBindings + ? "Use left-click to move around and right-click to create new skeleton nodes" + : "Use left-click to move around or to create/select/move nodes. Right-click opens a context menu with further options."; + const disabledInfosForTools = useSelector(getDisabledInfoForTools); + const hasSkeleton = useSelector((state: OxalisState) => state.annotation?.skeleton != null); + const isReadOnly = useSelector( + (state: OxalisState) => !state.annotation.restrictions.allowUpdate, + ); + + if (!hasSkeleton || isReadOnly) { + return null; + } + + return ( + + + + ); +} + +function getIsVolumeModificationAllowed(state: OxalisState) { + const isReadOnly = !state.annotation.restrictions.allowUpdate; + const hasVolume = state.annotation?.volumes.length > 0; + return hasVolume && !isReadOnly && !hasEditableMapping(state); +} + +function BrushTool({ adaptedActiveTool }: { adaptedActiveTool: AnnotationTool }) { + const disabledInfosForTools = useSelector(getDisabledInfoForTools); + const isVolumeModificationAllowed = useSelector(getIsVolumeModificationAllowed); + if (!isVolumeModificationAllowed) { + return null; + } + return ( + + + {adaptedActiveTool === AnnotationToolEnum.BRUSH ? ( + + ) : null} + + ); +} + +function EraseBrushTool({ adaptedActiveTool }: { adaptedActiveTool: AnnotationTool }) { + const disabledInfosForTools = useSelector(getDisabledInfoForTools); + const showEraseTraceTool = + adaptedActiveTool === AnnotationToolEnum.TRACE || + adaptedActiveTool === AnnotationToolEnum.ERASE_TRACE; + const showEraseBrushTool = !showEraseTraceTool; + + const isVolumeModificationAllowed = useSelector(getIsVolumeModificationAllowed); + if (!isVolumeModificationAllowed) { + return null; + } + + return ( + + + {adaptedActiveTool === AnnotationToolEnum.ERASE_BRUSH ? ( + + ) : null} + + ); +} + +function TraceTool({ adaptedActiveTool }: { adaptedActiveTool: AnnotationTool }) { + const disabledInfosForTools = useSelector(getDisabledInfoForTools); + const isVolumeModificationAllowed = useSelector(getIsVolumeModificationAllowed); + if (!isVolumeModificationAllowed) { + return null; + } + return ( + + Trace Tool Icon + {adaptedActiveTool === AnnotationToolEnum.TRACE ? ( + + ) : null} + + ); +} + +function EraseTraceTool({ adaptedActiveTool }: { adaptedActiveTool: AnnotationTool }) { + const disabledInfosForTools = useSelector(getDisabledInfoForTools); + const showEraseTraceTool = + adaptedActiveTool === AnnotationToolEnum.TRACE || + adaptedActiveTool === AnnotationToolEnum.ERASE_TRACE; + const isVolumeModificationAllowed = useSelector(getIsVolumeModificationAllowed); + if (!isVolumeModificationAllowed) { + return null; + } + + return ( + + + {adaptedActiveTool === AnnotationToolEnum.ERASE_TRACE ? ( + + ) : null} + + ); +} + +function FillCellTool({ adaptedActiveTool }: { adaptedActiveTool: AnnotationTool }) { + const disabledInfosForTools = useSelector(getDisabledInfoForTools); + const isVolumeModificationAllowed = useSelector(getIsVolumeModificationAllowed); + if (!isVolumeModificationAllowed) { + return null; + } + + return ( + + + {adaptedActiveTool === AnnotationToolEnum.FILL_CELL ? ( + + ) : null} + + ); +} + +function PickCellTool() { + const disabledInfosForTools = useSelector(getDisabledInfoForTools); + const isVolumeModificationAllowed = useSelector(getIsVolumeModificationAllowed); + if (!isVolumeModificationAllowed) { + return null; + } + return ( + + + + ); +} + +function QuickSelectTool() { + const disabledInfosForTools = useSelector(getDisabledInfoForTools); + const isVolumeModificationAllowed = useSelector(getIsVolumeModificationAllowed); + if (!isVolumeModificationAllowed) { + return null; + } + return ( + + Quick Select Icon + + ); +} + +function BoundingBoxTool() { + const disabledInfosForTools = useSelector(getDisabledInfoForTools); + const isReadOnly = useSelector( + (state: OxalisState) => !state.annotation.restrictions.allowUpdate, + ); + if (isReadOnly) { + return null; + } + return ( + + Bounding Box Icon + + ); +} + +function ProofreadTool() { + const dispatch = useDispatch(); + const isAgglomerateMappingEnabled = useSelector(hasAgglomerateMapping); + const disabledInfosForTools = useSelector(getDisabledInfoForTools); + const areEditableMappingsEnabled = features().editableMappingsEnabled; + const hasSkeleton = useSelector((state: OxalisState) => state.annotation?.skeleton != null); + const hasVolume = useSelector((state: OxalisState) => state.annotation?.volumes.length > 0); + const isReadOnly = useSelector( + (state: OxalisState) => !state.annotation.restrictions.allowUpdate, + ); + + const mayProofread = hasSkeleton && hasVolume && !isReadOnly; + if (!mayProofread) { + return null; + } + + return ( + { + dispatch(ensureLayerMappingsAreLoadedAction()); + }} + > + + + ); +} + +function LineMeasurementTool() { + return ( + + + + ); +} + +function MaybeMultiSliceAnnotationInfoIcon() { + const maybeMagWithZoomStep = useSelector(getRenderableMagForActiveSegmentationTracing); + const labeledMag = maybeMagWithZoomStep != null ? maybeMagWithZoomStep.mag : null; + const hasMagWithHigherDimension = (labeledMag || []).some((val) => val > 1); + const maybeMultiSliceAnnotationInfoIcon = hasMagWithHigherDimension ? ( + + + + ) : null; + return maybeMultiSliceAnnotationInfoIcon; +} diff --git a/frontend/javascripts/oxalis/view/action-bar/view_modes_view.tsx b/frontend/javascripts/oxalis/view/action-bar/view_modes_view.tsx index fd6566c4bc4..d1992fd2445 100644 --- a/frontend/javascripts/oxalis/view/action-bar/view_modes_view.tsx +++ b/frontend/javascripts/oxalis/view/action-bar/view_modes_view.tsx @@ -44,7 +44,7 @@ class ViewModesView extends PureComponent { Store.dispatch(setViewModeAction(mode)); // Unfortunately, antd doesn't provide the original event here - // which is why we have to blur using document.activElement. + // which is why we have to blur using document.activeElement. // Additionally, we need a timeout since the blurring would be done // to early, otherwise. setTimeout(() => { @@ -85,54 +85,12 @@ class ViewModesView extends PureComponent { onClick: handleMenuClick, }; - const toolWorkspaceItems: MenuProps["items"] = [ - { - key: "1", - type: "group", - label: "Select Workflow", - children: [ - { - label: "All Tools", - key: "1", - }, - { - label: "View Only", - key: "2", - }, - { - label: "Volume Only", - key: "3", - }, - { - label: "Split Segments", - key: "4", - }, - ], - }, - ]; - - const toolWorkspaceMenuProps = { - items: toolWorkspaceItems, - onClick: () => {}, - }; - return ( - // The outer div is necessary for proper spacing. -
- - - - - - - - - -
+ + + ); } } diff --git a/frontend/javascripts/oxalis/view/action_bar_view.tsx b/frontend/javascripts/oxalis/view/action_bar_view.tsx index 2809d7befe4..758fd114d6a 100644 --- a/frontend/javascripts/oxalis/view/action_bar_view.tsx +++ b/frontend/javascripts/oxalis/view/action_bar_view.tsx @@ -1,6 +1,6 @@ import { createExplorational } from "admin/admin_rest_api"; import { withAuthentication } from "admin/auth/authentication_modal"; -import { Alert, Popover } from "antd"; +import { Alert, Popover, Space } from "antd"; import { AsyncButton, type AsyncButtonProps } from "components/async_clickables"; import { isUserAdminOrTeamManager } from "libs/utils"; import { ArbitraryVectorInput } from "libs/vector_input"; @@ -41,6 +41,7 @@ import { APIJobType, type AdditionalCoordinate } from "types/api_flow_types"; import { StartAIJobModal, type StartAIJobModalState } from "./action-bar/starting_job_modals"; import ButtonComponent from "./components/button_component"; import { NumberSliderSetting } from "./components/setting_input_views"; +import ToolWorkspaceView from "./action-bar/tool_workspace_view"; const VersionRestoreWarning = ( state.annotation.skeleton != null); + const is2d = useSelector((state: OxalisState) => is2dDataset(state.dataset)); + const controlMode = useSelector((state: OxalisState) => state.temporaryConfiguration.controlMode); + const isViewMode = controlMode === ControlModeEnum.VIEW; + + const isArbitrarySupported = hasSkeleton || isViewMode; + + // The outer div is necessary for proper spacing. + return ( +
+ + {isArbitrarySupported && !is2d ? : null} + + +
+ ); +} + class ActionBarView extends React.PureComponent { state: State = { isNewLayoutModalOpen: false, @@ -244,20 +262,10 @@ class ActionBarView extends React.PureComponent { } render() { - const { - dataset, - is2d, - isReadOnly, - showVersionRestore, - controlMode, - hasSkeleton, - layoutProps, - viewMode, - activeUser, - } = this.props; + const { dataset, is2d, showVersionRestore, controlMode, layoutProps, viewMode, activeUser } = + this.props; const isAdminOrDatasetManager = activeUser && isUserAdminOrTeamManager(activeUser); const isViewMode = controlMode === ControlModeEnum.VIEW; - const isArbitrarySupported = hasSkeleton || isViewMode; const getIsAIAnalysisEnabled = () => { const jobsEnabled = dataset.dataStore.jobsSupportedByAvailableWorkers.includes(APIJobType.INFER_NEURONS) || @@ -304,14 +312,12 @@ class ActionBarView extends React.PureComponent { {showVersionRestore ? VersionRestoreWarning : null} - {isArbitrarySupported && !is2d ? : null} + {getIsAIAnalysisEnabled() && isAdminOrDatasetManager ? this.renderStartAIJobButton(shouldDisableAIJobButton, tooltip) : null} {isViewMode ? this.renderStartTracingButton() : null} - {constants.MODES_PLANE.indexOf(viewMode) > -1 ? ( - - ) : null} + {constants.MODES_PLANE.indexOf(viewMode) > -1 ? : null} ({ activeUser: state.activeUser, controlMode: state.temporaryConfiguration.controlMode, showVersionRestore: state.uiInformation.showVersionRestore, - hasSkeleton: state.annotation.skeleton != null, - isReadOnly: !state.annotation.restrictions.allowUpdate, is2d: is2dDataset(state.dataset), viewMode: state.temporaryConfiguration.viewMode, aiJobModalState: state.uiInformation.aIJobModalState, diff --git a/frontend/javascripts/oxalis/view/plane_view.ts b/frontend/javascripts/oxalis/view/plane_view.ts index ec69635eb6d..7beac7f00bf 100644 --- a/frontend/javascripts/oxalis/view/plane_view.ts +++ b/frontend/javascripts/oxalis/view/plane_view.ts @@ -4,7 +4,7 @@ import VisibilityAwareRaycaster, { } from "libs/visibility_aware_raycaster"; import window from "libs/window"; import _ from "lodash"; -import type { OrthoViewMap, Vector3, Viewport } from "oxalis/constants"; +import type { OrthoViewMap, Viewport } from "oxalis/constants"; import Constants, { OrthoViewColors, OrthoViewValues, OrthoViews } from "oxalis/constants"; import getSceneController, { getSceneControllerOrNull, @@ -21,21 +21,6 @@ import * as THREE from "three"; // @ts-expect-error ts-migrate(7016) FIXME: Could not find a declaration file for module 'twee... Remove this comment to see the full error message import TWEEN from "tween.js"; -const createDirLight = ( - position: Vector3, - target: Vector3, - intensity: number, - parent: THREE.OrthographicCamera, -) => { - const dirLight = new THREE.DirectionalLight(0xffffff, intensity); - dirLight.color.setHSL(0.1, 1, 0.95); - dirLight.position.set(...position); - parent.add(dirLight); - parent.add(dirLight.target); - dirLight.target.position.set(...target); - return dirLight; -}; - const raycaster = new VisibilityAwareRaycaster(); let oldRaycasterHit: MeshSceneNode | null = null; const MESH_HOVER_THROTTLING_DELAY = 150; @@ -70,7 +55,6 @@ class PlaneView { } this.cameras = cameras; - // createDirLight([10, 10, 10], [0, 0, 10], 5, this.cameras[OrthoViews.TDView]); this.cameras[OrthoViews.PLANE_XY].position.z = -1; this.cameras[OrthoViews.PLANE_YZ].position.x = 1; this.cameras[OrthoViews.PLANE_XZ].position.y = 1; From 880026592152cc7c179862872b020e5d140a1f6e Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Wed, 9 Apr 2025 14:48:14 +0200 Subject: [PATCH 13/84] some clean up --- .../javascripts/oxalis/controller/renderer.ts | 2 - .../oxalis/controller/scene_controller.ts | 89 +------------------ .../model/bucket_data_handling/data_cube.ts | 19 ++-- frontend/javascripts/types/globals.d.ts | 1 + 4 files changed, 12 insertions(+), 99 deletions(-) diff --git a/frontend/javascripts/oxalis/controller/renderer.ts b/frontend/javascripts/oxalis/controller/renderer.ts index 3ebd0cf42fa..b300afb0a8e 100644 --- a/frontend/javascripts/oxalis/controller/renderer.ts +++ b/frontend/javascripts/oxalis/controller/renderer.ts @@ -40,8 +40,6 @@ function getRenderer(): THREE.WebGLRenderer { : {} ) as THREE.WebGLRenderer; - renderer.physicallyCorrectLights = true; - return renderer; } diff --git a/frontend/javascripts/oxalis/controller/scene_controller.ts b/frontend/javascripts/oxalis/controller/scene_controller.ts index 89f66985c88..ac9b68c8407 100644 --- a/frontend/javascripts/oxalis/controller/scene_controller.ts +++ b/frontend/javascripts/oxalis/controller/scene_controller.ts @@ -47,6 +47,7 @@ import { getVoxelPerUnit } from "oxalis/model/scaleinfo"; import { Model } from "oxalis/singletons"; import type { OxalisState, SkeletonTracing, UserBoundingBox } from "oxalis/store"; import Store from "oxalis/store"; +// @ts-ignore import PCA from "pca-js"; import * as THREE from "three"; import SegmentMeshController from "./segment_mesh_controller"; @@ -279,7 +280,9 @@ function computeBentSurfaceSplines(points: Vector3[]): THREE.Object3D[] { const prevCurvePoints = curvesByZ[zValues[curveIdx - 1]].points; const distActual = currentCurvePoints[0].distanceTo(prevCurvePoints[0]); - const distFlipped = currentCurvePoints.at(-1).distanceTo(prevCurvePoints[0]); + const distFlipped = (currentCurvePoints.at(-1) as THREE.Vector3).distanceTo( + prevCurvePoints[0], + ); const shouldFlip = distFlipped < distActual; if (shouldFlip) { @@ -386,8 +389,6 @@ function computeBentSurfaceSplines(points: Vector3[]): THREE.Object3D[] { geometry.computeVertexNormals(); // Smooth shading geometry.computeBoundsTree(); - window.bentGeometry = geometry; - // Material and Mesh const material = new THREE.MeshStandardMaterial({ color: 0x0077ff, // A soft blue color @@ -406,29 +407,6 @@ function computeBentSurfaceSplines(points: Vector3[]): THREE.Object3D[] { return objects; } -// function createNormalsVisualization(geometry: THREE.BufferGeometry, objects: THREE.Object3D[]) { -// const positions = geometry.attributes.position.array; -// const normals = geometry.attributes.normal.array; -// const normalLines: number[] = []; - -// for (let i = 0; i < positions.length; i += 3) { -// const v = new THREE.Vector3(positions[i], positions[i + 1], positions[i + 2]); -// const n = new THREE.Vector3(normals[i], normals[i + 1], normals[i + 2]); - -// const vEnd = v.clone().add(n.multiplyScalar(5)); // Scale normals for visibility - -// normalLines.push(v.x, v.y, v.z, vEnd.x, vEnd.y, vEnd.z); -// } - -// const normalGeometry = new THREE.BufferGeometry(); -// normalGeometry.setAttribute("position", new THREE.Float32BufferAttribute(normalLines, 3)); - -// const normalMaterial = new THREE.LineBasicMaterial({ color: 0xff0000 }); // Red for visibility -// const normalLinesMesh = new THREE.LineSegments(normalGeometry, normalMaterial); - -// objects.push(normalLinesMesh); // Add to objects list instead of scene.add() -// } - function generatePlanePoints(planeMesh: THREE.Mesh): Vector3[] { const points: THREE.Vector3[] = []; const width = planeMesh.geometry.parameters.width; @@ -513,54 +491,6 @@ function createBentSurfaceGeometry(points: Vector3[], rows: number, cols: number return mesh; } -function generateTPSMesh(points, scale, resolution = 20) { - if (points.length < 3) { - throw new Error("At least 3 points are needed to define a surface."); - } - - const sourcePoints = points.map(projectToPlane); - const targetPoints = points.map((p) => [p[0], p[1], p[2]]); - - // Step 3: Create the TPS transformation - const tps = new TPS3D(sourcePoints, targetPoints, scale); - - // Step 4: Generate a grid of points in the base plane - const minX = Math.min(...sourcePoints.map((p) => p[0])); - const maxX = Math.max(...sourcePoints.map((p) => p[0])); - const minY = Math.min(...sourcePoints.map((p) => p[1])); - const maxY = Math.max(...sourcePoints.map((p) => p[1])); - - const gridPoints = []; - for (let i = 0; i <= resolution; i++) { - for (let j = 0; j <= resolution; j++) { - const x = minX + (i / resolution) * (maxX - minX); - const y = minY + (j / resolution) * (maxY - minY); - const transformed = tps.transform(x, y, 0); - gridPoints.push(new THREE.Vector3(transformed[0], transformed[1], transformed[2])); - } - } - - // Step 5: Perform Delaunay triangulation to create faces - const delaunay = Delaunator.from(gridPoints.map((p) => [p.x, p.y])); - const indices = delaunay.triangles; - - // Step 6: Convert data into THREE.BufferGeometry - const geometry = new THREE.BufferGeometry(); - const positions = new Float32Array(gridPoints.length * 3); - - gridPoints.forEach((p, i) => { - positions[i * 3] = p.x; - positions[i * 3 + 1] = p.y; - positions[i * 3 + 2] = p.z; - }); - - geometry.setAttribute("position", new THREE.BufferAttribute(positions, 3)); - geometry.setIndex(new THREE.BufferAttribute(new Uint16Array(indices), 1)); - geometry.computeVertexNormals(); // Smooth shading - - return geometry; -} - class SceneController { skeletons: Record = {}; current: number; @@ -796,17 +726,6 @@ class SceneController { } addBentSurface(points: Vector3[]) { - // const meshGeometry = generateTPSMesh(points, [1, 1, 1], 30); - // // const material = new THREE.MeshStandardMaterial({ color: 0x88ccff, wireframe: true }); - // const material = new THREE.MeshLambertMaterial({ - // color: "green", - // wireframe: true, - // }); - // material.side = THREE.FrontSide; - // // material.transparent = true; - // const surfaceMesh = new THREE.Mesh(meshGeometry, material); - // this.rootNode.add(surfaceMesh); - if (points.length === 0) { return () => {}; } diff --git a/frontend/javascripts/oxalis/model/bucket_data_handling/data_cube.ts b/frontend/javascripts/oxalis/model/bucket_data_handling/data_cube.ts index ff002e8430c..109f141fea2 100644 --- a/frontend/javascripts/oxalis/model/bucket_data_handling/data_cube.ts +++ b/frontend/javascripts/oxalis/model/bucket_data_handling/data_cube.ts @@ -726,13 +726,13 @@ class DataCube { const neighbourBucket = this.getOrCreateBucket(neighbourBucketAddress); let shouldSkip = false; - if (window.bentGeometry) { + if (window.bentMesh) { const currentGlobalPosition = V3.add( currentGlobalBucketPosition, V3.scale3(neighbourVoxelXyz, currentMag), ); const intersects = checkLineIntersection( - window.bentGeometry, + window.bentMesh, originGlobalPosition, currentGlobalPosition, ); @@ -758,15 +758,9 @@ class DataCube { }); let shouldSkip = false; - if (window.bentGeometry) { - // const target = {}; - // window.bentGeometry.boundsTree.closestPointToPoint( - // new THREE.Vector3(...currentGlobalPosition), - // target, - // ); - + if (window.bentMesh) { const intersects = checkLineIntersection( - window.bentGeometry, + window.bentMesh, originGlobalPosition, currentGlobalPosition, ); @@ -1038,7 +1032,8 @@ class DataCube { export default DataCube; // Function to check intersection -function checkLineIntersection(geometry: THREE.BufferGeometry, _pointA: Vector3, _pointB: Vector3) { +function checkLineIntersection(bentMesh: THREE.Mesh, _pointA: Vector3, _pointB: Vector3) { + const geometry = bentMesh.geometry; // Create BVH from geometry if not already built if (!geometry.boundsTree) { geometry.computeBoundsTree(); @@ -1060,7 +1055,7 @@ function checkLineIntersection(geometry: THREE.BufferGeometry, _pointA: Vector3, raycaster.far = pointA.distanceTo(pointB); // Limit to segment length raycaster.firstHitOnly = true; - const intersects = raycaster.intersectObject(window.bentMesh, true); + const intersects = raycaster.intersectObject(bentMesh, true); const retval = intersects.length > 0; // Returns true if an intersection is found return retval; diff --git a/frontend/javascripts/types/globals.d.ts b/frontend/javascripts/types/globals.d.ts index 4a80b22b3a3..8d7e51fec86 100644 --- a/frontend/javascripts/types/globals.d.ts +++ b/frontend/javascripts/types/globals.d.ts @@ -8,6 +8,7 @@ declare global { DEV: WkDev; apiReady: ApiType["apiReady"] }; + bentMesh: THREE.Mesh } } From 6bad426d25ff8f227b62c9b50269abe11ad573fb Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Wed, 9 Apr 2025 14:58:57 +0200 Subject: [PATCH 14/84] fix ts errors --- frontend/javascripts/libs/UpdatableTexture.ts | 16 +++++----------- .../libs/cuckoo/abstract_cuckoo_table.ts | 2 +- frontend/javascripts/libs/window.ts | 1 + frontend/javascripts/oxalis/default_state.ts | 1 + 4 files changed, 8 insertions(+), 12 deletions(-) diff --git a/frontend/javascripts/libs/UpdatableTexture.ts b/frontend/javascripts/libs/UpdatableTexture.ts index 19bf0de14ca..31bc83b3616 100644 --- a/frontend/javascripts/libs/UpdatableTexture.ts +++ b/frontend/javascripts/libs/UpdatableTexture.ts @@ -33,10 +33,9 @@ class UpdatableTexture extends THREE.Texture { mapping?: THREE.Mapping, wrapS?: THREE.Wrapping, wrapT?: THREE.Wrapping, - magFilter?: THREE.TextureFilter, - minFilter?: THREE.TextureFilter, + magFilter?: THREE.MagnificationTextureFilter, + minFilter?: THREE.MinificationTextureFilter, anisotropy?: number, - encoding?: THREE.TextureEncoding, ) { const imageData = { width, height, data: new Uint32Array(0) }; @@ -51,7 +50,6 @@ class UpdatableTexture extends THREE.Texture { format, type, anisotropy, - encoding, ); this.magFilter = magFilter !== undefined ? magFilter : THREE.LinearFilter; @@ -65,15 +63,11 @@ class UpdatableTexture extends THREE.Texture { setRenderer(renderer: THREE.WebGLRenderer) { this.renderer = renderer; this.gl = this.renderer.getContext() as WebGL2RenderingContext; - this.utils = new THREE.WebGLUtils( - this.gl, - this.renderer.extensions, - this.renderer.capabilities, - ); + this.utils = new THREE.WebGLUtils(this.gl, this.renderer.extensions); } isInitialized() { - return this.renderer.properties.get(this).__webglTexture != null; + return (this.renderer.properties.get(this) as any).__webglTexture != null; } update(src: TypedArray, x: number, y: number, width: number, height: number) { @@ -94,7 +88,7 @@ class UpdatableTexture extends THREE.Texture { this.renderer.initTexture(this); } const activeTexture = this.gl.getParameter(this.gl.TEXTURE_BINDING_2D); - const textureProperties = this.renderer.properties.get(this); + const textureProperties = this.renderer.properties.get(this) as any; this.gl.bindTexture(this.gl.TEXTURE_2D, textureProperties.__webglTexture); originalTexSubImage2D( diff --git a/frontend/javascripts/libs/cuckoo/abstract_cuckoo_table.ts b/frontend/javascripts/libs/cuckoo/abstract_cuckoo_table.ts index fc306fb77c4..ed50c738a00 100644 --- a/frontend/javascripts/libs/cuckoo/abstract_cuckoo_table.ts +++ b/frontend/javascripts/libs/cuckoo/abstract_cuckoo_table.ts @@ -32,7 +32,7 @@ export abstract class AbstractCuckooTable { return THREE.UnsignedIntType; } - static getTextureFormat() { + static getTextureFormat(): THREE.PixelFormat { return THREE.RGBAIntegerFormat; } diff --git a/frontend/javascripts/libs/window.ts b/frontend/javascripts/libs/window.ts index 2435d4d64a6..479452c3ab2 100644 --- a/frontend/javascripts/libs/window.ts +++ b/frontend/javascripts/libs/window.ts @@ -2,6 +2,7 @@ import type TextureBucketManager from "oxalis/model/bucket_data_handling/texture_bucket_manager"; import type { ArbitraryFunction, ArbitraryObject } from "types/globals"; +import type * as THREE from "three"; // mockRequire("libs/window", myFakeWindow); const removeEventListener = ( diff --git a/frontend/javascripts/oxalis/default_state.ts b/frontend/javascripts/oxalis/default_state.ts index 4492e5fa365..aafedf1d899 100644 --- a/frontend/javascripts/oxalis/default_state.ts +++ b/frontend/javascripts/oxalis/default_state.ts @@ -101,6 +101,7 @@ const defaultState: OxalisState = { }, renderWatermark: true, antialiasRendering: false, + toolWorkspace: "ALL_TOOLS", }, temporaryConfiguration: { viewMode: Constants.MODE_PLANE_TRACING, From c05b06d2cbcdb21fd941b9a9daba8da159af9332 Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Wed, 9 Apr 2025 14:59:31 +0200 Subject: [PATCH 15/84] linting --- frontend/javascripts/libs/window.ts | 2 +- .../oxalis/controller/scene_controller.ts | 6 +++--- .../oxalis/controller/splitting_stuff.ts | 2 +- .../model/bucket_data_handling/data_cube.ts | 2 +- .../oxalis/model/sagas/mesh_saga.ts | 20 +++++++++---------- .../oxalis/view/action_bar_view.tsx | 2 +- 6 files changed, 17 insertions(+), 17 deletions(-) diff --git a/frontend/javascripts/libs/window.ts b/frontend/javascripts/libs/window.ts index 479452c3ab2..79649c44917 100644 --- a/frontend/javascripts/libs/window.ts +++ b/frontend/javascripts/libs/window.ts @@ -1,8 +1,8 @@ // This module should be used to access the window object, so it can be mocked in the unit tests import type TextureBucketManager from "oxalis/model/bucket_data_handling/texture_bucket_manager"; -import type { ArbitraryFunction, ArbitraryObject } from "types/globals"; import type * as THREE from "three"; +import type { ArbitraryFunction, ArbitraryObject } from "types/globals"; // mockRequire("libs/window", myFakeWindow); const removeEventListener = ( diff --git a/frontend/javascripts/oxalis/controller/scene_controller.ts b/frontend/javascripts/oxalis/controller/scene_controller.ts index ac9b68c8407..b7668380e1e 100644 --- a/frontend/javascripts/oxalis/controller/scene_controller.ts +++ b/frontend/javascripts/oxalis/controller/scene_controller.ts @@ -61,11 +61,11 @@ import { WkDevFlags } from "oxalis/api/wk_dev"; import { orderPointsMST } from "./splitting_stuff"; import { - computeBoundsTree, - disposeBoundsTree, + acceleratedRaycast, computeBatchedBoundsTree, + computeBoundsTree, disposeBatchedBoundsTree, - acceleratedRaycast, + disposeBoundsTree, } from "three-mesh-bvh"; // Add the extension functions diff --git a/frontend/javascripts/oxalis/controller/splitting_stuff.ts b/frontend/javascripts/oxalis/controller/splitting_stuff.ts index fb05fa73ef4..15c79b505b7 100644 --- a/frontend/javascripts/oxalis/controller/splitting_stuff.ts +++ b/frontend/javascripts/oxalis/controller/splitting_stuff.ts @@ -1,4 +1,4 @@ -import * as THREE from "three"; +import type * as THREE from "three"; class DisjointSet { private parent: number[]; diff --git a/frontend/javascripts/oxalis/model/bucket_data_handling/data_cube.ts b/frontend/javascripts/oxalis/model/bucket_data_handling/data_cube.ts index 109f141fea2..3330356ba78 100644 --- a/frontend/javascripts/oxalis/model/bucket_data_handling/data_cube.ts +++ b/frontend/javascripts/oxalis/model/bucket_data_handling/data_cube.ts @@ -32,10 +32,10 @@ import { globalPositionToBucketPosition } from "oxalis/model/helpers/position_co import { VoxelNeighborQueue2D, VoxelNeighborQueue3D } from "oxalis/model/volumetracing/volumelayer"; import type { Mapping } from "oxalis/store"; import Store from "oxalis/store"; +import * as THREE from "three"; import type { AdditionalAxis, BucketDataArray, ElementClass } from "types/api_flow_types"; import type { AdditionalCoordinate } from "types/api_flow_types"; import type { MagInfo } from "../helpers/mag_info"; -import * as THREE from "three"; const warnAboutTooManyAllocations = _.once(() => { const msg = diff --git a/frontend/javascripts/oxalis/model/sagas/mesh_saga.ts b/frontend/javascripts/oxalis/model/sagas/mesh_saga.ts index 212772a2ecf..f2aacfd9c01 100644 --- a/frontend/javascripts/oxalis/model/sagas/mesh_saga.ts +++ b/frontend/javascripts/oxalis/model/sagas/mesh_saga.ts @@ -1,13 +1,3 @@ -import { saveAs } from "file-saver"; -import { mergeBufferGeometries } from "libs/BufferGeometryUtils"; -import Deferred from "libs/async/deferred"; -import ErrorHandling from "libs/error_handling"; -import { V3 } from "libs/mjs"; -import { areVec3AlmostEqual, chunkDynamically, sleep } from "libs/utils"; -import _ from "lodash"; -import type { ActionPattern } from "redux-saga/effects"; -import type { APIDataset, APIMeshFile, APISegmentationLayer } from "types/api_flow_types"; -import type * as THREE from "three"; import { computeAdHocMesh, getBucketPositionsForAdHocMesh, @@ -15,12 +5,19 @@ import { meshApi, sendAnalyticsEvent, } from "admin/admin_rest_api"; +import { saveAs } from "file-saver"; +import { mergeBufferGeometries } from "libs/BufferGeometryUtils"; import ThreeDMap from "libs/ThreeDMap"; +import Deferred from "libs/async/deferred"; import processTaskWithPool from "libs/async/task_pool"; import { getDracoLoader } from "libs/draco"; +import ErrorHandling from "libs/error_handling"; +import { V3 } from "libs/mjs"; import exportToStl from "libs/stl_exporter"; import Toast from "libs/toast"; +import { areVec3AlmostEqual, chunkDynamically, sleep } from "libs/utils"; import Zip from "libs/zipjs_wrapper"; +import _ from "lodash"; import messages from "messages"; import { WkDevFlags } from "oxalis/api/wk_dev"; import type { Vector3 } from "oxalis/constants"; @@ -73,7 +70,10 @@ import { Model } from "oxalis/singletons"; import Store from "oxalis/store"; import { stlMeshConstants } from "oxalis/view/right-border-tabs/segments_tab/segments_view"; import { getBaseSegmentationName } from "oxalis/view/right-border-tabs/segments_tab/segments_view_helper"; +import type { ActionPattern } from "redux-saga/effects"; +import type * as THREE from "three"; import { actionChannel, all, call, put, race, take, takeEvery } from "typed-redux-saga"; +import type { APIDataset, APIMeshFile, APISegmentationLayer } from "types/api_flow_types"; import type { AdditionalCoordinate } from "types/api_flow_types"; import { getAdditionalCoordinatesAsString } from "../accessors/flycam_accessor"; import type { FlycamAction } from "../actions/flycam_actions"; diff --git a/frontend/javascripts/oxalis/view/action_bar_view.tsx b/frontend/javascripts/oxalis/view/action_bar_view.tsx index 758fd114d6a..aa5ebae6fa8 100644 --- a/frontend/javascripts/oxalis/view/action_bar_view.tsx +++ b/frontend/javascripts/oxalis/view/action_bar_view.tsx @@ -39,9 +39,9 @@ import { useHistory } from "react-router-dom"; import type { APIDataset, APIUser } from "types/api_flow_types"; import { APIJobType, type AdditionalCoordinate } from "types/api_flow_types"; import { StartAIJobModal, type StartAIJobModalState } from "./action-bar/starting_job_modals"; +import ToolWorkspaceView from "./action-bar/tool_workspace_view"; import ButtonComponent from "./components/button_component"; import { NumberSliderSetting } from "./components/setting_input_views"; -import ToolWorkspaceView from "./action-bar/tool_workspace_view"; const VersionRestoreWarning = ( Date: Wed, 9 Apr 2025 15:53:26 +0200 Subject: [PATCH 16/84] only generate bent surface when split workspace is active --- .../oxalis/controller/scene_controller.ts | 1 - .../oxalis/model/sagas/bent_surface_saga.ts | 26 ++++---- .../oxalis/view/action-bar/toolbar_view.tsx | 63 ++++++++++--------- 3 files changed, 50 insertions(+), 40 deletions(-) diff --git a/frontend/javascripts/oxalis/controller/scene_controller.ts b/frontend/javascripts/oxalis/controller/scene_controller.ts index b7668380e1e..2cb877091af 100644 --- a/frontend/javascripts/oxalis/controller/scene_controller.ts +++ b/frontend/javascripts/oxalis/controller/scene_controller.ts @@ -244,7 +244,6 @@ function computeBentSurfaceTPS(points: Vector3[]): THREE.Object3D[] { function computeBentSurfaceSplines(points: Vector3[]): THREE.Object3D[] { const objects: THREE.Object3D[] = []; - console.log("fresh!"); const unfilteredPointsByZ = _.groupBy(points, (p) => p[2]); const pointsByZ = _.omitBy(unfilteredPointsByZ, (value) => value.length < 2); diff --git a/frontend/javascripts/oxalis/model/sagas/bent_surface_saga.ts b/frontend/javascripts/oxalis/model/sagas/bent_surface_saga.ts index 10771e73243..10452700aa3 100644 --- a/frontend/javascripts/oxalis/model/sagas/bent_surface_saga.ts +++ b/frontend/javascripts/oxalis/model/sagas/bent_surface_saga.ts @@ -5,23 +5,25 @@ import { call, takeEvery } from "typed-redux-saga"; import { getActiveTree } from "../accessors/skeletontracing_accessor"; import { ensureWkReady } from "./ready_sagas"; import { takeWithBatchActionSupport } from "./saga_helpers"; +import type { Action } from "../actions/actions"; +import type { ActionPattern } from "redux-saga/effects"; let cleanUpFn: (() => void) | null = null; -function* createBentSurface() { +function* updateBentSurface() { if (cleanUpFn != null) { cleanUpFn(); cleanUpFn = null; } - const sceneController = yield* call(() => getSceneController()); + const isSplitWorkspace = yield* select( + (state) => state.userConfiguration.toolWorkspace === "SPLIT_SEGMENTS", + ); + if (!isSplitWorkspace) { + return; + } - // const points: Vector3[] = [ - // [40, 50, 60], - // [50, 70, 60], - // [80, 70, 90], - // [50, 60, 80], - // ]; + const sceneController = yield* call(() => getSceneController()); const activeTree = yield* select((state) => getActiveTree(state.annotation.skeleton)); // biome-ignore lint/complexity/useOptionalChain: @@ -41,7 +43,7 @@ export function* bentSurfaceSaga(): Saga { yield* ensureWkReady(); // initial rendering - yield* call(createBentSurface); + yield* call(updateBentSurface); yield* takeEvery( [ "SET_ACTIVE_TREE", @@ -51,8 +53,10 @@ export function* bentSurfaceSaga(): Saga { "SET_TREE_VISIBILITY", "TOGGLE_TREE", "SET_NODE_POSITION", - ], - createBentSurface, + (action: Action) => + action.type === "UPDATE_USER_SETTING" && action.propertyName === "toolWorkspace", + ] as ActionPattern, + updateBentSurface, ); } diff --git a/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx b/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx index eb3e7e3d1b1..bd791a5c8cf 100644 --- a/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx +++ b/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx @@ -394,6 +394,9 @@ function SkeletonSpecificButtons() { const isContinuousNodeCreationEnabled = useSelector( (state: OxalisState) => state.userConfiguration.continuousNodeCreation, ); + const isSplitWorkspace = useSelector( + (state: OxalisState) => state.userConfiguration.toolWorkspace === "SPLIT_SEGMENTS", + ); const toggleContinuousNodeCreation = () => dispatch(updateUserSettingAction("continuousNodeCreation", !isContinuousNodeCreationEnabled)); @@ -433,34 +436,38 @@ function SkeletonSpecificButtons() { }} > - - Single Node Tree Mode - - - Merger Mode - + {isSplitWorkspace ? null : ( + + Single Node Tree Mode + + )} + {isSplitWorkspace ? null : ( + + Merger Mode + + )} Date: Wed, 9 Apr 2025 15:56:40 +0200 Subject: [PATCH 17/84] remove lots of unused code (from old delauney and tps based approaches) --- frontend/javascripts/oxalis/api/wk_dev.ts | 1 - .../oxalis/controller/scene_controller.ts | 266 +----------------- .../oxalis/controller/splitting_stuff.ts | 18 -- .../oxalis/model/sagas/bent_surface_saga.ts | 4 +- package.json | 3 - yarn.lock | 33 --- 6 files changed, 3 insertions(+), 322 deletions(-) diff --git a/frontend/javascripts/oxalis/api/wk_dev.ts b/frontend/javascripts/oxalis/api/wk_dev.ts index 8ead784ad2a..0e94cac317d 100644 --- a/frontend/javascripts/oxalis/api/wk_dev.ts +++ b/frontend/javascripts/oxalis/api/wk_dev.ts @@ -32,7 +32,6 @@ export const WkDevFlags = { datasetComposition: { allowThinPlateSplines: false, }, - splittingStrategy: "splines", }; export default class WkDev { diff --git a/frontend/javascripts/oxalis/controller/scene_controller.ts b/frontend/javascripts/oxalis/controller/scene_controller.ts index 2cb877091af..a1f69e730ba 100644 --- a/frontend/javascripts/oxalis/controller/scene_controller.ts +++ b/frontend/javascripts/oxalis/controller/scene_controller.ts @@ -47,17 +47,11 @@ import { getVoxelPerUnit } from "oxalis/model/scaleinfo"; import { Model } from "oxalis/singletons"; import type { OxalisState, SkeletonTracing, UserBoundingBox } from "oxalis/store"; import Store from "oxalis/store"; -// @ts-ignore -import PCA from "pca-js"; import * as THREE from "three"; import SegmentMeshController from "./segment_mesh_controller"; const CUBE_COLOR = 0x999999; const LAYER_CUBE_COLOR = 0xffff99; - -import Delaunator from "delaunator"; -import TPS3D from "libs/thin_plate_spline"; -import { WkDevFlags } from "oxalis/api/wk_dev"; import { orderPointsMST } from "./splitting_stuff"; import { @@ -77,171 +71,6 @@ THREE.BatchedMesh.prototype.computeBoundsTree = computeBatchedBoundsTree; THREE.BatchedMesh.prototype.disposeBoundsTree = disposeBatchedBoundsTree; THREE.BatchedMesh.prototype.raycast = acceleratedRaycast; -type EigenData = { eigenvalue: number; vector: number[] }; - -function _createPointCloud(points: Vector3[], color: string) { - // Convert points to Three.js geometry - const geometry = new THREE.BufferGeometry(); - const vertices = new Float32Array(_.flatten(points)); - geometry.setAttribute("position", new THREE.BufferAttribute(vertices, 3)); - - // Create point material and add to objects list - const material = new THREE.PointsMaterial({ color, size: 5 }); - - const pointCloud = new THREE.Points(geometry, material); - return pointCloud; -} - -const rows = 100; -const cols = 100; - -function computeBentSurfaceDelauny(points3D: Vector3[]): THREE.Object3D[] { - const objects: THREE.Object3D[] = []; - // Your precomputed 2D projection (same order as points3D) - - const { projectedLocalPoints } = projectPoints(points3D); - - // Compute Delaunay triangulation on the projected 2D points - const delaunay = Delaunator.from(projectedLocalPoints.map((vec) => [vec.x, vec.y])); - const indices = delaunay.triangles; // Triangle indices - - // Flatten 3D vertex positions for BufferGeometry - const vertices = points3D.flat(); - - // Create BufferGeometry - const geometry = new THREE.BufferGeometry(); - geometry.setAttribute("position", new THREE.Float32BufferAttribute(vertices, 3)); - geometry.setIndex(Array.from(indices)); - geometry.computeVertexNormals(); // Compute normals for shading - - const material = new THREE.MeshLambertMaterial({ - color: "green", - wireframe: false, - }); - material.side = THREE.DoubleSide; - // material.transparent = true; - const surfaceMesh = new THREE.Mesh(geometry, material); - objects.push(surfaceMesh); - return objects; -} - -function projectPoints(points: Vector3[]) { - const eigenData: EigenData[] = PCA.getEigenVectors(points); - - const adData = PCA.computeAdjustedData(points, eigenData[0], eigenData[1]); - const compressed = adData.formattedAdjustedData; - const uncompressed = PCA.computeOriginalData(compressed, adData.selectedVectors, adData.avgData); - console.log("uncompressed", uncompressed); - - const projectedPoints: Vector3[] = uncompressed.originalData; - - // Align the plane with the principal components - const normal = new THREE.Vector3(...eigenData[2].vector); - const quaternion = new THREE.Quaternion().setFromUnitVectors(new THREE.Vector3(0, 0, 1), normal); - const quaternionInv = quaternion.clone().invert(); - - // Transform projectedPoints into the plane’s local coordinate system - const projectedLocalPoints = projectedPoints.map((p) => { - const worldPoint = new THREE.Vector3(...p); - return worldPoint.applyQuaternion(quaternionInv); // Move to local plane space - }); - return { projectedPoints, projectedLocalPoints, eigenData }; -} - -function computeBentSurfaceTPS(points: Vector3[]): THREE.Object3D[] { - const objects: THREE.Object3D[] = []; - const { projectedPoints, projectedLocalPoints, eigenData } = projectPoints(points); - // objects.push(createPointCloud(points, "red")); - // objects.push(createPointCloud(projectedPoints, "blue")); - - // todop: adapt scale - const scale = [1, 1, 1] as Vector3; - const tps = new TPS3D(projectedPoints, points, scale); - - // Align the plane with the principal components - const normal = new THREE.Vector3(...eigenData[2].vector); - const quaternion = new THREE.Quaternion().setFromUnitVectors(new THREE.Vector3(0, 0, 1), normal); - const quaternionInv = quaternion.clone().invert(); - - const mean = points.reduce( - (acc, p) => acc.add(new THREE.Vector3(...p).divideScalar(points.length)), - new THREE.Vector3(0, 0, 0), - ); - const projectedMean = mean.clone().applyQuaternion(quaternionInv); - - // Compute min/max bounds in local plane space - let minX = Number.POSITIVE_INFINITY, - maxX = Number.NEGATIVE_INFINITY, - minY = Number.POSITIVE_INFINITY, - maxY = Number.NEGATIVE_INFINITY; - projectedLocalPoints.forEach((p) => { - minX = Math.min(minX, p.x); - maxX = Math.max(maxX, p.x); - minY = Math.min(minY, p.y); - maxY = Math.max(maxY, p.y); - }); - - // Compute exact plane size based on bounds - const planeSizeX = 2 * Math.max(maxX - projectedMean.x, projectedMean.x - minX); - const planeSizeY = 2 * Math.max(maxY - projectedMean.y, projectedMean.y - minY); - - // Define the plane using the first two principal components - // const planeSizeX = Math.sqrt(eigenData[0].eigenvalue) * 10; - // const planeSizeY = Math.sqrt(eigenData[1].eigenvalue) * 10; - - const planeGeometry = new THREE.PlaneGeometry(planeSizeX, planeSizeY); - const planeMaterial = new THREE.MeshBasicMaterial({ - color: 0x00ff00, - side: THREE.DoubleSide, - opacity: 0.5, - transparent: true, - }); - const plane = new THREE.Mesh(planeGeometry, planeMaterial); - - plane.setRotationFromQuaternion(quaternion); - - // const centerLocal = new THREE.Vector3((minX + maxX) / 2, (minY + maxY) / 2, 0); - // centerLocal.applyMatrix4(plane.matrixWorld); - plane.position.copy(mean); - - plane.updateMatrixWorld(); - - // objects.push(plane); - - const gridPoints = generatePlanePoints(plane); - const bentSurfacePoints = gridPoints.map((point) => tps.transform(...point)); - - // objects.push(createPointCloud(gridPoints, "purple")); - // objects.push(createPointCloud(bentSurfacePoints, "orange")); - - const bentMesh = createBentSurfaceGeometry(bentSurfacePoints, rows, cols); - objects.push(bentMesh); - - // const light = new THREE.DirectionalLight(0xffffff, 1); - // light.position.set(100, 150, 100); // Above and slightly in front of the points - // light.lookAt(60, 60, 75); // Aim at the center of the point set - // light.updateMatrixWorld(); - - // const lightHelper = new THREE.DirectionalLightHelper(light, 10, 0xff0000); // The size of the helper - - // const arrowHelper = new THREE.ArrowHelper( - // light.position - // .clone() - // .normalize(), // Direction - // new THREE.Vector3(60, 60, 75), // Start position (light target) - // 20, // Arrow length - // 0xff0000, // Color (red) - // ); - - // light.castShadow = true; - - // objects.push(light, lightHelper, arrowHelper); - - // createNormalsVisualization(bentMesh.geometry, objects); - - return objects; -} - function computeBentSurfaceSplines(points: Vector3[]): THREE.Object3D[] { const objects: THREE.Object3D[] = []; @@ -406,90 +235,6 @@ function computeBentSurfaceSplines(points: Vector3[]): THREE.Object3D[] { return objects; } -function generatePlanePoints(planeMesh: THREE.Mesh): Vector3[] { - const points: THREE.Vector3[] = []; - const width = planeMesh.geometry.parameters.width; - const height = planeMesh.geometry.parameters.height; - - // Use the full transformation matrix of the plane - const planeMatrix = planeMesh.matrixWorld.clone(); - - for (let i = 0; i < rows; i++) { - for (let j = 0; j < cols; j++) { - const x = (i / (rows - 1) - 0.5) * width; - const y = (j / (cols - 1) - 0.5) * height; - let point = new THREE.Vector3(x, y, 0); - - point = point.applyMatrix4(planeMatrix); - points.push(point); - } - } - return points.map((vec) => [vec.x, vec.y, vec.z]); -} - -function createBentSurfaceGeometry(points: Vector3[], rows: number, cols: number): THREE.Mesh { - const geometry = new THREE.BufferGeometry(); - - // Flattened position array - const positions = new Float32Array(points.length * 3); - points.forEach((p, i) => { - positions[i * 3] = p[0]; - positions[i * 3 + 1] = p[1]; - positions[i * 3 + 2] = p[2]; - }); - - // Create indices for two triangles per quad - const indices: number[] = []; - for (let i = 0; i < rows - 1; i++) { - for (let j = 0; j < cols - 1; j++) { - const a = i * cols + j; - const b = i * cols + (j + 1); - const c = (i + 1) * cols + j; - const d = (i + 1) * cols + (j + 1); - - // Two triangles per quad - indices.push(a, b, d); - indices.push(a, d, c); - } - } - - // Apply to geometry - geometry.setAttribute("position", new THREE.BufferAttribute(positions, 3)); - geometry.setIndex(indices); - geometry.computeVertexNormals(); // Generate normals for lighting - - const material = new THREE.MeshStandardMaterial({ - color: 0x0077ff, // A soft blue color - metalness: 0.5, // Slight metallic effect - roughness: 1, // Some surface roughness for a natural look - side: THREE.DoubleSide, // Render both sides - flatShading: false, // Ensures smooth shading with computed normals - }); - - // const material = new THREE.MeshLambertMaterial({ - // color: "blue", - // emissive: "green", - // side: THREE.DoubleSide, - // transparent: true, - // }); - - // const material = new THREE.MeshPhysicalMaterial({ - // color: 0x0077ff, - // metalness: 0.3, - // roughness: 0.5, - // clearcoat: 0.5, // Adds extra reflection - // side: THREE.DoubleSide, - // }); - - // const material = new THREE.MeshNormalMaterial({ side: THREE.DoubleSide }); - - // material.transparent = true; - const mesh = new THREE.Mesh(geometry, material); - mesh.receiveShadow = true; - mesh.castShadow = true; - return mesh; -} - class SceneController { skeletons: Record = {}; current: number; @@ -731,16 +476,7 @@ class SceneController { let objs: THREE.Object3D[] = []; try { - if (WkDevFlags.splittingStrategy === "tps") { - objs = computeBentSurfaceTPS(points); - } else if (WkDevFlags.splittingStrategy === "splines") { - objs = computeBentSurfaceSplines(points); - } else if (WkDevFlags.splittingStrategy === "delauny") { - objs = computeBentSurfaceDelauny(points); - } else { - Toast.error("Unknown splitting strategy. Use tps or splines or delauny"); - return () => {}; - } + objs = computeBentSurfaceSplines(points); } catch (exc) { console.error(exc); Toast.error("Could not compute surface"); diff --git a/frontend/javascripts/oxalis/controller/splitting_stuff.ts b/frontend/javascripts/oxalis/controller/splitting_stuff.ts index 15c79b505b7..c835f54e03b 100644 --- a/frontend/javascripts/oxalis/controller/splitting_stuff.ts +++ b/frontend/javascripts/oxalis/controller/splitting_stuff.ts @@ -108,21 +108,3 @@ export function orderPointsMST(points: THREE.Vector3[]): THREE.Vector3[] { return bestOrder.map((index) => points[index]); } - -export function enforceConsistentDirection(points: THREE.Vector3[]): THREE.Vector3[] { - if (points.length < 2) return points; - - const first = points[0]; - const last = points[points.length - 1]; - - // Check if the curve follows top-left → bottom-right order - const dx = last.x - first.x; - const dy = last.y - first.y; - const maxDelta = Math.abs(dx) > Math.abs(dy) ? dx : dy; - - if (maxDelta < 0) { - // The curve is flipped (going bottom-right → top-left), so reverse it - return points.reverse(); - } - return points; -} diff --git a/frontend/javascripts/oxalis/model/sagas/bent_surface_saga.ts b/frontend/javascripts/oxalis/model/sagas/bent_surface_saga.ts index 10452700aa3..5bfdef44022 100644 --- a/frontend/javascripts/oxalis/model/sagas/bent_surface_saga.ts +++ b/frontend/javascripts/oxalis/model/sagas/bent_surface_saga.ts @@ -1,12 +1,12 @@ import getSceneController from "oxalis/controller/scene_controller_provider"; import type { Saga } from "oxalis/model/sagas/effect-generators"; import { select } from "oxalis/model/sagas/effect-generators"; +import type { ActionPattern } from "redux-saga/effects"; import { call, takeEvery } from "typed-redux-saga"; import { getActiveTree } from "../accessors/skeletontracing_accessor"; +import type { Action } from "../actions/actions"; import { ensureWkReady } from "./ready_sagas"; import { takeWithBatchActionSupport } from "./saga_helpers"; -import type { Action } from "../actions/actions"; -import type { ActionPattern } from "redux-saga/effects"; let cleanUpFn: (() => void) | null = null; diff --git a/package.json b/package.json index 71c8bc1fa33..098cb8d052b 100644 --- a/package.json +++ b/package.json @@ -15,7 +15,6 @@ "@types/color-hash": "^1.0.2", "@types/cwise": "^1.0.4", "@types/dagre": "^0.7.48", - "@types/delaunator": "^5", "@types/file-saver": "^2.0.5", "@types/lodash": "^4.17.4", "@types/lz-string": "^1.3.34", @@ -159,7 +158,6 @@ "dayjs": "^1.11.13", "deep-for-each": "^2.0.3", "deep-freeze": "0.0.1", - "delaunator": "^5.0.1", "dice-coefficient": "^2.1.0", "distance-transform": "^1.0.2", "esbuild-loader": "^4.1.0", @@ -185,7 +183,6 @@ "ndarray-moments": "^1.0.0", "ndarray-ops": "^1.2.2", "pako": "^2.1.0", - "pca-js": "^1.0.2", "pretty-bytes": "^5.1.0", "process": "^0.11.10", "protobufjs": "^6.11.4", diff --git a/yarn.lock b/yarn.lock index ebf2c3ddf1c..a25e7e86899 100644 --- a/yarn.lock +++ b/yarn.lock @@ -2394,13 +2394,6 @@ __metadata: languageName: node linkType: hard -"@types/delaunator@npm:^5": - version: 5.0.3 - resolution: "@types/delaunator@npm:5.0.3" - checksum: 10c0/4d6a5be512a382f6b7185e372d0569635a4877e1d04b90c86ce48ad3270f04bf944e0edf4ea6810bf2e65aacc3c52ee836ab7c329bcad3f3478375c5ed0a3611 - languageName: node - linkType: hard - "@types/eslint-scope@npm:^3.7.3": version: 3.7.3 resolution: "@types/eslint-scope@npm:3.7.3" @@ -5314,15 +5307,6 @@ __metadata: languageName: node linkType: hard -"delaunator@npm:^5.0.1": - version: 5.0.1 - resolution: "delaunator@npm:5.0.1" - dependencies: - robust-predicates: "npm:^3.0.2" - checksum: 10c0/3d7ea4d964731c5849af33fec0a271bc6753487b331fd7d43ccb17d77834706e1c383e6ab8fda0032da955e7576d1083b9603cdaf9cbdfd6b3ebd1fb8bb675a5 - languageName: node - linkType: hard - "delayed-stream@npm:~1.0.0": version: 1.0.0 resolution: "delayed-stream@npm:1.0.0" @@ -10566,13 +10550,6 @@ __metadata: languageName: node linkType: hard -"pca-js@npm:^1.0.2": - version: 1.0.2 - resolution: "pca-js@npm:1.0.2" - checksum: 10c0/65daa653d338959e588890bef631ce313da593722bff0e9e16dcc0428fa37d181c59662d17893a75118535f90ddd61576533ad27794d6346e15049ffbdda77c4 - languageName: node - linkType: hard - "pend@npm:~1.2.0": version: 1.2.0 resolution: "pend@npm:1.2.0" @@ -12578,13 +12555,6 @@ __metadata: languageName: node linkType: hard -"robust-predicates@npm:^3.0.2": - version: 3.0.2 - resolution: "robust-predicates@npm:3.0.2" - checksum: 10c0/4ecd53649f1c2d49529c85518f2fa69ffb2f7a4453f7fd19c042421c7b4d76c3efb48bc1c740c8f7049346d7cb58cf08ee0c9adaae595cc23564d360adb1fde4 - languageName: node - linkType: hard - "rrweb-cssom@npm:^0.6.0": version: 0.6.0 resolution: "rrweb-cssom@npm:0.6.0" @@ -14691,7 +14661,6 @@ __metadata: "@types/color-hash": "npm:^1.0.2" "@types/cwise": "npm:^1.0.4" "@types/dagre": "npm:^0.7.48" - "@types/delaunator": "npm:^5" "@types/file-saver": "npm:^2.0.5" "@types/lodash": "npm:^4.17.4" "@types/lz-string": "npm:^1.3.34" @@ -14733,7 +14702,6 @@ __metadata: dayjs: "npm:^1.11.13" deep-for-each: "npm:^2.0.3" deep-freeze: "npm:0.0.1" - delaunator: "npm:^5.0.1" dependency-cruiser: "npm:^16.10.0" dice-coefficient: "npm:^2.1.0" distance-transform: "npm:^1.0.2" @@ -14775,7 +14743,6 @@ __metadata: ndarray-ops: "npm:^1.2.2" node-fetch: "npm:^2.6.7" pako: "npm:^2.1.0" - pca-js: "npm:^1.0.2" pg: "npm:^7.4.1" pixelmatch: "npm:^5.2.0" pngjs: "npm:^3.3.3" From 0c6ae1bee5be66e046106103e0a9460367d310f7 Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Wed, 9 Apr 2025 17:41:16 +0200 Subject: [PATCH 18/84] don't show edges if tree was created in split-workspace; more clean up --- .../oxalis/controller/scene_controller.ts | 48 ++++++++++++------- .../model/bucket_data_handling/data_cube.ts | 12 +++-- .../model/reducers/skeletontracing_reducer.ts | 10 +++- .../oxalis/model/sagas/bent_surface_saga.ts | 2 +- .../oxalis/view/action-bar/toolbar_view.tsx | 1 + 5 files changed, 50 insertions(+), 23 deletions(-) diff --git a/frontend/javascripts/oxalis/controller/scene_controller.ts b/frontend/javascripts/oxalis/controller/scene_controller.ts index a1f69e730ba..57abb4e2bd2 100644 --- a/frontend/javascripts/oxalis/controller/scene_controller.ts +++ b/frontend/javascripts/oxalis/controller/scene_controller.ts @@ -71,8 +71,11 @@ THREE.BatchedMesh.prototype.computeBoundsTree = computeBatchedBoundsTree; THREE.BatchedMesh.prototype.disposeBoundsTree = disposeBatchedBoundsTree; THREE.BatchedMesh.prototype.raycast = acceleratedRaycast; -function computeBentSurfaceSplines(points: Vector3[]): THREE.Object3D[] { - const objects: THREE.Object3D[] = []; +function computeBentSurfaceSplines(points: Vector3[]): { + splines: THREE.Object3D[]; + surfaceMesh: THREE.Mesh; +} { + const splines: THREE.Object3D[] = []; const unfilteredPointsByZ = _.groupBy(points, (p) => p[2]); const pointsByZ = _.omitBy(unfilteredPointsByZ, (value) => value.length < 2); @@ -91,9 +94,9 @@ function computeBentSurfaceSplines(points: Vector3[]): THREE.Object3D[] { zValues.map((zValue, curveIdx) => { let adaptedZ = zValue; if (zValue === minZ) { - adaptedZ -= 0.5; + adaptedZ -= 0.1; } else if (zValue === maxZ) { - adaptedZ += 0.5; + adaptedZ += 0.1; } const points2D = orderPointsMST( pointsByZ[zValue].map((p) => new THREE.Vector3(p[0], p[1], adaptedZ)), @@ -169,7 +172,7 @@ function computeBentSurfaceSplines(points: Vector3[]): THREE.Object3D[] { const geometry = new THREE.BufferGeometry().setFromPoints(curvePoints); const material = new THREE.LineBasicMaterial({ color: 0xff0000 }); const splineObject = new THREE.Line(geometry, material); - objects.push(splineObject); + splines.push(splineObject); }); // Generate grid of points @@ -229,10 +232,10 @@ function computeBentSurfaceSplines(points: Vector3[]): THREE.Object3D[] { wireframe: false, }); const surfaceMesh = new THREE.Mesh(geometry, material); - window.bentMesh = surfaceMesh; - - objects.push(surfaceMesh); - return objects; + return { + splines, + surfaceMesh, + }; } class SceneController { @@ -261,6 +264,7 @@ class SceneController { // meshesRootGroup!: THREE.Object3D; segmentMeshController: SegmentMeshController; storePropertyUnsubscribers: Array<() => void>; + surfaceMesh: THREE.Mesh | null = null; // This class collects all the meshes displayed in the Skeleton View and updates position and scale of each // element depending on the provided flycam. @@ -474,9 +478,12 @@ class SceneController { return () => {}; } - let objs: THREE.Object3D[] = []; + let surfaceMesh: THREE.Mesh | null = null; + let splines: THREE.Object3D[] = []; try { - objs = computeBentSurfaceSplines(points); + const objects = computeBentSurfaceSplines(points); + surfaceMesh = objects.surfaceMesh; + splines = objects.splines; } catch (exc) { console.error(exc); Toast.error("Could not compute surface"); @@ -484,18 +491,26 @@ class SceneController { } const surfaceGroup = new THREE.Group(); - for (const obj of objs) { - surfaceGroup.add(obj); + if (surfaceMesh != null) { + surfaceGroup.add(surfaceMesh); + } + for (const spline of splines) { + surfaceGroup.add(spline); } this.rootGroup.add(surfaceGroup); - // surfaceGroup.scale.copy(new THREE.Vector3(...Store.getState().dataset.dataSource.scale.factor)); + this.surfaceMesh = surfaceMesh; return () => { this.rootGroup.remove(surfaceGroup); + this.surfaceMesh = null; }; } + getBentSurface() { + return this.surfaceMesh; + } + addSkeleton( skeletonTracingSelector: (arg0: OxalisState) => Maybe, supportsPicking: boolean, @@ -561,9 +576,8 @@ class SceneController { this.taskBoundingBox?.updateForCam(id); this.segmentMeshController.meshesLODRootGroup.visible = id === OrthoViews.TDView; - // todop - if (window.bentMesh != null) { - window.bentMesh.visible = id === OrthoViews.TDView; + if (this.surfaceMesh != null) { + this.surfaceMesh.visible = id === OrthoViews.TDView; } // this.segmentMeshController.meshesLODRootGroup.visible = false; this.annotationToolsGeometryGroup.visible = id !== OrthoViews.TDView; diff --git a/frontend/javascripts/oxalis/model/bucket_data_handling/data_cube.ts b/frontend/javascripts/oxalis/model/bucket_data_handling/data_cube.ts index 3330356ba78..dfe22fef7ce 100644 --- a/frontend/javascripts/oxalis/model/bucket_data_handling/data_cube.ts +++ b/frontend/javascripts/oxalis/model/bucket_data_handling/data_cube.ts @@ -36,6 +36,7 @@ import * as THREE from "three"; import type { AdditionalAxis, BucketDataArray, ElementClass } from "types/api_flow_types"; import type { AdditionalCoordinate } from "types/api_flow_types"; import type { MagInfo } from "../helpers/mag_info"; +import getSceneController from "oxalis/controller/scene_controller_provider"; const warnAboutTooManyAllocations = _.once(() => { const msg = @@ -542,6 +543,9 @@ class DataCube { // not all of the target area in the neighbour bucket might be filled. const floodfillBoundingBox = new BoundingBox(_floodfillBoundingBox); + const sceneController = getSceneController(); + const isSplitWorkspace = Store.getState().userConfiguration.toolWorkspace === "SPLIT_SEGMENTS"; + const splitBoundaryMesh = isSplitWorkspace ? sceneController.getBentSurface() : null; // Helper function to convert between xyz and uvw (both directions) const transpose = (voxel: Vector3): Vector3 => @@ -726,13 +730,13 @@ class DataCube { const neighbourBucket = this.getOrCreateBucket(neighbourBucketAddress); let shouldSkip = false; - if (window.bentMesh) { + if (splitBoundaryMesh) { const currentGlobalPosition = V3.add( currentGlobalBucketPosition, V3.scale3(neighbourVoxelXyz, currentMag), ); const intersects = checkLineIntersection( - window.bentMesh, + splitBoundaryMesh, originGlobalPosition, currentGlobalPosition, ); @@ -758,9 +762,9 @@ class DataCube { }); let shouldSkip = false; - if (window.bentMesh) { + if (splitBoundaryMesh) { const intersects = checkLineIntersection( - window.bentMesh, + splitBoundaryMesh, originGlobalPosition, currentGlobalPosition, ); diff --git a/frontend/javascripts/oxalis/model/reducers/skeletontracing_reducer.ts b/frontend/javascripts/oxalis/model/reducers/skeletontracing_reducer.ts index b7c387be0b6..bd16d16c6e7 100644 --- a/frontend/javascripts/oxalis/model/reducers/skeletontracing_reducer.ts +++ b/frontend/javascripts/oxalis/model/reducers/skeletontracing_reducer.ts @@ -828,7 +828,15 @@ function SkeletonTracingReducer(state: OxalisState, action: Action): OxalisState case "CREATE_TREE": { const { timestamp } = action; - return createTree(state, timestamp) + const isSplitWorkspaceActive = state.userConfiguration.toolWorkspace === "SPLIT_SEGMENTS"; + return createTree( + state, + timestamp, + undefined, + undefined, + undefined, + isSplitWorkspaceActive, + ) .map((tree) => { if (action.treeIdCallback) { action.treeIdCallback(tree.treeId); diff --git a/frontend/javascripts/oxalis/model/sagas/bent_surface_saga.ts b/frontend/javascripts/oxalis/model/sagas/bent_surface_saga.ts index 5bfdef44022..8d7b40b5782 100644 --- a/frontend/javascripts/oxalis/model/sagas/bent_surface_saga.ts +++ b/frontend/javascripts/oxalis/model/sagas/bent_surface_saga.ts @@ -30,7 +30,6 @@ function* updateBentSurface() { if (activeTree != null && activeTree.isVisible) { const nodes = Array.from(activeTree.nodes.values()); const points = nodes.map((node) => node.untransformedPosition); - console.log("points", points); if (points.length > 3) { cleanUpFn = sceneController.addBentSurface(points); } @@ -50,6 +49,7 @@ export function* bentSurfaceSaga(): Saga { "SET_ACTIVE_TREE_BY_NAME", "CREATE_NODE", "DELETE_NODE", + "DELETE_TREE", "SET_TREE_VISIBILITY", "TOGGLE_TREE", "SET_NODE_POSITION", diff --git a/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx b/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx index bd791a5c8cf..28e15b69bb7 100644 --- a/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx +++ b/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx @@ -58,6 +58,7 @@ import { updateUserSettingAction } from "oxalis/model/actions/settings_actions"; import { createTreeAction, setMergerModeEnabledAction, + setTreeEdgeVisibilityAction, } from "oxalis/model/actions/skeletontracing_actions"; import { setToolAction, showQuickSelectSettingsAction } from "oxalis/model/actions/ui_actions"; import { From 92c7c18a69a361c02f4af64b92e8fe5430a303bf Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Wed, 9 Apr 2025 17:48:49 +0200 Subject: [PATCH 19/84] rename some stuff --- ...ompute_split_boundary_mesh_with_splines.ts | 279 ++++++++++++++++++ .../oxalis/controller/scene_controller.ts | 195 +----------- .../oxalis/controller/splitting_stuff.ts | 110 ------- .../model/bucket_data_handling/data_cube.ts | 2 +- .../oxalis/model/sagas/root_saga.ts | 4 +- ...ce_saga.ts => split_boundary_mesh_saga.ts} | 12 +- .../view/action-bar/tool_workspace_view.tsx | 63 ++++ 7 files changed, 365 insertions(+), 300 deletions(-) create mode 100644 frontend/javascripts/oxalis/controller/compute_split_boundary_mesh_with_splines.ts delete mode 100644 frontend/javascripts/oxalis/controller/splitting_stuff.ts rename frontend/javascripts/oxalis/model/sagas/{bent_surface_saga.ts => split_boundary_mesh_saga.ts} (87%) create mode 100644 frontend/javascripts/oxalis/view/action-bar/tool_workspace_view.tsx diff --git a/frontend/javascripts/oxalis/controller/compute_split_boundary_mesh_with_splines.ts b/frontend/javascripts/oxalis/controller/compute_split_boundary_mesh_with_splines.ts new file mode 100644 index 00000000000..e3725735166 --- /dev/null +++ b/frontend/javascripts/oxalis/controller/compute_split_boundary_mesh_with_splines.ts @@ -0,0 +1,279 @@ +import _ from "lodash"; +import * as THREE from "three"; +import type { Vector3 } from "oxalis/constants"; + +export default function computeSplitBoundaryMeshWithSplines(points: Vector3[]): { + splines: THREE.Object3D[]; + splitBoundaryMesh: THREE.Mesh; +} { + const splines: THREE.Object3D[] = []; + + const unfilteredPointsByZ = _.groupBy(points, (p) => p[2]); + const pointsByZ = _.omitBy(unfilteredPointsByZ, (value) => value.length < 2); + + const zValues = Object.keys(pointsByZ) + .map((el) => Number(el)) + .sort(); + + const minZ = Math.min(...zValues); + const maxZ = Math.max(...zValues); + + const curvesByZ: Record = {}; + + // Create curves for existing z-values + const curves = _.compact( + zValues.map((zValue, curveIdx) => { + let adaptedZ = zValue; + if (zValue === minZ) { + adaptedZ -= 0.1; + } else if (zValue === maxZ) { + adaptedZ += 0.1; + } + const points2D = orderPointsMST( + pointsByZ[zValue].map((p) => new THREE.Vector3(p[0], p[1], adaptedZ)), + ); + + if (points2D.length < 2) { + return null; + } + + if (curveIdx > 0) { + const currentCurvePoints = points2D; + const prevCurvePoints = curvesByZ[zValues[curveIdx - 1]].points; + + const distActual = currentCurvePoints[0].distanceTo(prevCurvePoints[0]); + const distFlipped = (currentCurvePoints.at(-1) as THREE.Vector3).distanceTo( + prevCurvePoints[0], + ); + + const shouldFlip = distFlipped < distActual; + if (shouldFlip) { + points2D.reverse(); + } + } + + const curve = new THREE.CatmullRomCurve3(points2D); + curvesByZ[zValue] = curve; + return curve; + }), + ); + + // Number of points per curve + const numPoints = 50; + + // Sort z-values for interpolation + const sortedZValues = Object.keys(curvesByZ) + .map(Number) + .sort((a, b) => a - b); + + // Interpolate missing z-values + for (let z = minZ; z <= maxZ; z++) { + if (curvesByZ[z]) continue; // Skip if curve already exists + + // Find nearest lower and upper z-values + const lowerZ = Math.max(...sortedZValues.filter((v) => v < z)); + const upperZ = Math.min(...sortedZValues.filter((v) => v > z)); + + if (lowerZ === Number.NEGATIVE_INFINITY || upperZ === Number.POSITIVE_INFINITY) continue; + + // Get the two adjacent curves and sample 50 points from each + const lowerCurvePoints = curvesByZ[lowerZ].getPoints(numPoints); + const upperCurvePoints = curvesByZ[upperZ].getPoints(numPoints); + + // Interpolate between corresponding points + const interpolatedPoints = lowerCurvePoints.map((lowerPoint, i) => { + const upperPoint = upperCurvePoints[i]; + const alpha = (z - lowerZ) / (upperZ - lowerZ); // Interpolation factor + + return new THREE.Vector3( + THREE.MathUtils.lerp(lowerPoint.x, upperPoint.x, alpha), + THREE.MathUtils.lerp(lowerPoint.y, upperPoint.y, alpha), + z, + ); + }); + + // Create the interpolated curve + const interpolatedCurve = new THREE.CatmullRomCurve3(interpolatedPoints); + curvesByZ[z] = interpolatedCurve; + } + + // Generate and display all curves + Object.values(curvesByZ).forEach((curve) => { + const curvePoints = curve.getPoints(50); + const geometry = new THREE.BufferGeometry().setFromPoints(curvePoints); + const material = new THREE.LineBasicMaterial({ color: 0xff0000 }); + const splineObject = new THREE.Line(geometry, material); + splines.push(splineObject); + }); + + // Generate grid of points + const gridPoints = curves.map((curve) => curve.getPoints(numPoints - 1)); + + // Flatten into a single array of vertices + const vertices: number[] = []; + const indices = []; + + gridPoints.forEach((row) => { + row.forEach((point) => { + vertices.push(point.x, point.y, point.z); // Store as flat array for BufferGeometry + }); + }); + + // Connect vertices with triangles + // console.group("Computing indices"); + for (let i = 0; i < curves.length - 1; i++) { + // console.group("Curve i=" + i); + for (let j = 0; j < numPoints - 1; j++) { + // console.group("Point j=" + j); + let current = i * numPoints + j; + let next = (i + 1) * numPoints + j; + + // const printFace = (x, y, z) => { + // return [vertices[3 * x], vertices[3 * y], vertices[3 * z]]; + // }; + + // console.log("Creating faces with", { current, next }); + // console.log("First face:", printFace(current, next, current + 1)); + // console.log("Second face:", printFace(next, next + 1, current + 1)); + // Two triangles per quad + indices.push(current, next, current + 1); + indices.push(next, next + 1, current + 1); + // console.groupEnd(); + } + // console.groupEnd(); + } + // console.groupEnd(); + + // Convert to Three.js BufferGeometry + const geometry = new THREE.BufferGeometry(); + geometry.setAttribute("position", new THREE.Float32BufferAttribute(vertices, 3)); + geometry.setIndex(indices); + geometry.computeVertexNormals(); // Smooth shading + geometry.computeBoundsTree(); + + // Material and Mesh + const material = new THREE.MeshStandardMaterial({ + color: 0x0077ff, // A soft blue color + metalness: 0.5, // Slight metallic effect + roughness: 1, // Some surface roughness for a natural look + side: THREE.DoubleSide, // Render both sides + flatShading: false, // Ensures smooth shading with computed normals + opacity: 0.8, + transparent: true, + wireframe: false, + }); + const splitBoundaryMesh = new THREE.Mesh(geometry, material); + return { + splines, + splitBoundaryMesh, + }; +} + +class DisjointSet { + private parent: number[]; + private rank: number[]; + + constructor(n: number) { + this.parent = Array.from({ length: n }, (_, i) => i); + this.rank = Array(n).fill(0); + } + + find(i: number): number { + if (this.parent[i] !== i) this.parent[i] = this.find(this.parent[i]); + return this.parent[i]; + } + + union(i: number, j: number): void { + let rootI = this.find(i), + rootJ = this.find(j); + if (rootI !== rootJ) { + if (this.rank[rootI] > this.rank[rootJ]) this.parent[rootJ] = rootI; + else if (this.rank[rootI] < this.rank[rootJ]) this.parent[rootI] = rootJ; + else { + this.parent[rootJ] = rootI; + this.rank[rootI]++; + } + } + } +} + +interface Edge { + i: number; + j: number; + dist: number; +} + +function computeMST(points: THREE.Vector3[]): number[][] { + const edges: Edge[] = []; + const numPoints = points.length; + + // Create all possible edges with distances + for (let i = 0; i < numPoints; i++) { + for (let j = i + 1; j < numPoints; j++) { + const dist = points[i].distanceTo(points[j]); + edges.push({ i, j, dist }); + } + } + + // Sort edges by distance (Kruskal's Algorithm) + edges.sort((a, b) => a.dist - b.dist); + + // Compute MST using Kruskal’s Algorithm + const ds = new DisjointSet(numPoints); + const mst: number[][] = Array.from({ length: numPoints }, () => []); + + for (const { i, j } of edges) { + if (ds.find(i) !== ds.find(j)) { + ds.union(i, j); + mst[i].push(j); + mst[j].push(i); + } + } + + return mst; +} + +function traverseMstDfs(mst: number[][], startIdx = 0): number[] { + const visited = new Set(); + const orderedPoints: number[] = []; + + function dfs(node: number) { + if (visited.has(node)) return; + visited.add(node); + orderedPoints.push(node); + for (let neighbor of mst[node]) { + dfs(neighbor); + } + } + + dfs(startIdx); + return orderedPoints; +} + +function computePathLength(points: THREE.Vector3[], order: number[]): number { + let length = 0; + for (let i = 0; i < order.length - 1; i++) { + length += points[order[i]].distanceTo(points[order[i + 1]]); + } + return length; +} + +export function orderPointsMST(points: THREE.Vector3[]): THREE.Vector3[] { + if (points.length === 0) return []; + + const mst = computeMST(points); + let bestOrder: number[] = []; + let minLength = Number.POSITIVE_INFINITY; + + for (let startIdx = 0; startIdx < points.length; startIdx++) { + const order = traverseMstDfs(mst, startIdx); + const length = computePathLength(points, order); + + if (length < minLength) { + minLength = length; + bestOrder = order; + } + } + + return bestOrder.map((index) => points[index]); +} diff --git a/frontend/javascripts/oxalis/controller/scene_controller.ts b/frontend/javascripts/oxalis/controller/scene_controller.ts index 57abb4e2bd2..bc8629e601f 100644 --- a/frontend/javascripts/oxalis/controller/scene_controller.ts +++ b/frontend/javascripts/oxalis/controller/scene_controller.ts @@ -52,7 +52,6 @@ import SegmentMeshController from "./segment_mesh_controller"; const CUBE_COLOR = 0x999999; const LAYER_CUBE_COLOR = 0xffff99; -import { orderPointsMST } from "./splitting_stuff"; import { acceleratedRaycast, @@ -61,6 +60,7 @@ import { disposeBatchedBoundsTree, disposeBoundsTree, } from "three-mesh-bvh"; +import computeSplitBoundaryMeshWithSplines from "./compute_split_boundary_mesh_with_splines"; // Add the extension functions THREE.BufferGeometry.prototype.computeBoundsTree = computeBoundsTree; @@ -71,173 +71,6 @@ THREE.BatchedMesh.prototype.computeBoundsTree = computeBatchedBoundsTree; THREE.BatchedMesh.prototype.disposeBoundsTree = disposeBatchedBoundsTree; THREE.BatchedMesh.prototype.raycast = acceleratedRaycast; -function computeBentSurfaceSplines(points: Vector3[]): { - splines: THREE.Object3D[]; - surfaceMesh: THREE.Mesh; -} { - const splines: THREE.Object3D[] = []; - - const unfilteredPointsByZ = _.groupBy(points, (p) => p[2]); - const pointsByZ = _.omitBy(unfilteredPointsByZ, (value) => value.length < 2); - - const zValues = Object.keys(pointsByZ) - .map((el) => Number(el)) - .sort(); - - const minZ = Math.min(...zValues); - const maxZ = Math.max(...zValues); - - const curvesByZ: Record = {}; - - // Create curves for existing z-values - const curves = _.compact( - zValues.map((zValue, curveIdx) => { - let adaptedZ = zValue; - if (zValue === minZ) { - adaptedZ -= 0.1; - } else if (zValue === maxZ) { - adaptedZ += 0.1; - } - const points2D = orderPointsMST( - pointsByZ[zValue].map((p) => new THREE.Vector3(p[0], p[1], adaptedZ)), - ); - - if (points2D.length < 2) { - return null; - } - - if (curveIdx > 0) { - const currentCurvePoints = points2D; - const prevCurvePoints = curvesByZ[zValues[curveIdx - 1]].points; - - const distActual = currentCurvePoints[0].distanceTo(prevCurvePoints[0]); - const distFlipped = (currentCurvePoints.at(-1) as THREE.Vector3).distanceTo( - prevCurvePoints[0], - ); - - const shouldFlip = distFlipped < distActual; - if (shouldFlip) { - points2D.reverse(); - } - } - - const curve = new THREE.CatmullRomCurve3(points2D); - curvesByZ[zValue] = curve; - return curve; - }), - ); - - // Number of points per curve - const numPoints = 50; - - // Sort z-values for interpolation - const sortedZValues = Object.keys(curvesByZ) - .map(Number) - .sort((a, b) => a - b); - - // Interpolate missing z-values - for (let z = minZ; z <= maxZ; z++) { - if (curvesByZ[z]) continue; // Skip if curve already exists - - // Find nearest lower and upper z-values - const lowerZ = Math.max(...sortedZValues.filter((v) => v < z)); - const upperZ = Math.min(...sortedZValues.filter((v) => v > z)); - - if (lowerZ === Number.NEGATIVE_INFINITY || upperZ === Number.POSITIVE_INFINITY) continue; - - // Get the two adjacent curves and sample 50 points from each - const lowerCurvePoints = curvesByZ[lowerZ].getPoints(numPoints); - const upperCurvePoints = curvesByZ[upperZ].getPoints(numPoints); - - // Interpolate between corresponding points - const interpolatedPoints = lowerCurvePoints.map((lowerPoint, i) => { - const upperPoint = upperCurvePoints[i]; - const alpha = (z - lowerZ) / (upperZ - lowerZ); // Interpolation factor - - return new THREE.Vector3( - THREE.MathUtils.lerp(lowerPoint.x, upperPoint.x, alpha), - THREE.MathUtils.lerp(lowerPoint.y, upperPoint.y, alpha), - z, - ); - }); - - // Create the interpolated curve - const interpolatedCurve = new THREE.CatmullRomCurve3(interpolatedPoints); - curvesByZ[z] = interpolatedCurve; - } - - // Generate and display all curves - Object.values(curvesByZ).forEach((curve) => { - const curvePoints = curve.getPoints(50); - const geometry = new THREE.BufferGeometry().setFromPoints(curvePoints); - const material = new THREE.LineBasicMaterial({ color: 0xff0000 }); - const splineObject = new THREE.Line(geometry, material); - splines.push(splineObject); - }); - - // Generate grid of points - const gridPoints = curves.map((curve) => curve.getPoints(numPoints - 1)); - - // Flatten into a single array of vertices - const vertices: number[] = []; - const indices = []; - - gridPoints.forEach((row) => { - row.forEach((point) => { - vertices.push(point.x, point.y, point.z); // Store as flat array for BufferGeometry - }); - }); - - // Connect vertices with triangles - // console.group("Computing indices"); - for (let i = 0; i < curves.length - 1; i++) { - // console.group("Curve i=" + i); - for (let j = 0; j < numPoints - 1; j++) { - // console.group("Point j=" + j); - let current = i * numPoints + j; - let next = (i + 1) * numPoints + j; - - // const printFace = (x, y, z) => { - // return [vertices[3 * x], vertices[3 * y], vertices[3 * z]]; - // }; - - // console.log("Creating faces with", { current, next }); - // console.log("First face:", printFace(current, next, current + 1)); - // console.log("Second face:", printFace(next, next + 1, current + 1)); - // Two triangles per quad - indices.push(current, next, current + 1); - indices.push(next, next + 1, current + 1); - // console.groupEnd(); - } - // console.groupEnd(); - } - // console.groupEnd(); - - // Convert to Three.js BufferGeometry - const geometry = new THREE.BufferGeometry(); - geometry.setAttribute("position", new THREE.Float32BufferAttribute(vertices, 3)); - geometry.setIndex(indices); - geometry.computeVertexNormals(); // Smooth shading - geometry.computeBoundsTree(); - - // Material and Mesh - const material = new THREE.MeshStandardMaterial({ - color: 0x0077ff, // A soft blue color - metalness: 0.5, // Slight metallic effect - roughness: 1, // Some surface roughness for a natural look - side: THREE.DoubleSide, // Render both sides - flatShading: false, // Ensures smooth shading with computed normals - opacity: 0.8, - transparent: true, - wireframe: false, - }); - const surfaceMesh = new THREE.Mesh(geometry, material); - return { - splines, - surfaceMesh, - }; -} - class SceneController { skeletons: Record = {}; current: number; @@ -264,7 +97,7 @@ class SceneController { // meshesRootGroup!: THREE.Object3D; segmentMeshController: SegmentMeshController; storePropertyUnsubscribers: Array<() => void>; - surfaceMesh: THREE.Mesh | null = null; + splitBoundaryMesh: THREE.Mesh | null = null; // This class collects all the meshes displayed in the Skeleton View and updates position and scale of each // element depending on the provided flycam. @@ -473,16 +306,16 @@ class SceneController { this.stopPlaneMode(); } - addBentSurface(points: Vector3[]) { + addSplitBoundaryMesh(points: Vector3[]) { if (points.length === 0) { return () => {}; } - let surfaceMesh: THREE.Mesh | null = null; + let splitBoundaryMesh: THREE.Mesh | null = null; let splines: THREE.Object3D[] = []; try { - const objects = computeBentSurfaceSplines(points); - surfaceMesh = objects.surfaceMesh; + const objects = computeSplitBoundaryMeshWithSplines(points); + splitBoundaryMesh = objects.splitBoundaryMesh; splines = objects.splines; } catch (exc) { console.error(exc); @@ -491,24 +324,24 @@ class SceneController { } const surfaceGroup = new THREE.Group(); - if (surfaceMesh != null) { - surfaceGroup.add(surfaceMesh); + if (splitBoundaryMesh != null) { + surfaceGroup.add(splitBoundaryMesh); } for (const spline of splines) { surfaceGroup.add(spline); } this.rootGroup.add(surfaceGroup); - this.surfaceMesh = surfaceMesh; + this.splitBoundaryMesh = splitBoundaryMesh; return () => { this.rootGroup.remove(surfaceGroup); - this.surfaceMesh = null; + this.splitBoundaryMesh = null; }; } - getBentSurface() { - return this.surfaceMesh; + getSplitBoundaryMesh() { + return this.splitBoundaryMesh; } addSkeleton( @@ -576,8 +409,8 @@ class SceneController { this.taskBoundingBox?.updateForCam(id); this.segmentMeshController.meshesLODRootGroup.visible = id === OrthoViews.TDView; - if (this.surfaceMesh != null) { - this.surfaceMesh.visible = id === OrthoViews.TDView; + if (this.splitBoundaryMesh != null) { + this.splitBoundaryMesh.visible = id === OrthoViews.TDView; } // this.segmentMeshController.meshesLODRootGroup.visible = false; this.annotationToolsGeometryGroup.visible = id !== OrthoViews.TDView; diff --git a/frontend/javascripts/oxalis/controller/splitting_stuff.ts b/frontend/javascripts/oxalis/controller/splitting_stuff.ts deleted file mode 100644 index c835f54e03b..00000000000 --- a/frontend/javascripts/oxalis/controller/splitting_stuff.ts +++ /dev/null @@ -1,110 +0,0 @@ -import type * as THREE from "three"; - -class DisjointSet { - private parent: number[]; - private rank: number[]; - - constructor(n: number) { - this.parent = Array.from({ length: n }, (_, i) => i); - this.rank = Array(n).fill(0); - } - - find(i: number): number { - if (this.parent[i] !== i) this.parent[i] = this.find(this.parent[i]); - return this.parent[i]; - } - - union(i: number, j: number): void { - let rootI = this.find(i), - rootJ = this.find(j); - if (rootI !== rootJ) { - if (this.rank[rootI] > this.rank[rootJ]) this.parent[rootJ] = rootI; - else if (this.rank[rootI] < this.rank[rootJ]) this.parent[rootI] = rootJ; - else { - this.parent[rootJ] = rootI; - this.rank[rootI]++; - } - } - } -} - -interface Edge { - i: number; - j: number; - dist: number; -} - -function computeMST(points: THREE.Vector3[]): number[][] { - const edges: Edge[] = []; - const numPoints = points.length; - - // Create all possible edges with distances - for (let i = 0; i < numPoints; i++) { - for (let j = i + 1; j < numPoints; j++) { - const dist = points[i].distanceTo(points[j]); - edges.push({ i, j, dist }); - } - } - - // Sort edges by distance (Kruskal's Algorithm) - edges.sort((a, b) => a.dist - b.dist); - - // Compute MST using Kruskal’s Algorithm - const ds = new DisjointSet(numPoints); - const mst: number[][] = Array.from({ length: numPoints }, () => []); - - for (const { i, j } of edges) { - if (ds.find(i) !== ds.find(j)) { - ds.union(i, j); - mst[i].push(j); - mst[j].push(i); - } - } - - return mst; -} - -function traverseMST_DFS(mst: number[][], startIdx = 0): number[] { - const visited = new Set(); - const orderedPoints: number[] = []; - - function dfs(node: number) { - if (visited.has(node)) return; - visited.add(node); - orderedPoints.push(node); - for (let neighbor of mst[node]) { - dfs(neighbor); - } - } - - dfs(startIdx); - return orderedPoints; -} - -function computePathLength(points: THREE.Vector3[], order: number[]): number { - let length = 0; - for (let i = 0; i < order.length - 1; i++) { - length += points[order[i]].distanceTo(points[order[i + 1]]); - } - return length; -} - -export function orderPointsMST(points: THREE.Vector3[]): THREE.Vector3[] { - if (points.length === 0) return []; - - const mst = computeMST(points); - let bestOrder: number[] = []; - let minLength = Number.POSITIVE_INFINITY; - - for (let startIdx = 0; startIdx < points.length; startIdx++) { - const order = traverseMST_DFS(mst, startIdx); - const length = computePathLength(points, order); - - if (length < minLength) { - minLength = length; - bestOrder = order; - } - } - - return bestOrder.map((index) => points[index]); -} diff --git a/frontend/javascripts/oxalis/model/bucket_data_handling/data_cube.ts b/frontend/javascripts/oxalis/model/bucket_data_handling/data_cube.ts index dfe22fef7ce..b3a2af96dd7 100644 --- a/frontend/javascripts/oxalis/model/bucket_data_handling/data_cube.ts +++ b/frontend/javascripts/oxalis/model/bucket_data_handling/data_cube.ts @@ -545,7 +545,7 @@ class DataCube { const floodfillBoundingBox = new BoundingBox(_floodfillBoundingBox); const sceneController = getSceneController(); const isSplitWorkspace = Store.getState().userConfiguration.toolWorkspace === "SPLIT_SEGMENTS"; - const splitBoundaryMesh = isSplitWorkspace ? sceneController.getBentSurface() : null; + const splitBoundaryMesh = isSplitWorkspace ? sceneController.getSplitBoundaryMesh() : null; // Helper function to convert between xyz and uvw (both directions) const transpose = (voxel: Vector3): Vector3 => diff --git a/frontend/javascripts/oxalis/model/sagas/root_saga.ts b/frontend/javascripts/oxalis/model/sagas/root_saga.ts index f163ca7b8c9..971060c6ce7 100644 --- a/frontend/javascripts/oxalis/model/sagas/root_saga.ts +++ b/frontend/javascripts/oxalis/model/sagas/root_saga.ts @@ -21,7 +21,7 @@ import { race } from "redux-saga/effects"; import { all, call, cancel, fork, put, take, takeEvery } from "typed-redux-saga"; import type { EscalateErrorAction } from "../actions/actions"; import { setIsWkReadyAction } from "../actions/ui_actions"; -import bentSurfaceSaga from "./bent_surface_saga"; +import splitBoundaryMeshSaga from "./split_boundary_mesh_saga"; import maintainMaximumZoomForAllMagsSaga from "./flycam_info_cache_saga"; import { warnIfEmailIsUnverified } from "./user_saga"; @@ -83,7 +83,7 @@ function* restartableSaga(): Saga { call(handleAdditionalCoordinateUpdate), call(maintainMaximumZoomForAllMagsSaga), ...DatasetSagas.map((saga) => call(saga)), - call(bentSurfaceSaga), + call(splitBoundaryMeshSaga), ]); } catch (err) { rootSagaCrashed = true; diff --git a/frontend/javascripts/oxalis/model/sagas/bent_surface_saga.ts b/frontend/javascripts/oxalis/model/sagas/split_boundary_mesh_saga.ts similarity index 87% rename from frontend/javascripts/oxalis/model/sagas/bent_surface_saga.ts rename to frontend/javascripts/oxalis/model/sagas/split_boundary_mesh_saga.ts index 8d7b40b5782..973400a45f8 100644 --- a/frontend/javascripts/oxalis/model/sagas/bent_surface_saga.ts +++ b/frontend/javascripts/oxalis/model/sagas/split_boundary_mesh_saga.ts @@ -10,7 +10,7 @@ import { takeWithBatchActionSupport } from "./saga_helpers"; let cleanUpFn: (() => void) | null = null; -function* updateBentSurface() { +function* updateSplitBoundaryMesh() { if (cleanUpFn != null) { cleanUpFn(); cleanUpFn = null; @@ -31,18 +31,18 @@ function* updateBentSurface() { const nodes = Array.from(activeTree.nodes.values()); const points = nodes.map((node) => node.untransformedPosition); if (points.length > 3) { - cleanUpFn = sceneController.addBentSurface(points); + cleanUpFn = sceneController.addSplitBoundaryMesh(points); } } } -export function* bentSurfaceSaga(): Saga { +export function* splitBoundaryMeshSaga(): Saga { cleanUpFn = null; yield* takeWithBatchActionSupport("INITIALIZE_SKELETONTRACING"); yield* ensureWkReady(); // initial rendering - yield* call(updateBentSurface); + yield* call(updateSplitBoundaryMesh); yield* takeEvery( [ "SET_ACTIVE_TREE", @@ -56,8 +56,8 @@ export function* bentSurfaceSaga(): Saga { (action: Action) => action.type === "UPDATE_USER_SETTING" && action.propertyName === "toolWorkspace", ] as ActionPattern, - updateBentSurface, + updateSplitBoundaryMesh, ); } -export default bentSurfaceSaga; +export default splitBoundaryMeshSaga; diff --git a/frontend/javascripts/oxalis/view/action-bar/tool_workspace_view.tsx b/frontend/javascripts/oxalis/view/action-bar/tool_workspace_view.tsx new file mode 100644 index 00000000000..d1577256fd1 --- /dev/null +++ b/frontend/javascripts/oxalis/view/action-bar/tool_workspace_view.tsx @@ -0,0 +1,63 @@ +import { Button, Dropdown, type MenuProps } from "antd"; +import { + // setToolWorkspaceAction, + updateUserSettingAction, +} from "oxalis/model/actions/settings_actions"; +import { Store } from "oxalis/singletons"; +import type { ToolWorkspace } from "oxalis/store"; + +export default function ToolWorkspaceView() { + const toolWorkspaceItems: MenuProps["items"] = [ + { + key: "1", + type: "group", + label: "Select Workflow", + children: [ + { + label: "All Tools", + key: "ALL_TOOLS", + }, + { + label: "Read Only", + key: "READ_ONLY_TOOLS", + }, + { + label: "Volume", + key: "VOLUME_ANNOTATION", + }, + { + label: "Split Segments", + key: "SPLIT_SEGMENTS", + }, + ], + }, + ]; + + const handleMenuClick: MenuProps["onClick"] = (args) => { + const toolWorkspace = args.key; + Store.dispatch(updateUserSettingAction("toolWorkspace", toolWorkspace as ToolWorkspace)); + // Unfortunately, antd doesn't provide the original event here + // which is why we have to blur using document.activeElement. + // Additionally, we need a timeout since the blurring would be done + // to early, otherwise. + setTimeout(() => { + if (document.activeElement != null) { + // @ts-expect-error ts-migrate(2339) FIXME: Property 'blur' does not exist on type 'Element'. + document.activeElement.blur(); + } + }, 100); + }; + + const toolWorkspaceMenuProps = { + items: toolWorkspaceItems, + onClick: handleMenuClick, + }; + + return ( + + + + ); +} From 26a1c1b100df48d08abd35f0b46522b59146be44 Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Wed, 9 Apr 2025 17:49:18 +0200 Subject: [PATCH 20/84] linting --- .../controller/compute_split_boundary_mesh_with_splines.ts | 2 +- .../javascripts/oxalis/model/bucket_data_handling/data_cube.ts | 2 +- frontend/javascripts/oxalis/model/sagas/root_saga.ts | 2 +- frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx | 1 - 4 files changed, 3 insertions(+), 4 deletions(-) diff --git a/frontend/javascripts/oxalis/controller/compute_split_boundary_mesh_with_splines.ts b/frontend/javascripts/oxalis/controller/compute_split_boundary_mesh_with_splines.ts index e3725735166..dab4a9f483c 100644 --- a/frontend/javascripts/oxalis/controller/compute_split_boundary_mesh_with_splines.ts +++ b/frontend/javascripts/oxalis/controller/compute_split_boundary_mesh_with_splines.ts @@ -1,6 +1,6 @@ import _ from "lodash"; -import * as THREE from "three"; import type { Vector3 } from "oxalis/constants"; +import * as THREE from "three"; export default function computeSplitBoundaryMeshWithSplines(points: Vector3[]): { splines: THREE.Object3D[]; diff --git a/frontend/javascripts/oxalis/model/bucket_data_handling/data_cube.ts b/frontend/javascripts/oxalis/model/bucket_data_handling/data_cube.ts index b3a2af96dd7..fa187490296 100644 --- a/frontend/javascripts/oxalis/model/bucket_data_handling/data_cube.ts +++ b/frontend/javascripts/oxalis/model/bucket_data_handling/data_cube.ts @@ -17,6 +17,7 @@ import type { Vector3, } from "oxalis/constants"; import constants, { MappingStatusEnum } from "oxalis/constants"; +import getSceneController from "oxalis/controller/scene_controller_provider"; import { getMappingInfo } from "oxalis/model/accessors/dataset_accessor"; import { getSomeTracing } from "oxalis/model/accessors/tracing_accessor"; import BoundingBox from "oxalis/model/bucket_data_handling/bounding_box"; @@ -36,7 +37,6 @@ import * as THREE from "three"; import type { AdditionalAxis, BucketDataArray, ElementClass } from "types/api_flow_types"; import type { AdditionalCoordinate } from "types/api_flow_types"; import type { MagInfo } from "../helpers/mag_info"; -import getSceneController from "oxalis/controller/scene_controller_provider"; const warnAboutTooManyAllocations = _.once(() => { const msg = diff --git a/frontend/javascripts/oxalis/model/sagas/root_saga.ts b/frontend/javascripts/oxalis/model/sagas/root_saga.ts index 971060c6ce7..e6aaf9645e7 100644 --- a/frontend/javascripts/oxalis/model/sagas/root_saga.ts +++ b/frontend/javascripts/oxalis/model/sagas/root_saga.ts @@ -21,8 +21,8 @@ import { race } from "redux-saga/effects"; import { all, call, cancel, fork, put, take, takeEvery } from "typed-redux-saga"; import type { EscalateErrorAction } from "../actions/actions"; import { setIsWkReadyAction } from "../actions/ui_actions"; -import splitBoundaryMeshSaga from "./split_boundary_mesh_saga"; import maintainMaximumZoomForAllMagsSaga from "./flycam_info_cache_saga"; +import splitBoundaryMeshSaga from "./split_boundary_mesh_saga"; import { warnIfEmailIsUnverified } from "./user_saga"; let rootSagaCrashed = false; diff --git a/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx b/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx index 28e15b69bb7..bd791a5c8cf 100644 --- a/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx +++ b/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx @@ -58,7 +58,6 @@ import { updateUserSettingAction } from "oxalis/model/actions/settings_actions"; import { createTreeAction, setMergerModeEnabledAction, - setTreeEdgeVisibilityAction, } from "oxalis/model/actions/skeletontracing_actions"; import { setToolAction, showQuickSelectSettingsAction } from "oxalis/model/actions/ui_actions"; import { From 664c8d776318621db469cf8d70d5cd5410f956f4 Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Wed, 9 Apr 2025 17:50:26 +0200 Subject: [PATCH 21/84] move file --- frontend/javascripts/oxalis/controller/scene_controller.ts | 2 +- .../compute_split_boundary_mesh_with_splines.ts | 0 2 files changed, 1 insertion(+), 1 deletion(-) rename frontend/javascripts/oxalis/{controller => geometries}/compute_split_boundary_mesh_with_splines.ts (100%) diff --git a/frontend/javascripts/oxalis/controller/scene_controller.ts b/frontend/javascripts/oxalis/controller/scene_controller.ts index bc8629e601f..6c9c5405a6b 100644 --- a/frontend/javascripts/oxalis/controller/scene_controller.ts +++ b/frontend/javascripts/oxalis/controller/scene_controller.ts @@ -53,6 +53,7 @@ import SegmentMeshController from "./segment_mesh_controller"; const CUBE_COLOR = 0x999999; const LAYER_CUBE_COLOR = 0xffff99; +import computeSplitBoundaryMeshWithSplines from "oxalis/geometries/compute_split_boundary_mesh_with_splines"; import { acceleratedRaycast, computeBatchedBoundsTree, @@ -60,7 +61,6 @@ import { disposeBatchedBoundsTree, disposeBoundsTree, } from "three-mesh-bvh"; -import computeSplitBoundaryMeshWithSplines from "./compute_split_boundary_mesh_with_splines"; // Add the extension functions THREE.BufferGeometry.prototype.computeBoundsTree = computeBoundsTree; diff --git a/frontend/javascripts/oxalis/controller/compute_split_boundary_mesh_with_splines.ts b/frontend/javascripts/oxalis/geometries/compute_split_boundary_mesh_with_splines.ts similarity index 100% rename from frontend/javascripts/oxalis/controller/compute_split_boundary_mesh_with_splines.ts rename to frontend/javascripts/oxalis/geometries/compute_split_boundary_mesh_with_splines.ts From fa80d3c95151a0500d13db3e13424eaed9e865e4 Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Wed, 9 Apr 2025 17:53:14 +0200 Subject: [PATCH 22/84] fix bug --- .../oxalis/model/reducers/skeletontracing_reducer.ts | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/frontend/javascripts/oxalis/model/reducers/skeletontracing_reducer.ts b/frontend/javascripts/oxalis/model/reducers/skeletontracing_reducer.ts index bd16d16c6e7..7367dcdee98 100644 --- a/frontend/javascripts/oxalis/model/reducers/skeletontracing_reducer.ts +++ b/frontend/javascripts/oxalis/model/reducers/skeletontracing_reducer.ts @@ -835,7 +835,9 @@ function SkeletonTracingReducer(state: OxalisState, action: Action): OxalisState undefined, undefined, undefined, - isSplitWorkspaceActive, + // Don't show edges for trees that were created in the split workspace, + // because spline curves will be shown for each section by default. + !isSplitWorkspaceActive, ) .map((tree) => { if (action.treeIdCallback) { From 9ec00b5c50cdd814a1204e75d4253229a73b2f3b Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Thu, 10 Apr 2025 08:21:42 +0200 Subject: [PATCH 23/84] wip: add badge dot to workspace dropdown --- .../view/action-bar/tool_workspace_view.tsx | 18 ++++++++++++++---- .../oxalis/view/action-bar/toolbar_view.tsx | 2 +- .../oxalis/view/action-bar/view_modes_view.tsx | 3 ++- 3 files changed, 17 insertions(+), 6 deletions(-) diff --git a/frontend/javascripts/oxalis/view/action-bar/tool_workspace_view.tsx b/frontend/javascripts/oxalis/view/action-bar/tool_workspace_view.tsx index d1577256fd1..ab51f780f65 100644 --- a/frontend/javascripts/oxalis/view/action-bar/tool_workspace_view.tsx +++ b/frontend/javascripts/oxalis/view/action-bar/tool_workspace_view.tsx @@ -1,10 +1,11 @@ -import { Button, Dropdown, type MenuProps } from "antd"; +import { Badge, Button, Dropdown, type MenuProps } from "antd"; import { // setToolWorkspaceAction, updateUserSettingAction, } from "oxalis/model/actions/settings_actions"; import { Store } from "oxalis/singletons"; import type { ToolWorkspace } from "oxalis/store"; +import { NARROW_BUTTON_STYLE } from "./toolbar_view"; export default function ToolWorkspaceView() { const toolWorkspaceItems: MenuProps["items"] = [ @@ -55,9 +56,18 @@ export default function ToolWorkspaceView() { return ( - + + + ); } diff --git a/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx b/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx index bd791a5c8cf..b130684a083 100644 --- a/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx +++ b/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx @@ -88,7 +88,7 @@ import type { MenuInfo } from "rc-menu/lib/interface"; import { APIJobType } from "types/api_flow_types"; import { QuickSelectControls } from "./quick_select_settings"; -const NARROW_BUTTON_STYLE = { +export const NARROW_BUTTON_STYLE = { paddingLeft: 10, paddingRight: 8, }; diff --git a/frontend/javascripts/oxalis/view/action-bar/view_modes_view.tsx b/frontend/javascripts/oxalis/view/action-bar/view_modes_view.tsx index d1992fd2445..7a98c950221 100644 --- a/frontend/javascripts/oxalis/view/action-bar/view_modes_view.tsx +++ b/frontend/javascripts/oxalis/view/action-bar/view_modes_view.tsx @@ -12,6 +12,7 @@ import { PureComponent } from "react"; import { connect } from "react-redux"; import type { Dispatch } from "redux"; import type { EmptyObject } from "types/globals"; +import { NARROW_BUTTON_STYLE } from "./toolbar_view"; type StateProps = { viewMode: ViewMode; @@ -87,7 +88,7 @@ class ViewModesView extends PureComponent { return ( - From f6f3bb991db12c507e7b9c1f7de1416b9c4bf5a9 Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Thu, 10 Apr 2025 16:19:53 +0200 Subject: [PATCH 24/84] fix missing type import --- frontend/javascripts/libs/compute_bvh_async.ts | 1 + 1 file changed, 1 insertion(+) diff --git a/frontend/javascripts/libs/compute_bvh_async.ts b/frontend/javascripts/libs/compute_bvh_async.ts index 78d0a2b7127..0c4b88db88b 100644 --- a/frontend/javascripts/libs/compute_bvh_async.ts +++ b/frontend/javascripts/libs/compute_bvh_async.ts @@ -1,3 +1,4 @@ +import type * as THREE from "three"; import type { MeshBVH } from "three-mesh-bvh"; // @ts-ignore import { GenerateMeshBVHWorker } from "three-mesh-bvh/src/workers/GenerateMeshBVHWorker"; From 97c35cdae2c7b736c0a1fb64a8aa88b4356d6a79 Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Fri, 11 Apr 2025 16:17:34 +0200 Subject: [PATCH 25/84] refactor annotation tool enums --- frontend/javascripts/oxalis/api/api_latest.ts | 19 +- frontend/javascripts/oxalis/constants.ts | 55 +--- .../controller/combinations/tool_controls.ts | 73 +++-- .../controller/segment_mesh_controller.ts | 5 +- .../oxalis/controller/td_controller.tsx | 5 +- .../controller/viewmodes/plane_controller.tsx | 72 +++-- frontend/javascripts/oxalis/default_state.ts | 3 +- .../materials/plane_material_factory.ts | 4 +- .../oxalis/model/accessors/tool_accessor.ts | 283 +++++++++++++----- .../model/accessors/volumetracing_accessor.ts | 22 +- .../oxalis/model/actions/ui_actions.ts | 4 +- .../oxalis/model/reducers/reducer_helpers.ts | 16 +- .../model/reducers/skeletontracing_reducer.ts | 6 +- .../oxalis/model/reducers/ui_reducer.ts | 4 +- .../model/sagas/annotation_tool_saga.ts | 4 +- .../oxalis/model/sagas/proofread_saga.ts | 9 +- .../oxalis/model/sagas/undo_saga.ts | 4 +- .../model/sagas/volume/floodfill_saga.tsx | 4 +- .../oxalis/model/sagas/volumetracing_saga.tsx | 19 +- .../oxalis/model_initialization.ts | 4 +- frontend/javascripts/oxalis/store.ts | 4 +- .../oxalis/view/action-bar/toolbar_view.tsx | 178 ++++++----- .../view/components/command_palette.tsx | 6 +- .../javascripts/oxalis/view/context_menu.tsx | 24 +- .../view/distance_measurement_tooltip.tsx | 8 +- .../javascripts/oxalis/view/input_catcher.tsx | 14 +- .../left-border-tabs/layer_settings_tab.tsx | 9 +- .../javascripts/oxalis/view/plane_view.ts | 11 +- .../javascripts/oxalis/view/statusbar.tsx | 9 +- .../test/api/api_volume_latest.spec.ts | 12 +- .../test/fixtures/volumetracing_object.ts | 4 +- .../reducers/volumetracing_reducer.spec.ts | 32 +- .../annotation_tool_disabled_info.spec.ts | 50 ++-- .../test/sagas/annotation_tool_saga.spec.ts | 34 +-- .../volumetracing/bucket_eviction_helper.ts | 4 +- .../volumetracing/volumetracing_saga.spec.ts | 16 +- .../volumetracing_saga_integration.spec.ts | 28 +- 37 files changed, 584 insertions(+), 474 deletions(-) diff --git a/frontend/javascripts/oxalis/api/api_latest.ts b/frontend/javascripts/oxalis/api/api_latest.ts index 6f9cc561630..1f56d507d92 100644 --- a/frontend/javascripts/oxalis/api/api_latest.ts +++ b/frontend/javascripts/oxalis/api/api_latest.ts @@ -18,7 +18,7 @@ import window, { location } from "libs/window"; import _ from "lodash"; import messages from "messages"; import type { - AnnotationTool, + AnnotationToolId, BoundingBoxType, BucketAddress, ControlMode, @@ -30,10 +30,10 @@ import type { import Constants, { ControlModeEnum, OrthoViews, - AnnotationToolEnum, TDViewDisplayModeEnum, MappingStatusEnum, EMPTY_OBJECT, + AnnotationTool, } from "oxalis/constants"; import { rotate3DViewTo } from "oxalis/controller/camera_controller"; import { loadAgglomerateSkeletonForSegmentId } from "oxalis/controller/combinations/segmentation_handlers"; @@ -1481,8 +1481,8 @@ class TracingApi { * Returns the active tool which is either * "MOVE", "SKELETON", "TRACE", "BRUSH", "FILL_CELL" or "PICK_CELL" */ - getAnnotationTool(): AnnotationTool { - return Store.getState().uiInformation.activeTool; + getAnnotationTool(): AnnotationToolId { + return Store.getState().uiInformation.activeTool.id; } /** @@ -1490,10 +1490,11 @@ class TracingApi { * "MOVE", "SKELETON", "TRACE", "BRUSH", "FILL_CELL" or "PICK_CELL" * _Volume tracing only!_ */ - setAnnotationTool(tool: AnnotationTool) { - if (AnnotationToolEnum[tool] == null) { + setAnnotationTool(toolId: AnnotationToolId) { + const tool = AnnotationTool[toolId]; + if (tool == null) { throw new Error( - `Annotation tool has to be one of: "${Object.keys(AnnotationToolEnum).join('", "')}".`, + `Annotation tool has to be one of: "${Object.keys(AnnotationTool).join('", "')}".`, ); } @@ -1503,14 +1504,14 @@ class TracingApi { /** * Deprecated! Use getAnnotationTool instead. */ - getVolumeTool(): AnnotationTool { + getVolumeTool(): AnnotationToolId { return this.getAnnotationTool(); } /** * Deprecated! Use setAnnotationTool instead. */ - setVolumeTool(tool: AnnotationTool) { + setVolumeTool(tool: AnnotationToolId) { this.setAnnotationTool(tool); } diff --git a/frontend/javascripts/oxalis/constants.ts b/frontend/javascripts/oxalis/constants.ts index 56944295c8e..c3d4d12c012 100644 --- a/frontend/javascripts/oxalis/constants.ts +++ b/frontend/javascripts/oxalis/constants.ts @@ -1,5 +1,16 @@ import type { AdditionalCoordinate } from "types/api_flow_types"; +export { + AnnotationTool, + AnnotationToolType, + AnnotationToolId, + VolumeTools, + AvailableToolsInViewMode, + MeasurementTools, + ToolsWithOverwriteCapabilities, + ToolsWithInterpolationCapabilities, +} from "./model/accessors/tool_accessor"; + export const ViewModeValues = ["orthogonal", "flight", "oblique"] as ViewMode[]; export const ViewModeValuesIndices = { @@ -181,51 +192,7 @@ export enum ControlModeEnum { VIEW = "VIEW", } export type ControlMode = keyof typeof ControlModeEnum; -export enum AnnotationToolEnum { - MOVE = "MOVE", - SKELETON = "SKELETON", - BRUSH = "BRUSH", - ERASE_BRUSH = "ERASE_BRUSH", - TRACE = "TRACE", - ERASE_TRACE = "ERASE_TRACE", - FILL_CELL = "FILL_CELL", - PICK_CELL = "PICK_CELL", - QUICK_SELECT = "QUICK_SELECT", - BOUNDING_BOX = "BOUNDING_BOX", - PROOFREAD = "PROOFREAD", - LINE_MEASUREMENT = "LINE_MEASUREMENT", - AREA_MEASUREMENT = "AREA_MEASUREMENT", -} -export const VolumeTools: Array = [ - AnnotationToolEnum.BRUSH, - AnnotationToolEnum.ERASE_BRUSH, - AnnotationToolEnum.TRACE, - AnnotationToolEnum.ERASE_TRACE, - AnnotationToolEnum.FILL_CELL, - AnnotationToolEnum.PICK_CELL, - AnnotationToolEnum.QUICK_SELECT, -]; -export const ToolsWithOverwriteCapabilities: Array = [ - AnnotationToolEnum.TRACE, - AnnotationToolEnum.BRUSH, - AnnotationToolEnum.ERASE_TRACE, - AnnotationToolEnum.ERASE_BRUSH, - AnnotationToolEnum.QUICK_SELECT, -]; -export const ToolsWithInterpolationCapabilities: Array = [ - AnnotationToolEnum.TRACE, - AnnotationToolEnum.BRUSH, - AnnotationToolEnum.QUICK_SELECT, -]; - -export const MeasurementTools: Array = [ - AnnotationToolEnum.LINE_MEASUREMENT, - AnnotationToolEnum.AREA_MEASUREMENT, -]; - -export const AvailableToolsInViewMode = [...MeasurementTools, AnnotationToolEnum.MOVE]; -export type AnnotationTool = keyof typeof AnnotationToolEnum; export enum ContourModeEnum { DRAW = "DRAW", DELETE = "DELETE", diff --git a/frontend/javascripts/oxalis/controller/combinations/tool_controls.ts b/frontend/javascripts/oxalis/controller/combinations/tool_controls.ts index cae8a4dfd5e..936df3299a4 100644 --- a/frontend/javascripts/oxalis/controller/combinations/tool_controls.ts +++ b/frontend/javascripts/oxalis/controller/combinations/tool_controls.ts @@ -3,8 +3,16 @@ import type { ModifierKeys } from "libs/input"; import { V3 } from "libs/mjs"; import * as Utils from "libs/utils"; import { document } from "libs/window"; -import type { AnnotationTool, OrthoView, Point2, Vector3, Viewport } from "oxalis/constants"; -import { AnnotationToolEnum, ContourModeEnum, OrthoViews } from "oxalis/constants"; +import { + AnnotationTool, + ContourModeEnum, + OrthoViews, + type AnnotationToolType, + type OrthoView, + type Point2, + type Vector3, + type Viewport, +} from "oxalis/constants"; import { type SelectedEdge, createBoundingBoxAndGetEdges, @@ -139,7 +147,7 @@ export class MoveTool { }, leftDoubleClick: (pos: Point2, _plane: OrthoView, _event: MouseEvent, _isTouch: boolean) => { const { uiInformation } = Store.getState(); - const isMoveToolActive = uiInformation.activeTool === AnnotationToolEnum.MOVE; + const isMoveToolActive = uiInformation.activeTool === AnnotationTool.MOVE; if (isMoveToolActive) { // We want to select the clicked segment ID only in the MOVE tool. This method is @@ -194,7 +202,7 @@ export class MoveTool { } static getActionDescriptors( - _activeTool: AnnotationTool, + _activeTool: AnnotationToolType, useLegacyBindings: boolean, shiftKey: boolean, _ctrlOrMetaKey: boolean, @@ -360,7 +368,7 @@ export class SkeletonTool { } static getActionDescriptors( - _activeTool: AnnotationTool, + _activeTool: AnnotationToolType, useLegacyBindings: boolean, shiftKey: boolean, ctrlOrMetaKey: boolean, @@ -487,7 +495,7 @@ export class DrawTool { } static getActionDescriptors( - activeTool: AnnotationTool, + activeTool: AnnotationToolType, useLegacyBindings: boolean, _shiftKey: boolean, _ctrlOrMetaKey: boolean, @@ -499,11 +507,11 @@ export class DrawTool { if (!useLegacyBindings) { rightClick = "Context Menu"; } else { - rightClick = `Erase (${activeTool === AnnotationToolEnum.BRUSH ? "Brush" : "Trace"})`; + rightClick = `Erase (${activeTool === AnnotationTool.BRUSH ? "Brush" : "Trace"})`; } return { - leftDrag: activeTool === AnnotationToolEnum.BRUSH ? "Brush" : "Trace", + leftDrag: activeTool === AnnotationTool.BRUSH ? "Brush" : "Trace", rightClick, }; } @@ -546,7 +554,7 @@ export class EraseTool { } static getActionDescriptors( - activeTool: AnnotationTool, + activeTool: AnnotationToolType, _useLegacyBindings: boolean, _shiftKey: boolean, _ctrlOrMetaKey: boolean, @@ -554,7 +562,7 @@ export class EraseTool { _isTDViewportActive: boolean, ): ActionDescriptor { return { - leftDrag: `Erase (${activeTool === AnnotationToolEnum.ERASE_BRUSH ? "Brush" : "Trace"})`, + leftDrag: `Erase (${activeTool === AnnotationTool.ERASE_BRUSH ? "Brush" : "Trace"})`, rightClick: "Context Menu", }; } @@ -571,7 +579,7 @@ export class PickCellTool { } static getActionDescriptors( - _activeTool: AnnotationTool, + _activeTool: AnnotationToolType, _useLegacyBindings: boolean, _shiftKey: boolean, _ctrlOrMetaKey: boolean, @@ -602,7 +610,7 @@ export class FillCellTool { } static getActionDescriptors( - _activeTool: AnnotationTool, + _activeTool: AnnotationToolType, _useLegacyBindings: boolean, _shiftKey: boolean, _ctrlOrMetaKey: boolean, @@ -681,7 +689,7 @@ export class BoundingBoxTool { } static getActionDescriptors( - _activeTool: AnnotationTool, + _activeTool: AnnotationToolType, _useLegacyBindings: boolean, _shiftKey: boolean, ctrlOrMetaKey: boolean, @@ -810,7 +818,7 @@ export class QuickSelectTool { } static getActionDescriptors( - _activeTool: AnnotationTool, + _activeTool: AnnotationToolType, _useLegacyBindings: boolean, shiftKey: boolean, _ctrlOrMetaKey: boolean, @@ -934,7 +942,7 @@ export class LineMeasurementTool { } static getActionDescriptors( - _activeTool: AnnotationTool, + _activeTool: AnnotationToolType, _useLegacyBindings: boolean, _shiftKey: boolean, _ctrlOrMetaKey: boolean, @@ -1013,7 +1021,7 @@ export class AreaMeasurementTool { } static getActionDescriptors( - _activeTool: AnnotationTool, + _activeTool: AnnotationToolType, _useLegacyBindings: boolean, _shiftKey: boolean, _ctrlOrMetaKey: boolean, @@ -1073,7 +1081,7 @@ export class ProofreadTool { } static getActionDescriptors( - _activeTool: AnnotationTool, + _activeTool: AnnotationToolType, _useLegacyBindings: boolean, shiftKey: boolean, ctrlOrMetaKey: boolean, @@ -1114,20 +1122,21 @@ export class ProofreadTool { static onToolDeselected() {} } const toolToToolClass = { - [AnnotationToolEnum.MOVE]: MoveTool, - [AnnotationToolEnum.SKELETON]: SkeletonTool, - [AnnotationToolEnum.BOUNDING_BOX]: BoundingBoxTool, - [AnnotationToolEnum.QUICK_SELECT]: QuickSelectTool, - [AnnotationToolEnum.PROOFREAD]: ProofreadTool, - [AnnotationToolEnum.BRUSH]: DrawTool, - [AnnotationToolEnum.TRACE]: DrawTool, - [AnnotationToolEnum.ERASE_TRACE]: EraseTool, - [AnnotationToolEnum.ERASE_BRUSH]: EraseTool, - [AnnotationToolEnum.FILL_CELL]: FillCellTool, - [AnnotationToolEnum.PICK_CELL]: PickCellTool, - [AnnotationToolEnum.LINE_MEASUREMENT]: LineMeasurementTool, - [AnnotationToolEnum.AREA_MEASUREMENT]: AreaMeasurementTool, + // todop + [AnnotationTool.MOVE.id]: MoveTool, + [AnnotationTool.SKELETON.id]: SkeletonTool, + [AnnotationTool.BOUNDING_BOX.id]: BoundingBoxTool, + [AnnotationTool.QUICK_SELECT.id]: QuickSelectTool, + [AnnotationTool.PROOFREAD.id]: ProofreadTool, + [AnnotationTool.BRUSH.id]: DrawTool, + [AnnotationTool.TRACE.id]: DrawTool, + [AnnotationTool.ERASE_TRACE.id]: EraseTool, + [AnnotationTool.ERASE_BRUSH.id]: EraseTool, + [AnnotationTool.FILL_CELL.id]: FillCellTool, + [AnnotationTool.PICK_CELL.id]: PickCellTool, + [AnnotationTool.LINE_MEASUREMENT.id]: LineMeasurementTool, + [AnnotationTool.AREA_MEASUREMENT.id]: AreaMeasurementTool, }; -export function getToolClassForAnnotationTool(activeTool: AnnotationTool) { - return toolToToolClass[activeTool]; +export function getToolClassForAnnotationTool(activeTool: AnnotationToolType) { + return toolToToolClass[activeTool.id]; } diff --git a/frontend/javascripts/oxalis/controller/segment_mesh_controller.ts b/frontend/javascripts/oxalis/controller/segment_mesh_controller.ts index 9b6af2d9fc5..99af4118fe0 100644 --- a/frontend/javascripts/oxalis/controller/segment_mesh_controller.ts +++ b/frontend/javascripts/oxalis/controller/segment_mesh_controller.ts @@ -1,7 +1,7 @@ import app from "app"; import { mergeVertices } from "libs/BufferGeometryUtils"; import _ from "lodash"; -import type { Vector2, Vector3 } from "oxalis/constants"; +import { AnnotationTool, type Vector2, type Vector3 } from "oxalis/constants"; import CustomLOD from "oxalis/controller/custom_lod"; import { getAdditionalCoordinatesAsString } from "oxalis/model/accessors/flycam_accessor"; import { @@ -420,7 +420,8 @@ export default class SegmentMeshController { // appearance. // 2) Clear old partial ranges if necessary. // 3) Update the appearance. - const isProofreadingMode = Store.getState().uiInformation.activeTool === "PROOFREAD"; + const isProofreadingMode = + Store.getState().uiInformation.activeTool === AnnotationTool.PROOFREAD; if (highlightState != null && !isProofreadingMode) { // If the proofreading mode is not active and highlightState is not null, diff --git a/frontend/javascripts/oxalis/controller/td_controller.tsx b/frontend/javascripts/oxalis/controller/td_controller.tsx index 5cc53e3b742..c8bc57779e0 100644 --- a/frontend/javascripts/oxalis/controller/td_controller.tsx +++ b/frontend/javascripts/oxalis/controller/td_controller.tsx @@ -4,8 +4,7 @@ import TrackballControls from "libs/trackball_controls"; import * as Utils from "libs/utils"; import _ from "lodash"; import { - type AnnotationTool, - AnnotationToolEnum, + AnnotationTool, type OrthoView, type OrthoViewMap, OrthoViews, @@ -65,7 +64,7 @@ function getTDViewMouseControlsSkeleton(planeView: PlaneView): Record - activeTool === AnnotationToolEnum.PROOFREAD + activeTool === AnnotationTool.PROOFREAD ? ProofreadTool.onLeftClick(planeView, pos, plane, event, isTouch) : SkeletonTool.onLeftClick( planeView, diff --git a/frontend/javascripts/oxalis/controller/viewmodes/plane_controller.tsx b/frontend/javascripts/oxalis/controller/viewmodes/plane_controller.tsx index 31f7fed97b1..0bffabebcc8 100644 --- a/frontend/javascripts/oxalis/controller/viewmodes/plane_controller.tsx +++ b/frontend/javascripts/oxalis/controller/viewmodes/plane_controller.tsx @@ -3,8 +3,14 @@ import Toast from "libs/toast"; import * as Utils from "libs/utils"; import { document } from "libs/window"; import _ from "lodash"; -import type { AnnotationTool, OrthoView, OrthoViewMap } from "oxalis/constants"; -import { AnnotationToolEnum, OrthoViewValuesWithoutTDView, OrthoViews } from "oxalis/constants"; +import { + AnnotationTool, + type AnnotationToolId, + type AnnotationToolType, + type OrthoView, + type OrthoViewMap, +} from "oxalis/constants"; +import { OrthoViewValuesWithoutTDView, OrthoViews } from "oxalis/constants"; import * as MoveHandlers from "oxalis/controller/combinations/move_handlers"; import * as SkeletonHandlers from "oxalis/controller/combinations/skeleton_handlers"; import { @@ -102,7 +108,7 @@ const setTool = (tool: AnnotationTool) => { type StateProps = { annotation: StoreAnnotation; - activeTool: AnnotationTool; + activeTool: AnnotationToolType; }; type Props = StateProps; @@ -140,7 +146,7 @@ class SkeletonKeybindings { } static getExtendedKeyboardControls() { - return { s: () => setTool(AnnotationToolEnum.SKELETON) }; + return { s: () => setTool(AnnotationTool.SKELETON) }; } } @@ -170,14 +176,14 @@ class VolumeKeybindings { static getExtendedKeyboardControls() { return { - b: () => setTool(AnnotationToolEnum.BRUSH), - e: () => setTool(AnnotationToolEnum.ERASE_BRUSH), - l: () => setTool(AnnotationToolEnum.TRACE), - r: () => setTool(AnnotationToolEnum.ERASE_TRACE), - f: () => setTool(AnnotationToolEnum.FILL_CELL), - p: () => setTool(AnnotationToolEnum.PICK_CELL), - q: () => setTool(AnnotationToolEnum.QUICK_SELECT), - o: () => setTool(AnnotationToolEnum.PROOFREAD), + b: () => setTool(AnnotationTool.BRUSH), + e: () => setTool(AnnotationTool.ERASE_BRUSH), + l: () => setTool(AnnotationTool.TRACE), + r: () => setTool(AnnotationTool.ERASE_TRACE), + f: () => setTool(AnnotationTool.FILL_CELL), + p: () => setTool(AnnotationTool.PICK_CELL), + q: () => setTool(AnnotationTool.QUICK_SELECT), + o: () => setTool(AnnotationTool.PROOFREAD), }; } } @@ -203,7 +209,7 @@ class BoundingBoxKeybindings { }; static getExtendedKeyboardControls() { - return { x: () => setTool(AnnotationToolEnum.BOUNDING_BOX) }; + return { x: () => setTool(AnnotationTool.BOUNDING_BOX) }; } static createKeyDownAndUpHandler() { @@ -345,20 +351,20 @@ class PlaneController extends React.PureComponent { for (const controlKey of allControlKeys) { controls[controlKey] = this.createToolDependentMouseHandler({ - [AnnotationToolEnum.MOVE]: moveControls[controlKey], + [AnnotationTool.MOVE.id]: moveControls[controlKey], // @ts-expect-error ts-migrate(7053) FIXME: Element implicitly has an 'any' type because expre... Remove this comment to see the full error message - [AnnotationToolEnum.SKELETON]: skeletonControls[controlKey], - [AnnotationToolEnum.BRUSH]: drawControls[controlKey], - [AnnotationToolEnum.TRACE]: drawControls[controlKey], - [AnnotationToolEnum.ERASE_BRUSH]: eraseControls[controlKey], - [AnnotationToolEnum.ERASE_TRACE]: eraseControls[controlKey], - [AnnotationToolEnum.PICK_CELL]: pickCellControls[controlKey], - [AnnotationToolEnum.FILL_CELL]: fillCellControls[controlKey], - [AnnotationToolEnum.BOUNDING_BOX]: boundingBoxControls[controlKey], - [AnnotationToolEnum.QUICK_SELECT]: quickSelectControls[controlKey], - [AnnotationToolEnum.PROOFREAD]: proofreadControls[controlKey], - [AnnotationToolEnum.LINE_MEASUREMENT]: lineMeasurementControls[controlKey], - [AnnotationToolEnum.AREA_MEASUREMENT]: areaMeasurementControls[controlKey], + [AnnotationTool.SKELETON.id]: skeletonControls[controlKey], + [AnnotationTool.BRUSH.id]: drawControls[controlKey], + [AnnotationTool.TRACE.id]: drawControls[controlKey], + [AnnotationTool.ERASE_BRUSH.id]: eraseControls[controlKey], + [AnnotationTool.ERASE_TRACE.id]: eraseControls[controlKey], + [AnnotationTool.PICK_CELL.id]: pickCellControls[controlKey], + [AnnotationTool.FILL_CELL.id]: fillCellControls[controlKey], + [AnnotationTool.BOUNDING_BOX.id]: boundingBoxControls[controlKey], + [AnnotationTool.QUICK_SELECT.id]: quickSelectControls[controlKey], + [AnnotationTool.PROOFREAD.id]: proofreadControls[controlKey], + [AnnotationTool.LINE_MEASUREMENT.id]: lineMeasurementControls[controlKey], + [AnnotationTool.AREA_MEASUREMENT.id]: areaMeasurementControls[controlKey], }); } @@ -504,7 +510,7 @@ class PlaneController extends React.PureComponent { }; let extendedControls = { - m: () => setTool(AnnotationToolEnum.MOVE), + m: () => setTool(AnnotationTool.MOVE), 1: () => this.handleUpdateBrushSize("small"), 2: () => this.handleUpdateBrushSize("medium"), 3: () => this.handleUpdateBrushSize("large"), @@ -635,7 +641,7 @@ class PlaneController extends React.PureComponent { const tool = this.props.activeTool; switch (tool) { - case AnnotationToolEnum.MOVE: { + case AnnotationTool.MOVE: { if (viewHandler != null) { viewHandler(...args); } else if (skeletonHandler != null) { @@ -645,7 +651,7 @@ class PlaneController extends React.PureComponent { return; } - case AnnotationToolEnum.SKELETON: { + case AnnotationTool.SKELETON: { if (skeletonHandler != null) { skeletonHandler(...args); } else if (viewHandler != null) { @@ -655,7 +661,7 @@ class PlaneController extends React.PureComponent { return; } - case AnnotationToolEnum.BOUNDING_BOX: { + case AnnotationTool.BOUNDING_BOX: { if (boundingBoxHandler != null) { boundingBoxHandler(...args); } else if (viewHandler != null) { @@ -677,12 +683,12 @@ class PlaneController extends React.PureComponent { } createToolDependentMouseHandler( - toolToHandlerMap: Record) => any>, + toolToHandlerMap: Record) => any>, ): (...args: Array) => any { return (...args) => { const tool = this.props.activeTool; - const handler = toolToHandlerMap[tool]; - const fallbackHandler = toolToHandlerMap[AnnotationToolEnum.MOVE]; + const handler = toolToHandlerMap[tool.id]; + const fallbackHandler = toolToHandlerMap[AnnotationTool.MOVE.id]; if (handler != null) { handler(...args); diff --git a/frontend/javascripts/oxalis/default_state.ts b/frontend/javascripts/oxalis/default_state.ts index aafedf1d899..ccfdd0618e0 100644 --- a/frontend/javascripts/oxalis/default_state.ts +++ b/frontend/javascripts/oxalis/default_state.ts @@ -6,6 +6,7 @@ import Constants, { TDViewDisplayModeEnum, InterpolationModeEnum, UnitLong, + AnnotationTool, } from "oxalis/constants"; import constants from "oxalis/constants"; import type { OxalisState } from "oxalis/store"; @@ -232,7 +233,7 @@ const defaultState: OxalisState = { activeOrganization: null, uiInformation: { globalProgress: 0, - activeTool: "MOVE", + activeTool: AnnotationTool.MOVE, activeUserBoundingBoxId: null, showDropzoneModal: false, showVersionRestore: false, diff --git a/frontend/javascripts/oxalis/geometries/materials/plane_material_factory.ts b/frontend/javascripts/oxalis/geometries/materials/plane_material_factory.ts index faffe55edd5..9f187d7029e 100644 --- a/frontend/javascripts/oxalis/geometries/materials/plane_material_factory.ts +++ b/frontend/javascripts/oxalis/geometries/materials/plane_material_factory.ts @@ -7,7 +7,7 @@ import _ from "lodash"; import { WkDevFlags } from "oxalis/api/wk_dev"; import { BLEND_MODES, Identity4x4, type OrthoView, type Vector3 } from "oxalis/constants"; import { - AnnotationToolEnum, + AnnotationTool, MappingStatusEnum, OrthoViewValues, OrthoViews, @@ -885,7 +885,7 @@ class PlaneMaterialFactory { (storeState) => storeState.uiInformation.activeTool, (annotationTool) => { this.uniforms.showBrush.value = isBrushTool(annotationTool); - this.uniforms.isProofreading.value = annotationTool === AnnotationToolEnum.PROOFREAD; + this.uniforms.isProofreading.value = annotationTool === AnnotationTool.PROOFREAD; }, true, ), diff --git a/frontend/javascripts/oxalis/model/accessors/tool_accessor.ts b/frontend/javascripts/oxalis/model/accessors/tool_accessor.ts index 94d4af90b0a..54b0d6a325d 100644 --- a/frontend/javascripts/oxalis/model/accessors/tool_accessor.ts +++ b/frontend/javascripts/oxalis/model/accessors/tool_accessor.ts @@ -4,8 +4,7 @@ import { isFeatureAllowedByPricingPlan, } from "admin/organization/pricing_plan_utils"; import memoizeOne from "memoize-one"; -import { type AnnotationTool, IdentityTransform } from "oxalis/constants"; -import { AnnotationToolEnum } from "oxalis/constants"; +import { IdentityTransform } from "oxalis/constants"; import { getVisibleSegmentationLayer } from "oxalis/model/accessors/dataset_accessor"; import { isMagRestrictionViolated } from "oxalis/model/accessors/flycam_accessor"; import { @@ -21,22 +20,157 @@ import { reuseInstanceOnEquality } from "./accessor_helpers"; import { getTransformsPerLayer } from "./dataset_layer_transformation_accessor"; import { isSkeletonLayerTransformed, isSkeletonLayerVisible } from "./skeletontracing_accessor"; -export const TOOL_NAMES = { - MOVE: "Move", - SKELETON: "Skeleton", - BRUSH: "Brush", - ERASE_BRUSH: "Erase (via Brush)", - TRACE: "Trace", - ERASE_TRACE: "Erase", - FILL_CELL: "Fill Tool", - PICK_CELL: "Segment Picker", - QUICK_SELECT: "Quick Select Tool", - BOUNDING_BOX: "Bounding Box Tool", - PROOFREAD: "Proofreading Tool", - LINE_MEASUREMENT: "Measurement Tool", - AREA_MEASUREMENT: "Area Measurement Tool", +abstract class AbstractAnnotationTool { + static id: keyof typeof _AnnotationToolHelper; + static readableName: string; + static hasOverwriteCapabilities: boolean = false; + static hasInterpolationCapabilities: boolean = false; +} + +export type AnnotationToolId = (typeof AbstractAnnotationTool)["id"]; + +const _AnnotationToolHelper = { + MOVE: "MOVE", + SKELETON: "SKELETON", + BRUSH: "BRUSH", + ERASE_BRUSH: "ERASE_BRUSH", + TRACE: "TRACE", + ERASE_TRACE: "ERASE_TRACE", + FILL_CELL: "FILL_CELL", + PICK_CELL: "PICK_CELL", + QUICK_SELECT: "QUICK_SELECT", + BOUNDING_BOX: "BOUNDING_BOX", + PROOFREAD: "PROOFREAD", + LINE_MEASUREMENT: "LINE_MEASUREMENT", + AREA_MEASUREMENT: "AREA_MEASUREMENT", +} as const; + +class MoveTool extends AbstractAnnotationTool { + static id = _AnnotationToolHelper.MOVE; + readableName = "Move"; +} +class SkeletonTool extends AbstractAnnotationTool { + static id = _AnnotationToolHelper.SKELETON; + readableName = "Skeleton"; +} +class BrushTool extends AbstractAnnotationTool { + static id = _AnnotationToolHelper.BRUSH; + static readableName = "Brush"; +} +class EraseBrushTool extends AbstractAnnotationTool { + static id = _AnnotationToolHelper.ERASE_BRUSH; + static readableName = "Erase (via Brush)"; +} +class TraceTool extends AbstractAnnotationTool { + static id = _AnnotationToolHelper.TRACE; + static readableName = "Trace"; +} +class EraseTraceTool extends AbstractAnnotationTool { + static id = _AnnotationToolHelper.ERASE_TRACE; + static readableName = "Erase"; +} +class FillCellTool extends AbstractAnnotationTool { + static id = _AnnotationToolHelper.FILL_CELL; + static readableName = "Fill Tool"; +} +class PickCellTool extends AbstractAnnotationTool { + static id = _AnnotationToolHelper.PICK_CELL; + static readableName = "Segment Picker"; +} +class QuickSelectTool extends AbstractAnnotationTool { + static id = _AnnotationToolHelper.QUICK_SELECT; + static readableName = "Quick Select Tool"; +} +class BoundingBoxTool extends AbstractAnnotationTool { + static id = _AnnotationToolHelper.BOUNDING_BOX; + static readableName = "Bounding Box Tool"; +} +class ProofreadTool extends AbstractAnnotationTool { + static id = _AnnotationToolHelper.PROOFREAD; + static readableName = "Proofreading Tool"; +} +class LineMeasurementTool extends AbstractAnnotationTool { + static id = _AnnotationToolHelper.LINE_MEASUREMENT; + static readableName = "Measurement Tool"; +} +class AreaMeasurementTool extends AbstractAnnotationTool { + static id = _AnnotationToolHelper.AREA_MEASUREMENT; + static readableName = "Area Measurement Tool"; +} + +export const AnnotationTool = { + MOVE: MoveTool, + SKELETON: SkeletonTool, + BRUSH: BrushTool, + ERASE_BRUSH: EraseBrushTool, + TRACE: TraceTool, + ERASE_TRACE: EraseTraceTool, + FILL_CELL: FillCellTool, + PICK_CELL: PickCellTool, + QUICK_SELECT: QuickSelectTool, + BOUNDING_BOX: BoundingBoxTool, + PROOFREAD: ProofreadTool, + LINE_MEASUREMENT: LineMeasurementTool, + AREA_MEASUREMENT: AreaMeasurementTool, }; +export type AnnotationTool = (typeof AnnotationTool)[keyof typeof AnnotationTool]; + +// todop: remove again +export type AnnotationToolType = AnnotationTool; +// export type AnnotationToolType = typeof AbstractAnnotationTool; + +export const ToolCollections = { + ALL_TOOLS: Object.values(AnnotationTool), + VOLUME_TOOLS: [ + AnnotationTool.BRUSH, + AnnotationTool.ERASE_BRUSH, + AnnotationTool.TRACE, + AnnotationTool.ERASE_TRACE, + AnnotationTool.FILL_CELL, + AnnotationTool.PICK_CELL, + AnnotationTool.QUICK_SELECT, + ] as AnnotationTool[], + READ_ONLY_TOOLS: [ + AnnotationTool.MOVE, + AnnotationTool.LINE_MEASUREMENT, + AnnotationTool.AREA_MEASUREMENT, + ] as AnnotationTool[], +}; + +export const VolumeTools = ToolCollections.VOLUME_TOOLS; + +export type ToolCollection = keyof typeof ToolCollections; + +export const ToolsWithOverwriteCapabilities = [ + AnnotationTool.TRACE, + AnnotationTool.BRUSH, + AnnotationTool.ERASE_TRACE, + AnnotationTool.ERASE_BRUSH, + AnnotationTool.QUICK_SELECT, + // todop: remove as...? +] as const as AnnotationTool[]; +export const ToolsWithInterpolationCapabilities = [ + AnnotationTool.TRACE, + AnnotationTool.BRUSH, + AnnotationTool.QUICK_SELECT, +] as const as AnnotationTool[]; + +export const MeasurementTools = [ + AnnotationTool.LINE_MEASUREMENT, + AnnotationTool.AREA_MEASUREMENT, +] as const as AnnotationTool[]; + +export const AvailableToolsInViewMode = [...MeasurementTools, AnnotationTool.MOVE]; + +export type ToolWorkspace = + | "ALL_TOOLS" + | "READ_ONLY_TOOLS" + | "VOLUME_ANNOTATION" + | "SPLIT_SEGMENTS"; + +export function getAvailableTools(_state: OxalisState) {} + const zoomInToUseToolMessage = "Please zoom in further to use this tool. If you want to edit volume data on this zoom level, create an annotation with restricted magnifications from the extended annotation menu in the dashboard."; @@ -79,19 +213,19 @@ const getExplanationForDisabledVolume = ( return "Volume annotation is currently disabled."; }; -export function isVolumeDrawingTool(activeTool: AnnotationTool): boolean { +export function isVolumeDrawingTool(activeTool: AnnotationToolType): boolean { return ( - activeTool === AnnotationToolEnum.TRACE || - activeTool === AnnotationToolEnum.BRUSH || - activeTool === AnnotationToolEnum.ERASE_TRACE || - activeTool === AnnotationToolEnum.ERASE_BRUSH + activeTool === AnnotationTool.TRACE || + activeTool === AnnotationTool.BRUSH || + activeTool === AnnotationTool.ERASE_TRACE || + activeTool === AnnotationTool.ERASE_BRUSH ); } -export function isBrushTool(activeTool: AnnotationTool): boolean { - return activeTool === AnnotationToolEnum.BRUSH || activeTool === AnnotationToolEnum.ERASE_BRUSH; +export function isBrushTool(activeTool: AnnotationToolType): boolean { + return activeTool === AnnotationTool.BRUSH || activeTool === AnnotationTool.ERASE_BRUSH; } -export function isTraceTool(activeTool: AnnotationTool): boolean { - return activeTool === AnnotationToolEnum.TRACE || activeTool === AnnotationToolEnum.ERASE_TRACE; +export function isTraceTool(activeTool: AnnotationToolType): boolean { + return activeTool === AnnotationTool.TRACE || activeTool === AnnotationTool.ERASE_TRACE; } const noSkeletonsExplanation = "This annotation does not have a skeleton. Please convert it to a hybrid annotation."; @@ -110,10 +244,10 @@ const NOT_DISABLED_INFO = { }; const ALWAYS_ENABLED_TOOL_INFOS = { - [AnnotationToolEnum.MOVE]: NOT_DISABLED_INFO, - [AnnotationToolEnum.LINE_MEASUREMENT]: NOT_DISABLED_INFO, - [AnnotationToolEnum.AREA_MEASUREMENT]: NOT_DISABLED_INFO, - [AnnotationToolEnum.BOUNDING_BOX]: NOT_DISABLED_INFO, + [AnnotationTool.MOVE.id]: NOT_DISABLED_INFO, + [AnnotationTool.LINE_MEASUREMENT.id]: NOT_DISABLED_INFO, + [AnnotationTool.AREA_MEASUREMENT.id]: NOT_DISABLED_INFO, + [AnnotationTool.BOUNDING_BOX.id]: NOT_DISABLED_INFO, }; function _getSkeletonToolInfo( @@ -123,7 +257,7 @@ function _getSkeletonToolInfo( ) { if (!hasSkeleton) { return { - [AnnotationToolEnum.SKELETON]: { + [AnnotationTool.SKELETON.id]: { isDisabled: true, explanation: noSkeletonsExplanation, }, @@ -132,7 +266,7 @@ function _getSkeletonToolInfo( if (!areSkeletonsVisible) { return { - [AnnotationToolEnum.SKELETON]: { + [AnnotationTool.SKELETON.id]: { isDisabled: true, explanation: disabledSkeletonExplanation, }, @@ -141,7 +275,7 @@ function _getSkeletonToolInfo( if (isSkeletonLayerTransformed) { return { - [AnnotationToolEnum.SKELETON]: { + [AnnotationTool.SKELETON.id]: { isDisabled: true, explanation: "Skeleton annotation is disabled because the skeleton layer is transformed. Use the left sidebar to render the skeleton layer without any transformations.", @@ -150,7 +284,7 @@ function _getSkeletonToolInfo( } return { - [AnnotationToolEnum.SKELETON]: NOT_DISABLED_INFO, + [AnnotationTool.SKELETON.id]: NOT_DISABLED_INFO, }; } const getSkeletonToolInfo = memoizeOne(_getSkeletonToolInfo); @@ -180,14 +314,14 @@ function _getDisabledInfoWhenVolumeIsDisabled( explanation: genericDisabledExplanation, }; return { - [AnnotationToolEnum.BRUSH]: disabledInfo, - [AnnotationToolEnum.ERASE_BRUSH]: disabledInfo, - [AnnotationToolEnum.TRACE]: disabledInfo, - [AnnotationToolEnum.ERASE_TRACE]: disabledInfo, - [AnnotationToolEnum.FILL_CELL]: disabledInfo, - [AnnotationToolEnum.QUICK_SELECT]: disabledInfo, - [AnnotationToolEnum.PICK_CELL]: disabledInfo, - [AnnotationToolEnum.PROOFREAD]: { + [AnnotationTool.BRUSH.id]: disabledInfo, + [AnnotationTool.ERASE_BRUSH.id]: disabledInfo, + [AnnotationTool.TRACE.id]: disabledInfo, + [AnnotationTool.ERASE_TRACE.id]: disabledInfo, + [AnnotationTool.FILL_CELL.id]: disabledInfo, + [AnnotationTool.QUICK_SELECT.id]: disabledInfo, + [AnnotationTool.PICK_CELL.id]: disabledInfo, + [AnnotationTool.PROOFREAD.id]: { isDisabled: isVolumeDisabled, explanation: genericDisabledExplanation, }, @@ -259,32 +393,32 @@ function _getVolumeDisabledWhenVolumeIsEnabled( ); return { - [AnnotationToolEnum.BRUSH]: { + [AnnotationTool.BRUSH.id]: { isDisabled: isZoomStepTooHighForBrushing, explanation: zoomInToUseToolMessage, }, - [AnnotationToolEnum.ERASE_BRUSH]: { + [AnnotationTool.ERASE_BRUSH.id]: { isDisabled: isZoomStepTooHighForBrushing, explanation: zoomInToUseToolMessage, }, - [AnnotationToolEnum.ERASE_TRACE]: { + [AnnotationTool.ERASE_TRACE.id]: { isDisabled: isZoomStepTooHighForTracing, explanation: zoomInToUseToolMessage, }, - [AnnotationToolEnum.TRACE]: { + [AnnotationTool.TRACE.id]: { isDisabled: isZoomStepTooHighForTracing, explanation: zoomInToUseToolMessage, }, - [AnnotationToolEnum.FILL_CELL]: { + [AnnotationTool.FILL_CELL.id]: { isDisabled: isZoomStepTooHighForFilling, explanation: zoomInToUseToolMessage, }, - [AnnotationToolEnum.PICK_CELL]: NOT_DISABLED_INFO, - [AnnotationToolEnum.QUICK_SELECT]: { + [AnnotationTool.PICK_CELL.id]: NOT_DISABLED_INFO, + [AnnotationTool.QUICK_SELECT.id]: { isDisabled: isZoomStepTooHighForFilling, explanation: zoomInToUseToolMessage, }, - [AnnotationToolEnum.PROOFREAD]: getDisabledInfoForProofreadTool( + [AnnotationTool.PROOFREAD.id]: getDisabledInfoForProofreadTool( hasSkeleton, agglomerateState, isProofReadingToolAllowed, @@ -353,9 +487,9 @@ function getDisabledVolumeInfo(state: OxalisState) { : // Volume tools are not ALL disabled, but some of them might be. getVolumeDisabledWhenVolumeIsEnabled( hasSkeleton, - isVolumeAnnotationDisallowedForZoom(AnnotationToolEnum.BRUSH, state), - isVolumeAnnotationDisallowedForZoom(AnnotationToolEnum.TRACE, state), - isVolumeAnnotationDisallowedForZoom(AnnotationToolEnum.FILL_CELL, state), + isVolumeAnnotationDisallowedForZoom(AnnotationTool.BRUSH, state), + isVolumeAnnotationDisallowedForZoom(AnnotationTool.TRACE, state), + isVolumeAnnotationDisallowedForZoom(AnnotationTool.FILL_CELL, state), isUneditableMappingLocked, hasAgglomerateMapping(state), state.activeOrganization, @@ -364,7 +498,7 @@ function getDisabledVolumeInfo(state: OxalisState) { } const getVolumeDisabledWhenVolumeIsEnabled = memoizeOne(_getVolumeDisabledWhenVolumeIsEnabled); -const _getDisabledInfoForTools = (state: OxalisState): Record => { +const _getDisabledInfoForTools = (state: OxalisState): Record => { const { annotation } = state; const hasSkeleton = annotation.skeleton != null; const skeletonToolInfo = getSkeletonToolInfo( @@ -385,42 +519,42 @@ export const getDisabledInfoForTools = reuseInstanceOnEquality( ); export function adaptActiveToolToShortcuts( - activeTool: AnnotationTool, + activeTool: AnnotationToolType, isShiftPressed: boolean, isControlOrMetaPressed: boolean, isAltPressed: boolean, -): AnnotationTool { +): AnnotationToolType { if (!isShiftPressed && !isControlOrMetaPressed && !isAltPressed) { // No modifier is pressed return activeTool; } if ( - activeTool === AnnotationToolEnum.MOVE || - activeTool === AnnotationToolEnum.QUICK_SELECT || - activeTool === AnnotationToolEnum.PROOFREAD || - activeTool === AnnotationToolEnum.LINE_MEASUREMENT || - activeTool === AnnotationToolEnum.AREA_MEASUREMENT + activeTool === AnnotationTool.MOVE || + activeTool === AnnotationTool.QUICK_SELECT || + activeTool === AnnotationTool.PROOFREAD || + activeTool === AnnotationTool.LINE_MEASUREMENT || + activeTool === AnnotationTool.AREA_MEASUREMENT ) { // These tools do not have any modifier-related behavior currently (except for ALT // which is already handled below) } else if ( - activeTool === AnnotationToolEnum.ERASE_BRUSH || - activeTool === AnnotationToolEnum.ERASE_TRACE + activeTool === AnnotationTool.ERASE_BRUSH || + activeTool === AnnotationTool.ERASE_TRACE ) { if (isShiftPressed) { if (isControlOrMetaPressed) { - return AnnotationToolEnum.FILL_CELL; + return AnnotationTool.FILL_CELL; } else { - return AnnotationToolEnum.PICK_CELL; + return AnnotationTool.PICK_CELL; } } } else { - if (activeTool === AnnotationToolEnum.SKELETON) { + if (activeTool === AnnotationTool.SKELETON) { // The "skeleton" tool is not changed right now (since actions such as moving a node // don't have a dedicated tool). The only exception is "Alt" which switches to the move tool. if (isAltPressed && !isControlOrMetaPressed && !isShiftPressed) { - return AnnotationToolEnum.MOVE; + return AnnotationTool.MOVE; } return activeTool; @@ -429,13 +563,13 @@ export function adaptActiveToolToShortcuts( if (isShiftPressed && !isAltPressed) { if (!isControlOrMetaPressed) { // Only shift is pressed. Switch to the picker - return AnnotationToolEnum.PICK_CELL; + return AnnotationTool.PICK_CELL; } else { // Control and shift switch to the eraser - if (activeTool === AnnotationToolEnum.BRUSH) { - return AnnotationToolEnum.ERASE_BRUSH; - } else if (activeTool === AnnotationToolEnum.TRACE) { - return AnnotationToolEnum.ERASE_TRACE; + if (activeTool === AnnotationTool.BRUSH) { + return AnnotationTool.ERASE_BRUSH; + } else if (activeTool === AnnotationTool.TRACE) { + return AnnotationTool.ERASE_TRACE; } } } @@ -443,15 +577,16 @@ export function adaptActiveToolToShortcuts( if (isAltPressed) { // Alt switches to the move tool - return AnnotationToolEnum.MOVE; + return AnnotationTool.MOVE; } return activeTool; } export const getLabelForTool = (tool: AnnotationTool) => { - const toolName = TOOL_NAMES[tool]; - if (toolName.endsWith("Tool")) { + // todop + const toolName = AnnotationTool[tool.id]; + if (toolName.readableName.endsWith("Tool")) { return toolName; } return `${toolName} Tool`; diff --git a/frontend/javascripts/oxalis/model/accessors/volumetracing_accessor.ts b/frontend/javascripts/oxalis/model/accessors/volumetracing_accessor.ts index bc1fe8fe4fd..f811971203c 100644 --- a/frontend/javascripts/oxalis/model/accessors/volumetracing_accessor.ts +++ b/frontend/javascripts/oxalis/model/accessors/volumetracing_accessor.ts @@ -3,13 +3,14 @@ import _ from "lodash"; import memoizeOne from "memoize-one"; import messages from "messages"; import Constants, { - type AnnotationTool, + AnnotationTool, + type AnnotationToolId, type ContourMode, MappingStatusEnum, type Vector3, type Vector4, + VolumeTools, } from "oxalis/constants"; -import { AnnotationToolEnum, VolumeTools } from "oxalis/constants"; import { reuseInstanceOnEquality } from "oxalis/model/accessors/accessor_helpers"; import { getDataLayers, @@ -213,15 +214,15 @@ export function getContourTracingMode(volumeTracing: VolumeTracing): ContourMode return contourTracingMode; } -const MAG_THRESHOLDS_FOR_ZOOM: Partial> = { +const MAG_THRESHOLDS_FOR_ZOOM: Partial> = { // Note that these are relative to the lowest existing mag index. // A threshold of 1 indicates that the respective tool can be used in the // lowest existing magnification as well as the next highest one. - [AnnotationToolEnum.TRACE]: 1, - [AnnotationToolEnum.ERASE_TRACE]: 1, - [AnnotationToolEnum.BRUSH]: 3, - [AnnotationToolEnum.ERASE_BRUSH]: 3, - [AnnotationToolEnum.FILL_CELL]: 1, + [AnnotationTool.TRACE.id]: 1, + [AnnotationTool.ERASE_TRACE.id]: 1, + [AnnotationTool.BRUSH.id]: 3, + [AnnotationTool.ERASE_BRUSH.id]: 3, + [AnnotationTool.FILL_CELL.id]: 1, }; export function isVolumeTool(tool: AnnotationTool): boolean { return VolumeTools.indexOf(tool) > -1; @@ -232,7 +233,7 @@ export function isVolumeAnnotationDisallowedForZoom(tool: AnnotationTool, state: return true; } - const threshold = MAG_THRESHOLDS_FOR_ZOOM[tool]; + const threshold = MAG_THRESHOLDS_FOR_ZOOM[tool.id]; if (threshold == null) { // If there is no threshold for the provided tool, it doesn't need to be @@ -864,8 +865,7 @@ export function needsLocalHdf5Mapping(state: OxalisState, layerName: string) { // An annotation that has an editable mapping is likely proofread a lot. // Switching between tools should not require a reload which is why // needsLocalHdf5Mapping() will always return true in that case. - volumeTracing.hasEditableMapping || - state.uiInformation.activeTool === AnnotationToolEnum.PROOFREAD + volumeTracing.hasEditableMapping || state.uiInformation.activeTool === AnnotationTool.PROOFREAD ); } diff --git a/frontend/javascripts/oxalis/model/actions/ui_actions.ts b/frontend/javascripts/oxalis/model/actions/ui_actions.ts index 3cc188cffc3..a3587fdf385 100644 --- a/frontend/javascripts/oxalis/model/actions/ui_actions.ts +++ b/frontend/javascripts/oxalis/model/actions/ui_actions.ts @@ -1,4 +1,4 @@ -import type { AnnotationTool, OrthoView, Vector3 } from "oxalis/constants"; +import type { AnnotationToolType, OrthoView, Vector3 } from "oxalis/constants"; import type { BorderOpenStatus, OxalisState, Theme } from "oxalis/store"; import type { StartAIJobModalState } from "oxalis/view/action-bar/starting_job_modals"; @@ -107,7 +107,7 @@ export const setHasOrganizationsAction = (value: boolean) => type: "SET_HAS_ORGANIZATIONS", value, }) as const; -export const setToolAction = (tool: AnnotationTool) => +export const setToolAction = (tool: AnnotationToolType) => ({ type: "SET_TOOL", tool, diff --git a/frontend/javascripts/oxalis/model/reducers/reducer_helpers.ts b/frontend/javascripts/oxalis/model/reducers/reducer_helpers.ts index 7fd0a5c090f..fc17e2a3433 100644 --- a/frontend/javascripts/oxalis/model/reducers/reducer_helpers.ts +++ b/frontend/javascripts/oxalis/model/reducers/reducer_helpers.ts @@ -1,7 +1,7 @@ import Maybe from "data.maybe"; import * as Utils from "libs/utils"; -import { AnnotationToolEnum } from "oxalis/constants"; -import type { AnnotationTool, BoundingBoxType } from "oxalis/constants"; +import { AnnotationTool } from "oxalis/constants"; +import type { AnnotationToolType, BoundingBoxType } from "oxalis/constants"; import { getDisabledInfoForTools } from "oxalis/model/accessors/tool_accessor"; import { isVolumeAnnotationDisallowedForZoom, @@ -141,9 +141,9 @@ export function convertServerAdditionalAxesToFrontEnd( })); } -export function getNextTool(state: OxalisState): AnnotationTool | null { +export function getNextTool(state: OxalisState): AnnotationToolType | null { const disabledToolInfo = getDisabledInfoForTools(state); - const tools = Object.keys(AnnotationToolEnum) as AnnotationTool[]; + const tools = Object.values(AnnotationTool); const currentToolIndex = tools.indexOf(state.uiInformation.activeTool); // Search for the next tool which is not disabled. @@ -154,16 +154,16 @@ export function getNextTool(state: OxalisState): AnnotationTool | null { ) { const newTool = tools[newToolIndex % tools.length]; - if (!disabledToolInfo[newTool].isDisabled) { + if (!disabledToolInfo[newTool.id].isDisabled) { return newTool; } } return null; } -export function getPreviousTool(state: OxalisState): AnnotationTool | null { +export function getPreviousTool(state: OxalisState): AnnotationToolType | null { const disabledToolInfo = getDisabledInfoForTools(state); - const tools = Object.keys(AnnotationToolEnum) as AnnotationTool[]; + const tools = Object.values(AnnotationTool); const currentToolIndex = tools.indexOf(state.uiInformation.activeTool); // Search backwards for the next tool which is not disabled. @@ -174,7 +174,7 @@ export function getPreviousTool(state: OxalisState): AnnotationTool | null { ) { const newTool = tools[(tools.length + newToolIndex) % tools.length]; - if (!disabledToolInfo[newTool].isDisabled) { + if (!disabledToolInfo[newTool.id].isDisabled) { return newTool; } } diff --git a/frontend/javascripts/oxalis/model/reducers/skeletontracing_reducer.ts b/frontend/javascripts/oxalis/model/reducers/skeletontracing_reducer.ts index 7367dcdee98..723e454861d 100644 --- a/frontend/javascripts/oxalis/model/reducers/skeletontracing_reducer.ts +++ b/frontend/javascripts/oxalis/model/reducers/skeletontracing_reducer.ts @@ -4,7 +4,7 @@ import ColorGenerator from "libs/color_generator"; import Toast from "libs/toast"; import * as Utils from "libs/utils"; import _ from "lodash"; -import Constants, { AnnotationToolEnum, TreeTypeEnum } from "oxalis/constants"; +import Constants, { AnnotationTool, TreeTypeEnum } from "oxalis/constants"; import { findTreeByNodeId, getNodeAndTree, @@ -690,7 +690,7 @@ function SkeletonTracingReducer(state: OxalisState, action: Action): OxalisState return state; } const isProofreadingActive = - state.uiInformation.activeTool === AnnotationToolEnum.PROOFREAD; + state.uiInformation.activeTool === AnnotationTool.PROOFREAD; const treeType = isProofreadingActive ? TreeTypeEnum.AGGLOMERATE : TreeTypeEnum.DEFAULT; const sourceTreeMaybe = getNodeAndTree(skeletonTracing, sourceNodeId, null, treeType); const targetTreeMaybe = getNodeAndTree(skeletonTracing, targetNodeId, null, treeType); @@ -965,7 +965,7 @@ function SkeletonTracingReducer(state: OxalisState, action: Action): OxalisState case "MERGE_TREES": { const { sourceNodeId, targetNodeId } = action; const isProofreadingActive = - state.uiInformation.activeTool === AnnotationToolEnum.PROOFREAD; + state.uiInformation.activeTool === AnnotationTool.PROOFREAD; const treeType = isProofreadingActive ? TreeTypeEnum.AGGLOMERATE : TreeTypeEnum.DEFAULT; const oldTrees = skeletonTracing.trees; const mergeResult = mergeTrees(oldTrees, sourceNodeId, targetNodeId, treeType); diff --git a/frontend/javascripts/oxalis/model/reducers/ui_reducer.ts b/frontend/javascripts/oxalis/model/reducers/ui_reducer.ts index 181e8dbc86e..5a75a20ea87 100644 --- a/frontend/javascripts/oxalis/model/reducers/ui_reducer.ts +++ b/frontend/javascripts/oxalis/model/reducers/ui_reducer.ts @@ -1,4 +1,4 @@ -import { AnnotationToolEnum, AvailableToolsInViewMode } from "oxalis/constants"; +import { type AnnotationTool, AvailableToolsInViewMode } from "oxalis/constants"; import defaultState from "oxalis/default_state"; import type { Action } from "oxalis/model/actions/actions"; import { updateKey, updateKey2 } from "oxalis/model/helpers/deep_update"; @@ -69,7 +69,7 @@ function UiReducer(state: OxalisState, action: Action): OxalisState { case "SET_TOOL": { if (!state.annotation.restrictions.allowUpdate) { - if (AvailableToolsInViewMode.includes(AnnotationToolEnum[action.tool])) { + if ((AvailableToolsInViewMode as AnnotationTool[]).includes(action.tool)) { return setToolReducer(state, action.tool); } return state; diff --git a/frontend/javascripts/oxalis/model/sagas/annotation_tool_saga.ts b/frontend/javascripts/oxalis/model/sagas/annotation_tool_saga.ts index b3cf6f33633..946e7e5d692 100644 --- a/frontend/javascripts/oxalis/model/sagas/annotation_tool_saga.ts +++ b/frontend/javascripts/oxalis/model/sagas/annotation_tool_saga.ts @@ -1,4 +1,4 @@ -import { AnnotationToolEnum, MeasurementTools } from "oxalis/constants"; +import { AnnotationTool, MeasurementTools } from "oxalis/constants"; import { getToolClassForAnnotationTool } from "oxalis/controller/combinations/tool_controls"; import getSceneController from "oxalis/controller/scene_controller_provider"; import { @@ -45,7 +45,7 @@ export function* watchToolReset(): Saga { if (MeasurementTools.indexOf(activeTool) >= 0) { const sceneController = yield* call(() => getSceneController()); const geometry = - activeTool === AnnotationToolEnum.AREA_MEASUREMENT + activeTool === AnnotationTool.AREA_MEASUREMENT ? sceneController.areaMeasurementGeometry : sceneController.lineMeasurementGeometry; geometry.hide(); diff --git a/frontend/javascripts/oxalis/model/sagas/proofread_saga.ts b/frontend/javascripts/oxalis/model/sagas/proofread_saga.ts index d10bee7c37d..3a926bdb843 100644 --- a/frontend/javascripts/oxalis/model/sagas/proofread_saga.ts +++ b/frontend/javascripts/oxalis/model/sagas/proofread_saga.ts @@ -9,12 +9,7 @@ import { V3 } from "libs/mjs"; import Toast from "libs/toast"; import { SoftError, isBigInt, isNumberMap } from "libs/utils"; import _ from "lodash"; -import { - AnnotationToolEnum, - MappingStatusEnum, - TreeTypeEnum, - type Vector3, -} from "oxalis/constants"; +import { AnnotationTool, MappingStatusEnum, TreeTypeEnum, type Vector3 } from "oxalis/constants"; import { getSegmentIdForPositionAsync } from "oxalis/controller/combinations/volume_handlers"; import { getLayerByName, @@ -329,7 +324,7 @@ function* handleSkeletonProofreadingAction(action: Action): Saga { const isModifyingAnyAgglomerateSkeletons = sourceTree.type === TreeTypeEnum.AGGLOMERATE || targetTree.type === TreeTypeEnum.AGGLOMERATE; const isProofreadingToolActive = yield* select( - (state) => state.uiInformation.activeTool === AnnotationToolEnum.PROOFREAD, + (state) => state.uiInformation.activeTool === AnnotationTool.PROOFREAD, ); if (isProofreadingToolActive && !isModifyingOnlyAgglomerateSkeletons) { diff --git a/frontend/javascripts/oxalis/model/sagas/undo_saga.ts b/frontend/javascripts/oxalis/model/sagas/undo_saga.ts index 780862408cd..d3530c28af3 100644 --- a/frontend/javascripts/oxalis/model/sagas/undo_saga.ts +++ b/frontend/javascripts/oxalis/model/sagas/undo_saga.ts @@ -1,7 +1,7 @@ import createProgressCallback from "libs/progress_callback"; import Toast from "libs/toast"; import messages from "messages"; -import { AnnotationToolEnum } from "oxalis/constants"; +import { AnnotationTool } from "oxalis/constants"; import { enforceSkeletonTracing } from "oxalis/model/accessors/skeletontracing_accessor"; import { getUserBoundingBoxesFromState } from "oxalis/model/accessors/tracing_accessor"; import { @@ -554,7 +554,7 @@ function* applyStateOfStack( } const activeTool = yield* select((state) => state.uiInformation.activeTool); - if (activeTool === AnnotationToolEnum.PROOFREAD) { + if (activeTool === AnnotationTool.PROOFREAD) { const warningMessage = direction === "undo" ? messages["undo.no_undo_during_proofread"] diff --git a/frontend/javascripts/oxalis/model/sagas/volume/floodfill_saga.tsx b/frontend/javascripts/oxalis/model/sagas/volume/floodfill_saga.tsx index 9f80222789d..f66f2197243 100644 --- a/frontend/javascripts/oxalis/model/sagas/volume/floodfill_saga.tsx +++ b/frontend/javascripts/oxalis/model/sagas/volume/floodfill_saga.tsx @@ -10,7 +10,7 @@ import type { Vector2, Vector3, } from "oxalis/constants"; -import Constants, { AnnotationToolEnum, FillModeEnum, Unicode } from "oxalis/constants"; +import Constants, { AnnotationTool, FillModeEnum, Unicode } from "oxalis/constants"; import _ from "lodash"; import { getDatasetBoundingBox, getMagInfo } from "oxalis/model/accessors/dataset_accessor"; @@ -156,7 +156,7 @@ function* handleFloodFill(floodFillAction: FloodFillAction): Saga { const allowUpdate = yield* select((state) => state.annotation.restrictions.allowUpdate); const disabledInfosForTools = yield* select(getDisabledInfoForTools); - if (!allowUpdate || disabledInfosForTools[AnnotationToolEnum.FILL_CELL].isDisabled) { + if (!allowUpdate || disabledInfosForTools[AnnotationTool.FILL_CELL.id].isDisabled) { return; } diff --git a/frontend/javascripts/oxalis/model/sagas/volumetracing_saga.tsx b/frontend/javascripts/oxalis/model/sagas/volumetracing_saga.tsx index c78880a664d..a53d1d625e5 100644 --- a/frontend/javascripts/oxalis/model/sagas/volumetracing_saga.tsx +++ b/frontend/javascripts/oxalis/model/sagas/volumetracing_saga.tsx @@ -3,19 +3,8 @@ import { V3 } from "libs/mjs"; import Toast from "libs/toast"; import _ from "lodash"; import memoizeOne from "memoize-one"; -import type { - AnnotationTool, - ContourMode, - OrthoView, - OverwriteMode, - Vector3, -} from "oxalis/constants"; -import { - AnnotationToolEnum, - ContourModeEnum, - OrthoViews, - OverwriteModeEnum, -} from "oxalis/constants"; +import type { ContourMode, OrthoView, OverwriteMode, Vector3 } from "oxalis/constants"; +import { AnnotationTool, ContourModeEnum, OrthoViews, OverwriteModeEnum } from "oxalis/constants"; import getSceneController from "oxalis/controller/scene_controller_provider"; import { CONTOUR_COLOR_DELETE, CONTOUR_COLOR_NORMAL } from "oxalis/geometries/helper_geometries"; @@ -194,7 +183,7 @@ export function* editVolumeLayerAsync(): Saga { continue; } - if (activeTool === AnnotationToolEnum.MOVE) { + if (activeTool === AnnotationTool.MOVE) { // This warning can be helpful when debugging tests. console.warn("Volume actions are ignored since current tool is the move tool."); continue; @@ -403,7 +392,7 @@ export function* ensureToolIsAllowedInMag(): Saga { }); if (isMagTooLow) { - yield* put(setToolAction(AnnotationToolEnum.MOVE)); + yield* put(setToolAction(AnnotationTool.MOVE)); } } } diff --git a/frontend/javascripts/oxalis/model_initialization.ts b/frontend/javascripts/oxalis/model_initialization.ts index c7ec8433e33..ec8bd0c3ba9 100644 --- a/frontend/javascripts/oxalis/model_initialization.ts +++ b/frontend/javascripts/oxalis/model_initialization.ts @@ -19,7 +19,7 @@ import Toast from "libs/toast"; import * as Utils from "libs/utils"; import _ from "lodash"; import messages from "messages"; -import constants, { ControlModeEnum, AnnotationToolEnum, type Vector3 } from "oxalis/constants"; +import constants, { ControlModeEnum, AnnotationTool, type Vector3 } from "oxalis/constants"; import type { PartialUrlManagerState, UrlStateByLayer } from "oxalis/controller/url_manager"; import UrlManager from "oxalis/controller/url_manager"; import { @@ -409,7 +409,7 @@ function setInitialTool() { // We are in a annotation which contains a skeleton. Due to the // enabled legacy-bindings, the user can expect to immediately create new nodes // with right click. Therefore, switch to the skeleton tool. - Store.dispatch(setToolAction(AnnotationToolEnum.SKELETON)); + Store.dispatch(setToolAction(AnnotationTool.SKELETON)); } } diff --git a/frontend/javascripts/oxalis/store.ts b/frontend/javascripts/oxalis/store.ts index fedae95875a..22446e7f9cf 100644 --- a/frontend/javascripts/oxalis/store.ts +++ b/frontend/javascripts/oxalis/store.ts @@ -1,7 +1,7 @@ import type DiffableMap from "libs/diffable_map"; import type { Matrix4x4 } from "libs/mjs"; import type { - AnnotationTool, + AnnotationToolType, BoundingBoxType, ContourMode, ControlMode, @@ -557,7 +557,7 @@ type UiInformation = { readonly showAddScriptModal: boolean; readonly aIJobModalState: StartAIJobModalState; readonly showRenderAnimationModal: boolean; - readonly activeTool: AnnotationTool; + readonly activeTool: AnnotationToolType; readonly activeUserBoundingBoxId: number | null | undefined; readonly storedLayouts: Record; readonly isImportingMesh: boolean; diff --git a/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx b/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx index b130684a083..f0a9cc6d961 100644 --- a/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx +++ b/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx @@ -24,8 +24,7 @@ import { useDispatch, useSelector } from "react-redux"; import { useKeyPress, usePrevious } from "libs/react_hooks"; import { document } from "libs/window"; import { - type AnnotationTool, - AnnotationToolEnum, + AnnotationTool, FillModeEnum, type InterpolationMode, InterpolationModeEnum, @@ -40,7 +39,7 @@ import { } from "oxalis/constants"; import { getActiveTree } from "oxalis/model/accessors/skeletontracing_accessor"; import { - TOOL_NAMES, + type AnnotationToolType, adaptActiveToolToShortcuts, getDisabledInfoForTools, } from "oxalis/model/accessors/tool_accessor"; @@ -860,7 +859,7 @@ export default function ToolbarView() { const toolWorkspace = useSelector((state: OxalisState) => state.userConfiguration.toolWorkspace); const [lastForcefullyDisabledTool, setLastForcefullyDisabledTool] = - useState(null); + useState(null); const activeTool = useSelector((state: OxalisState) => state.uiInformation.activeTool); @@ -869,24 +868,24 @@ export default function ToolbarView() { // Even though the volume toolbar is disabled, the user can still cycle through // the tools via the w shortcut. In that case, the effect-hook is re-executed // and the tool is switched to MOVE. - const disabledInfoForCurrentTool = disabledInfosForTools[activeTool]; + const disabledInfoForCurrentTool = disabledInfosForTools[activeTool.id]; const isLastForcefullyDisabledToolAvailable = lastForcefullyDisabledTool != null && - !disabledInfosForTools[lastForcefullyDisabledTool].isDisabled; + !disabledInfosForTools[lastForcefullyDisabledTool.id].isDisabled; useEffect(() => { if (disabledInfoForCurrentTool.isDisabled) { setLastForcefullyDisabledTool(activeTool); - Store.dispatch(setToolAction(AnnotationToolEnum.MOVE)); + Store.dispatch(setToolAction(AnnotationTool.MOVE)); } else if ( lastForcefullyDisabledTool != null && isLastForcefullyDisabledToolAvailable && - activeTool === AnnotationToolEnum.MOVE + activeTool === AnnotationTool.MOVE ) { // Re-enable the tool that was disabled before. setLastForcefullyDisabledTool(null); Store.dispatch(setToolAction(lastForcefullyDisabledTool)); - } else if (activeTool !== AnnotationToolEnum.MOVE) { + } else if (activeTool !== AnnotationTool.MOVE) { // Forget the last disabled tool as another tool besides the move tool was selected. setLastForcefullyDisabledTool(null); } @@ -976,18 +975,18 @@ function ToolSpecificSettings({ isShiftPressed, }: { hasSkeleton: boolean; - adaptedActiveTool: AnnotationTool; + adaptedActiveTool: AnnotationToolType; hasVolume: boolean; isControlOrMetaPressed: boolean; isShiftPressed: boolean; }) { - const showSkeletonButtons = hasSkeleton && adaptedActiveTool === AnnotationToolEnum.SKELETON; - const showNewBoundingBoxButton = adaptedActiveTool === AnnotationToolEnum.BOUNDING_BOX; + const showSkeletonButtons = hasSkeleton && adaptedActiveTool === AnnotationTool.SKELETON; + const showNewBoundingBoxButton = adaptedActiveTool === AnnotationTool.BOUNDING_BOX; const showCreateCellButton = hasVolume && VolumeTools.includes(adaptedActiveTool); const showChangeBrushSizeButton = showCreateCellButton && - (adaptedActiveTool === AnnotationToolEnum.BRUSH || - adaptedActiveTool === AnnotationToolEnum.ERASE_BRUSH); + (adaptedActiveTool === AnnotationTool.BRUSH || + adaptedActiveTool === AnnotationTool.ERASE_BRUSH); const dispatch = useDispatch(); const quickSelectConfig = useSelector( (state: OxalisState) => state.userConfiguration.quickSelect, @@ -1040,7 +1039,10 @@ function ToolSpecificSettings({ visible={ToolsWithOverwriteCapabilities.includes(adaptedActiveTool)} /> - {adaptedActiveTool === "QUICK_SELECT" && ( + { + // todop: search for Tool.id to get these? + } + {adaptedActiveTool.id === "QUICK_SELECT" && ( <> ) : null} - {adaptedActiveTool === AnnotationToolEnum.FILL_CELL ? : null} + {adaptedActiveTool === AnnotationTool.FILL_CELL ? : null} - {adaptedActiveTool === AnnotationToolEnum.PROOFREAD && areEditableMappingsEnabled ? ( + {adaptedActiveTool === AnnotationTool.PROOFREAD && areEditableMappingsEnabled ? ( ) : null} @@ -1279,7 +1281,7 @@ function MeasurementToolSwitch({ activeTool }: { activeTool: AnnotationTool }) { Measurement Tool Icon @@ -1288,7 +1290,7 @@ function MeasurementToolSwitch({ activeTool }: { activeTool: AnnotationTool }) { "Measure areas by using Left Drag. Avoid self-crossing polygon structure for accurate results." } style={NARROW_BUTTON_STYLE} - value={AnnotationToolEnum.AREA_MEASUREMENT} + value={AnnotationTool.AREA_MEASUREMENT.id} > @@ -1333,15 +1335,15 @@ function SkeletonTool() { return ( @@ -1355,7 +1357,7 @@ function getIsVolumeModificationAllowed(state: OxalisState) { return hasVolume && !isReadOnly && !hasEditableMapping(state); } -function BrushTool({ adaptedActiveTool }: { adaptedActiveTool: AnnotationTool }) { +function BrushTool({ adaptedActiveTool }: { adaptedActiveTool: AnnotationToolType }) { const disabledInfosForTools = useSelector(getDisabledInfoForTools); const isVolumeModificationAllowed = useSelector(getIsVolumeModificationAllowed); if (!isVolumeModificationAllowed) { @@ -1363,32 +1365,29 @@ function BrushTool({ adaptedActiveTool }: { adaptedActiveTool: AnnotationTool }) } return ( - {adaptedActiveTool === AnnotationToolEnum.BRUSH ? ( - - ) : null} + {adaptedActiveTool === AnnotationTool.BRUSH ? : null} ); } -function EraseBrushTool({ adaptedActiveTool }: { adaptedActiveTool: AnnotationTool }) { +function EraseBrushTool({ adaptedActiveTool }: { adaptedActiveTool: AnnotationToolType }) { const disabledInfosForTools = useSelector(getDisabledInfoForTools); const showEraseTraceTool = - adaptedActiveTool === AnnotationToolEnum.TRACE || - adaptedActiveTool === AnnotationToolEnum.ERASE_TRACE; + adaptedActiveTool === AnnotationTool.TRACE || adaptedActiveTool === AnnotationTool.ERASE_TRACE; const showEraseBrushTool = !showEraseTraceTool; const isVolumeModificationAllowed = useSelector(getIsVolumeModificationAllowed); @@ -1398,31 +1397,31 @@ function EraseBrushTool({ adaptedActiveTool }: { adaptedActiveTool: AnnotationTo return ( - {adaptedActiveTool === AnnotationToolEnum.ERASE_BRUSH ? ( + {adaptedActiveTool === AnnotationTool.ERASE_BRUSH ? ( ) : null} ); } -function TraceTool({ adaptedActiveTool }: { adaptedActiveTool: AnnotationTool }) { +function TraceTool({ adaptedActiveTool }: { adaptedActiveTool: AnnotationToolType }) { const disabledInfosForTools = useSelector(getDisabledInfoForTools); const isVolumeModificationAllowed = useSelector(getIsVolumeModificationAllowed); if (!isVolumeModificationAllowed) { @@ -1430,33 +1429,30 @@ function TraceTool({ adaptedActiveTool }: { adaptedActiveTool: AnnotationTool }) } return ( Trace Tool Icon - {adaptedActiveTool === AnnotationToolEnum.TRACE ? ( - - ) : null} + {adaptedActiveTool === AnnotationTool.TRACE ? : null} ); } -function EraseTraceTool({ adaptedActiveTool }: { adaptedActiveTool: AnnotationTool }) { +function EraseTraceTool({ adaptedActiveTool }: { adaptedActiveTool: AnnotationToolType }) { const disabledInfosForTools = useSelector(getDisabledInfoForTools); const showEraseTraceTool = - adaptedActiveTool === AnnotationToolEnum.TRACE || - adaptedActiveTool === AnnotationToolEnum.ERASE_TRACE; + adaptedActiveTool === AnnotationTool.TRACE || adaptedActiveTool === AnnotationTool.ERASE_TRACE; const isVolumeModificationAllowed = useSelector(getIsVolumeModificationAllowed); if (!isVolumeModificationAllowed) { return null; @@ -1464,31 +1460,31 @@ function EraseTraceTool({ adaptedActiveTool }: { adaptedActiveTool: AnnotationTo return ( - {adaptedActiveTool === AnnotationToolEnum.ERASE_TRACE ? ( + {adaptedActiveTool === AnnotationTool.ERASE_TRACE ? ( ) : null} ); } -function FillCellTool({ adaptedActiveTool }: { adaptedActiveTool: AnnotationTool }) { +function FillCellTool({ adaptedActiveTool }: { adaptedActiveTool: AnnotationToolType }) { const disabledInfosForTools = useSelector(getDisabledInfoForTools); const isVolumeModificationAllowed = useSelector(getIsVolumeModificationAllowed); if (!isVolumeModificationAllowed) { @@ -1497,20 +1493,20 @@ function FillCellTool({ adaptedActiveTool }: { adaptedActiveTool: AnnotationTool return ( - {adaptedActiveTool === AnnotationToolEnum.FILL_CELL ? ( + {adaptedActiveTool === AnnotationTool.FILL_CELL ? ( ) : null} @@ -1525,16 +1521,16 @@ function PickCellTool() { } return ( @@ -1549,17 +1545,17 @@ function QuickSelectTool() { } return ( Quick Select Icon @@ -1577,17 +1573,17 @@ function BoundingBoxTool() { } return ( Bounding Box Icon @@ -1613,22 +1609,22 @@ function ProofreadTool() { return ( { dispatch(ensureLayerMappingsAreLoadedAction()); }} @@ -1636,7 +1632,7 @@ function ProofreadTool() { @@ -1647,11 +1643,11 @@ function ProofreadTool() { function LineMeasurementTool() { return ( diff --git a/frontend/javascripts/oxalis/view/components/command_palette.tsx b/frontend/javascripts/oxalis/view/components/command_palette.tsx index 35abc014f4c..a820d5461f7 100644 --- a/frontend/javascripts/oxalis/view/components/command_palette.tsx +++ b/frontend/javascripts/oxalis/view/components/command_palette.tsx @@ -3,7 +3,7 @@ import { capitalize, getPhraseFromCamelCaseString } from "libs/utils"; import * as Utils from "libs/utils"; import _ from "lodash"; import { getAdministrationSubMenu } from "navbar"; -import { AnnotationToolEnum, AvailableToolsInViewMode } from "oxalis/constants"; +import { AnnotationTool, AvailableToolsInViewMode } from "oxalis/constants"; import { getLabelForTool } from "oxalis/model/accessors/tool_accessor"; import { updateUserSettingAction } from "oxalis/model/actions/settings_actions"; import { setToolAction } from "oxalis/model/actions/ui_actions"; @@ -159,9 +159,9 @@ export const CommandPalette = ({ label }: { label: string | JSX.Element | null } const getToolEntries = () => { if (!isInTracingView) return []; const commands: CommandWithoutId[] = []; - let availableTools = Object.keys(AnnotationToolEnum) as [keyof typeof AnnotationToolEnum]; + let availableTools = Object.values(AnnotationTool); if (isViewMode || !restrictions.allowUpdate) { - availableTools = AvailableToolsInViewMode as [keyof typeof AnnotationToolEnum]; + availableTools = AvailableToolsInViewMode; } availableTools.forEach((tool) => { commands.push({ diff --git a/frontend/javascripts/oxalis/view/context_menu.tsx b/frontend/javascripts/oxalis/view/context_menu.tsx index 5438c759af2..5291707b8c6 100644 --- a/frontend/javascripts/oxalis/view/context_menu.tsx +++ b/frontend/javascripts/oxalis/view/context_menu.tsx @@ -27,8 +27,7 @@ import { hexToRgb, rgbToHex, roundTo, truncateStringToLength } from "libs/utils" import messages from "messages"; import { AltOrOptionKey, - type AnnotationTool, - AnnotationToolEnum, + AnnotationTool, CtrlOrCmdKey, LongUnitToShortUnitMap, type OrthoView, @@ -58,7 +57,10 @@ import { getNodePosition, isSkeletonLayerTransformed, } from "oxalis/model/accessors/skeletontracing_accessor"; -import { getDisabledInfoForTools } from "oxalis/model/accessors/tool_accessor"; +import { + type AnnotationToolType, + getDisabledInfoForTools, +} from "oxalis/model/accessors/tool_accessor"; import { maybeGetSomeTracing } from "oxalis/model/accessors/tracing_accessor"; import { getActiveCellId, @@ -166,7 +168,7 @@ type StateProps = { currentMeshFile: APIMeshFile | null | undefined; currentConnectomeFile: APIConnectomeFile | null | undefined; volumeTracing: VolumeTracing | null | undefined; - activeTool: AnnotationTool; + activeTool: AnnotationToolType; useLegacyBindings: boolean; userBoundingBoxes: Array; mappingInfo: ActiveMappingInfo; @@ -184,7 +186,7 @@ type NodeContextMenuOptionsProps = Props & { type NoNodeContextMenuProps = Props & { viewport: OrthoView; segmentIdAtPosition: number; - activeTool: AnnotationTool; + activeTool: AnnotationToolType; infoRows: ItemType[]; }; @@ -416,7 +418,7 @@ function getMeshItems( return []; } const state = Store.getState(); - const isProofreadingActive = state.uiInformation.activeTool === AnnotationToolEnum.PROOFREAD; + const isProofreadingActive = state.uiInformation.activeTool === AnnotationTool.PROOFREAD; const activeCellId = getActiveCellId(volumeTracing); const { activeUnmappedSegmentId } = volumeTracing; const segments = getSegmentsForLayer(state, volumeTracing.tracingId); @@ -571,7 +573,7 @@ function getNodeContextMenuOptions({ currentMeshFile, }: NodeContextMenuOptionsProps): ItemType[] { const state = Store.getState(); - const isProofreadingActive = state.uiInformation.activeTool === AnnotationToolEnum.PROOFREAD; + const isProofreadingActive = state.uiInformation.activeTool === AnnotationTool.PROOFREAD; const isVolumeModificationAllowed = !hasEditableMapping(state); if (skeletonTracing == null) { @@ -774,7 +776,7 @@ function getBoundingBoxMenuOptions({ }: NoNodeContextMenuProps): ItemType[] { if (globalPosition == null) return []; - const isBoundingBoxToolActive = activeTool === AnnotationToolEnum.BOUNDING_BOX; + const isBoundingBoxToolActive = activeTool === AnnotationTool.BOUNDING_BOX; const newBoundingBoxMenuItem: ItemType = { key: "add-new-bounding-box", onClick: () => { @@ -943,7 +945,7 @@ function getNoNodeContextMenuOptions(props: NoNodeContextMenuProps): ItemType[] const isAgglomerateMappingEnabled = hasAgglomerateMapping(state); const isConnectomeMappingEnabled = hasConnectomeFile(state); - const isProofreadingActive = state.uiInformation.activeTool === AnnotationToolEnum.PROOFREAD; + const isProofreadingActive = state.uiInformation.activeTool === AnnotationTool.PROOFREAD; Store.dispatch(maybeFetchMeshFilesAction(visibleSegmentationLayer, dataset, false)); @@ -1021,7 +1023,7 @@ function getNoNodeContextMenuOptions(props: NoNodeContextMenuProps): ItemType[] }); const isVolumeBasedToolActive = VolumeTools.includes(activeTool); - const isBoundingBoxToolActive = activeTool === AnnotationToolEnum.BOUNDING_BOX; + const isBoundingBoxToolActive = activeTool === AnnotationTool.BOUNDING_BOX; const skeletonActions: ItemType[] = skeletonTracing != null && globalPosition != null && allowUpdate ? [ @@ -1235,7 +1237,7 @@ function getNoNodeContextMenuOptions(props: NoNodeContextMenuProps): ItemType[] : []; const boundingBoxActions = getBoundingBoxMenuOptions(props); - const isSkeletonToolActive = activeTool === AnnotationToolEnum.SKELETON; + const isSkeletonToolActive = activeTool === AnnotationTool.SKELETON; let allActions: ItemType[] = []; const meshRelatedItems = getMeshItems( diff --git a/frontend/javascripts/oxalis/view/distance_measurement_tooltip.tsx b/frontend/javascripts/oxalis/view/distance_measurement_tooltip.tsx index 4bb5f5a8d1f..630653a71d8 100644 --- a/frontend/javascripts/oxalis/view/distance_measurement_tooltip.tsx +++ b/frontend/javascripts/oxalis/view/distance_measurement_tooltip.tsx @@ -9,7 +9,7 @@ import { } from "libs/format_utils"; import { clamp } from "libs/utils"; import { - AnnotationToolEnum, + AnnotationTool, LongUnitToShortUnitMap, MeasurementTools, type Vector3, @@ -60,7 +60,7 @@ export default function DistanceMeasurementTooltip() { const currentPosition = getPosition(flycam); const { areaMeasurementGeometry, lineMeasurementGeometry } = getSceneController(); const activeGeometry = - activeTool === AnnotationToolEnum.LINE_MEASUREMENT + activeTool === AnnotationTool.LINE_MEASUREMENT ? lineMeasurementGeometry : areaMeasurementGeometry; const orthoView = activeGeometry.viewport; @@ -91,14 +91,14 @@ export default function DistanceMeasurementTooltip() { let valueInMetricUnit = ""; const notScalingFactor = [1, 1, 1] as Vector3; - if (activeTool === AnnotationToolEnum.LINE_MEASUREMENT) { + if (activeTool === AnnotationTool.LINE_MEASUREMENT) { const { lineMeasurementGeometry } = getSceneController(); valueInVx = formatLengthAsVx(lineMeasurementGeometry.getDistance(notScalingFactor), 1); valueInMetricUnit = formatNumberToLength( lineMeasurementGeometry.getDistance(voxelSize.factor), LongUnitToShortUnitMap[voxelSize.unit], ); - } else if (activeTool === AnnotationToolEnum.AREA_MEASUREMENT) { + } else if (activeTool === AnnotationTool.AREA_MEASUREMENT) { const { areaMeasurementGeometry } = getSceneController(); valueInVx = formatAreaAsVx(areaMeasurementGeometry.getArea(notScalingFactor), 1); valueInMetricUnit = formatNumberToArea( diff --git a/frontend/javascripts/oxalis/view/input_catcher.tsx b/frontend/javascripts/oxalis/view/input_catcher.tsx index 90cc29d3eec..1be91cada25 100644 --- a/frontend/javascripts/oxalis/view/input_catcher.tsx +++ b/frontend/javascripts/oxalis/view/input_catcher.tsx @@ -2,12 +2,7 @@ import { useEffectOnlyOnce, useKeyPress } from "libs/react_hooks"; import { waitForCondition } from "libs/utils"; import _ from "lodash"; import type { Rect, Viewport, ViewportRects } from "oxalis/constants"; -import { - AnnotationToolEnum, - ArbitraryViewport, - ArbitraryViews, - OrthoViews, -} from "oxalis/constants"; +import { AnnotationTool, ArbitraryViewport, ArbitraryViews, OrthoViews } from "oxalis/constants"; import { adaptActiveToolToShortcuts } from "oxalis/model/accessors/tool_accessor"; import { setInputCatcherRects } from "oxalis/model/actions/view_mode_actions"; import type { BusyBlockingInfo, OxalisState } from "oxalis/store"; @@ -97,6 +92,7 @@ export function recalculateInputCatcherSizes() { } } +// todop const cursorForTool = { MOVE: "move", SKELETON: "crosshair", @@ -142,9 +138,9 @@ function InputCatcher({ const adaptedTool = viewportID === ArbitraryViews.arbitraryViewport - ? AnnotationToolEnum.SKELETON + ? AnnotationTool.SKELETON : viewportID === OrthoViews.TDView - ? AnnotationToolEnum.MOVE + ? AnnotationTool.MOVE : adaptActiveToolToShortcuts( activeTool, isShiftPressed, @@ -160,7 +156,7 @@ function InputCatcher({
{ /> ); - const isProofreadingMode = this.props.activeTool === "PROOFREAD"; + const isProofreadingMode = this.props.activeTool === AnnotationTool.PROOFREAD; const isSelectiveVisibilityDisabled = isProofreadingMode; const selectiveVisibilitySwitch = ( diff --git a/frontend/javascripts/oxalis/view/plane_view.ts b/frontend/javascripts/oxalis/view/plane_view.ts index 7651c6a1c86..9f363f3e5a8 100644 --- a/frontend/javascripts/oxalis/view/plane_view.ts +++ b/frontend/javascripts/oxalis/view/plane_view.ts @@ -3,7 +3,12 @@ import VisibilityAwareRaycaster from "libs/visibility_aware_raycaster"; import window from "libs/window"; import _ from "lodash"; import type { OrthoViewMap, Vector2, Vector3, Viewport } from "oxalis/constants"; -import Constants, { OrthoViewColors, OrthoViewValues, OrthoViews } from "oxalis/constants"; +import Constants, { + AnnotationTool, + OrthoViewColors, + OrthoViewValues, + OrthoViews, +} from "oxalis/constants"; import type { VertexSegmentMapping } from "oxalis/controller/mesh_helpers"; import getSceneController, { getSceneControllerOrNull, @@ -183,7 +188,7 @@ class PlaneView { // Check whether we are hitting the same object as before, since we can return early // in this case. - if (storeState.uiInformation.activeTool === "PROOFREAD") { + if (storeState.uiInformation.activeTool === AnnotationTool.PROOFREAD) { if (hitObject == null && oldRaycasterHit == null) { return null; } @@ -321,7 +326,7 @@ class PlaneView { // If the proofreading tool is not active, pretend that // activeUnmappedSegmentId is null so that no super-voxel // is highlighted. - return storeState.uiInformation.activeTool === "PROOFREAD" + return storeState.uiInformation.activeTool === AnnotationTool.PROOFREAD ? segmentationTracing.activeUnmappedSegmentId : null; }, diff --git a/frontend/javascripts/oxalis/view/statusbar.tsx b/frontend/javascripts/oxalis/view/statusbar.tsx index ca51444ba9d..84083690d76 100644 --- a/frontend/javascripts/oxalis/view/statusbar.tsx +++ b/frontend/javascripts/oxalis/view/statusbar.tsx @@ -18,7 +18,7 @@ import { hasVisibleUint64Segmentation, } from "oxalis/model/accessors/dataset_accessor"; import { getActiveMagInfo } from "oxalis/model/accessors/flycam_accessor"; -import { adaptActiveToolToShortcuts } from "oxalis/model/accessors/tool_accessor"; +import { adaptActiveToolToShortcuts, AnnotationTool } from "oxalis/model/accessors/tool_accessor"; import { calculateGlobalPos, isPlaneMode as getIsPlaneMode, @@ -194,8 +194,11 @@ function ShortcutsInfo() { if (!isPlaneMode) { let actionDescriptor = null; if (hasSkeleton && isShiftPressed) { - actionDescriptor = getToolClassForAnnotationTool("SKELETON").getActionDescriptors( - "SKELETON", + // todop + actionDescriptor = getToolClassForAnnotationTool( + AnnotationTool.SKELETON, + ).getActionDescriptors( + AnnotationTool.SKELETON, useLegacyBindings, isShiftPressed, isControlOrMetaPressed, diff --git a/frontend/javascripts/test/api/api_volume_latest.spec.ts b/frontend/javascripts/test/api/api_volume_latest.spec.ts index 0da73f65f5f..1e946c73024 100644 --- a/frontend/javascripts/test/api/api_volume_latest.spec.ts +++ b/frontend/javascripts/test/api/api_volume_latest.spec.ts @@ -1,6 +1,6 @@ // @ts-nocheck import "test/mocks/lz4"; -import { AnnotationToolEnum } from "oxalis/constants"; +import { AnnotationTool } from "oxalis/constants"; import { __setupOxalis } from "test/helpers/apiHelpers"; import test from "ava"; import window from "libs/window"; @@ -21,14 +21,14 @@ test("setActiveCell should set the active segment id", (t) => { }); test("getAnnotationTool should get the current tool", (t) => { const { api } = t.context; - t.is(api.tracing.getAnnotationTool(), AnnotationToolEnum.MOVE); + t.is(api.tracing.getAnnotationTool(), AnnotationTool.MOVE); }); test("setAnnotationTool should set the current tool", (t) => { const { api } = t.context; - api.tracing.setAnnotationTool(AnnotationToolEnum.TRACE); - t.is(api.tracing.getAnnotationTool(), AnnotationToolEnum.TRACE); - api.tracing.setAnnotationTool(AnnotationToolEnum.BRUSH); - t.is(api.tracing.getAnnotationTool(), AnnotationToolEnum.BRUSH); + api.tracing.setAnnotationTool(AnnotationTool.TRACE); + t.is(api.tracing.getAnnotationTool(), AnnotationTool.TRACE); + api.tracing.setAnnotationTool(AnnotationTool.BRUSH); + t.is(api.tracing.getAnnotationTool(), AnnotationTool.BRUSH); }); test("setAnnotationTool should throw an error for an invalid tool", (t) => { const { api } = t.context; diff --git a/frontend/javascripts/test/fixtures/volumetracing_object.ts b/frontend/javascripts/test/fixtures/volumetracing_object.ts index 1d828556996..6b94d53fcf3 100644 --- a/frontend/javascripts/test/fixtures/volumetracing_object.ts +++ b/frontend/javascripts/test/fixtures/volumetracing_object.ts @@ -1,11 +1,11 @@ import update from "immutability-helper"; -import Constants, { AnnotationToolEnum } from "oxalis/constants"; +import Constants, { AnnotationTool } from "oxalis/constants"; import defaultState from "oxalis/default_state"; const volumeTracing = { type: "volume", activeCellId: 0, - activeTool: AnnotationToolEnum.MOVE, + activeTool: AnnotationTool.MOVE, largestSegmentId: 0, contourList: [], lastLabelActions: [], diff --git a/frontend/javascripts/test/reducers/volumetracing_reducer.spec.ts b/frontend/javascripts/test/reducers/volumetracing_reducer.spec.ts index 093d6e2258d..eb7ee431785 100644 --- a/frontend/javascripts/test/reducers/volumetracing_reducer.spec.ts +++ b/frontend/javascripts/test/reducers/volumetracing_reducer.spec.ts @@ -1,7 +1,7 @@ import "test/mocks/lz4"; import update from "immutability-helper"; import Maybe from "data.maybe"; -import { AnnotationToolEnum, type Vector3 } from "oxalis/constants"; +import { AnnotationTool, type Vector3 } from "oxalis/constants"; import * as VolumeTracingActions from "oxalis/model/actions/volumetracing_actions"; import * as UiActions from "oxalis/model/actions/ui_actions"; import VolumeTracingReducer from "oxalis/model/reducers/volumetracing_reducer"; @@ -135,15 +135,15 @@ test("VolumeTracing should create cells and only update the largestSegmentId aft }); test("VolumeTracing should set trace/view tool", (t) => { - const setToolAction = UiActions.setToolAction(AnnotationToolEnum.TRACE); + const setToolAction = UiActions.setToolAction(AnnotationTool.TRACE); // Change tool to Trace const newState = UiReducer(initialState, setToolAction); t.not(newState, initialState); - t.is(newState.uiInformation.activeTool, AnnotationToolEnum.TRACE); + t.is(newState.uiInformation.activeTool, AnnotationTool.TRACE); }); test("VolumeTracing should not allow to set trace tool if getActiveMagIndexForLayer(zoomStep, 'tracingId') is > 1", (t) => { - const setToolAction = UiActions.setToolAction(AnnotationToolEnum.TRACE); + const setToolAction = UiActions.setToolAction(AnnotationTool.TRACE); const alteredState = update(initialState, { flycam: { zoomStep: { @@ -157,7 +157,7 @@ test("VolumeTracing should not allow to set trace tool if getActiveMagIndexForLa const newState = UiReducer(alteredState, setToolAction); t.is(alteredState, newState); // Tool should not have changed - t.is(newState.uiInformation.activeTool, AnnotationToolEnum.MOVE); + t.is(newState.uiInformation.activeTool, AnnotationTool.MOVE); }); test("VolumeTracing should cycle trace/view/brush tool", (t) => { @@ -165,29 +165,29 @@ test("VolumeTracing should cycle trace/view/brush tool", (t) => { // Cycle tool to Brush let newState = UiReducer(initialState, cycleToolAction()); - t.is(newState.uiInformation.activeTool, AnnotationToolEnum.BRUSH); + t.is(newState.uiInformation.activeTool, AnnotationTool.BRUSH); newState = UiReducer(newState, cycleToolAction()); - t.is(newState.uiInformation.activeTool, AnnotationToolEnum.ERASE_BRUSH); + t.is(newState.uiInformation.activeTool, AnnotationTool.ERASE_BRUSH); // Cycle tool to Trace newState = UiReducer(newState, cycleToolAction()); - t.is(newState.uiInformation.activeTool, AnnotationToolEnum.TRACE); + t.is(newState.uiInformation.activeTool, AnnotationTool.TRACE); newState = UiReducer(newState, cycleToolAction()); - t.is(newState.uiInformation.activeTool, AnnotationToolEnum.ERASE_TRACE); + t.is(newState.uiInformation.activeTool, AnnotationTool.ERASE_TRACE); newState = UiReducer(newState, cycleToolAction()); - t.is(newState.uiInformation.activeTool, AnnotationToolEnum.FILL_CELL); + t.is(newState.uiInformation.activeTool, AnnotationTool.FILL_CELL); newState = UiReducer(newState, cycleToolAction()); - t.is(newState.uiInformation.activeTool, AnnotationToolEnum.PICK_CELL); + t.is(newState.uiInformation.activeTool, AnnotationTool.PICK_CELL); newState = UiReducer(newState, cycleToolAction()); - t.is(newState.uiInformation.activeTool, AnnotationToolEnum.QUICK_SELECT); + t.is(newState.uiInformation.activeTool, AnnotationTool.QUICK_SELECT); newState = UiReducer(newState, cycleToolAction()); - t.is(newState.uiInformation.activeTool, AnnotationToolEnum.BOUNDING_BOX); + t.is(newState.uiInformation.activeTool, AnnotationTool.BOUNDING_BOX); newState = UiReducer(newState, cycleToolAction()); - t.is(newState.uiInformation.activeTool, AnnotationToolEnum.LINE_MEASUREMENT); + t.is(newState.uiInformation.activeTool, AnnotationTool.LINE_MEASUREMENT); newState = UiReducer(newState, cycleToolAction()); - t.is(newState.uiInformation.activeTool, AnnotationToolEnum.AREA_MEASUREMENT); + t.is(newState.uiInformation.activeTool, AnnotationTool.AREA_MEASUREMENT); // Cycle tool back to MOVE newState = UiReducer(newState, cycleToolAction()); - t.is(newState.uiInformation.activeTool, AnnotationToolEnum.MOVE); + t.is(newState.uiInformation.activeTool, AnnotationTool.MOVE); }); test("VolumeTracing should update its lastLabelActions", (t) => { diff --git a/frontend/javascripts/test/sagas/annotation_tool_disabled_info.spec.ts b/frontend/javascripts/test/sagas/annotation_tool_disabled_info.spec.ts index 11b828fa2b0..61b65d935b0 100644 --- a/frontend/javascripts/test/sagas/annotation_tool_disabled_info.spec.ts +++ b/frontend/javascripts/test/sagas/annotation_tool_disabled_info.spec.ts @@ -3,12 +3,12 @@ import update from "immutability-helper"; import test from "ava"; import { getDisabledInfoForTools } from "oxalis/model/accessors/tool_accessor"; import { initialState } from "test/fixtures/hybridtracing_object"; -import { AnnotationToolEnum, VolumeTools } from "oxalis/constants"; +import { AnnotationTool, VolumeTools } from "oxalis/constants"; import type { CoordinateTransformation } from "types/api_flow_types"; const zoomSensitiveVolumeTools = VolumeTools.filter( - (name) => name !== AnnotationToolEnum.PICK_CELL, -) as AnnotationToolEnum[]; + (name) => name !== AnnotationTool.PICK_CELL, +) as AnnotationTool[]; const zoomedInInitialState = update(initialState, { flycam: { zoomStep: { $set: 0.1 } }, @@ -123,11 +123,11 @@ const rotatedState = update(initialState, { test("Zoomed in main tools should be enabled.", (t) => { const disabledInfo = getDisabledInfoForTools(zoomedInInitialState); - for (const toolName in AnnotationToolEnum) { - if (toolName === AnnotationToolEnum.PROOFREAD) { - t.assert(disabledInfo[toolName]?.isDisabled === true); + for (const tool of Object.values(AnnotationTool)) { + if (tool === AnnotationTool.PROOFREAD) { + t.assert(disabledInfo[tool.id]?.isDisabled === true); } else { - t.assert(disabledInfo[toolName as AnnotationToolEnum]?.isDisabled === false); + t.assert(disabledInfo[tool.id]?.isDisabled === false); } } }); @@ -135,31 +135,31 @@ test("Zoomed in main tools should be enabled.", (t) => { test("Volume tools should be disabled when zoomed out.", (t) => { const disabledInfo = getDisabledInfoForTools(zoomedOutState); - for (const toolName in AnnotationToolEnum) { + for (const tool of Object.values(AnnotationTool)) { if ( - toolName === AnnotationToolEnum.PROOFREAD || - zoomSensitiveVolumeTools.includes(toolName as AnnotationToolEnum) + tool === AnnotationTool.PROOFREAD || + zoomSensitiveVolumeTools.includes(tool as AnnotationTool) ) { - t.assert(disabledInfo[toolName as AnnotationToolEnum]?.isDisabled === true); + t.assert(disabledInfo[tool.id]?.isDisabled === true); } else { - t.assert(disabledInfo[toolName as AnnotationToolEnum]?.isDisabled === false); + t.assert(disabledInfo[tool.id]?.isDisabled === false); } } }); test("Tools should be disabled when dataset is rotated", (t) => { const toolsDisregardingRotation = [ - AnnotationToolEnum.MOVE, - AnnotationToolEnum.LINE_MEASUREMENT, - AnnotationToolEnum.AREA_MEASUREMENT, - AnnotationToolEnum.BOUNDING_BOX, - ]; + AnnotationTool.MOVE, + AnnotationTool.LINE_MEASUREMENT, + AnnotationTool.AREA_MEASUREMENT, + AnnotationTool.BOUNDING_BOX, + ] as AnnotationTool[]; const disabledInfo = getDisabledInfoForTools(rotatedState); - for (const toolName in AnnotationToolEnum) { - if (toolsDisregardingRotation.includes(toolName as AnnotationToolEnum)) { - t.assert(disabledInfo[toolName as AnnotationToolEnum]?.isDisabled === false); + for (const tool of Object.values(AnnotationTool)) { + if (toolsDisregardingRotation.includes(tool)) { + t.assert(disabledInfo[tool.id]?.isDisabled === false); } else { - t.assert(disabledInfo[toolName as AnnotationToolEnum]?.isDisabled === true); + t.assert(disabledInfo[tool.id]?.isDisabled === true); } } }); @@ -171,11 +171,11 @@ test("Tools should not be disabled when dataset rotation is toggled off", (t) => }, }); const disabledInfo = getDisabledInfoForTools(rotationTurnedOffState); - for (const toolName in AnnotationToolEnum) { - if (toolName === AnnotationToolEnum.PROOFREAD) { - t.assert(disabledInfo[toolName]?.isDisabled === true); + for (const tool of Object.values(AnnotationTool)) { + if (tool === AnnotationTool.PROOFREAD) { + t.assert(disabledInfo[tool.id]?.isDisabled === true); } else { - t.assert(disabledInfo[toolName as AnnotationToolEnum]?.isDisabled === false); + t.assert(disabledInfo[tool.id]?.isDisabled === false); } } }); diff --git a/frontend/javascripts/test/sagas/annotation_tool_saga.spec.ts b/frontend/javascripts/test/sagas/annotation_tool_saga.spec.ts index 1c90fe6598f..2a0f90279b6 100644 --- a/frontend/javascripts/test/sagas/annotation_tool_saga.spec.ts +++ b/frontend/javascripts/test/sagas/annotation_tool_saga.spec.ts @@ -1,13 +1,13 @@ import "test/mocks/lz4"; import test from "ava"; import _ from "lodash"; -import { AnnotationToolEnum, type AnnotationTool } from "oxalis/constants"; +import { AnnotationTool, type AnnotationToolType } from "oxalis/constants"; import mockRequire from "mock-require"; import { initialState } from "test/fixtures/volumetracing_object"; import sinon from "sinon"; const disabledInfoMock: { [key in any]?: any } = {}; -Object.values(AnnotationToolEnum).forEach((annotationTool) => { - disabledInfoMock[annotationTool] = { +Object.values(AnnotationTool).forEach((annotationTool) => { + disabledInfoMock[annotationTool.id] = { isDisabled: false, explanation: "", }; @@ -114,37 +114,37 @@ test.serial("Selecting another tool should trigger a deselection of the previous saga.next(wkReadyAction()); saga.next(newState.uiInformation.activeTool); - const cycleTool = (nextTool: AnnotationTool) => { + const cycleTool = (nextTool: AnnotationToolType) => { const action = setToolAction(nextTool); newState = UiReducer(newState, action); saga.next(action); saga.next(newState); }; - cycleTool(AnnotationToolEnum.SKELETON); + cycleTool(AnnotationTool.SKELETON); t.true(MoveTool.onToolDeselected.calledOnce); - cycleTool(AnnotationToolEnum.BRUSH); + cycleTool(AnnotationTool.BRUSH); t.true(SkeletonTool.onToolDeselected.calledOnce); - cycleTool(AnnotationToolEnum.ERASE_BRUSH); + cycleTool(AnnotationTool.ERASE_BRUSH); t.true(DrawTool.onToolDeselected.calledOnce); - cycleTool(AnnotationToolEnum.TRACE); + cycleTool(AnnotationTool.TRACE); t.true(EraseTool.onToolDeselected.calledOnce); - cycleTool(AnnotationToolEnum.ERASE_TRACE); + cycleTool(AnnotationTool.ERASE_TRACE); t.true(DrawTool.onToolDeselected.calledTwice); - cycleTool(AnnotationToolEnum.FILL_CELL); + cycleTool(AnnotationTool.FILL_CELL); t.true(EraseTool.onToolDeselected.calledTwice); - cycleTool(AnnotationToolEnum.PICK_CELL); + cycleTool(AnnotationTool.PICK_CELL); t.true(FillCellTool.onToolDeselected.calledOnce); - cycleTool(AnnotationToolEnum.BOUNDING_BOX); + cycleTool(AnnotationTool.BOUNDING_BOX); t.true(PickCellTool.onToolDeselected.calledOnce); - cycleTool(AnnotationToolEnum.PROOFREAD); + cycleTool(AnnotationTool.PROOFREAD); t.true(BoundingBoxTool.onToolDeselected.calledOnce); - cycleTool(AnnotationToolEnum.LINE_MEASUREMENT); + cycleTool(AnnotationTool.LINE_MEASUREMENT); t.true(ProofreadTool.onToolDeselected.calledOnce); - cycleTool(AnnotationToolEnum.AREA_MEASUREMENT); + cycleTool(AnnotationTool.AREA_MEASUREMENT); t.true(LineMeasurementTool.onToolDeselected.calledOnce); - cycleTool(AnnotationToolEnum.MOVE); + cycleTool(AnnotationTool.MOVE); t.true(AreaMeasurementTool.onToolDeselected.calledOnce); - cycleTool(AnnotationToolEnum.SKELETON); + cycleTool(AnnotationTool.SKELETON); t.true(MoveTool.onToolDeselected.calledTwice); }); diff --git a/frontend/javascripts/test/sagas/volumetracing/bucket_eviction_helper.ts b/frontend/javascripts/test/sagas/volumetracing/bucket_eviction_helper.ts index 84e212eeaca..0e1cbd3b3d5 100644 --- a/frontend/javascripts/test/sagas/volumetracing/bucket_eviction_helper.ts +++ b/frontend/javascripts/test/sagas/volumetracing/bucket_eviction_helper.ts @@ -3,7 +3,7 @@ import mockRequire from "mock-require"; import "test/sagas/saga_integration.mock"; import { createBucketResponseFunction } from "test/helpers/apiHelpers"; import Store from "oxalis/store"; -import { OrthoViews, AnnotationToolEnum } from "oxalis/constants"; +import { OrthoViews, AnnotationTool } from "oxalis/constants"; import { updateUserSettingAction } from "oxalis/model/actions/settings_actions"; const { setToolAction } = mockRequire.reRequire("oxalis/model/actions/ui_actions"); const { setPositionAction } = mockRequire.reRequire("oxalis/model/actions/flycam_actions"); @@ -42,7 +42,7 @@ export async function testLabelingManyBuckets(t: any, saveInbetween: boolean) { ]); Store.dispatch(updateUserSettingAction("brushSize", brushSize)); - Store.dispatch(setToolAction(AnnotationToolEnum.BRUSH)); + Store.dispatch(setToolAction(AnnotationTool.BRUSH)); Store.dispatch(setActiveCellAction(newCellId)); for (const paintPosition of paintPositions1) { diff --git a/frontend/javascripts/test/sagas/volumetracing/volumetracing_saga.spec.ts b/frontend/javascripts/test/sagas/volumetracing/volumetracing_saga.spec.ts index c8811e9ad20..5d61fa810e3 100644 --- a/frontend/javascripts/test/sagas/volumetracing/volumetracing_saga.spec.ts +++ b/frontend/javascripts/test/sagas/volumetracing/volumetracing_saga.spec.ts @@ -5,7 +5,7 @@ import _ from "lodash"; import type { APISegmentationLayer, ServerVolumeTracing } from "types/api_flow_types"; import { OrthoViews, - AnnotationToolEnum, + AnnotationTool, ContourModeEnum, OverwriteModeEnum, MappingStatusEnum, @@ -187,7 +187,7 @@ test("VolumeTracingSaga should create a volume layer (saga test)", (t) => { }); saga.next(volumeTracing); saga.next(OverwriteModeEnum.OVERWRITE_ALL); - saga.next(AnnotationToolEnum.BRUSH); + saga.next(AnnotationTool.BRUSH); saga.next(false); // pass labeled mag saga.next({ @@ -228,7 +228,7 @@ test("VolumeTracingSaga should add values to volume layer (saga test)", (t) => { }); saga.next(volumeTracing); saga.next(OverwriteModeEnum.OVERWRITE_ALL); - saga.next(AnnotationToolEnum.TRACE); + saga.next(AnnotationTool.TRACE); saga.next(false); saga.next({ mag: [1, 1, 1], @@ -279,7 +279,7 @@ test("VolumeTracingSaga should finish a volume layer (saga test)", (t) => { }); saga.next(volumeTracing); saga.next(OverwriteModeEnum.OVERWRITE_ALL); - saga.next(AnnotationToolEnum.TRACE); + saga.next(AnnotationTool.TRACE); saga.next(false); saga.next({ mag: [1, 1, 1], @@ -321,7 +321,7 @@ test("VolumeTracingSaga should finish a volume layer (saga test)", (t) => { call( finishLayer, volumeLayer, - AnnotationToolEnum.TRACE, + AnnotationTool.TRACE, ContourModeEnum.DRAW, OverwriteModeEnum.OVERWRITE_ALL, 0, @@ -342,7 +342,7 @@ test("VolumeTracingSaga should finish a volume layer in delete mode (saga test)" }); saga.next({ ...volumeTracing, contourTracingMode: ContourModeEnum.DELETE }); saga.next(OverwriteModeEnum.OVERWRITE_ALL); - saga.next(AnnotationToolEnum.TRACE); + saga.next(AnnotationTool.TRACE); saga.next(false); saga.next({ mag: [1, 1, 1], @@ -382,7 +382,7 @@ test("VolumeTracingSaga should finish a volume layer in delete mode (saga test)" call( finishLayer, volumeLayer, - AnnotationToolEnum.TRACE, + AnnotationTool.TRACE, ContourModeEnum.DELETE, OverwriteModeEnum.OVERWRITE_ALL, 0, @@ -420,7 +420,7 @@ test("VolumeTracingSaga should lock an active mapping upon first volume annotati }); saga.next(volumeTracing); saga.next(OverwriteModeEnum.OVERWRITE_ALL); - saga.next(AnnotationToolEnum.BRUSH); + saga.next(AnnotationTool.BRUSH); saga.next(false); // pass labeled mag saga.next({ diff --git a/frontend/javascripts/test/sagas/volumetracing/volumetracing_saga_integration.spec.ts b/frontend/javascripts/test/sagas/volumetracing/volumetracing_saga_integration.spec.ts index 0bbcf6bb286..e04279762e1 100644 --- a/frontend/javascripts/test/sagas/volumetracing/volumetracing_saga_integration.spec.ts +++ b/frontend/javascripts/test/sagas/volumetracing/volumetracing_saga_integration.spec.ts @@ -2,7 +2,7 @@ import "test/sagas/saga_integration.mock"; import _ from "lodash"; import Constants, { - AnnotationToolEnum, + AnnotationTool, ContourModeEnum, FillModeEnum, OrthoViews, @@ -92,7 +92,7 @@ test.serial("Executing a floodfill in mag 1", async (t) => { const newCellId = 2; Store.dispatch(updateUserSettingAction("brushSize", brushSize)); Store.dispatch(setPositionAction([0, 0, 43])); - Store.dispatch(setToolAction(AnnotationToolEnum.BRUSH)); + Store.dispatch(setToolAction(AnnotationTool.BRUSH)); Store.dispatch(setActiveCellAction(newCellId)); Store.dispatch(startEditingAction(paintCenter, OrthoViews.PLANE_XY)); Store.dispatch(addToLayerAction(paintCenter)); @@ -192,7 +192,7 @@ test.serial("Executing a floodfill in mag 2", async (t) => { const newCellId = 2; Store.dispatch(updateUserSettingAction("brushSize", brushSize)); Store.dispatch(setPositionAction([0, 0, 43])); - Store.dispatch(setToolAction(AnnotationToolEnum.BRUSH)); + Store.dispatch(setToolAction(AnnotationTool.BRUSH)); Store.dispatch(setActiveCellAction(newCellId)); Store.dispatch(startEditingAction(paintCenter, OrthoViews.PLANE_XY)); Store.dispatch(addToLayerAction(paintCenter)); @@ -364,7 +364,7 @@ test.serial("Brushing/Tracing with a new segment id should update the bucket dat const volumeTracingLayerName = t.context.api.data.getVolumeTracingLayerIds()[0]; Store.dispatch(updateUserSettingAction("brushSize", brushSize)); Store.dispatch(setPositionAction([0, 0, 0])); - Store.dispatch(setToolAction(AnnotationToolEnum.BRUSH)); + Store.dispatch(setToolAction(AnnotationTool.BRUSH)); Store.dispatch(setActiveCellAction(newCellId)); Store.dispatch(startEditingAction(paintCenter, OrthoViews.PLANE_XY)); Store.dispatch(addToLayerAction(paintCenter)); @@ -441,7 +441,7 @@ test.serial("Brushing/Tracing with already existing backend data", async (t) => t.is(await t.context.api.data.getDataValue(volumeTracingLayerName, paintCenter), oldCellId); Store.dispatch(updateUserSettingAction("brushSize", brushSize)); Store.dispatch(setPositionAction([0, 0, 0])); - Store.dispatch(setToolAction(AnnotationToolEnum.BRUSH)); + Store.dispatch(setToolAction(AnnotationTool.BRUSH)); Store.dispatch(setActiveCellAction(newCellId)); Store.dispatch(startEditingAction(paintCenter, OrthoViews.PLANE_XY)); Store.dispatch(addToLayerAction(paintCenter)); @@ -498,7 +498,7 @@ async function undoTestHelper( const volumeTracingLayerName = t.context.api.data.getVolumeTracingLayerIds()[0]; Store.dispatch(updateUserSettingAction("brushSize", brushSize)); Store.dispatch(setPositionAction([0, 0, 0])); - Store.dispatch(setToolAction(AnnotationToolEnum.BRUSH)); + Store.dispatch(setToolAction(AnnotationTool.BRUSH)); // Brush with ${newCellId} Store.dispatch(setActiveCellAction(newCellId)); Store.dispatch(startEditingAction(paintCenter, OrthoViews.PLANE_XY)); @@ -559,7 +559,7 @@ async function testBrushingWithUndo(t: ExecutionContext, assertBeforeRe Store.dispatch(updateUserSettingAction("overwriteMode", OverwriteModeEnum.OVERWRITE_ALL)); Store.dispatch(updateUserSettingAction("brushSize", brushSize)); Store.dispatch(setPositionAction([0, 0, 0])); - Store.dispatch(setToolAction(AnnotationToolEnum.BRUSH)); + Store.dispatch(setToolAction(AnnotationTool.BRUSH)); // Brush with ${newCellId} Store.dispatch(setActiveCellAction(newCellId)); Store.dispatch(startEditingAction(paintCenter, OrthoViews.PLANE_XY)); @@ -572,7 +572,7 @@ async function testBrushingWithUndo(t: ExecutionContext, assertBeforeRe Store.dispatch(finishEditingAction()); // Erase everything Store.dispatch(setContourTracingModeAction(ContourModeEnum.DELETE)); - Store.dispatch(setToolAction(AnnotationToolEnum.ERASE_BRUSH)); + Store.dispatch(setToolAction(AnnotationTool.ERASE_BRUSH)); Store.dispatch(startEditingAction(paintCenter, OrthoViews.PLANE_XY)); Store.dispatch(addToLayerAction(paintCenter)); Store.dispatch(finishEditingAction()); @@ -641,7 +641,7 @@ test.serial("Brushing/Tracing with undo (II)", async (t) => { const newCellId = 2; Store.dispatch(updateUserSettingAction("brushSize", brushSize)); Store.dispatch(setPositionAction([0, 0, 0])); - Store.dispatch(setToolAction(AnnotationToolEnum.BRUSH)); + Store.dispatch(setToolAction(AnnotationTool.BRUSH)); Store.dispatch(setActiveCellAction(newCellId)); Store.dispatch(startEditingAction(paintCenter, OrthoViews.PLANE_XY)); Store.dispatch(addToLayerAction(paintCenter)); @@ -677,7 +677,7 @@ test.serial("Brushing with undo and garbage collection", async (t: ExecutionCont const volumeTracingLayerName = t.context.api.data.getVolumeTracingLayerIds()[0]; Store.dispatch(updateUserSettingAction("brushSize", brushSize)); Store.dispatch(setPositionAction([0, 0, 0])); - Store.dispatch(setToolAction(AnnotationToolEnum.BRUSH)); + Store.dispatch(setToolAction(AnnotationTool.BRUSH)); // Brush with ${newCellId} Store.dispatch(setActiveCellAction(newCellId)); Store.dispatch(startEditingAction(paintCenter, OrthoViews.PLANE_XY)); @@ -732,7 +732,7 @@ test.serial("Brushing/Tracing with upsampling to unloaded data", async (t) => { Store.dispatch(updateUserSettingAction("overwriteMode", OverwriteModeEnum.OVERWRITE_EMPTY)); Store.dispatch(updateUserSettingAction("brushSize", brushSize)); Store.dispatch(setPositionAction([0, 0, 0])); - Store.dispatch(setToolAction(AnnotationToolEnum.BRUSH)); + Store.dispatch(setToolAction(AnnotationTool.BRUSH)); Store.dispatch(setActiveCellAction(newCellId)); Store.dispatch(startEditingAction(paintCenter, OrthoViews.PLANE_XY)); Store.dispatch(addToLayerAction(paintCenter)); @@ -780,7 +780,7 @@ async function eraseInMag4Helper(t: ExecutionContext, loadDataAtBeginni Store.dispatch(updateUserSettingAction("overwriteMode", OverwriteModeEnum.OVERWRITE_ALL)); Store.dispatch(updateUserSettingAction("brushSize", brushSize)); Store.dispatch(setPositionAction([0, 0, 0])); - Store.dispatch(setToolAction(AnnotationToolEnum.ERASE_BRUSH)); + Store.dispatch(setToolAction(AnnotationTool.ERASE_BRUSH)); Store.dispatch(startEditingAction(paintCenter, OrthoViews.PLANE_XY)); Store.dispatch(addToLayerAction(paintCenter)); Store.dispatch(finishEditingAction()); @@ -824,7 +824,7 @@ async function undoEraseInMag4Helper(t: ExecutionContext, loadBeforeUnd Store.dispatch(updateUserSettingAction("overwriteMode", OverwriteModeEnum.OVERWRITE_ALL)); Store.dispatch(updateUserSettingAction("brushSize", brushSize)); Store.dispatch(setPositionAction([0, 0, 0])); - Store.dispatch(setToolAction(AnnotationToolEnum.ERASE_BRUSH)); + Store.dispatch(setToolAction(AnnotationTool.ERASE_BRUSH)); Store.dispatch(startEditingAction(paintCenter, OrthoViews.PLANE_XY)); Store.dispatch(addToLayerAction(paintCenter)); Store.dispatch(finishEditingAction()); @@ -871,7 +871,7 @@ test.serial("Provoke race condition when bucket compression is very slow", async Store.dispatch(updateUserSettingAction("overwriteMode", OverwriteModeEnum.OVERWRITE_ALL)); Store.dispatch(updateUserSettingAction("brushSize", brushSize)); Store.dispatch(setPositionAction([0, 0, 0])); - Store.dispatch(setToolAction(AnnotationToolEnum.ERASE_BRUSH)); + Store.dispatch(setToolAction(AnnotationTool.ERASE_BRUSH)); Store.dispatch(startEditingAction(paintCenter, OrthoViews.PLANE_XY)); Store.dispatch(addToLayerAction(paintCenter)); Store.dispatch(finishEditingAction()); From 85696f4918fecc65670e5134e5729edf514ae4a7 Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Fri, 11 Apr 2025 16:24:50 +0200 Subject: [PATCH 26/84] remove AnnotationToolType in favor of AnnotationTool --- frontend/javascripts/oxalis/constants.ts | 1 - .../controller/combinations/tool_controls.ts | 25 +++++++++---------- .../controller/viewmodes/plane_controller.tsx | 3 +-- .../oxalis/model/accessors/tool_accessor.ts | 14 ++++------- .../oxalis/model/actions/ui_actions.ts | 4 +-- .../oxalis/model/reducers/reducer_helpers.ts | 6 ++--- frontend/javascripts/oxalis/store.ts | 4 +-- .../oxalis/view/action-bar/toolbar_view.tsx | 15 ++++++----- .../javascripts/oxalis/view/context_menu.tsx | 9 +++---- .../test/sagas/annotation_tool_saga.spec.ts | 4 +-- 10 files changed, 37 insertions(+), 48 deletions(-) diff --git a/frontend/javascripts/oxalis/constants.ts b/frontend/javascripts/oxalis/constants.ts index c3d4d12c012..055846c7694 100644 --- a/frontend/javascripts/oxalis/constants.ts +++ b/frontend/javascripts/oxalis/constants.ts @@ -2,7 +2,6 @@ import type { AdditionalCoordinate } from "types/api_flow_types"; export { AnnotationTool, - AnnotationToolType, AnnotationToolId, VolumeTools, AvailableToolsInViewMode, diff --git a/frontend/javascripts/oxalis/controller/combinations/tool_controls.ts b/frontend/javascripts/oxalis/controller/combinations/tool_controls.ts index 936df3299a4..af435c20028 100644 --- a/frontend/javascripts/oxalis/controller/combinations/tool_controls.ts +++ b/frontend/javascripts/oxalis/controller/combinations/tool_controls.ts @@ -7,7 +7,6 @@ import { AnnotationTool, ContourModeEnum, OrthoViews, - type AnnotationToolType, type OrthoView, type Point2, type Vector3, @@ -202,7 +201,7 @@ export class MoveTool { } static getActionDescriptors( - _activeTool: AnnotationToolType, + _activeTool: AnnotationTool, useLegacyBindings: boolean, shiftKey: boolean, _ctrlOrMetaKey: boolean, @@ -368,7 +367,7 @@ export class SkeletonTool { } static getActionDescriptors( - _activeTool: AnnotationToolType, + _activeTool: AnnotationTool, useLegacyBindings: boolean, shiftKey: boolean, ctrlOrMetaKey: boolean, @@ -495,7 +494,7 @@ export class DrawTool { } static getActionDescriptors( - activeTool: AnnotationToolType, + activeTool: AnnotationTool, useLegacyBindings: boolean, _shiftKey: boolean, _ctrlOrMetaKey: boolean, @@ -554,7 +553,7 @@ export class EraseTool { } static getActionDescriptors( - activeTool: AnnotationToolType, + activeTool: AnnotationTool, _useLegacyBindings: boolean, _shiftKey: boolean, _ctrlOrMetaKey: boolean, @@ -579,7 +578,7 @@ export class PickCellTool { } static getActionDescriptors( - _activeTool: AnnotationToolType, + _activeTool: AnnotationTool, _useLegacyBindings: boolean, _shiftKey: boolean, _ctrlOrMetaKey: boolean, @@ -610,7 +609,7 @@ export class FillCellTool { } static getActionDescriptors( - _activeTool: AnnotationToolType, + _activeTool: AnnotationTool, _useLegacyBindings: boolean, _shiftKey: boolean, _ctrlOrMetaKey: boolean, @@ -689,7 +688,7 @@ export class BoundingBoxTool { } static getActionDescriptors( - _activeTool: AnnotationToolType, + _activeTool: AnnotationTool, _useLegacyBindings: boolean, _shiftKey: boolean, ctrlOrMetaKey: boolean, @@ -818,7 +817,7 @@ export class QuickSelectTool { } static getActionDescriptors( - _activeTool: AnnotationToolType, + _activeTool: AnnotationTool, _useLegacyBindings: boolean, shiftKey: boolean, _ctrlOrMetaKey: boolean, @@ -942,7 +941,7 @@ export class LineMeasurementTool { } static getActionDescriptors( - _activeTool: AnnotationToolType, + _activeTool: AnnotationTool, _useLegacyBindings: boolean, _shiftKey: boolean, _ctrlOrMetaKey: boolean, @@ -1021,7 +1020,7 @@ export class AreaMeasurementTool { } static getActionDescriptors( - _activeTool: AnnotationToolType, + _activeTool: AnnotationTool, _useLegacyBindings: boolean, _shiftKey: boolean, _ctrlOrMetaKey: boolean, @@ -1081,7 +1080,7 @@ export class ProofreadTool { } static getActionDescriptors( - _activeTool: AnnotationToolType, + _activeTool: AnnotationTool, _useLegacyBindings: boolean, shiftKey: boolean, ctrlOrMetaKey: boolean, @@ -1137,6 +1136,6 @@ const toolToToolClass = { [AnnotationTool.LINE_MEASUREMENT.id]: LineMeasurementTool, [AnnotationTool.AREA_MEASUREMENT.id]: AreaMeasurementTool, }; -export function getToolClassForAnnotationTool(activeTool: AnnotationToolType) { +export function getToolClassForAnnotationTool(activeTool: AnnotationTool) { return toolToToolClass[activeTool.id]; } diff --git a/frontend/javascripts/oxalis/controller/viewmodes/plane_controller.tsx b/frontend/javascripts/oxalis/controller/viewmodes/plane_controller.tsx index 0bffabebcc8..c1a1fd3498c 100644 --- a/frontend/javascripts/oxalis/controller/viewmodes/plane_controller.tsx +++ b/frontend/javascripts/oxalis/controller/viewmodes/plane_controller.tsx @@ -6,7 +6,6 @@ import _ from "lodash"; import { AnnotationTool, type AnnotationToolId, - type AnnotationToolType, type OrthoView, type OrthoViewMap, } from "oxalis/constants"; @@ -108,7 +107,7 @@ const setTool = (tool: AnnotationTool) => { type StateProps = { annotation: StoreAnnotation; - activeTool: AnnotationToolType; + activeTool: AnnotationTool; }; type Props = StateProps; diff --git a/frontend/javascripts/oxalis/model/accessors/tool_accessor.ts b/frontend/javascripts/oxalis/model/accessors/tool_accessor.ts index 54b0d6a325d..a061b30c50d 100644 --- a/frontend/javascripts/oxalis/model/accessors/tool_accessor.ts +++ b/frontend/javascripts/oxalis/model/accessors/tool_accessor.ts @@ -116,10 +116,6 @@ export const AnnotationTool = { export type AnnotationTool = (typeof AnnotationTool)[keyof typeof AnnotationTool]; -// todop: remove again -export type AnnotationToolType = AnnotationTool; -// export type AnnotationToolType = typeof AbstractAnnotationTool; - export const ToolCollections = { ALL_TOOLS: Object.values(AnnotationTool), VOLUME_TOOLS: [ @@ -213,7 +209,7 @@ const getExplanationForDisabledVolume = ( return "Volume annotation is currently disabled."; }; -export function isVolumeDrawingTool(activeTool: AnnotationToolType): boolean { +export function isVolumeDrawingTool(activeTool: AnnotationTool): boolean { return ( activeTool === AnnotationTool.TRACE || activeTool === AnnotationTool.BRUSH || @@ -221,10 +217,10 @@ export function isVolumeDrawingTool(activeTool: AnnotationToolType): boolean { activeTool === AnnotationTool.ERASE_BRUSH ); } -export function isBrushTool(activeTool: AnnotationToolType): boolean { +export function isBrushTool(activeTool: AnnotationTool): boolean { return activeTool === AnnotationTool.BRUSH || activeTool === AnnotationTool.ERASE_BRUSH; } -export function isTraceTool(activeTool: AnnotationToolType): boolean { +export function isTraceTool(activeTool: AnnotationTool): boolean { return activeTool === AnnotationTool.TRACE || activeTool === AnnotationTool.ERASE_TRACE; } const noSkeletonsExplanation = @@ -519,11 +515,11 @@ export const getDisabledInfoForTools = reuseInstanceOnEquality( ); export function adaptActiveToolToShortcuts( - activeTool: AnnotationToolType, + activeTool: AnnotationTool, isShiftPressed: boolean, isControlOrMetaPressed: boolean, isAltPressed: boolean, -): AnnotationToolType { +): AnnotationTool { if (!isShiftPressed && !isControlOrMetaPressed && !isAltPressed) { // No modifier is pressed return activeTool; diff --git a/frontend/javascripts/oxalis/model/actions/ui_actions.ts b/frontend/javascripts/oxalis/model/actions/ui_actions.ts index a3587fdf385..3cc188cffc3 100644 --- a/frontend/javascripts/oxalis/model/actions/ui_actions.ts +++ b/frontend/javascripts/oxalis/model/actions/ui_actions.ts @@ -1,4 +1,4 @@ -import type { AnnotationToolType, OrthoView, Vector3 } from "oxalis/constants"; +import type { AnnotationTool, OrthoView, Vector3 } from "oxalis/constants"; import type { BorderOpenStatus, OxalisState, Theme } from "oxalis/store"; import type { StartAIJobModalState } from "oxalis/view/action-bar/starting_job_modals"; @@ -107,7 +107,7 @@ export const setHasOrganizationsAction = (value: boolean) => type: "SET_HAS_ORGANIZATIONS", value, }) as const; -export const setToolAction = (tool: AnnotationToolType) => +export const setToolAction = (tool: AnnotationTool) => ({ type: "SET_TOOL", tool, diff --git a/frontend/javascripts/oxalis/model/reducers/reducer_helpers.ts b/frontend/javascripts/oxalis/model/reducers/reducer_helpers.ts index fc17e2a3433..f4664df3171 100644 --- a/frontend/javascripts/oxalis/model/reducers/reducer_helpers.ts +++ b/frontend/javascripts/oxalis/model/reducers/reducer_helpers.ts @@ -1,7 +1,7 @@ import Maybe from "data.maybe"; import * as Utils from "libs/utils"; import { AnnotationTool } from "oxalis/constants"; -import type { AnnotationToolType, BoundingBoxType } from "oxalis/constants"; +import type { BoundingBoxType } from "oxalis/constants"; import { getDisabledInfoForTools } from "oxalis/model/accessors/tool_accessor"; import { isVolumeAnnotationDisallowedForZoom, @@ -141,7 +141,7 @@ export function convertServerAdditionalAxesToFrontEnd( })); } -export function getNextTool(state: OxalisState): AnnotationToolType | null { +export function getNextTool(state: OxalisState): AnnotationTool | null { const disabledToolInfo = getDisabledInfoForTools(state); const tools = Object.values(AnnotationTool); const currentToolIndex = tools.indexOf(state.uiInformation.activeTool); @@ -161,7 +161,7 @@ export function getNextTool(state: OxalisState): AnnotationToolType | null { return null; } -export function getPreviousTool(state: OxalisState): AnnotationToolType | null { +export function getPreviousTool(state: OxalisState): AnnotationTool | null { const disabledToolInfo = getDisabledInfoForTools(state); const tools = Object.values(AnnotationTool); const currentToolIndex = tools.indexOf(state.uiInformation.activeTool); diff --git a/frontend/javascripts/oxalis/store.ts b/frontend/javascripts/oxalis/store.ts index 22446e7f9cf..fedae95875a 100644 --- a/frontend/javascripts/oxalis/store.ts +++ b/frontend/javascripts/oxalis/store.ts @@ -1,7 +1,7 @@ import type DiffableMap from "libs/diffable_map"; import type { Matrix4x4 } from "libs/mjs"; import type { - AnnotationToolType, + AnnotationTool, BoundingBoxType, ContourMode, ControlMode, @@ -557,7 +557,7 @@ type UiInformation = { readonly showAddScriptModal: boolean; readonly aIJobModalState: StartAIJobModalState; readonly showRenderAnimationModal: boolean; - readonly activeTool: AnnotationToolType; + readonly activeTool: AnnotationTool; readonly activeUserBoundingBoxId: number | null | undefined; readonly storedLayouts: Record; readonly isImportingMesh: boolean; diff --git a/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx b/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx index f0a9cc6d961..97c08fdba8a 100644 --- a/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx +++ b/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx @@ -39,7 +39,6 @@ import { } from "oxalis/constants"; import { getActiveTree } from "oxalis/model/accessors/skeletontracing_accessor"; import { - type AnnotationToolType, adaptActiveToolToShortcuts, getDisabledInfoForTools, } from "oxalis/model/accessors/tool_accessor"; @@ -859,7 +858,7 @@ export default function ToolbarView() { const toolWorkspace = useSelector((state: OxalisState) => state.userConfiguration.toolWorkspace); const [lastForcefullyDisabledTool, setLastForcefullyDisabledTool] = - useState(null); + useState(null); const activeTool = useSelector((state: OxalisState) => state.uiInformation.activeTool); @@ -975,7 +974,7 @@ function ToolSpecificSettings({ isShiftPressed, }: { hasSkeleton: boolean; - adaptedActiveTool: AnnotationToolType; + adaptedActiveTool: AnnotationTool; hasVolume: boolean; isControlOrMetaPressed: boolean; isShiftPressed: boolean; @@ -1357,7 +1356,7 @@ function getIsVolumeModificationAllowed(state: OxalisState) { return hasVolume && !isReadOnly && !hasEditableMapping(state); } -function BrushTool({ adaptedActiveTool }: { adaptedActiveTool: AnnotationToolType }) { +function BrushTool({ adaptedActiveTool }: { adaptedActiveTool: AnnotationTool }) { const disabledInfosForTools = useSelector(getDisabledInfoForTools); const isVolumeModificationAllowed = useSelector(getIsVolumeModificationAllowed); if (!isVolumeModificationAllowed) { @@ -1384,7 +1383,7 @@ function BrushTool({ adaptedActiveTool }: { adaptedActiveTool: AnnotationToolTyp ); } -function EraseBrushTool({ adaptedActiveTool }: { adaptedActiveTool: AnnotationToolType }) { +function EraseBrushTool({ adaptedActiveTool }: { adaptedActiveTool: AnnotationTool }) { const disabledInfosForTools = useSelector(getDisabledInfoForTools); const showEraseTraceTool = adaptedActiveTool === AnnotationTool.TRACE || adaptedActiveTool === AnnotationTool.ERASE_TRACE; @@ -1421,7 +1420,7 @@ function EraseBrushTool({ adaptedActiveTool }: { adaptedActiveTool: AnnotationTo ); } -function TraceTool({ adaptedActiveTool }: { adaptedActiveTool: AnnotationToolType }) { +function TraceTool({ adaptedActiveTool }: { adaptedActiveTool: AnnotationTool }) { const disabledInfosForTools = useSelector(getDisabledInfoForTools); const isVolumeModificationAllowed = useSelector(getIsVolumeModificationAllowed); if (!isVolumeModificationAllowed) { @@ -1449,7 +1448,7 @@ function TraceTool({ adaptedActiveTool }: { adaptedActiveTool: AnnotationToolTyp ); } -function EraseTraceTool({ adaptedActiveTool }: { adaptedActiveTool: AnnotationToolType }) { +function EraseTraceTool({ adaptedActiveTool }: { adaptedActiveTool: AnnotationTool }) { const disabledInfosForTools = useSelector(getDisabledInfoForTools); const showEraseTraceTool = adaptedActiveTool === AnnotationTool.TRACE || adaptedActiveTool === AnnotationTool.ERASE_TRACE; @@ -1484,7 +1483,7 @@ function EraseTraceTool({ adaptedActiveTool }: { adaptedActiveTool: AnnotationTo ); } -function FillCellTool({ adaptedActiveTool }: { adaptedActiveTool: AnnotationToolType }) { +function FillCellTool({ adaptedActiveTool }: { adaptedActiveTool: AnnotationTool }) { const disabledInfosForTools = useSelector(getDisabledInfoForTools); const isVolumeModificationAllowed = useSelector(getIsVolumeModificationAllowed); if (!isVolumeModificationAllowed) { diff --git a/frontend/javascripts/oxalis/view/context_menu.tsx b/frontend/javascripts/oxalis/view/context_menu.tsx index 5291707b8c6..643dc20922a 100644 --- a/frontend/javascripts/oxalis/view/context_menu.tsx +++ b/frontend/javascripts/oxalis/view/context_menu.tsx @@ -57,10 +57,7 @@ import { getNodePosition, isSkeletonLayerTransformed, } from "oxalis/model/accessors/skeletontracing_accessor"; -import { - type AnnotationToolType, - getDisabledInfoForTools, -} from "oxalis/model/accessors/tool_accessor"; +import { getDisabledInfoForTools } from "oxalis/model/accessors/tool_accessor"; import { maybeGetSomeTracing } from "oxalis/model/accessors/tracing_accessor"; import { getActiveCellId, @@ -168,7 +165,7 @@ type StateProps = { currentMeshFile: APIMeshFile | null | undefined; currentConnectomeFile: APIConnectomeFile | null | undefined; volumeTracing: VolumeTracing | null | undefined; - activeTool: AnnotationToolType; + activeTool: AnnotationTool; useLegacyBindings: boolean; userBoundingBoxes: Array; mappingInfo: ActiveMappingInfo; @@ -186,7 +183,7 @@ type NodeContextMenuOptionsProps = Props & { type NoNodeContextMenuProps = Props & { viewport: OrthoView; segmentIdAtPosition: number; - activeTool: AnnotationToolType; + activeTool: AnnotationTool; infoRows: ItemType[]; }; diff --git a/frontend/javascripts/test/sagas/annotation_tool_saga.spec.ts b/frontend/javascripts/test/sagas/annotation_tool_saga.spec.ts index 2a0f90279b6..62b5167a326 100644 --- a/frontend/javascripts/test/sagas/annotation_tool_saga.spec.ts +++ b/frontend/javascripts/test/sagas/annotation_tool_saga.spec.ts @@ -1,7 +1,7 @@ import "test/mocks/lz4"; import test from "ava"; import _ from "lodash"; -import { AnnotationTool, type AnnotationToolType } from "oxalis/constants"; +import { AnnotationTool } from "oxalis/constants"; import mockRequire from "mock-require"; import { initialState } from "test/fixtures/volumetracing_object"; import sinon from "sinon"; @@ -114,7 +114,7 @@ test.serial("Selecting another tool should trigger a deselection of the previous saga.next(wkReadyAction()); saga.next(newState.uiInformation.activeTool); - const cycleTool = (nextTool: AnnotationToolType) => { + const cycleTool = (nextTool: AnnotationTool) => { const action = setToolAction(nextTool); newState = UiReducer(newState, action); saga.next(action); From a4bc77b308dac73c0b9519d8e54f9d16137c6e3e Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Fri, 11 Apr 2025 16:36:56 +0200 Subject: [PATCH 27/84] rename control classes to ....ToolController; clean up tool label code --- .../controller/combinations/tool_controls.ts | 61 +++++++++---------- .../oxalis/controller/td_controller.tsx | 9 ++- .../viewmodes/arbitrary_controller.tsx | 4 +- .../controller/viewmodes/plane_controller.tsx | 53 +++++++++------- .../oxalis/model/accessors/tool_accessor.ts | 36 ++++------- .../model/sagas/annotation_tool_saga.ts | 4 +- .../oxalis/view/action-bar/toolbar_view.tsx | 5 +- .../view/components/command_palette.tsx | 3 +- .../javascripts/oxalis/view/input_catcher.tsx | 5 +- .../javascripts/oxalis/view/statusbar.tsx | 7 +-- 10 files changed, 91 insertions(+), 96 deletions(-) diff --git a/frontend/javascripts/oxalis/controller/combinations/tool_controls.ts b/frontend/javascripts/oxalis/controller/combinations/tool_controls.ts index af435c20028..c0272ffa051 100644 --- a/frontend/javascripts/oxalis/controller/combinations/tool_controls.ts +++ b/frontend/javascripts/oxalis/controller/combinations/tool_controls.ts @@ -71,11 +71,11 @@ export type ActionDescriptor = { }; /* - This module contains classes for the different tools, such as MoveTool, SkeletonTool, DrawTool etc. + This module contains classes for the different tools, such as MoveToolController, SkeletonToolController, DrawToolController etc. Each tool class defines getMouseControls which declares how mouse bindings are mapped (depending on modifiers) to actions. For the actions, code from oxalis/controller/combinations is called. - If a tool does not define a specific mouse binding, the bindings of the MoveTool are used as a fallback. + If a tool does not define a specific mouse binding, the bindings of the MoveToolController are used as a fallback. See `createToolDependentMouseHandler` in plane_controller.js In general, each tool has to check the pressed modifiers and delegate to another tool if necessary. @@ -88,7 +88,7 @@ export type ActionDescriptor = { so that the returned hint of class X is only rendered if `adaptActiveToolToShortcuts` returns X. Therefore, the returned actions of a tool class should only refer to the actions of that tool class. */ -export class MoveTool { +export class MoveToolController { static getMouseControls(planeId: OrthoView, planeView: PlaneView): Record { return { scroll: (delta: number, type: ModifierKeys | null | undefined) => { @@ -191,7 +191,7 @@ export class MoveTool { MoveHandlers.handleMovePlane(delta); }, middleDownMove: MoveHandlers.handleMovePlane, - rightClick: MoveTool.createRightClickHandler(planeView), + rightClick: MoveToolController.createRightClickHandler(planeView), }; } @@ -225,7 +225,7 @@ export class MoveTool { static onToolDeselected() {} } -export class SkeletonTool { +export class SkeletonToolController { static getMouseControls(planeView: PlaneView) { const legacyRightClick = ( position: Point2, @@ -408,7 +408,7 @@ export class SkeletonTool { static onToolDeselected() {} } -export class DrawTool { +export class DrawToolController { static getPlaneMouseControls(_planeId: OrthoView, planeView: PlaneView): any { return { leftDownMove: (_delta: Point2, pos: Point2) => { @@ -517,7 +517,7 @@ export class DrawTool { static onToolDeselected() {} } -export class EraseTool { +export class EraseToolController { static getPlaneMouseControls(_planeId: OrthoView, planeView: PlaneView): any { return { leftDownMove: (_delta: Point2, pos: Point2) => { @@ -568,7 +568,7 @@ export class EraseTool { static onToolDeselected() {} } -export class PickCellTool { +export class PickCellToolController { static getPlaneMouseControls(_planeId: OrthoView): any { return { leftClick: (pos: Point2, _plane: OrthoView, _event: MouseEvent) => { @@ -593,7 +593,7 @@ export class PickCellTool { static onToolDeselected() {} } -export class FillCellTool { +export class FillCellToolController { static getPlaneMouseControls(_planeId: OrthoView): any { return { leftClick: (pos: Point2, plane: OrthoView, event: MouseEvent) => { @@ -624,7 +624,7 @@ export class FillCellTool { static onToolDeselected() {} } -export class BoundingBoxTool { +export class BoundingBoxToolController { static getPlaneMouseControls(planeId: OrthoView, planeView: PlaneView): any { let primarySelectedEdge: SelectedEdge | null | undefined = null; let secondarySelectedEdge: SelectedEdge | null | undefined = null; @@ -711,7 +711,7 @@ export class BoundingBoxTool { } } -export class QuickSelectTool { +export class QuickSelectToolController { static getPlaneMouseControls(_planeId: OrthoView, planeView: PlaneView): any { let startPos: Vector3 | null = null; let currentPos: Vector3 | null = null; @@ -856,7 +856,7 @@ function getDoubleClickGuard() { return doubleClickGuard; } -export class LineMeasurementTool { +export class LineMeasurementToolController { static initialPlane: OrthoView = OrthoViews.PLANE_XY; static isMeasuring = false; static getPlaneMouseControls(): any { @@ -964,7 +964,7 @@ export class LineMeasurementTool { } } -export class AreaMeasurementTool { +export class AreaMeasurementToolController { static initialPlane: OrthoView = OrthoViews.PLANE_XY; static isMeasuring = false; static getPlaneMouseControls(): any { @@ -1042,7 +1042,7 @@ export class AreaMeasurementTool { } } -export class ProofreadTool { +export class ProofreadToolController { static getPlaneMouseControls(_planeId: OrthoView, planeView: PlaneView): any { return { leftClick: (pos: Point2, plane: OrthoView, event: MouseEvent, isTouch: boolean) => { @@ -1120,22 +1120,21 @@ export class ProofreadTool { static onToolDeselected() {} } -const toolToToolClass = { - // todop - [AnnotationTool.MOVE.id]: MoveTool, - [AnnotationTool.SKELETON.id]: SkeletonTool, - [AnnotationTool.BOUNDING_BOX.id]: BoundingBoxTool, - [AnnotationTool.QUICK_SELECT.id]: QuickSelectTool, - [AnnotationTool.PROOFREAD.id]: ProofreadTool, - [AnnotationTool.BRUSH.id]: DrawTool, - [AnnotationTool.TRACE.id]: DrawTool, - [AnnotationTool.ERASE_TRACE.id]: EraseTool, - [AnnotationTool.ERASE_BRUSH.id]: EraseTool, - [AnnotationTool.FILL_CELL.id]: FillCellTool, - [AnnotationTool.PICK_CELL.id]: PickCellTool, - [AnnotationTool.LINE_MEASUREMENT.id]: LineMeasurementTool, - [AnnotationTool.AREA_MEASUREMENT.id]: AreaMeasurementTool, +const toolToToolController = { + [AnnotationTool.MOVE.id]: MoveToolController, + [AnnotationTool.SKELETON.id]: SkeletonToolController, + [AnnotationTool.BOUNDING_BOX.id]: BoundingBoxToolController, + [AnnotationTool.QUICK_SELECT.id]: QuickSelectToolController, + [AnnotationTool.PROOFREAD.id]: ProofreadToolController, + [AnnotationTool.BRUSH.id]: DrawToolController, + [AnnotationTool.TRACE.id]: DrawToolController, + [AnnotationTool.ERASE_TRACE.id]: EraseToolController, + [AnnotationTool.ERASE_BRUSH.id]: EraseToolController, + [AnnotationTool.FILL_CELL.id]: FillCellToolController, + [AnnotationTool.PICK_CELL.id]: PickCellToolController, + [AnnotationTool.LINE_MEASUREMENT.id]: LineMeasurementToolController, + [AnnotationTool.AREA_MEASUREMENT.id]: AreaMeasurementToolController, }; -export function getToolClassForAnnotationTool(activeTool: AnnotationTool) { - return toolToToolClass[activeTool.id]; +export function getToolControllerForAnnotationTool(activeTool: AnnotationTool) { + return toolToToolController[activeTool.id]; } diff --git a/frontend/javascripts/oxalis/controller/td_controller.tsx b/frontend/javascripts/oxalis/controller/td_controller.tsx index c8bc57779e0..95e23c16e6a 100644 --- a/frontend/javascripts/oxalis/controller/td_controller.tsx +++ b/frontend/javascripts/oxalis/controller/td_controller.tsx @@ -13,7 +13,10 @@ import { } from "oxalis/constants"; import CameraController from "oxalis/controller/camera_controller"; import { handleOpenContextMenu } from "oxalis/controller/combinations/skeleton_handlers"; -import { ProofreadTool, SkeletonTool } from "oxalis/controller/combinations/tool_controls"; +import { + ProofreadToolController, + SkeletonToolController, +} from "oxalis/controller/combinations/tool_controls"; import { getPosition } from "oxalis/model/accessors/flycam_accessor"; import { getActiveNode, getNodePosition } from "oxalis/model/accessors/skeletontracing_accessor"; import { getInputCatcherRect, getViewportScale } from "oxalis/model/accessors/view_mode_accessor"; @@ -65,8 +68,8 @@ function getTDViewMouseControlsSkeleton(planeView: PlaneView): Record activeTool === AnnotationTool.PROOFREAD - ? ProofreadTool.onLeftClick(planeView, pos, plane, event, isTouch) - : SkeletonTool.onLeftClick( + ? ProofreadToolController.onLeftClick(planeView, pos, plane, event, isTouch) + : SkeletonToolController.onLeftClick( planeView, pos, event.shiftKey, diff --git a/frontend/javascripts/oxalis/controller/viewmodes/arbitrary_controller.tsx b/frontend/javascripts/oxalis/controller/viewmodes/arbitrary_controller.tsx index 8403b7b0303..96b8076bb8c 100644 --- a/frontend/javascripts/oxalis/controller/viewmodes/arbitrary_controller.tsx +++ b/frontend/javascripts/oxalis/controller/viewmodes/arbitrary_controller.tsx @@ -46,7 +46,7 @@ import Store from "oxalis/store"; import ArbitraryView from "oxalis/view/arbitrary_view"; import { downloadScreenshot } from "oxalis/view/rendering_utils"; import * as React from "react"; -import { SkeletonTool } from "../combinations/tool_controls"; +import { SkeletonToolController } from "../combinations/tool_controls"; const arbitraryViewportId = "inputcatcher_arbitraryViewport"; type Props = { @@ -96,7 +96,7 @@ class ArbitraryController extends React.PureComponent { arbitraryViewportId, { leftClick: (pos: Point2, viewport: string, event: MouseEvent, isTouch: boolean) => { - SkeletonTool.onLeftClick( + SkeletonToolController.onLeftClick( this.arbitraryView, pos, event.shiftKey, diff --git a/frontend/javascripts/oxalis/controller/viewmodes/plane_controller.tsx b/frontend/javascripts/oxalis/controller/viewmodes/plane_controller.tsx index c1a1fd3498c..e6820538b08 100644 --- a/frontend/javascripts/oxalis/controller/viewmodes/plane_controller.tsx +++ b/frontend/javascripts/oxalis/controller/viewmodes/plane_controller.tsx @@ -13,17 +13,17 @@ import { OrthoViewValuesWithoutTDView, OrthoViews } from "oxalis/constants"; import * as MoveHandlers from "oxalis/controller/combinations/move_handlers"; import * as SkeletonHandlers from "oxalis/controller/combinations/skeleton_handlers"; import { - AreaMeasurementTool, - BoundingBoxTool, - DrawTool, - EraseTool, - FillCellTool, - LineMeasurementTool, - MoveTool, - PickCellTool, - ProofreadTool, - QuickSelectTool, - SkeletonTool, + AreaMeasurementToolController, + BoundingBoxToolController, + DrawToolController, + EraseToolController, + FillCellToolController, + LineMeasurementToolController, + MoveToolController, + PickCellToolController, + ProofreadToolController, + QuickSelectToolController, + SkeletonToolController, } from "oxalis/controller/combinations/tool_controls"; import * as VolumeHandlers from "oxalis/controller/combinations/volume_handlers"; import getSceneController, { @@ -320,17 +320,26 @@ class PlaneController extends React.PureComponent { } getPlaneMouseControls(planeId: OrthoView): MouseBindingMap { - const moveControls = MoveTool.getMouseControls(planeId, this.planeView); - const skeletonControls = SkeletonTool.getMouseControls(this.planeView); - const drawControls = DrawTool.getPlaneMouseControls(planeId, this.planeView); - const eraseControls = EraseTool.getPlaneMouseControls(planeId, this.planeView); - const fillCellControls = FillCellTool.getPlaneMouseControls(planeId); - const pickCellControls = PickCellTool.getPlaneMouseControls(planeId); - const boundingBoxControls = BoundingBoxTool.getPlaneMouseControls(planeId, this.planeView); - const quickSelectControls = QuickSelectTool.getPlaneMouseControls(planeId, this.planeView); - const proofreadControls = ProofreadTool.getPlaneMouseControls(planeId, this.planeView); - const lineMeasurementControls = LineMeasurementTool.getPlaneMouseControls(); - const areaMeasurementControls = AreaMeasurementTool.getPlaneMouseControls(); + const moveControls = MoveToolController.getMouseControls(planeId, this.planeView); + const skeletonControls = SkeletonToolController.getMouseControls(this.planeView); + const drawControls = DrawToolController.getPlaneMouseControls(planeId, this.planeView); + const eraseControls = EraseToolController.getPlaneMouseControls(planeId, this.planeView); + const fillCellControls = FillCellToolController.getPlaneMouseControls(planeId); + const pickCellControls = PickCellToolController.getPlaneMouseControls(planeId); + const boundingBoxControls = BoundingBoxToolController.getPlaneMouseControls( + planeId, + this.planeView, + ); + const quickSelectControls = QuickSelectToolController.getPlaneMouseControls( + planeId, + this.planeView, + ); + const proofreadControls = ProofreadToolController.getPlaneMouseControls( + planeId, + this.planeView, + ); + const lineMeasurementControls = LineMeasurementToolController.getPlaneMouseControls(); + const areaMeasurementControls = AreaMeasurementToolController.getPlaneMouseControls(); const allControlKeys = _.union( Object.keys(moveControls), diff --git a/frontend/javascripts/oxalis/model/accessors/tool_accessor.ts b/frontend/javascripts/oxalis/model/accessors/tool_accessor.ts index a061b30c50d..c6d383bcc12 100644 --- a/frontend/javascripts/oxalis/model/accessors/tool_accessor.ts +++ b/frontend/javascripts/oxalis/model/accessors/tool_accessor.ts @@ -47,27 +47,27 @@ const _AnnotationToolHelper = { class MoveTool extends AbstractAnnotationTool { static id = _AnnotationToolHelper.MOVE; - readableName = "Move"; + readableName = "Move Tool"; } class SkeletonTool extends AbstractAnnotationTool { static id = _AnnotationToolHelper.SKELETON; - readableName = "Skeleton"; + readableName = "Skeleton Tool"; } class BrushTool extends AbstractAnnotationTool { static id = _AnnotationToolHelper.BRUSH; - static readableName = "Brush"; + static readableName = "Brush Tool"; } class EraseBrushTool extends AbstractAnnotationTool { static id = _AnnotationToolHelper.ERASE_BRUSH; - static readableName = "Erase (via Brush)"; + static readableName = "Erase Tool (via Brush)"; } class TraceTool extends AbstractAnnotationTool { static id = _AnnotationToolHelper.TRACE; - static readableName = "Trace"; + static readableName = "Trace Tool"; } class EraseTraceTool extends AbstractAnnotationTool { static id = _AnnotationToolHelper.ERASE_TRACE; - static readableName = "Erase"; + static readableName = "Erase Tool"; } class FillCellTool extends AbstractAnnotationTool { static id = _AnnotationToolHelper.FILL_CELL; @@ -75,7 +75,7 @@ class FillCellTool extends AbstractAnnotationTool { } class PickCellTool extends AbstractAnnotationTool { static id = _AnnotationToolHelper.PICK_CELL; - static readableName = "Segment Picker"; + static readableName = "Segment Picker Tool"; } class QuickSelectTool extends AbstractAnnotationTool { static id = _AnnotationToolHelper.QUICK_SELECT; @@ -138,24 +138,23 @@ export const VolumeTools = ToolCollections.VOLUME_TOOLS; export type ToolCollection = keyof typeof ToolCollections; -export const ToolsWithOverwriteCapabilities = [ +export const ToolsWithOverwriteCapabilities: AnnotationTool[] = [ AnnotationTool.TRACE, AnnotationTool.BRUSH, AnnotationTool.ERASE_TRACE, AnnotationTool.ERASE_BRUSH, AnnotationTool.QUICK_SELECT, - // todop: remove as...? -] as const as AnnotationTool[]; -export const ToolsWithInterpolationCapabilities = [ +]; +export const ToolsWithInterpolationCapabilities: AnnotationTool[] = [ AnnotationTool.TRACE, AnnotationTool.BRUSH, AnnotationTool.QUICK_SELECT, -] as const as AnnotationTool[]; +]; -export const MeasurementTools = [ +export const MeasurementTools: AnnotationTool[] = [ AnnotationTool.LINE_MEASUREMENT, AnnotationTool.AREA_MEASUREMENT, -] as const as AnnotationTool[]; +]; export const AvailableToolsInViewMode = [...MeasurementTools, AnnotationTool.MOVE]; @@ -578,12 +577,3 @@ export function adaptActiveToolToShortcuts( return activeTool; } - -export const getLabelForTool = (tool: AnnotationTool) => { - // todop - const toolName = AnnotationTool[tool.id]; - if (toolName.readableName.endsWith("Tool")) { - return toolName; - } - return `${toolName} Tool`; -}; diff --git a/frontend/javascripts/oxalis/model/sagas/annotation_tool_saga.ts b/frontend/javascripts/oxalis/model/sagas/annotation_tool_saga.ts index 946e7e5d692..accaa357ab9 100644 --- a/frontend/javascripts/oxalis/model/sagas/annotation_tool_saga.ts +++ b/frontend/javascripts/oxalis/model/sagas/annotation_tool_saga.ts @@ -1,5 +1,5 @@ import { AnnotationTool, MeasurementTools } from "oxalis/constants"; -import { getToolClassForAnnotationTool } from "oxalis/controller/combinations/tool_controls"; +import { getToolControllerForAnnotationTool } from "oxalis/controller/combinations/tool_controls"; import getSceneController from "oxalis/controller/scene_controller_provider"; import { type CycleToolAction, @@ -31,7 +31,7 @@ export function* watchToolDeselection(): Saga { } if (executeDeselect) { - getToolClassForAnnotationTool(previousTool).onToolDeselected(); + getToolControllerForAnnotationTool(previousTool).onToolDeselected(); } previousTool = storeState.uiInformation.activeTool; diff --git a/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx b/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx index 97c08fdba8a..50d7045ffc0 100644 --- a/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx +++ b/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx @@ -1038,10 +1038,7 @@ function ToolSpecificSettings({ visible={ToolsWithOverwriteCapabilities.includes(adaptedActiveTool)} /> - { - // todop: search for Tool.id to get these? - } - {adaptedActiveTool.id === "QUICK_SELECT" && ( + {adaptedActiveTool === AnnotationTool.QUICK_SELECT && ( <> { commands.push({ - name: `Switch to ${getLabelForTool(tool)}`, + name: `Switch to ${tool.readableName}`, command: () => Store.dispatch(setToolAction(tool)), color: commandEntryColor, }); diff --git a/frontend/javascripts/oxalis/view/input_catcher.tsx b/frontend/javascripts/oxalis/view/input_catcher.tsx index 1be91cada25..6773287af2d 100644 --- a/frontend/javascripts/oxalis/view/input_catcher.tsx +++ b/frontend/javascripts/oxalis/view/input_catcher.tsx @@ -1,7 +1,7 @@ import { useEffectOnlyOnce, useKeyPress } from "libs/react_hooks"; import { waitForCondition } from "libs/utils"; import _ from "lodash"; -import type { Rect, Viewport, ViewportRects } from "oxalis/constants"; +import type { AnnotationToolId, Rect, Viewport, ViewportRects } from "oxalis/constants"; import { AnnotationTool, ArbitraryViewport, ArbitraryViews, OrthoViews } from "oxalis/constants"; import { adaptActiveToolToShortcuts } from "oxalis/model/accessors/tool_accessor"; import { setInputCatcherRects } from "oxalis/model/actions/view_mode_actions"; @@ -92,8 +92,7 @@ export function recalculateInputCatcherSizes() { } } -// todop -const cursorForTool = { +const cursorForTool: Record = { MOVE: "move", SKELETON: "crosshair", BRUSH: "url(/assets/images/paint-brush-solid-border.svg) 0 10,auto", diff --git a/frontend/javascripts/oxalis/view/statusbar.tsx b/frontend/javascripts/oxalis/view/statusbar.tsx index 84083690d76..8f0e18a94fb 100644 --- a/frontend/javascripts/oxalis/view/statusbar.tsx +++ b/frontend/javascripts/oxalis/view/statusbar.tsx @@ -10,7 +10,7 @@ import type { Vector3 } from "oxalis/constants"; import { AltOrOptionKey, MappingStatusEnum, OrthoViews } from "oxalis/constants"; import { type ActionDescriptor, - getToolClassForAnnotationTool, + getToolControllerForAnnotationTool, } from "oxalis/controller/combinations/tool_controls"; import { getMappingInfoOrNull, @@ -194,8 +194,7 @@ function ShortcutsInfo() { if (!isPlaneMode) { let actionDescriptor = null; if (hasSkeleton && isShiftPressed) { - // todop - actionDescriptor = getToolClassForAnnotationTool( + actionDescriptor = getToolControllerForAnnotationTool( AnnotationTool.SKELETON, ).getActionDescriptors( AnnotationTool.SKELETON, @@ -337,7 +336,7 @@ function ShortcutsInfo() { isControlOrMetaPressed, isAltPressed, ); - const actionDescriptor = getToolClassForAnnotationTool(adaptedTool).getActionDescriptors( + const actionDescriptor = getToolControllerForAnnotationTool(adaptedTool).getActionDescriptors( adaptedTool, useLegacyBindings, isShiftPressed, From 4ec5a0d1b946c3830b08b3e62a0de9ff60b5a1dd Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Fri, 11 Apr 2025 16:37:20 +0200 Subject: [PATCH 28/84] linting --- .../oxalis/controller/combinations/tool_controls.ts | 2 +- .../oxalis/model/reducers/skeletontracing_reducer.ts | 6 ++---- frontend/javascripts/oxalis/model/sagas/mesh_saga.ts | 2 +- frontend/javascripts/oxalis/view/statusbar.tsx | 2 +- 4 files changed, 5 insertions(+), 7 deletions(-) diff --git a/frontend/javascripts/oxalis/controller/combinations/tool_controls.ts b/frontend/javascripts/oxalis/controller/combinations/tool_controls.ts index c0272ffa051..b9a3b60312b 100644 --- a/frontend/javascripts/oxalis/controller/combinations/tool_controls.ts +++ b/frontend/javascripts/oxalis/controller/combinations/tool_controls.ts @@ -6,8 +6,8 @@ import { document } from "libs/window"; import { AnnotationTool, ContourModeEnum, - OrthoViews, type OrthoView, + OrthoViews, type Point2, type Vector3, type Viewport, diff --git a/frontend/javascripts/oxalis/model/reducers/skeletontracing_reducer.ts b/frontend/javascripts/oxalis/model/reducers/skeletontracing_reducer.ts index 723e454861d..4b110b10b4b 100644 --- a/frontend/javascripts/oxalis/model/reducers/skeletontracing_reducer.ts +++ b/frontend/javascripts/oxalis/model/reducers/skeletontracing_reducer.ts @@ -689,8 +689,7 @@ function SkeletonTracingReducer(state: OxalisState, action: Action): OxalisState if (sourceNodeId === targetNodeId) { return state; } - const isProofreadingActive = - state.uiInformation.activeTool === AnnotationTool.PROOFREAD; + const isProofreadingActive = state.uiInformation.activeTool === AnnotationTool.PROOFREAD; const treeType = isProofreadingActive ? TreeTypeEnum.AGGLOMERATE : TreeTypeEnum.DEFAULT; const sourceTreeMaybe = getNodeAndTree(skeletonTracing, sourceNodeId, null, treeType); const targetTreeMaybe = getNodeAndTree(skeletonTracing, targetNodeId, null, treeType); @@ -964,8 +963,7 @@ function SkeletonTracingReducer(state: OxalisState, action: Action): OxalisState case "MERGE_TREES": { const { sourceNodeId, targetNodeId } = action; - const isProofreadingActive = - state.uiInformation.activeTool === AnnotationTool.PROOFREAD; + const isProofreadingActive = state.uiInformation.activeTool === AnnotationTool.PROOFREAD; const treeType = isProofreadingActive ? TreeTypeEnum.AGGLOMERATE : TreeTypeEnum.DEFAULT; const oldTrees = skeletonTracing.trees; const mergeResult = mergeTrees(oldTrees, sourceNodeId, targetNodeId, treeType); diff --git a/frontend/javascripts/oxalis/model/sagas/mesh_saga.ts b/frontend/javascripts/oxalis/model/sagas/mesh_saga.ts index 4caafbc24ae..9aa89afc94a 100644 --- a/frontend/javascripts/oxalis/model/sagas/mesh_saga.ts +++ b/frontend/javascripts/oxalis/model/sagas/mesh_saga.ts @@ -6,6 +6,7 @@ import { sendAnalyticsEvent, } from "admin/admin_rest_api"; import { saveAs } from "file-saver"; +import { mergeGeometries } from "libs/BufferGeometryUtils"; import ThreeDMap from "libs/ThreeDMap"; import Deferred from "libs/async/deferred"; import processTaskWithPool from "libs/async/task_pool"; @@ -88,7 +89,6 @@ import type { } from "../actions/volumetracing_actions"; import type { MagInfo } from "../helpers/mag_info"; import { ensureSceneControllerReady, ensureWkReady } from "./ready_sagas"; -import { mergeGeometries } from "libs/BufferGeometryUtils"; export const NO_LOD_MESH_INDEX = -1; const MAX_RETRY_COUNT = 5; diff --git a/frontend/javascripts/oxalis/view/statusbar.tsx b/frontend/javascripts/oxalis/view/statusbar.tsx index 8f0e18a94fb..eaa24a83244 100644 --- a/frontend/javascripts/oxalis/view/statusbar.tsx +++ b/frontend/javascripts/oxalis/view/statusbar.tsx @@ -18,7 +18,7 @@ import { hasVisibleUint64Segmentation, } from "oxalis/model/accessors/dataset_accessor"; import { getActiveMagInfo } from "oxalis/model/accessors/flycam_accessor"; -import { adaptActiveToolToShortcuts, AnnotationTool } from "oxalis/model/accessors/tool_accessor"; +import { AnnotationTool, adaptActiveToolToShortcuts } from "oxalis/model/accessors/tool_accessor"; import { calculateGlobalPos, isPlaneMode as getIsPlaneMode, From 833db7d8324a76d22146f7d4dfed353894e132bf Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Fri, 11 Apr 2025 16:46:06 +0200 Subject: [PATCH 29/84] make use of hasOverwriteCapabilities properties etc --- frontend/javascripts/oxalis/constants.ts | 3 --- .../oxalis/model/accessors/tool_accessor.ts | 24 +++++++------------ .../oxalis/model/reducers/ui_reducer.ts | 5 ++-- .../sagas/volume/volume_interpolation_saga.ts | 3 +-- .../oxalis/view/action-bar/toolbar_view.tsx | 8 ++----- .../view/components/command_palette.tsx | 5 ++-- 6 files changed, 18 insertions(+), 30 deletions(-) diff --git a/frontend/javascripts/oxalis/constants.ts b/frontend/javascripts/oxalis/constants.ts index 055846c7694..e399dad2878 100644 --- a/frontend/javascripts/oxalis/constants.ts +++ b/frontend/javascripts/oxalis/constants.ts @@ -4,10 +4,7 @@ export { AnnotationTool, AnnotationToolId, VolumeTools, - AvailableToolsInViewMode, MeasurementTools, - ToolsWithOverwriteCapabilities, - ToolsWithInterpolationCapabilities, } from "./model/accessors/tool_accessor"; export const ViewModeValues = ["orthogonal", "flight", "oblique"] as ViewMode[]; diff --git a/frontend/javascripts/oxalis/model/accessors/tool_accessor.ts b/frontend/javascripts/oxalis/model/accessors/tool_accessor.ts index c6d383bcc12..f1a97a08cfd 100644 --- a/frontend/javascripts/oxalis/model/accessors/tool_accessor.ts +++ b/frontend/javascripts/oxalis/model/accessors/tool_accessor.ts @@ -56,19 +56,26 @@ class SkeletonTool extends AbstractAnnotationTool { class BrushTool extends AbstractAnnotationTool { static id = _AnnotationToolHelper.BRUSH; static readableName = "Brush Tool"; + static hasOverwriteCapabilities = true; + static hasInterpolationCapabilities = true; } class EraseBrushTool extends AbstractAnnotationTool { static id = _AnnotationToolHelper.ERASE_BRUSH; static readableName = "Erase Tool (via Brush)"; + static hasOverwriteCapabilities = true; } class TraceTool extends AbstractAnnotationTool { static id = _AnnotationToolHelper.TRACE; static readableName = "Trace Tool"; + static hasOverwriteCapabilities = true; + static hasInterpolationCapabilities = true; } class EraseTraceTool extends AbstractAnnotationTool { static id = _AnnotationToolHelper.ERASE_TRACE; static readableName = "Erase Tool"; + static hasOverwriteCapabilities = true; } + class FillCellTool extends AbstractAnnotationTool { static id = _AnnotationToolHelper.FILL_CELL; static readableName = "Fill Tool"; @@ -80,6 +87,8 @@ class PickCellTool extends AbstractAnnotationTool { class QuickSelectTool extends AbstractAnnotationTool { static id = _AnnotationToolHelper.QUICK_SELECT; static readableName = "Quick Select Tool"; + static hasOverwriteCapabilities = true; + static hasInterpolationCapabilities = true; } class BoundingBoxTool extends AbstractAnnotationTool { static id = _AnnotationToolHelper.BOUNDING_BOX; @@ -138,26 +147,11 @@ export const VolumeTools = ToolCollections.VOLUME_TOOLS; export type ToolCollection = keyof typeof ToolCollections; -export const ToolsWithOverwriteCapabilities: AnnotationTool[] = [ - AnnotationTool.TRACE, - AnnotationTool.BRUSH, - AnnotationTool.ERASE_TRACE, - AnnotationTool.ERASE_BRUSH, - AnnotationTool.QUICK_SELECT, -]; -export const ToolsWithInterpolationCapabilities: AnnotationTool[] = [ - AnnotationTool.TRACE, - AnnotationTool.BRUSH, - AnnotationTool.QUICK_SELECT, -]; - export const MeasurementTools: AnnotationTool[] = [ AnnotationTool.LINE_MEASUREMENT, AnnotationTool.AREA_MEASUREMENT, ]; -export const AvailableToolsInViewMode = [...MeasurementTools, AnnotationTool.MOVE]; - export type ToolWorkspace = | "ALL_TOOLS" | "READ_ONLY_TOOLS" diff --git a/frontend/javascripts/oxalis/model/reducers/ui_reducer.ts b/frontend/javascripts/oxalis/model/reducers/ui_reducer.ts index 5a75a20ea87..16ce171eae6 100644 --- a/frontend/javascripts/oxalis/model/reducers/ui_reducer.ts +++ b/frontend/javascripts/oxalis/model/reducers/ui_reducer.ts @@ -1,4 +1,4 @@ -import { type AnnotationTool, AvailableToolsInViewMode } from "oxalis/constants"; +import { type AnnotationTool } from "oxalis/constants"; import defaultState from "oxalis/default_state"; import type { Action } from "oxalis/model/actions/actions"; import { updateKey, updateKey2 } from "oxalis/model/helpers/deep_update"; @@ -9,6 +9,7 @@ import { } from "oxalis/model/reducers/reducer_helpers"; import { hideBrushReducer } from "oxalis/model/reducers/volumetracing_reducer_helpers"; import type { OxalisState } from "oxalis/store"; +import { ToolCollections } from "../accessors/tool_accessor"; function UiReducer(state: OxalisState, action: Action): OxalisState { switch (action.type) { @@ -69,7 +70,7 @@ function UiReducer(state: OxalisState, action: Action): OxalisState { case "SET_TOOL": { if (!state.annotation.restrictions.allowUpdate) { - if ((AvailableToolsInViewMode as AnnotationTool[]).includes(action.tool)) { + if (ToolCollections.READ_ONLY_TOOLS.includes(action.tool)) { return setToolReducer(state, action.tool); } return state; diff --git a/frontend/javascripts/oxalis/model/sagas/volume/volume_interpolation_saga.ts b/frontend/javascripts/oxalis/model/sagas/volume/volume_interpolation_saga.ts index 7b39e060680..e45125ee4f5 100644 --- a/frontend/javascripts/oxalis/model/sagas/volume/volume_interpolation_saga.ts +++ b/frontend/javascripts/oxalis/model/sagas/volume/volume_interpolation_saga.ts @@ -8,7 +8,6 @@ import { ContourModeEnum, InterpolationModeEnum, OrthoViews, - ToolsWithInterpolationCapabilities, type TypedArrayWithoutBigInt, type Vector3, } from "oxalis/constants"; @@ -267,7 +266,7 @@ export default function* maybeInterpolateSegmentationLayer(): Saga { if (!allowUpdate) return; const activeTool = yield* select((state) => state.uiInformation.activeTool); - if (!ToolsWithInterpolationCapabilities.includes(activeTool)) { + if (!activeTool.hasInterpolationCapabilities) { return; } diff --git a/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx b/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx index 50d7045ffc0..8b0cabb8e7b 100644 --- a/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx +++ b/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx @@ -32,8 +32,6 @@ import { MeasurementTools, type OverwriteMode, OverwriteModeEnum, - ToolsWithInterpolationCapabilities, - ToolsWithOverwriteCapabilities, Unicode, VolumeTools, } from "oxalis/constants"; @@ -1035,7 +1033,7 @@ function ToolSpecificSettings({ {adaptedActiveTool === AnnotationTool.QUICK_SELECT && ( @@ -1058,9 +1056,7 @@ function ToolSpecificSettings({ )} - {ToolsWithInterpolationCapabilities.includes(adaptedActiveTool) ? ( - - ) : null} + {adaptedActiveTool.hasOverwriteCapabilities ? : null} {adaptedActiveTool === AnnotationTool.FILL_CELL ? : null} diff --git a/frontend/javascripts/oxalis/view/components/command_palette.tsx b/frontend/javascripts/oxalis/view/components/command_palette.tsx index ad967c3f230..8a8a1aba114 100644 --- a/frontend/javascripts/oxalis/view/components/command_palette.tsx +++ b/frontend/javascripts/oxalis/view/components/command_palette.tsx @@ -3,7 +3,7 @@ import { capitalize, getPhraseFromCamelCaseString } from "libs/utils"; import * as Utils from "libs/utils"; import _ from "lodash"; import { getAdministrationSubMenu } from "navbar"; -import { AnnotationTool, AvailableToolsInViewMode } from "oxalis/constants"; +import { AnnotationTool } from "oxalis/constants"; import { updateUserSettingAction } from "oxalis/model/actions/settings_actions"; import { setToolAction } from "oxalis/model/actions/ui_actions"; import { Store } from "oxalis/singletons"; @@ -18,6 +18,7 @@ import { } from "../action-bar/tracing_actions_view"; import { viewDatasetMenu } from "../action-bar/view_dataset_actions_view"; import { commandPaletteDarkTheme, commandPaletteLightTheme } from "./command_palette_theme"; +import { ToolCollections } from "oxalis/model/accessors/tool_accessor"; type CommandWithoutId = Omit; @@ -160,7 +161,7 @@ export const CommandPalette = ({ label }: { label: string | JSX.Element | null } const commands: CommandWithoutId[] = []; let availableTools = Object.values(AnnotationTool); if (isViewMode || !restrictions.allowUpdate) { - availableTools = AvailableToolsInViewMode; + availableTools = ToolCollections.READ_ONLY_TOOLS; } availableTools.forEach((tool) => { commands.push({ From d2c9baa0882ef1a321de3c402242fed44dbe3b25 Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Fri, 11 Apr 2025 16:52:04 +0200 Subject: [PATCH 30/84] rename tool workspace to toolkit --- frontend/javascripts/oxalis/default_state.ts | 2 +- .../oxalis/model/accessors/tool_accessor.ts | 6 +----- .../oxalis/model/actions/settings_actions.ts | 9 -------- .../model/bucket_data_handling/data_cube.ts | 4 ++-- .../model/reducers/skeletontracing_reducer.ts | 6 +++--- .../model/sagas/split_boundary_mesh_saga.ts | 8 +++---- frontend/javascripts/oxalis/store.ts | 8 ++----- .../oxalis/view/action-bar/toolbar_view.tsx | 18 ++++++++-------- ...ace_view.tsx => toolkit_switcher_view.tsx} | 21 ++++++++----------- .../oxalis/view/action_bar_view.tsx | 4 ++-- 10 files changed, 33 insertions(+), 53 deletions(-) rename frontend/javascripts/oxalis/view/action-bar/{tool_workspace_view.tsx => toolkit_switcher_view.tsx} (74%) diff --git a/frontend/javascripts/oxalis/default_state.ts b/frontend/javascripts/oxalis/default_state.ts index ccfdd0618e0..0b62172f424 100644 --- a/frontend/javascripts/oxalis/default_state.ts +++ b/frontend/javascripts/oxalis/default_state.ts @@ -102,7 +102,7 @@ const defaultState: OxalisState = { }, renderWatermark: true, antialiasRendering: false, - toolWorkspace: "ALL_TOOLS", + activeToolkit: "ALL_TOOLS", }, temporaryConfiguration: { viewMode: Constants.MODE_PLANE_TRACING, diff --git a/frontend/javascripts/oxalis/model/accessors/tool_accessor.ts b/frontend/javascripts/oxalis/model/accessors/tool_accessor.ts index f1a97a08cfd..9ee297a78b1 100644 --- a/frontend/javascripts/oxalis/model/accessors/tool_accessor.ts +++ b/frontend/javascripts/oxalis/model/accessors/tool_accessor.ts @@ -152,11 +152,7 @@ export const MeasurementTools: AnnotationTool[] = [ AnnotationTool.AREA_MEASUREMENT, ]; -export type ToolWorkspace = - | "ALL_TOOLS" - | "READ_ONLY_TOOLS" - | "VOLUME_ANNOTATION" - | "SPLIT_SEGMENTS"; +export type Toolkit = "ALL_TOOLS" | "READ_ONLY_TOOLS" | "VOLUME_ANNOTATION" | "SPLIT_SEGMENTS"; export function getAvailableTools(_state: OxalisState) {} diff --git a/frontend/javascripts/oxalis/model/actions/settings_actions.ts b/frontend/javascripts/oxalis/model/actions/settings_actions.ts index 5570fec333a..ed702176124 100644 --- a/frontend/javascripts/oxalis/model/actions/settings_actions.ts +++ b/frontend/javascripts/oxalis/model/actions/settings_actions.ts @@ -6,7 +6,6 @@ import type { Mapping, MappingType, TemporaryConfiguration, - ToolWorkspace, UserConfiguration, } from "oxalis/store"; import type { APIHistogramData } from "types/api_flow_types"; @@ -18,7 +17,6 @@ export type ToggleTemporarySettingAction = ReturnType; export type InitializeSettingsAction = ReturnType; type SetViewModeAction = ReturnType; -type SetToolWorkspaceAction = ReturnType; type SetHistogramDataForLayerAction = ReturnType; export type ReloadHistogramAction = ReturnType; export type ClipHistogramAction = ReturnType; @@ -42,7 +40,6 @@ export type SettingAction = | InitializeSettingsAction | UpdateLayerSettingAction | SetViewModeAction - | SetToolWorkspaceAction | SetFlightmodeRecordingAction | SetControlModeAction | SetMappingEnabledAction @@ -121,12 +118,6 @@ export const setViewModeAction = (viewMode: ViewMode) => viewMode, }) as const; -export const setToolWorkspaceAction = (toolWorkspace: ToolWorkspace) => - ({ - type: "SET_TOOL_WORKSPACE", - toolWorkspace, - }) as const; - export const setHistogramDataForLayerAction = ( layerName: string, histogramData: APIHistogramData | null | undefined, diff --git a/frontend/javascripts/oxalis/model/bucket_data_handling/data_cube.ts b/frontend/javascripts/oxalis/model/bucket_data_handling/data_cube.ts index fa187490296..7147adafe12 100644 --- a/frontend/javascripts/oxalis/model/bucket_data_handling/data_cube.ts +++ b/frontend/javascripts/oxalis/model/bucket_data_handling/data_cube.ts @@ -544,8 +544,8 @@ class DataCube { const floodfillBoundingBox = new BoundingBox(_floodfillBoundingBox); const sceneController = getSceneController(); - const isSplitWorkspace = Store.getState().userConfiguration.toolWorkspace === "SPLIT_SEGMENTS"; - const splitBoundaryMesh = isSplitWorkspace ? sceneController.getSplitBoundaryMesh() : null; + const isSplitToolkit = Store.getState().userConfiguration.activeToolkit === "SPLIT_SEGMENTS"; + const splitBoundaryMesh = isSplitToolkit ? sceneController.getSplitBoundaryMesh() : null; // Helper function to convert between xyz and uvw (both directions) const transpose = (voxel: Vector3): Vector3 => diff --git a/frontend/javascripts/oxalis/model/reducers/skeletontracing_reducer.ts b/frontend/javascripts/oxalis/model/reducers/skeletontracing_reducer.ts index 4b110b10b4b..f62398f123a 100644 --- a/frontend/javascripts/oxalis/model/reducers/skeletontracing_reducer.ts +++ b/frontend/javascripts/oxalis/model/reducers/skeletontracing_reducer.ts @@ -827,16 +827,16 @@ function SkeletonTracingReducer(state: OxalisState, action: Action): OxalisState case "CREATE_TREE": { const { timestamp } = action; - const isSplitWorkspaceActive = state.userConfiguration.toolWorkspace === "SPLIT_SEGMENTS"; + const isSplitToolkitActive = state.userConfiguration.activeToolkit === "SPLIT_SEGMENTS"; return createTree( state, timestamp, undefined, undefined, undefined, - // Don't show edges for trees that were created in the split workspace, + // Don't show edges for trees that were created in the split toolkit, // because spline curves will be shown for each section by default. - !isSplitWorkspaceActive, + !isSplitToolkitActive, ) .map((tree) => { if (action.treeIdCallback) { diff --git a/frontend/javascripts/oxalis/model/sagas/split_boundary_mesh_saga.ts b/frontend/javascripts/oxalis/model/sagas/split_boundary_mesh_saga.ts index 973400a45f8..1044d3986ab 100644 --- a/frontend/javascripts/oxalis/model/sagas/split_boundary_mesh_saga.ts +++ b/frontend/javascripts/oxalis/model/sagas/split_boundary_mesh_saga.ts @@ -16,10 +16,10 @@ function* updateSplitBoundaryMesh() { cleanUpFn = null; } - const isSplitWorkspace = yield* select( - (state) => state.userConfiguration.toolWorkspace === "SPLIT_SEGMENTS", + const isSplitToolkit = yield* select( + (state) => state.userConfiguration.activeToolkit === "SPLIT_SEGMENTS", ); - if (!isSplitWorkspace) { + if (!isSplitToolkit) { return; } @@ -54,7 +54,7 @@ export function* splitBoundaryMeshSaga(): Saga { "TOGGLE_TREE", "SET_NODE_POSITION", (action: Action) => - action.type === "UPDATE_USER_SETTING" && action.propertyName === "toolWorkspace", + action.type === "UPDATE_USER_SETTING" && action.propertyName === "activeToolkit", ] as ActionPattern, updateSplitBoundaryMesh, ); diff --git a/frontend/javascripts/oxalis/store.ts b/frontend/javascripts/oxalis/store.ts index fedae95875a..14d51ba6df6 100644 --- a/frontend/javascripts/oxalis/store.ts +++ b/frontend/javascripts/oxalis/store.ts @@ -372,11 +372,7 @@ export type QuickSelectConfig = { readonly dilateValue: number; }; -export type ToolWorkspace = - | "ALL_TOOLS" - | "READ_ONLY_TOOLS" - | "VOLUME_ANNOTATION" - | "SPLIT_SEGMENTS"; +export type Toolkit = "ALL_TOOLS" | "READ_ONLY_TOOLS" | "VOLUME_ANNOTATION" | "SPLIT_SEGMENTS"; export type UserConfiguration = { readonly autoSaveLayouts: boolean; @@ -419,7 +415,7 @@ export type UserConfiguration = { readonly quickSelect: QuickSelectConfig; readonly renderWatermark: boolean; readonly antialiasRendering: boolean; - readonly toolWorkspace: ToolWorkspace; + readonly activeToolkit: Toolkit; }; export type RecommendedConfiguration = Partial< UserConfiguration & diff --git a/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx b/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx index 8b0cabb8e7b..e69637671f1 100644 --- a/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx +++ b/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx @@ -390,8 +390,8 @@ function SkeletonSpecificButtons() { const isContinuousNodeCreationEnabled = useSelector( (state: OxalisState) => state.userConfiguration.continuousNodeCreation, ); - const isSplitWorkspace = useSelector( - (state: OxalisState) => state.userConfiguration.toolWorkspace === "SPLIT_SEGMENTS", + const isSplitToolkit = useSelector( + (state: OxalisState) => state.userConfiguration.activeToolkit === "SPLIT_SEGMENTS", ); const toggleContinuousNodeCreation = () => dispatch(updateUserSettingAction("continuousNodeCreation", !isContinuousNodeCreationEnabled)); @@ -432,7 +432,7 @@ function SkeletonSpecificButtons() { }} > - {isSplitWorkspace ? null : ( + {isSplitToolkit ? null : ( )} - {isSplitWorkspace ? null : ( + {isSplitToolkit ? null : ( state.annotation?.volumes.length > 0); const hasSkeleton = useSelector((state: OxalisState) => state.annotation?.skeleton != null); - const toolWorkspace = useSelector((state: OxalisState) => state.userConfiguration.toolWorkspace); + const toolkit = useSelector((state: OxalisState) => state.userConfiguration.activeToolkit); const [lastForcefullyDisabledTool, setLastForcefullyDisabledTool] = useState(null); @@ -906,7 +906,7 @@ export default function ToolbarView() { return ( <> - {toolWorkspace === "ALL_TOOLS" ? ( + {toolkit === "ALL_TOOLS" ? ( <> @@ -922,7 +922,7 @@ export default function ToolbarView() { ) : null} - {toolWorkspace === "READ_ONLY_TOOLS" ? ( + {toolkit === "READ_ONLY_TOOLS" ? ( <> @@ -930,7 +930,7 @@ export default function ToolbarView() { ) : null} - {toolWorkspace === "VOLUME_ANNOTATION" ? ( + {toolkit === "VOLUME_ANNOTATION" ? ( <> @@ -942,7 +942,7 @@ export default function ToolbarView() { ) : null} - {toolWorkspace === "SPLIT_SEGMENTS" ? ( + {toolkit === "SPLIT_SEGMENTS" ? ( <> diff --git a/frontend/javascripts/oxalis/view/action-bar/tool_workspace_view.tsx b/frontend/javascripts/oxalis/view/action-bar/toolkit_switcher_view.tsx similarity index 74% rename from frontend/javascripts/oxalis/view/action-bar/tool_workspace_view.tsx rename to frontend/javascripts/oxalis/view/action-bar/toolkit_switcher_view.tsx index ab51f780f65..90c7e5c640d 100644 --- a/frontend/javascripts/oxalis/view/action-bar/tool_workspace_view.tsx +++ b/frontend/javascripts/oxalis/view/action-bar/toolkit_switcher_view.tsx @@ -1,14 +1,11 @@ import { Badge, Button, Dropdown, type MenuProps } from "antd"; -import { - // setToolWorkspaceAction, - updateUserSettingAction, -} from "oxalis/model/actions/settings_actions"; +import { updateUserSettingAction } from "oxalis/model/actions/settings_actions"; import { Store } from "oxalis/singletons"; -import type { ToolWorkspace } from "oxalis/store"; +import type { Toolkit } from "oxalis/store"; import { NARROW_BUTTON_STYLE } from "./toolbar_view"; -export default function ToolWorkspaceView() { - const toolWorkspaceItems: MenuProps["items"] = [ +export default function ToolkitView() { + const toolkitItems: MenuProps["items"] = [ { key: "1", type: "group", @@ -35,8 +32,8 @@ export default function ToolWorkspaceView() { ]; const handleMenuClick: MenuProps["onClick"] = (args) => { - const toolWorkspace = args.key; - Store.dispatch(updateUserSettingAction("toolWorkspace", toolWorkspace as ToolWorkspace)); + const toolkit = args.key; + Store.dispatch(updateUserSettingAction("activeToolkit", toolkit as Toolkit)); // Unfortunately, antd doesn't provide the original event here // which is why we have to blur using document.activeElement. // Additionally, we need a timeout since the blurring would be done @@ -49,13 +46,13 @@ export default function ToolWorkspaceView() { }, 100); }; - const toolWorkspaceMenuProps = { - items: toolWorkspaceItems, + const toolkitMenuProps = { + items: toolkitItems, onClick: handleMenuClick, }; return ( - + {isArbitrarySupported && !is2d ? : null} - +
); From 72ffdd15830ce1ba9c3c8b202d79cad79a175842 Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Fri, 11 Apr 2025 17:01:31 +0200 Subject: [PATCH 31/84] use toolkit collection in toolbar --- .../oxalis/model/accessors/tool_accessor.ts | 9 +- frontend/javascripts/oxalis/store.ts | 3 +- .../oxalis/view/action-bar/toolbar_view.tsx | 88 +++++++++---------- .../view/action-bar/toolkit_switcher_view.tsx | 4 +- 4 files changed, 54 insertions(+), 50 deletions(-) diff --git a/frontend/javascripts/oxalis/model/accessors/tool_accessor.ts b/frontend/javascripts/oxalis/model/accessors/tool_accessor.ts index 9ee297a78b1..ced7be4ad22 100644 --- a/frontend/javascripts/oxalis/model/accessors/tool_accessor.ts +++ b/frontend/javascripts/oxalis/model/accessors/tool_accessor.ts @@ -141,6 +141,13 @@ export const ToolCollections = { AnnotationTool.LINE_MEASUREMENT, AnnotationTool.AREA_MEASUREMENT, ] as AnnotationTool[], + SPLIT_SEGMENTS: [ + AnnotationTool.MOVE, + AnnotationTool.SKELETON, + AnnotationTool.FILL_CELL, + AnnotationTool.PICK_CELL, + AnnotationTool.BOUNDING_BOX, + ], }; export const VolumeTools = ToolCollections.VOLUME_TOOLS; @@ -152,7 +159,7 @@ export const MeasurementTools: AnnotationTool[] = [ AnnotationTool.AREA_MEASUREMENT, ]; -export type Toolkit = "ALL_TOOLS" | "READ_ONLY_TOOLS" | "VOLUME_ANNOTATION" | "SPLIT_SEGMENTS"; +export type Toolkit = keyof typeof ToolCollections; export function getAvailableTools(_state: OxalisState) {} diff --git a/frontend/javascripts/oxalis/store.ts b/frontend/javascripts/oxalis/store.ts index 14d51ba6df6..4efe2df7548 100644 --- a/frontend/javascripts/oxalis/store.ts +++ b/frontend/javascripts/oxalis/store.ts @@ -72,6 +72,7 @@ import type { import FlycamInfoCacheReducer from "./model/reducers/flycam_info_cache_reducer"; import OrganizationReducer from "./model/reducers/organization_reducer"; import type { StartAIJobModalState } from "./view/action-bar/starting_job_modals"; +import type { Toolkit } from "./model/accessors/tool_accessor"; export type MutableCommentType = { content: string; @@ -372,8 +373,6 @@ export type QuickSelectConfig = { readonly dilateValue: number; }; -export type Toolkit = "ALL_TOOLS" | "READ_ONLY_TOOLS" | "VOLUME_ANNOTATION" | "SPLIT_SEGMENTS"; - export type UserConfiguration = { readonly autoSaveLayouts: boolean; readonly autoRenderMeshInProofreading: boolean; diff --git a/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx b/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx index e69637671f1..1af53bd7b82 100644 --- a/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx +++ b/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx @@ -39,6 +39,7 @@ import { getActiveTree } from "oxalis/model/accessors/skeletontracing_accessor"; import { adaptActiveToolToShortcuts, getDisabledInfoForTools, + ToolCollections, } from "oxalis/model/accessors/tool_accessor"; import { getActiveSegmentationTracing, @@ -906,51 +907,7 @@ export default function ToolbarView() { return ( <> - {toolkit === "ALL_TOOLS" ? ( - <> - - - - - - - - - - - - - - ) : null} - {toolkit === "READ_ONLY_TOOLS" ? ( - <> - - - - - ) : null} - - {toolkit === "VOLUME_ANNOTATION" ? ( - <> - - - - - - - - - - ) : null} - {toolkit === "SPLIT_SEGMENTS" ? ( - <> - - - - - - - ) : null} + {ToolCollections[toolkit].map((tool) => getButtonForTool(tool, adaptedActiveTool))} ; + } + case AnnotationTool.SKELETON: { + return ; + } + case AnnotationTool.BRUSH: { + return ; + } + case AnnotationTool.ERASE_BRUSH: { + return ; + } + case AnnotationTool.TRACE: { + return ; + } + case AnnotationTool.ERASE_TRACE: { + return ; + } + case AnnotationTool.FILL_CELL: { + return ; + } + case AnnotationTool.PICK_CELL: { + return ; + } + case AnnotationTool.QUICK_SELECT: { + return ; + } + case AnnotationTool.BOUNDING_BOX: { + return ; + } + case AnnotationTool.PROOFREAD: { + return ; + } + case AnnotationTool.LINE_MEASUREMENT: { + return ; + } + } +} + function MaybeMultiSliceAnnotationInfoIcon() { const maybeMagWithZoomStep = useSelector(getRenderableMagForActiveSegmentationTracing); const labeledMag = maybeMagWithZoomStep != null ? maybeMagWithZoomStep.mag : null; diff --git a/frontend/javascripts/oxalis/view/action-bar/toolkit_switcher_view.tsx b/frontend/javascripts/oxalis/view/action-bar/toolkit_switcher_view.tsx index 90c7e5c640d..9571be5ca9d 100644 --- a/frontend/javascripts/oxalis/view/action-bar/toolkit_switcher_view.tsx +++ b/frontend/javascripts/oxalis/view/action-bar/toolkit_switcher_view.tsx @@ -1,7 +1,7 @@ import { Badge, Button, Dropdown, type MenuProps } from "antd"; import { updateUserSettingAction } from "oxalis/model/actions/settings_actions"; import { Store } from "oxalis/singletons"; -import type { Toolkit } from "oxalis/store"; +import type { Toolkit } from "oxalis/model/accessors/tool_accessor"; import { NARROW_BUTTON_STYLE } from "./toolbar_view"; export default function ToolkitView() { @@ -21,7 +21,7 @@ export default function ToolkitView() { }, { label: "Volume", - key: "VOLUME_ANNOTATION", + key: "VOLUME_TOOLS", }, { label: "Split Segments", From 0488b7db3a04fb0919f8f0c0020cba00390a4dba Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Fri, 11 Apr 2025 17:09:21 +0200 Subject: [PATCH 32/84] fix cycling of tools --- frontend/javascripts/oxalis/constants.ts | 2 +- .../javascripts/oxalis/model/accessors/tool_accessor.ts | 4 ++-- .../javascripts/oxalis/model/reducers/reducer_helpers.ts | 8 ++++---- frontend/javascripts/oxalis/model/reducers/ui_reducer.ts | 1 - frontend/javascripts/oxalis/store.ts | 2 +- .../javascripts/oxalis/view/action-bar/toolbar_view.tsx | 2 +- .../oxalis/view/action-bar/toolkit_switcher_view.tsx | 2 +- .../oxalis/view/components/command_palette.tsx | 2 +- 8 files changed, 11 insertions(+), 12 deletions(-) diff --git a/frontend/javascripts/oxalis/constants.ts b/frontend/javascripts/oxalis/constants.ts index e399dad2878..4cdf36597f4 100644 --- a/frontend/javascripts/oxalis/constants.ts +++ b/frontend/javascripts/oxalis/constants.ts @@ -2,7 +2,7 @@ import type { AdditionalCoordinate } from "types/api_flow_types"; export { AnnotationTool, - AnnotationToolId, + type AnnotationToolId, VolumeTools, MeasurementTools, } from "./model/accessors/tool_accessor"; diff --git a/frontend/javascripts/oxalis/model/accessors/tool_accessor.ts b/frontend/javascripts/oxalis/model/accessors/tool_accessor.ts index ced7be4ad22..56556de5ba2 100644 --- a/frontend/javascripts/oxalis/model/accessors/tool_accessor.ts +++ b/frontend/javascripts/oxalis/model/accessors/tool_accessor.ts @@ -126,7 +126,7 @@ export const AnnotationTool = { export type AnnotationTool = (typeof AnnotationTool)[keyof typeof AnnotationTool]; export const ToolCollections = { - ALL_TOOLS: Object.values(AnnotationTool), + ALL_TOOLS: Object.values(AnnotationTool) as AnnotationTool[], VOLUME_TOOLS: [ AnnotationTool.BRUSH, AnnotationTool.ERASE_BRUSH, @@ -147,7 +147,7 @@ export const ToolCollections = { AnnotationTool.FILL_CELL, AnnotationTool.PICK_CELL, AnnotationTool.BOUNDING_BOX, - ], + ] as AnnotationTool[], }; export const VolumeTools = ToolCollections.VOLUME_TOOLS; diff --git a/frontend/javascripts/oxalis/model/reducers/reducer_helpers.ts b/frontend/javascripts/oxalis/model/reducers/reducer_helpers.ts index f4664df3171..dfec63af6b7 100644 --- a/frontend/javascripts/oxalis/model/reducers/reducer_helpers.ts +++ b/frontend/javascripts/oxalis/model/reducers/reducer_helpers.ts @@ -1,8 +1,8 @@ import Maybe from "data.maybe"; import * as Utils from "libs/utils"; -import { AnnotationTool } from "oxalis/constants"; +import type { AnnotationTool } from "oxalis/constants"; import type { BoundingBoxType } from "oxalis/constants"; -import { getDisabledInfoForTools } from "oxalis/model/accessors/tool_accessor"; +import { ToolCollections, getDisabledInfoForTools } from "oxalis/model/accessors/tool_accessor"; import { isVolumeAnnotationDisallowedForZoom, isVolumeTool, @@ -143,7 +143,7 @@ export function convertServerAdditionalAxesToFrontEnd( export function getNextTool(state: OxalisState): AnnotationTool | null { const disabledToolInfo = getDisabledInfoForTools(state); - const tools = Object.values(AnnotationTool); + const tools = ToolCollections[state.userConfiguration.activeToolkit]; const currentToolIndex = tools.indexOf(state.uiInformation.activeTool); // Search for the next tool which is not disabled. @@ -163,7 +163,7 @@ export function getNextTool(state: OxalisState): AnnotationTool | null { } export function getPreviousTool(state: OxalisState): AnnotationTool | null { const disabledToolInfo = getDisabledInfoForTools(state); - const tools = Object.values(AnnotationTool); + const tools = ToolCollections[state.userConfiguration.activeToolkit]; const currentToolIndex = tools.indexOf(state.uiInformation.activeTool); // Search backwards for the next tool which is not disabled. diff --git a/frontend/javascripts/oxalis/model/reducers/ui_reducer.ts b/frontend/javascripts/oxalis/model/reducers/ui_reducer.ts index 16ce171eae6..f4d33e9a550 100644 --- a/frontend/javascripts/oxalis/model/reducers/ui_reducer.ts +++ b/frontend/javascripts/oxalis/model/reducers/ui_reducer.ts @@ -1,4 +1,3 @@ -import { type AnnotationTool } from "oxalis/constants"; import defaultState from "oxalis/default_state"; import type { Action } from "oxalis/model/actions/actions"; import { updateKey, updateKey2 } from "oxalis/model/helpers/deep_update"; diff --git a/frontend/javascripts/oxalis/store.ts b/frontend/javascripts/oxalis/store.ts index 4efe2df7548..c84981d6183 100644 --- a/frontend/javascripts/oxalis/store.ts +++ b/frontend/javascripts/oxalis/store.ts @@ -69,10 +69,10 @@ import type { ServerEditableMapping, TracingType, } from "types/api_flow_types"; +import type { Toolkit } from "./model/accessors/tool_accessor"; import FlycamInfoCacheReducer from "./model/reducers/flycam_info_cache_reducer"; import OrganizationReducer from "./model/reducers/organization_reducer"; import type { StartAIJobModalState } from "./view/action-bar/starting_job_modals"; -import type { Toolkit } from "./model/accessors/tool_accessor"; export type MutableCommentType = { content: string; diff --git a/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx b/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx index 1af53bd7b82..159ea820204 100644 --- a/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx +++ b/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx @@ -37,9 +37,9 @@ import { } from "oxalis/constants"; import { getActiveTree } from "oxalis/model/accessors/skeletontracing_accessor"; import { + ToolCollections, adaptActiveToolToShortcuts, getDisabledInfoForTools, - ToolCollections, } from "oxalis/model/accessors/tool_accessor"; import { getActiveSegmentationTracing, diff --git a/frontend/javascripts/oxalis/view/action-bar/toolkit_switcher_view.tsx b/frontend/javascripts/oxalis/view/action-bar/toolkit_switcher_view.tsx index 9571be5ca9d..d87807ffa5f 100644 --- a/frontend/javascripts/oxalis/view/action-bar/toolkit_switcher_view.tsx +++ b/frontend/javascripts/oxalis/view/action-bar/toolkit_switcher_view.tsx @@ -1,7 +1,7 @@ import { Badge, Button, Dropdown, type MenuProps } from "antd"; +import type { Toolkit } from "oxalis/model/accessors/tool_accessor"; import { updateUserSettingAction } from "oxalis/model/actions/settings_actions"; import { Store } from "oxalis/singletons"; -import type { Toolkit } from "oxalis/model/accessors/tool_accessor"; import { NARROW_BUTTON_STYLE } from "./toolbar_view"; export default function ToolkitView() { diff --git a/frontend/javascripts/oxalis/view/components/command_palette.tsx b/frontend/javascripts/oxalis/view/components/command_palette.tsx index 8a8a1aba114..5e08c3edb29 100644 --- a/frontend/javascripts/oxalis/view/components/command_palette.tsx +++ b/frontend/javascripts/oxalis/view/components/command_palette.tsx @@ -4,6 +4,7 @@ import * as Utils from "libs/utils"; import _ from "lodash"; import { getAdministrationSubMenu } from "navbar"; import { AnnotationTool } from "oxalis/constants"; +import { ToolCollections } from "oxalis/model/accessors/tool_accessor"; import { updateUserSettingAction } from "oxalis/model/actions/settings_actions"; import { setToolAction } from "oxalis/model/actions/ui_actions"; import { Store } from "oxalis/singletons"; @@ -18,7 +19,6 @@ import { } from "../action-bar/tracing_actions_view"; import { viewDatasetMenu } from "../action-bar/view_dataset_actions_view"; import { commandPaletteDarkTheme, commandPaletteLightTheme } from "./command_palette_theme"; -import { ToolCollections } from "oxalis/model/accessors/tool_accessor"; type CommandWithoutId = Omit; From cfc5527f5206b866b9f834c603f7920dbb155b27 Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Fri, 11 Apr 2025 17:28:06 +0200 Subject: [PATCH 33/84] fix some cyclic imports --- frontend/javascripts/oxalis/api/api_latest.ts | 3 +-- frontend/javascripts/oxalis/constants.ts | 7 ------- .../oxalis/controller/combinations/tool_controls.ts | 2 +- .../oxalis/controller/segment_mesh_controller.ts | 3 ++- frontend/javascripts/oxalis/controller/td_controller.tsx | 2 +- .../oxalis/controller/viewmodes/plane_controller.tsx | 8 ++------ frontend/javascripts/oxalis/default_state.ts | 2 +- .../geometries/materials/plane_material_factory.ts | 9 ++------- .../oxalis/model/accessors/volumetracing_accessor.ts | 6 ++++-- frontend/javascripts/oxalis/model/actions/ui_actions.ts | 3 ++- .../javascripts/oxalis/model/reducers/reducer_helpers.ts | 2 +- .../oxalis/model/reducers/skeletontracing_reducer.ts | 3 ++- .../oxalis/model/sagas/annotation_tool_saga.ts | 2 +- .../javascripts/oxalis/model/sagas/proofread_saga.ts | 3 ++- frontend/javascripts/oxalis/model/sagas/undo_saga.ts | 2 +- .../oxalis/model/sagas/volume/floodfill_saga.tsx | 6 +++--- .../oxalis/model/sagas/volumetracing_saga.tsx | 3 ++- .../oxalis/model/volumetracing/volumelayer.ts | 3 ++- frontend/javascripts/oxalis/model_initialization.ts | 3 ++- frontend/javascripts/oxalis/store.ts | 2 +- .../javascripts/oxalis/view/action-bar/toolbar_view.tsx | 6 ++++-- .../oxalis/view/components/command_palette.tsx | 2 +- frontend/javascripts/oxalis/view/context_menu.tsx | 4 ++-- .../oxalis/view/distance_measurement_tooltip.tsx | 8 ++------ frontend/javascripts/oxalis/view/input_catcher.tsx | 5 +++-- .../oxalis/view/left-border-tabs/layer_settings_tab.tsx | 8 ++------ frontend/javascripts/oxalis/view/plane_view.ts | 8 ++------ frontend/javascripts/test/api/api_volume_latest.spec.ts | 2 +- .../javascripts/test/fixtures/volumetracing_object.ts | 3 ++- .../test/reducers/volumetracing_reducer.spec.ts | 3 ++- .../test/sagas/annotation_tool_disabled_info.spec.ts | 2 +- .../javascripts/test/sagas/annotation_tool_saga.spec.ts | 2 +- .../test/sagas/volumetracing/bucket_eviction_helper.ts | 3 ++- .../test/sagas/volumetracing/volumetracing_saga.spec.ts | 2 +- .../volumetracing/volumetracing_saga_integration.spec.ts | 2 +- 35 files changed, 60 insertions(+), 74 deletions(-) diff --git a/frontend/javascripts/oxalis/api/api_latest.ts b/frontend/javascripts/oxalis/api/api_latest.ts index 1f56d507d92..863fea2702f 100644 --- a/frontend/javascripts/oxalis/api/api_latest.ts +++ b/frontend/javascripts/oxalis/api/api_latest.ts @@ -17,8 +17,8 @@ import { coalesce } from "libs/utils"; import window, { location } from "libs/window"; import _ from "lodash"; import messages from "messages"; +import { AnnotationTool, type AnnotationToolId } from "oxalis/model/accessors/tool_accessor"; import type { - AnnotationToolId, BoundingBoxType, BucketAddress, ControlMode, @@ -33,7 +33,6 @@ import Constants, { TDViewDisplayModeEnum, MappingStatusEnum, EMPTY_OBJECT, - AnnotationTool, } from "oxalis/constants"; import { rotate3DViewTo } from "oxalis/controller/camera_controller"; import { loadAgglomerateSkeletonForSegmentId } from "oxalis/controller/combinations/segmentation_handlers"; diff --git a/frontend/javascripts/oxalis/constants.ts b/frontend/javascripts/oxalis/constants.ts index 4cdf36597f4..82df6784877 100644 --- a/frontend/javascripts/oxalis/constants.ts +++ b/frontend/javascripts/oxalis/constants.ts @@ -1,12 +1,5 @@ import type { AdditionalCoordinate } from "types/api_flow_types"; -export { - AnnotationTool, - type AnnotationToolId, - VolumeTools, - MeasurementTools, -} from "./model/accessors/tool_accessor"; - export const ViewModeValues = ["orthogonal", "flight", "oblique"] as ViewMode[]; export const ViewModeValuesIndices = { diff --git a/frontend/javascripts/oxalis/controller/combinations/tool_controls.ts b/frontend/javascripts/oxalis/controller/combinations/tool_controls.ts index b9a3b60312b..4f11023ed95 100644 --- a/frontend/javascripts/oxalis/controller/combinations/tool_controls.ts +++ b/frontend/javascripts/oxalis/controller/combinations/tool_controls.ts @@ -3,8 +3,8 @@ import type { ModifierKeys } from "libs/input"; import { V3 } from "libs/mjs"; import * as Utils from "libs/utils"; import { document } from "libs/window"; +import { AnnotationTool } from "oxalis/model/accessors/tool_accessor"; import { - AnnotationTool, ContourModeEnum, type OrthoView, OrthoViews, diff --git a/frontend/javascripts/oxalis/controller/segment_mesh_controller.ts b/frontend/javascripts/oxalis/controller/segment_mesh_controller.ts index 99af4118fe0..06e162eea83 100644 --- a/frontend/javascripts/oxalis/controller/segment_mesh_controller.ts +++ b/frontend/javascripts/oxalis/controller/segment_mesh_controller.ts @@ -1,7 +1,8 @@ import app from "app"; import { mergeVertices } from "libs/BufferGeometryUtils"; import _ from "lodash"; -import { AnnotationTool, type Vector2, type Vector3 } from "oxalis/constants"; +import { AnnotationTool } from "oxalis/model/accessors/tool_accessor"; +import type { Vector2, Vector3 } from "oxalis/constants"; import CustomLOD from "oxalis/controller/custom_lod"; import { getAdditionalCoordinatesAsString } from "oxalis/model/accessors/flycam_accessor"; import { diff --git a/frontend/javascripts/oxalis/controller/td_controller.tsx b/frontend/javascripts/oxalis/controller/td_controller.tsx index 95e23c16e6a..86a459bb130 100644 --- a/frontend/javascripts/oxalis/controller/td_controller.tsx +++ b/frontend/javascripts/oxalis/controller/td_controller.tsx @@ -3,8 +3,8 @@ import { V3 } from "libs/mjs"; import TrackballControls from "libs/trackball_controls"; import * as Utils from "libs/utils"; import _ from "lodash"; +import { AnnotationTool } from "oxalis/model/accessors/tool_accessor"; import { - AnnotationTool, type OrthoView, type OrthoViewMap, OrthoViews, diff --git a/frontend/javascripts/oxalis/controller/viewmodes/plane_controller.tsx b/frontend/javascripts/oxalis/controller/viewmodes/plane_controller.tsx index e6820538b08..91838eba2b0 100644 --- a/frontend/javascripts/oxalis/controller/viewmodes/plane_controller.tsx +++ b/frontend/javascripts/oxalis/controller/viewmodes/plane_controller.tsx @@ -3,12 +3,8 @@ import Toast from "libs/toast"; import * as Utils from "libs/utils"; import { document } from "libs/window"; import _ from "lodash"; -import { - AnnotationTool, - type AnnotationToolId, - type OrthoView, - type OrthoViewMap, -} from "oxalis/constants"; +import { AnnotationTool, type AnnotationToolId } from "oxalis/model/accessors/tool_accessor"; +import type { OrthoView, OrthoViewMap } from "oxalis/constants"; import { OrthoViewValuesWithoutTDView, OrthoViews } from "oxalis/constants"; import * as MoveHandlers from "oxalis/controller/combinations/move_handlers"; import * as SkeletonHandlers from "oxalis/controller/combinations/skeleton_handlers"; diff --git a/frontend/javascripts/oxalis/default_state.ts b/frontend/javascripts/oxalis/default_state.ts index 0b62172f424..f999798c74e 100644 --- a/frontend/javascripts/oxalis/default_state.ts +++ b/frontend/javascripts/oxalis/default_state.ts @@ -6,8 +6,8 @@ import Constants, { TDViewDisplayModeEnum, InterpolationModeEnum, UnitLong, - AnnotationTool, } from "oxalis/constants"; +import { AnnotationTool } from "oxalis/model/accessors/tool_accessor"; import constants from "oxalis/constants"; import type { OxalisState } from "oxalis/store"; import { getSystemColorTheme } from "theme"; diff --git a/frontend/javascripts/oxalis/geometries/materials/plane_material_factory.ts b/frontend/javascripts/oxalis/geometries/materials/plane_material_factory.ts index 9f187d7029e..9d7f73177c9 100644 --- a/frontend/javascripts/oxalis/geometries/materials/plane_material_factory.ts +++ b/frontend/javascripts/oxalis/geometries/materials/plane_material_factory.ts @@ -6,13 +6,8 @@ import * as Utils from "libs/utils"; import _ from "lodash"; import { WkDevFlags } from "oxalis/api/wk_dev"; import { BLEND_MODES, Identity4x4, type OrthoView, type Vector3 } from "oxalis/constants"; -import { - AnnotationTool, - MappingStatusEnum, - OrthoViewValues, - OrthoViews, - ViewModeValues, -} from "oxalis/constants"; +import { AnnotationTool } from "oxalis/model/accessors/tool_accessor"; +import { MappingStatusEnum, OrthoViewValues, OrthoViews, ViewModeValues } from "oxalis/constants"; import { getColorLayers, getDataLayers, diff --git a/frontend/javascripts/oxalis/model/accessors/volumetracing_accessor.ts b/frontend/javascripts/oxalis/model/accessors/volumetracing_accessor.ts index f811971203c..6752699ce4f 100644 --- a/frontend/javascripts/oxalis/model/accessors/volumetracing_accessor.ts +++ b/frontend/javascripts/oxalis/model/accessors/volumetracing_accessor.ts @@ -2,14 +2,16 @@ import { V3 } from "libs/mjs"; import _ from "lodash"; import memoizeOne from "memoize-one"; import messages from "messages"; -import Constants, { +import { AnnotationTool, + VolumeTools, type AnnotationToolId, +} from "oxalis/model/accessors/tool_accessor"; +import Constants, { type ContourMode, MappingStatusEnum, type Vector3, type Vector4, - VolumeTools, } from "oxalis/constants"; import { reuseInstanceOnEquality } from "oxalis/model/accessors/accessor_helpers"; import { diff --git a/frontend/javascripts/oxalis/model/actions/ui_actions.ts b/frontend/javascripts/oxalis/model/actions/ui_actions.ts index 3cc188cffc3..dfff51a9648 100644 --- a/frontend/javascripts/oxalis/model/actions/ui_actions.ts +++ b/frontend/javascripts/oxalis/model/actions/ui_actions.ts @@ -1,4 +1,5 @@ -import type { AnnotationTool, OrthoView, Vector3 } from "oxalis/constants"; +import type { AnnotationTool } from "oxalis/model/accessors/tool_accessor"; +import type { OrthoView, Vector3 } from "oxalis/constants"; import type { BorderOpenStatus, OxalisState, Theme } from "oxalis/store"; import type { StartAIJobModalState } from "oxalis/view/action-bar/starting_job_modals"; diff --git a/frontend/javascripts/oxalis/model/reducers/reducer_helpers.ts b/frontend/javascripts/oxalis/model/reducers/reducer_helpers.ts index dfec63af6b7..991e75c3352 100644 --- a/frontend/javascripts/oxalis/model/reducers/reducer_helpers.ts +++ b/frontend/javascripts/oxalis/model/reducers/reducer_helpers.ts @@ -1,6 +1,6 @@ import Maybe from "data.maybe"; import * as Utils from "libs/utils"; -import type { AnnotationTool } from "oxalis/constants"; +import type { AnnotationTool } from "oxalis/model/accessors/tool_accessor"; import type { BoundingBoxType } from "oxalis/constants"; import { ToolCollections, getDisabledInfoForTools } from "oxalis/model/accessors/tool_accessor"; import { diff --git a/frontend/javascripts/oxalis/model/reducers/skeletontracing_reducer.ts b/frontend/javascripts/oxalis/model/reducers/skeletontracing_reducer.ts index f62398f123a..498ec546333 100644 --- a/frontend/javascripts/oxalis/model/reducers/skeletontracing_reducer.ts +++ b/frontend/javascripts/oxalis/model/reducers/skeletontracing_reducer.ts @@ -4,7 +4,8 @@ import ColorGenerator from "libs/color_generator"; import Toast from "libs/toast"; import * as Utils from "libs/utils"; import _ from "lodash"; -import Constants, { AnnotationTool, TreeTypeEnum } from "oxalis/constants"; +import Constants, { TreeTypeEnum } from "oxalis/constants"; +import { AnnotationTool } from "oxalis/model/accessors/tool_accessor"; import { findTreeByNodeId, getNodeAndTree, diff --git a/frontend/javascripts/oxalis/model/sagas/annotation_tool_saga.ts b/frontend/javascripts/oxalis/model/sagas/annotation_tool_saga.ts index accaa357ab9..a428b81618a 100644 --- a/frontend/javascripts/oxalis/model/sagas/annotation_tool_saga.ts +++ b/frontend/javascripts/oxalis/model/sagas/annotation_tool_saga.ts @@ -1,4 +1,4 @@ -import { AnnotationTool, MeasurementTools } from "oxalis/constants"; +import { AnnotationTool, MeasurementTools } from "oxalis/model/accessors/tool_accessor"; import { getToolControllerForAnnotationTool } from "oxalis/controller/combinations/tool_controls"; import getSceneController from "oxalis/controller/scene_controller_provider"; import { diff --git a/frontend/javascripts/oxalis/model/sagas/proofread_saga.ts b/frontend/javascripts/oxalis/model/sagas/proofread_saga.ts index 3a926bdb843..39b6f0f0232 100644 --- a/frontend/javascripts/oxalis/model/sagas/proofread_saga.ts +++ b/frontend/javascripts/oxalis/model/sagas/proofread_saga.ts @@ -9,7 +9,8 @@ import { V3 } from "libs/mjs"; import Toast from "libs/toast"; import { SoftError, isBigInt, isNumberMap } from "libs/utils"; import _ from "lodash"; -import { AnnotationTool, MappingStatusEnum, TreeTypeEnum, type Vector3 } from "oxalis/constants"; +import { AnnotationTool } from "oxalis/model/accessors/tool_accessor"; +import { MappingStatusEnum, TreeTypeEnum, type Vector3 } from "oxalis/constants"; import { getSegmentIdForPositionAsync } from "oxalis/controller/combinations/volume_handlers"; import { getLayerByName, diff --git a/frontend/javascripts/oxalis/model/sagas/undo_saga.ts b/frontend/javascripts/oxalis/model/sagas/undo_saga.ts index d3530c28af3..e8d4fd5f146 100644 --- a/frontend/javascripts/oxalis/model/sagas/undo_saga.ts +++ b/frontend/javascripts/oxalis/model/sagas/undo_saga.ts @@ -1,7 +1,7 @@ import createProgressCallback from "libs/progress_callback"; import Toast from "libs/toast"; import messages from "messages"; -import { AnnotationTool } from "oxalis/constants"; +import { AnnotationTool } from "oxalis/model/accessors/tool_accessor"; import { enforceSkeletonTracing } from "oxalis/model/accessors/skeletontracing_accessor"; import { getUserBoundingBoxesFromState } from "oxalis/model/accessors/tracing_accessor"; import { diff --git a/frontend/javascripts/oxalis/model/sagas/volume/floodfill_saga.tsx b/frontend/javascripts/oxalis/model/sagas/volume/floodfill_saga.tsx index f66f2197243..832e17686ab 100644 --- a/frontend/javascripts/oxalis/model/sagas/volume/floodfill_saga.tsx +++ b/frontend/javascripts/oxalis/model/sagas/volume/floodfill_saga.tsx @@ -1,3 +1,4 @@ +import _ from "lodash"; import { V2, V3 } from "libs/mjs"; import createProgressCallback, { type ProgressCallback } from "libs/progress_callback"; import Toast from "libs/toast"; @@ -10,9 +11,8 @@ import type { Vector2, Vector3, } from "oxalis/constants"; -import Constants, { AnnotationTool, FillModeEnum, Unicode } from "oxalis/constants"; - -import _ from "lodash"; +import { AnnotationTool } from "oxalis/model/accessors/tool_accessor"; +import Constants, { FillModeEnum, Unicode } from "oxalis/constants"; import { getDatasetBoundingBox, getMagInfo } from "oxalis/model/accessors/dataset_accessor"; import { getActiveMagIndexForLayer } from "oxalis/model/accessors/flycam_accessor"; import { getDisabledInfoForTools } from "oxalis/model/accessors/tool_accessor"; diff --git a/frontend/javascripts/oxalis/model/sagas/volumetracing_saga.tsx b/frontend/javascripts/oxalis/model/sagas/volumetracing_saga.tsx index a53d1d625e5..efc31af8256 100644 --- a/frontend/javascripts/oxalis/model/sagas/volumetracing_saga.tsx +++ b/frontend/javascripts/oxalis/model/sagas/volumetracing_saga.tsx @@ -4,7 +4,8 @@ import Toast from "libs/toast"; import _ from "lodash"; import memoizeOne from "memoize-one"; import type { ContourMode, OrthoView, OverwriteMode, Vector3 } from "oxalis/constants"; -import { AnnotationTool, ContourModeEnum, OrthoViews, OverwriteModeEnum } from "oxalis/constants"; +import { AnnotationTool } from "oxalis/model/accessors/tool_accessor"; +import { ContourModeEnum, OrthoViews, OverwriteModeEnum } from "oxalis/constants"; import getSceneController from "oxalis/controller/scene_controller_provider"; import { CONTOUR_COLOR_DELETE, CONTOUR_COLOR_NORMAL } from "oxalis/geometries/helper_geometries"; diff --git a/frontend/javascripts/oxalis/model/volumetracing/volumelayer.ts b/frontend/javascripts/oxalis/model/volumetracing/volumelayer.ts index ba64630a8b5..9e945792545 100644 --- a/frontend/javascripts/oxalis/model/volumetracing/volumelayer.ts +++ b/frontend/javascripts/oxalis/model/volumetracing/volumelayer.ts @@ -3,7 +3,8 @@ import { V2, V3 } from "libs/mjs"; import Toast from "libs/toast"; import _ from "lodash"; import messages from "messages"; -import type { AnnotationTool, OrthoView, Vector2, Vector3 } from "oxalis/constants"; +import type { AnnotationTool } from "oxalis/model/accessors/tool_accessor"; +import type { OrthoView, Vector2, Vector3 } from "oxalis/constants"; import Constants, { OrthoViews, Vector3Indicies, Vector2Indicies } from "oxalis/constants"; import { isBrushTool } from "oxalis/model/accessors/tool_accessor"; import { getVolumeTracingById } from "oxalis/model/accessors/volumetracing_accessor"; diff --git a/frontend/javascripts/oxalis/model_initialization.ts b/frontend/javascripts/oxalis/model_initialization.ts index ec8bd0c3ba9..a11f8d2d03c 100644 --- a/frontend/javascripts/oxalis/model_initialization.ts +++ b/frontend/javascripts/oxalis/model_initialization.ts @@ -19,7 +19,8 @@ import Toast from "libs/toast"; import * as Utils from "libs/utils"; import _ from "lodash"; import messages from "messages"; -import constants, { ControlModeEnum, AnnotationTool, type Vector3 } from "oxalis/constants"; +import { AnnotationTool } from "oxalis/model/accessors/tool_accessor"; +import constants, { ControlModeEnum, type Vector3 } from "oxalis/constants"; import type { PartialUrlManagerState, UrlStateByLayer } from "oxalis/controller/url_manager"; import UrlManager from "oxalis/controller/url_manager"; import { diff --git a/frontend/javascripts/oxalis/store.ts b/frontend/javascripts/oxalis/store.ts index c84981d6183..dee76c21706 100644 --- a/frontend/javascripts/oxalis/store.ts +++ b/frontend/javascripts/oxalis/store.ts @@ -1,7 +1,7 @@ import type DiffableMap from "libs/diffable_map"; import type { Matrix4x4 } from "libs/mjs"; +import type { AnnotationTool } from "oxalis/model/accessors/tool_accessor"; import type { - AnnotationTool, BoundingBoxType, ContourMode, ControlMode, diff --git a/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx b/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx index 159ea820204..3cdc7657ec1 100644 --- a/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx +++ b/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx @@ -25,15 +25,17 @@ import { useKeyPress, usePrevious } from "libs/react_hooks"; import { document } from "libs/window"; import { AnnotationTool, + MeasurementTools, + VolumeTools, +} from "oxalis/model/accessors/tool_accessor"; +import { FillModeEnum, type InterpolationMode, InterpolationModeEnum, MappingStatusEnum, - MeasurementTools, type OverwriteMode, OverwriteModeEnum, Unicode, - VolumeTools, } from "oxalis/constants"; import { getActiveTree } from "oxalis/model/accessors/skeletontracing_accessor"; import { diff --git a/frontend/javascripts/oxalis/view/components/command_palette.tsx b/frontend/javascripts/oxalis/view/components/command_palette.tsx index 5e08c3edb29..43c4c2a1a5a 100644 --- a/frontend/javascripts/oxalis/view/components/command_palette.tsx +++ b/frontend/javascripts/oxalis/view/components/command_palette.tsx @@ -3,7 +3,7 @@ import { capitalize, getPhraseFromCamelCaseString } from "libs/utils"; import * as Utils from "libs/utils"; import _ from "lodash"; import { getAdministrationSubMenu } from "navbar"; -import { AnnotationTool } from "oxalis/constants"; +import { AnnotationTool } from "oxalis/model/accessors/tool_accessor"; import { ToolCollections } from "oxalis/model/accessors/tool_accessor"; import { updateUserSettingAction } from "oxalis/model/actions/settings_actions"; import { setToolAction } from "oxalis/model/actions/ui_actions"; diff --git a/frontend/javascripts/oxalis/view/context_menu.tsx b/frontend/javascripts/oxalis/view/context_menu.tsx index 643dc20922a..97289c58f13 100644 --- a/frontend/javascripts/oxalis/view/context_menu.tsx +++ b/frontend/javascripts/oxalis/view/context_menu.tsx @@ -25,15 +25,15 @@ import Shortcut from "libs/shortcut_component"; import Toast from "libs/toast"; import { hexToRgb, rgbToHex, roundTo, truncateStringToLength } from "libs/utils"; import messages from "messages"; + +import { AnnotationTool, VolumeTools } from "oxalis/model/accessors/tool_accessor"; import { AltOrOptionKey, - AnnotationTool, CtrlOrCmdKey, LongUnitToShortUnitMap, type OrthoView, type UnitLong, type Vector3, - VolumeTools, } from "oxalis/constants"; import { loadAgglomerateSkeletonAtPosition, diff --git a/frontend/javascripts/oxalis/view/distance_measurement_tooltip.tsx b/frontend/javascripts/oxalis/view/distance_measurement_tooltip.tsx index 630653a71d8..a9ed7577fe3 100644 --- a/frontend/javascripts/oxalis/view/distance_measurement_tooltip.tsx +++ b/frontend/javascripts/oxalis/view/distance_measurement_tooltip.tsx @@ -8,12 +8,8 @@ import { formatNumberToLength, } from "libs/format_utils"; import { clamp } from "libs/utils"; -import { - AnnotationTool, - LongUnitToShortUnitMap, - MeasurementTools, - type Vector3, -} from "oxalis/constants"; +import { AnnotationTool, MeasurementTools } from "oxalis/model/accessors/tool_accessor"; +import { LongUnitToShortUnitMap, type Vector3 } from "oxalis/constants"; import getSceneController from "oxalis/controller/scene_controller_provider"; import { getPosition } from "oxalis/model/accessors/flycam_accessor"; import { diff --git a/frontend/javascripts/oxalis/view/input_catcher.tsx b/frontend/javascripts/oxalis/view/input_catcher.tsx index 6773287af2d..34b13a04300 100644 --- a/frontend/javascripts/oxalis/view/input_catcher.tsx +++ b/frontend/javascripts/oxalis/view/input_catcher.tsx @@ -1,8 +1,9 @@ import { useEffectOnlyOnce, useKeyPress } from "libs/react_hooks"; import { waitForCondition } from "libs/utils"; import _ from "lodash"; -import type { AnnotationToolId, Rect, Viewport, ViewportRects } from "oxalis/constants"; -import { AnnotationTool, ArbitraryViewport, ArbitraryViews, OrthoViews } from "oxalis/constants"; +import { AnnotationTool, type AnnotationToolId } from "oxalis/model/accessors/tool_accessor"; +import type { Rect, Viewport, ViewportRects } from "oxalis/constants"; +import { ArbitraryViewport, ArbitraryViews, OrthoViews } from "oxalis/constants"; import { adaptActiveToolToShortcuts } from "oxalis/model/accessors/tool_accessor"; import { setInputCatcherRects } from "oxalis/model/actions/view_mode_actions"; import type { BusyBlockingInfo, OxalisState } from "oxalis/store"; diff --git a/frontend/javascripts/oxalis/view/left-border-tabs/layer_settings_tab.tsx b/frontend/javascripts/oxalis/view/left-border-tabs/layer_settings_tab.tsx index c7ee50e8b43..6d2d3912e28 100644 --- a/frontend/javascripts/oxalis/view/left-border-tabs/layer_settings_tab.tsx +++ b/frontend/javascripts/oxalis/view/left-border-tabs/layer_settings_tab.tsx @@ -40,12 +40,8 @@ import { settingsTooltips, } from "messages"; import type { Vector3 } from "oxalis/constants"; -import Constants, { - AnnotationTool, - ControlModeEnum, - IdentityTransform, - MappingStatusEnum, -} from "oxalis/constants"; +import { AnnotationTool } from "oxalis/model/accessors/tool_accessor"; +import Constants, { ControlModeEnum, IdentityTransform, MappingStatusEnum } from "oxalis/constants"; import defaultState from "oxalis/default_state"; import { getDefaultValueRangeOfLayer, diff --git a/frontend/javascripts/oxalis/view/plane_view.ts b/frontend/javascripts/oxalis/view/plane_view.ts index 9f363f3e5a8..a365453b1b2 100644 --- a/frontend/javascripts/oxalis/view/plane_view.ts +++ b/frontend/javascripts/oxalis/view/plane_view.ts @@ -3,12 +3,8 @@ import VisibilityAwareRaycaster from "libs/visibility_aware_raycaster"; import window from "libs/window"; import _ from "lodash"; import type { OrthoViewMap, Vector2, Vector3, Viewport } from "oxalis/constants"; -import Constants, { - AnnotationTool, - OrthoViewColors, - OrthoViewValues, - OrthoViews, -} from "oxalis/constants"; +import { AnnotationTool } from "oxalis/model/accessors/tool_accessor"; +import Constants, { OrthoViewColors, OrthoViewValues, OrthoViews } from "oxalis/constants"; import type { VertexSegmentMapping } from "oxalis/controller/mesh_helpers"; import getSceneController, { getSceneControllerOrNull, diff --git a/frontend/javascripts/test/api/api_volume_latest.spec.ts b/frontend/javascripts/test/api/api_volume_latest.spec.ts index 1e946c73024..43ccbf08c33 100644 --- a/frontend/javascripts/test/api/api_volume_latest.spec.ts +++ b/frontend/javascripts/test/api/api_volume_latest.spec.ts @@ -1,6 +1,6 @@ // @ts-nocheck import "test/mocks/lz4"; -import { AnnotationTool } from "oxalis/constants"; +import { AnnotationTool } from "oxalis/model/accessors/tool_accessor"; import { __setupOxalis } from "test/helpers/apiHelpers"; import test from "ava"; import window from "libs/window"; diff --git a/frontend/javascripts/test/fixtures/volumetracing_object.ts b/frontend/javascripts/test/fixtures/volumetracing_object.ts index 6b94d53fcf3..c421d4e5460 100644 --- a/frontend/javascripts/test/fixtures/volumetracing_object.ts +++ b/frontend/javascripts/test/fixtures/volumetracing_object.ts @@ -1,5 +1,6 @@ import update from "immutability-helper"; -import Constants, { AnnotationTool } from "oxalis/constants"; +import { AnnotationTool } from "oxalis/model/accessors/tool_accessor"; +import Constants from "oxalis/constants"; import defaultState from "oxalis/default_state"; const volumeTracing = { diff --git a/frontend/javascripts/test/reducers/volumetracing_reducer.spec.ts b/frontend/javascripts/test/reducers/volumetracing_reducer.spec.ts index eb7ee431785..fabbcf3f781 100644 --- a/frontend/javascripts/test/reducers/volumetracing_reducer.spec.ts +++ b/frontend/javascripts/test/reducers/volumetracing_reducer.spec.ts @@ -1,7 +1,8 @@ import "test/mocks/lz4"; import update from "immutability-helper"; import Maybe from "data.maybe"; -import { AnnotationTool, type Vector3 } from "oxalis/constants"; +import { AnnotationTool } from "oxalis/model/accessors/tool_accessor"; +import type { Vector3 } from "oxalis/constants"; import * as VolumeTracingActions from "oxalis/model/actions/volumetracing_actions"; import * as UiActions from "oxalis/model/actions/ui_actions"; import VolumeTracingReducer from "oxalis/model/reducers/volumetracing_reducer"; diff --git a/frontend/javascripts/test/sagas/annotation_tool_disabled_info.spec.ts b/frontend/javascripts/test/sagas/annotation_tool_disabled_info.spec.ts index 61b65d935b0..81e6d2be06f 100644 --- a/frontend/javascripts/test/sagas/annotation_tool_disabled_info.spec.ts +++ b/frontend/javascripts/test/sagas/annotation_tool_disabled_info.spec.ts @@ -3,7 +3,7 @@ import update from "immutability-helper"; import test from "ava"; import { getDisabledInfoForTools } from "oxalis/model/accessors/tool_accessor"; import { initialState } from "test/fixtures/hybridtracing_object"; -import { AnnotationTool, VolumeTools } from "oxalis/constants"; +import { AnnotationTool, VolumeTools } from "oxalis/model/accessors/tool_accessor"; import type { CoordinateTransformation } from "types/api_flow_types"; const zoomSensitiveVolumeTools = VolumeTools.filter( diff --git a/frontend/javascripts/test/sagas/annotation_tool_saga.spec.ts b/frontend/javascripts/test/sagas/annotation_tool_saga.spec.ts index 62b5167a326..3ff8b605c72 100644 --- a/frontend/javascripts/test/sagas/annotation_tool_saga.spec.ts +++ b/frontend/javascripts/test/sagas/annotation_tool_saga.spec.ts @@ -1,7 +1,7 @@ import "test/mocks/lz4"; import test from "ava"; import _ from "lodash"; -import { AnnotationTool } from "oxalis/constants"; +import { AnnotationTool } from "oxalis/model/accessors/tool_accessor"; import mockRequire from "mock-require"; import { initialState } from "test/fixtures/volumetracing_object"; import sinon from "sinon"; diff --git a/frontend/javascripts/test/sagas/volumetracing/bucket_eviction_helper.ts b/frontend/javascripts/test/sagas/volumetracing/bucket_eviction_helper.ts index 0e1cbd3b3d5..0bedf1bc82f 100644 --- a/frontend/javascripts/test/sagas/volumetracing/bucket_eviction_helper.ts +++ b/frontend/javascripts/test/sagas/volumetracing/bucket_eviction_helper.ts @@ -3,7 +3,8 @@ import mockRequire from "mock-require"; import "test/sagas/saga_integration.mock"; import { createBucketResponseFunction } from "test/helpers/apiHelpers"; import Store from "oxalis/store"; -import { OrthoViews, AnnotationTool } from "oxalis/constants"; +import { AnnotationTool } from "oxalis/model/accessors/tool_accessor"; +import { OrthoViews } from "oxalis/constants"; import { updateUserSettingAction } from "oxalis/model/actions/settings_actions"; const { setToolAction } = mockRequire.reRequire("oxalis/model/actions/ui_actions"); const { setPositionAction } = mockRequire.reRequire("oxalis/model/actions/flycam_actions"); diff --git a/frontend/javascripts/test/sagas/volumetracing/volumetracing_saga.spec.ts b/frontend/javascripts/test/sagas/volumetracing/volumetracing_saga.spec.ts index 5d61fa810e3..90ef0ff9987 100644 --- a/frontend/javascripts/test/sagas/volumetracing/volumetracing_saga.spec.ts +++ b/frontend/javascripts/test/sagas/volumetracing/volumetracing_saga.spec.ts @@ -3,9 +3,9 @@ import { take, put, call } from "redux-saga/effects"; import update from "immutability-helper"; import _ from "lodash"; import type { APISegmentationLayer, ServerVolumeTracing } from "types/api_flow_types"; +import { AnnotationTool } from "oxalis/model/accessors/tool_accessor"; import { OrthoViews, - AnnotationTool, ContourModeEnum, OverwriteModeEnum, MappingStatusEnum, diff --git a/frontend/javascripts/test/sagas/volumetracing/volumetracing_saga_integration.spec.ts b/frontend/javascripts/test/sagas/volumetracing/volumetracing_saga_integration.spec.ts index e04279762e1..6516518b4e5 100644 --- a/frontend/javascripts/test/sagas/volumetracing/volumetracing_saga_integration.spec.ts +++ b/frontend/javascripts/test/sagas/volumetracing/volumetracing_saga_integration.spec.ts @@ -1,8 +1,8 @@ /* eslint-disable no-await-in-loop */ import "test/sagas/saga_integration.mock"; import _ from "lodash"; +import { AnnotationTool } from "oxalis/model/accessors/tool_accessor"; import Constants, { - AnnotationTool, ContourModeEnum, FillModeEnum, OrthoViews, From a8d0e54c9138561d91fdcf8b953ab883d2f74edd Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Fri, 11 Apr 2025 22:56:02 +0200 Subject: [PATCH 34/84] fix more cyclic dependencies and multiple bugs --- frontend/javascripts/oxalis/api/api_latest.ts | 2 +- .../controller/combinations/tool_controls.ts | 2 +- .../controller/segment_mesh_controller.ts | 2 +- .../oxalis/controller/td_controller.tsx | 2 +- .../controller/viewmodes/plane_controller.tsx | 2 +- frontend/javascripts/oxalis/default_state.ts | 2 +- .../materials/plane_material_factory.ts | 2 +- .../model/accessors/disabled_tool_accessor.ts | 356 ++++++++++++++++++ .../oxalis/model/accessors/tool_accessor.ts | 356 +----------------- .../model/accessors/volumetracing_accessor.ts | 10 +- .../oxalis/model/actions/ui_actions.ts | 2 +- .../oxalis/model/reducers/reducer_helpers.ts | 5 +- .../model/reducers/skeletontracing_reducer.ts | 2 +- .../model/sagas/annotation_tool_saga.ts | 2 +- .../oxalis/model/sagas/proofread_saga.ts | 2 +- .../oxalis/model/sagas/undo_saga.ts | 2 +- .../model/sagas/volume/floodfill_saga.tsx | 6 +- .../oxalis/model/sagas/volumetracing_saga.tsx | 2 +- .../oxalis/model/volumetracing/volumelayer.ts | 2 +- .../oxalis/model_initialization.ts | 2 +- frontend/javascripts/oxalis/store.ts | 2 +- .../oxalis/view/action-bar/toolbar_view.tsx | 56 +-- .../view/action-bar/toolkit_switcher_view.tsx | 2 +- .../javascripts/oxalis/view/context_menu.tsx | 4 +- .../view/distance_measurement_tooltip.tsx | 2 +- .../javascripts/oxalis/view/input_catcher.tsx | 2 +- .../left-border-tabs/layer_settings_tab.tsx | 2 +- .../javascripts/oxalis/view/plane_view.ts | 2 +- .../javascripts/oxalis/view/statusbar.tsx | 4 +- .../annotation_tool_disabled_info.spec.ts | 2 +- 30 files changed, 425 insertions(+), 416 deletions(-) create mode 100644 frontend/javascripts/oxalis/model/accessors/disabled_tool_accessor.ts diff --git a/frontend/javascripts/oxalis/api/api_latest.ts b/frontend/javascripts/oxalis/api/api_latest.ts index 863fea2702f..c9bd0c61c7b 100644 --- a/frontend/javascripts/oxalis/api/api_latest.ts +++ b/frontend/javascripts/oxalis/api/api_latest.ts @@ -17,7 +17,6 @@ import { coalesce } from "libs/utils"; import window, { location } from "libs/window"; import _ from "lodash"; import messages from "messages"; -import { AnnotationTool, type AnnotationToolId } from "oxalis/model/accessors/tool_accessor"; import type { BoundingBoxType, BucketAddress, @@ -68,6 +67,7 @@ import { getTreeGroupsMap, mapGroups, } from "oxalis/model/accessors/skeletontracing_accessor"; +import { AnnotationTool, type AnnotationToolId } from "oxalis/model/accessors/tool_accessor"; import { getActiveCellId, getActiveSegmentationTracing, diff --git a/frontend/javascripts/oxalis/controller/combinations/tool_controls.ts b/frontend/javascripts/oxalis/controller/combinations/tool_controls.ts index 4f11023ed95..eb41046b362 100644 --- a/frontend/javascripts/oxalis/controller/combinations/tool_controls.ts +++ b/frontend/javascripts/oxalis/controller/combinations/tool_controls.ts @@ -3,7 +3,6 @@ import type { ModifierKeys } from "libs/input"; import { V3 } from "libs/mjs"; import * as Utils from "libs/utils"; import { document } from "libs/window"; -import { AnnotationTool } from "oxalis/model/accessors/tool_accessor"; import { ContourModeEnum, type OrthoView, @@ -30,6 +29,7 @@ import { import * as SkeletonHandlers from "oxalis/controller/combinations/skeleton_handlers"; import * as VolumeHandlers from "oxalis/controller/combinations/volume_handlers"; import getSceneController from "oxalis/controller/scene_controller_provider"; +import { AnnotationTool } from "oxalis/model/accessors/tool_accessor"; import { isBrushTool } from "oxalis/model/accessors/tool_accessor"; import { calculateGlobalPos } from "oxalis/model/accessors/view_mode_accessor"; import { diff --git a/frontend/javascripts/oxalis/controller/segment_mesh_controller.ts b/frontend/javascripts/oxalis/controller/segment_mesh_controller.ts index 06e162eea83..79b09e9a813 100644 --- a/frontend/javascripts/oxalis/controller/segment_mesh_controller.ts +++ b/frontend/javascripts/oxalis/controller/segment_mesh_controller.ts @@ -1,10 +1,10 @@ import app from "app"; import { mergeVertices } from "libs/BufferGeometryUtils"; import _ from "lodash"; -import { AnnotationTool } from "oxalis/model/accessors/tool_accessor"; import type { Vector2, Vector3 } from "oxalis/constants"; import CustomLOD from "oxalis/controller/custom_lod"; import { getAdditionalCoordinatesAsString } from "oxalis/model/accessors/flycam_accessor"; +import { AnnotationTool } from "oxalis/model/accessors/tool_accessor"; import { getActiveSegmentationTracing, getSegmentColorAsHSLA, diff --git a/frontend/javascripts/oxalis/controller/td_controller.tsx b/frontend/javascripts/oxalis/controller/td_controller.tsx index 86a459bb130..8217438daec 100644 --- a/frontend/javascripts/oxalis/controller/td_controller.tsx +++ b/frontend/javascripts/oxalis/controller/td_controller.tsx @@ -3,7 +3,6 @@ import { V3 } from "libs/mjs"; import TrackballControls from "libs/trackball_controls"; import * as Utils from "libs/utils"; import _ from "lodash"; -import { AnnotationTool } from "oxalis/model/accessors/tool_accessor"; import { type OrthoView, type OrthoViewMap, @@ -19,6 +18,7 @@ import { } from "oxalis/controller/combinations/tool_controls"; import { getPosition } from "oxalis/model/accessors/flycam_accessor"; import { getActiveNode, getNodePosition } from "oxalis/model/accessors/skeletontracing_accessor"; +import { AnnotationTool } from "oxalis/model/accessors/tool_accessor"; import { getInputCatcherRect, getViewportScale } from "oxalis/model/accessors/view_mode_accessor"; import { getActiveSegmentationTracing } from "oxalis/model/accessors/volumetracing_accessor"; import { setPositionAction } from "oxalis/model/actions/flycam_actions"; diff --git a/frontend/javascripts/oxalis/controller/viewmodes/plane_controller.tsx b/frontend/javascripts/oxalis/controller/viewmodes/plane_controller.tsx index 91838eba2b0..ab272315753 100644 --- a/frontend/javascripts/oxalis/controller/viewmodes/plane_controller.tsx +++ b/frontend/javascripts/oxalis/controller/viewmodes/plane_controller.tsx @@ -3,7 +3,6 @@ import Toast from "libs/toast"; import * as Utils from "libs/utils"; import { document } from "libs/window"; import _ from "lodash"; -import { AnnotationTool, type AnnotationToolId } from "oxalis/model/accessors/tool_accessor"; import type { OrthoView, OrthoViewMap } from "oxalis/constants"; import { OrthoViewValuesWithoutTDView, OrthoViews } from "oxalis/constants"; import * as MoveHandlers from "oxalis/controller/combinations/move_handlers"; @@ -31,6 +30,7 @@ import { getMoveOffset, getPosition, } from "oxalis/model/accessors/flycam_accessor"; +import { AnnotationTool, type AnnotationToolId } from "oxalis/model/accessors/tool_accessor"; import { calculateGlobalPos } from "oxalis/model/accessors/view_mode_accessor"; import { getActiveSegmentationTracing, diff --git a/frontend/javascripts/oxalis/default_state.ts b/frontend/javascripts/oxalis/default_state.ts index f999798c74e..af548a9392b 100644 --- a/frontend/javascripts/oxalis/default_state.ts +++ b/frontend/javascripts/oxalis/default_state.ts @@ -7,8 +7,8 @@ import Constants, { InterpolationModeEnum, UnitLong, } from "oxalis/constants"; -import { AnnotationTool } from "oxalis/model/accessors/tool_accessor"; import constants from "oxalis/constants"; +import { AnnotationTool } from "oxalis/model/accessors/tool_accessor"; import type { OxalisState } from "oxalis/store"; import { getSystemColorTheme } from "theme"; import type { diff --git a/frontend/javascripts/oxalis/geometries/materials/plane_material_factory.ts b/frontend/javascripts/oxalis/geometries/materials/plane_material_factory.ts index 9d7f73177c9..8a6ed05452c 100644 --- a/frontend/javascripts/oxalis/geometries/materials/plane_material_factory.ts +++ b/frontend/javascripts/oxalis/geometries/materials/plane_material_factory.ts @@ -6,7 +6,6 @@ import * as Utils from "libs/utils"; import _ from "lodash"; import { WkDevFlags } from "oxalis/api/wk_dev"; import { BLEND_MODES, Identity4x4, type OrthoView, type Vector3 } from "oxalis/constants"; -import { AnnotationTool } from "oxalis/model/accessors/tool_accessor"; import { MappingStatusEnum, OrthoViewValues, OrthoViews, ViewModeValues } from "oxalis/constants"; import { getColorLayers, @@ -31,6 +30,7 @@ import { getUnrenderableLayerInfosForCurrentZoom, getZoomValue, } from "oxalis/model/accessors/flycam_accessor"; +import { AnnotationTool } from "oxalis/model/accessors/tool_accessor"; import { isBrushTool } from "oxalis/model/accessors/tool_accessor"; import { calculateGlobalPos, getViewportExtents } from "oxalis/model/accessors/view_mode_accessor"; import { diff --git a/frontend/javascripts/oxalis/model/accessors/disabled_tool_accessor.ts b/frontend/javascripts/oxalis/model/accessors/disabled_tool_accessor.ts new file mode 100644 index 00000000000..15f25ec5c6a --- /dev/null +++ b/frontend/javascripts/oxalis/model/accessors/disabled_tool_accessor.ts @@ -0,0 +1,356 @@ +import { + PricingPlanEnum, + getFeatureNotAvailableInPlanMessage, + isFeatureAllowedByPricingPlan, +} from "admin/organization/pricing_plan_utils"; +import memoizeOne from "memoize-one"; +import { IdentityTransform } from "oxalis/constants"; +import { getVisibleSegmentationLayer } from "oxalis/model/accessors/dataset_accessor"; +import { isMagRestrictionViolated } from "oxalis/model/accessors/flycam_accessor"; +import type { OxalisState } from "oxalis/store"; +import type { APIOrganization, APIUser } from "types/api_flow_types"; +import { reuseInstanceOnEquality } from "./accessor_helpers"; +import { getTransformsPerLayer } from "./dataset_layer_transformation_accessor"; +import { isSkeletonLayerTransformed, isSkeletonLayerVisible } from "./skeletontracing_accessor"; + +import { + type AgglomerateState, + getActiveSegmentationTracing, + getRenderableMagForSegmentationTracing, + hasAgglomerateMapping, + isVolumeAnnotationDisallowedForZoom, +} from "oxalis/model/accessors/volumetracing_accessor"; +import { AnnotationTool, type AnnotationToolId } from "./tool_accessor"; + +type DisabledInfo = { + isDisabled: boolean; + explanation: string; +}; + +const NOT_DISABLED_INFO = { + isDisabled: false, + explanation: "", +}; + +const zoomInToUseToolMessage = + "Please zoom in further to use this tool. If you want to edit volume data on this zoom level, create an annotation with restricted magnifications from the extended annotation menu in the dashboard."; + +const noSkeletonsExplanation = + "This annotation does not have a skeleton. Please convert it to a hybrid annotation."; + +const disabledSkeletonExplanation = + "Currently all trees are invisible. To use this tool, make the skeleton layer visible by toggling the button in the left sidebar."; + +const getExplanationForDisabledVolume = ( + isSegmentationTracingVisible: boolean, + isInMergerMode: boolean, + isSegmentationTracingVisibleForMag: boolean, + isZoomInvalidForTracing: boolean, + isEditableMappingActive: boolean, + isSegmentationTracingTransformed: boolean, + isJSONMappingActive: boolean, +) => { + if (!isSegmentationTracingVisible) { + return "Volume annotation is disabled since no segmentation tracing layer is enabled. Enable one in the left settings sidebar or make a segmentation layer editable via the lock icon."; + } + + if (isZoomInvalidForTracing) { + return "Volume annotation is disabled since the current zoom value is not in the required range. Please adjust the zoom level."; + } + + if (isInMergerMode) { + return "Volume annotation is disabled while the merger mode is active."; + } + + if (!isSegmentationTracingVisibleForMag) { + return "Volume annotation is disabled since no segmentation data can be shown at the current magnification. Please adjust the zoom level."; + } + + if (isEditableMappingActive) { + return "Volume annotation is disabled while an editable mapping is active."; + } + + if (isSegmentationTracingTransformed) { + return "Volume annotation is disabled because the visible segmentation layer is transformed. Use the left sidebar to render the segmentation layer without any transformations."; + } + if (isJSONMappingActive) { + return "Volume annotation is disabled because a JSON mapping is currently active for the the visible segmentation layer. Disable the JSON mapping to enable volume annotation."; + } + + return "Volume annotation is currently disabled."; +}; + +const ALWAYS_ENABLED_TOOL_INFOS = { + [AnnotationTool.MOVE.id]: NOT_DISABLED_INFO, + [AnnotationTool.LINE_MEASUREMENT.id]: NOT_DISABLED_INFO, + [AnnotationTool.AREA_MEASUREMENT.id]: NOT_DISABLED_INFO, + [AnnotationTool.BOUNDING_BOX.id]: NOT_DISABLED_INFO, +}; + +function _getSkeletonToolInfo( + hasSkeleton: boolean, + isSkeletonLayerTransformed: boolean, + areSkeletonsVisible: boolean, +) { + if (!hasSkeleton) { + return { + [AnnotationTool.SKELETON.id]: { + isDisabled: true, + explanation: noSkeletonsExplanation, + }, + }; + } + + if (!areSkeletonsVisible) { + return { + [AnnotationTool.SKELETON.id]: { + isDisabled: true, + explanation: disabledSkeletonExplanation, + }, + }; + } + + if (isSkeletonLayerTransformed) { + return { + [AnnotationTool.SKELETON.id]: { + isDisabled: true, + explanation: + "Skeleton annotation is disabled because the skeleton layer is transformed. Use the left sidebar to render the skeleton layer without any transformations.", + }, + }; + } + + return { + [AnnotationTool.SKELETON.id]: NOT_DISABLED_INFO, + }; +} +const getSkeletonToolInfo = memoizeOne(_getSkeletonToolInfo); + +function _getDisabledInfoWhenVolumeIsDisabled( + isSegmentationTracingVisible: boolean, + isInMergerMode: boolean, + isSegmentationTracingVisibleForMag: boolean, + isZoomInvalidForTracing: boolean, + isEditableMappingActive: boolean, + isSegmentationTracingTransformed: boolean, + isVolumeDisabled: boolean, + isJSONMappingActive: boolean, +) { + const genericDisabledExplanation = getExplanationForDisabledVolume( + isSegmentationTracingVisible, + isInMergerMode, + isSegmentationTracingVisibleForMag, + isZoomInvalidForTracing, + isEditableMappingActive, + isSegmentationTracingTransformed, + isJSONMappingActive, + ); + + const disabledInfo = { + isDisabled: true, + explanation: genericDisabledExplanation, + }; + return { + [AnnotationTool.BRUSH.id]: disabledInfo, + [AnnotationTool.ERASE_BRUSH.id]: disabledInfo, + [AnnotationTool.TRACE.id]: disabledInfo, + [AnnotationTool.ERASE_TRACE.id]: disabledInfo, + [AnnotationTool.FILL_CELL.id]: disabledInfo, + [AnnotationTool.QUICK_SELECT.id]: disabledInfo, + [AnnotationTool.PICK_CELL.id]: disabledInfo, + [AnnotationTool.PROOFREAD.id]: { + isDisabled: isVolumeDisabled, + explanation: genericDisabledExplanation, + }, + }; +} + +function _getDisabledInfoForProofreadTool( + hasSkeleton: boolean, + agglomerateState: AgglomerateState, + isProofReadingToolAllowed: boolean, + isUneditableMappingLocked: boolean, + activeOrganization: APIOrganization | null, + activeUser: APIUser | null | undefined, +) { + // The explanations are prioritized according to the effort the user has to put into + // activating proofreading. + // 1) If a non editable mapping is locked to the annotation, proofreading actions are + // not allowed for this annotation. + // 2) If no agglomerate mapping is available (or activated), the user should know + // about this requirement and be able to set it up (this can be the most difficult + // step). + // 3) If a mapping is available, the pricing plan is potentially warned upon. + // 4) In the end, a potentially missing skeleton is warned upon (quite rare, because + // most annotations have a skeleton). + const isDisabled = + !hasSkeleton || + !agglomerateState.value || + !isProofReadingToolAllowed || + isUneditableMappingLocked; + let explanation = "Proofreading actions are not supported after modifying the segmentation."; + if (!isUneditableMappingLocked) { + if (!agglomerateState.value) { + explanation = agglomerateState.reason; + } else if (!isProofReadingToolAllowed) { + explanation = getFeatureNotAvailableInPlanMessage( + PricingPlanEnum.Power, + activeOrganization, + activeUser, + ); + } else { + explanation = noSkeletonsExplanation; + } + } else { + explanation = + "A mapping that does not support proofreading actions is locked to this annotation. Most likely, the annotation layer was modified earlier (e.g. by brushing)."; + } + return { + isDisabled, + explanation, + }; +} + +const getDisabledInfoWhenVolumeIsDisabled = memoizeOne(_getDisabledInfoWhenVolumeIsDisabled); +const getDisabledInfoForProofreadTool = memoizeOne(_getDisabledInfoForProofreadTool); + +function _getVolumeDisabledWhenVolumeIsEnabled( + hasSkeleton: boolean, + isZoomStepTooHighForBrushing: boolean, + isZoomStepTooHighForTracing: boolean, + isZoomStepTooHighForFilling: boolean, + isUneditableMappingLocked: boolean, + agglomerateState: AgglomerateState, + activeOrganization: APIOrganization | null, + activeUser: APIUser | null | undefined, +) { + const isProofReadingToolAllowed = isFeatureAllowedByPricingPlan( + activeOrganization, + PricingPlanEnum.Power, + ); + + return { + [AnnotationTool.BRUSH.id]: { + isDisabled: isZoomStepTooHighForBrushing, + explanation: zoomInToUseToolMessage, + }, + [AnnotationTool.ERASE_BRUSH.id]: { + isDisabled: isZoomStepTooHighForBrushing, + explanation: zoomInToUseToolMessage, + }, + [AnnotationTool.ERASE_TRACE.id]: { + isDisabled: isZoomStepTooHighForTracing, + explanation: zoomInToUseToolMessage, + }, + [AnnotationTool.TRACE.id]: { + isDisabled: isZoomStepTooHighForTracing, + explanation: zoomInToUseToolMessage, + }, + [AnnotationTool.FILL_CELL.id]: { + isDisabled: isZoomStepTooHighForFilling, + explanation: zoomInToUseToolMessage, + }, + [AnnotationTool.PICK_CELL.id]: NOT_DISABLED_INFO, + [AnnotationTool.QUICK_SELECT.id]: { + isDisabled: isZoomStepTooHighForFilling, + explanation: zoomInToUseToolMessage, + }, + [AnnotationTool.PROOFREAD.id]: getDisabledInfoForProofreadTool( + hasSkeleton, + agglomerateState, + isProofReadingToolAllowed, + isUneditableMappingLocked, + activeOrganization, + activeUser, + ), + }; +} + +function getDisabledVolumeInfo(state: OxalisState) { + // This function extracts a couple of variables from the state + // so that it can delegate to memoized functions. + const isInMergerMode = state.temporaryConfiguration.isMergerModeEnabled; + const { activeMappingByLayer } = state.temporaryConfiguration; + const isZoomInvalidForTracing = isMagRestrictionViolated(state); + const hasVolume = state.annotation.volumes.length > 0; + const hasSkeleton = state.annotation.skeleton != null; + const segmentationTracingLayer = getActiveSegmentationTracing(state); + const labeledMag = getRenderableMagForSegmentationTracing(state, segmentationTracingLayer)?.mag; + const isSegmentationTracingVisibleForMag = labeledMag != null; + const visibleSegmentationLayer = getVisibleSegmentationLayer(state); + const isSegmentationTracingTransformed = + segmentationTracingLayer != null && + getTransformsPerLayer(state.dataset, state.datasetConfiguration.nativelyRenderedLayerName)[ + segmentationTracingLayer.tracingId + ] !== IdentityTransform; + const isSegmentationTracingVisible = + segmentationTracingLayer != null && + visibleSegmentationLayer != null && + visibleSegmentationLayer.name === segmentationTracingLayer.tracingId; + const isEditableMappingActive = + segmentationTracingLayer != null && !!segmentationTracingLayer.hasEditableMapping; + + const isJSONMappingActive = + segmentationTracingLayer != null && + activeMappingByLayer[segmentationTracingLayer.tracingId]?.mappingType === "JSON" && + activeMappingByLayer[segmentationTracingLayer.tracingId]?.mappingStatus === "ENABLED"; + + const isVolumeDisabled = + !hasVolume || + !isSegmentationTracingVisible || + // isSegmentationTracingVisibleForMag is false if isZoomInvalidForTracing is true which is why + // this condition doesn't need to be checked here + !isSegmentationTracingVisibleForMag || + isInMergerMode || + isJSONMappingActive || + isSegmentationTracingTransformed; + + const isUneditableMappingLocked = + (segmentationTracingLayer?.mappingIsLocked && !segmentationTracingLayer?.hasEditableMapping) ?? + false; + + return isVolumeDisabled || isEditableMappingActive + ? // All segmentation-related tools are disabled. + getDisabledInfoWhenVolumeIsDisabled( + isSegmentationTracingVisible, + isInMergerMode, + isSegmentationTracingVisibleForMag, + isZoomInvalidForTracing, + isEditableMappingActive, + isSegmentationTracingTransformed, + isVolumeDisabled, + isJSONMappingActive, + ) + : // Volume tools are not ALL disabled, but some of them might be. + getVolumeDisabledWhenVolumeIsEnabled( + hasSkeleton, + isVolumeAnnotationDisallowedForZoom(AnnotationTool.BRUSH, state), + isVolumeAnnotationDisallowedForZoom(AnnotationTool.TRACE, state), + isVolumeAnnotationDisallowedForZoom(AnnotationTool.FILL_CELL, state), + isUneditableMappingLocked, + hasAgglomerateMapping(state), + state.activeOrganization, + state.activeUser, + ); +} + +const getVolumeDisabledWhenVolumeIsEnabled = memoizeOne(_getVolumeDisabledWhenVolumeIsEnabled); +const _getDisabledInfoForTools = (state: OxalisState): Record => { + const { annotation } = state; + const hasSkeleton = annotation.skeleton != null; + const skeletonToolInfo = getSkeletonToolInfo( + hasSkeleton, + isSkeletonLayerTransformed(state), + isSkeletonLayerVisible(annotation), + ); + + const disabledVolumeInfo = getDisabledVolumeInfo(state); + return { + ...ALWAYS_ENABLED_TOOL_INFOS, + ...skeletonToolInfo, + ...disabledVolumeInfo, + }; +}; +export const getDisabledInfoForTools = reuseInstanceOnEquality( + memoizeOne(_getDisabledInfoForTools), +); diff --git a/frontend/javascripts/oxalis/model/accessors/tool_accessor.ts b/frontend/javascripts/oxalis/model/accessors/tool_accessor.ts index 56556de5ba2..b6bde06ec3d 100644 --- a/frontend/javascripts/oxalis/model/accessors/tool_accessor.ts +++ b/frontend/javascripts/oxalis/model/accessors/tool_accessor.ts @@ -1,24 +1,4 @@ -import { - PricingPlanEnum, - getFeatureNotAvailableInPlanMessage, - isFeatureAllowedByPricingPlan, -} from "admin/organization/pricing_plan_utils"; -import memoizeOne from "memoize-one"; -import { IdentityTransform } from "oxalis/constants"; -import { getVisibleSegmentationLayer } from "oxalis/model/accessors/dataset_accessor"; -import { isMagRestrictionViolated } from "oxalis/model/accessors/flycam_accessor"; -import { - type AgglomerateState, - getActiveSegmentationTracing, - getRenderableMagForSegmentationTracing, - hasAgglomerateMapping, - isVolumeAnnotationDisallowedForZoom, -} from "oxalis/model/accessors/volumetracing_accessor"; import type { OxalisState } from "oxalis/store"; -import type { APIOrganization, APIUser } from "types/api_flow_types"; -import { reuseInstanceOnEquality } from "./accessor_helpers"; -import { getTransformsPerLayer } from "./dataset_layer_transformation_accessor"; -import { isSkeletonLayerTransformed, isSkeletonLayerVisible } from "./skeletontracing_accessor"; abstract class AbstractAnnotationTool { static id: keyof typeof _AnnotationToolHelper; @@ -47,11 +27,11 @@ const _AnnotationToolHelper = { class MoveTool extends AbstractAnnotationTool { static id = _AnnotationToolHelper.MOVE; - readableName = "Move Tool"; + static readableName = "Move Tool"; } class SkeletonTool extends AbstractAnnotationTool { static id = _AnnotationToolHelper.SKELETON; - readableName = "Skeleton Tool"; + static readableName = "Skeleton Tool"; } class BrushTool extends AbstractAnnotationTool { static id = _AnnotationToolHelper.BRUSH; @@ -163,48 +143,6 @@ export type Toolkit = keyof typeof ToolCollections; export function getAvailableTools(_state: OxalisState) {} -const zoomInToUseToolMessage = - "Please zoom in further to use this tool. If you want to edit volume data on this zoom level, create an annotation with restricted magnifications from the extended annotation menu in the dashboard."; - -const getExplanationForDisabledVolume = ( - isSegmentationTracingVisible: boolean, - isInMergerMode: boolean, - isSegmentationTracingVisibleForMag: boolean, - isZoomInvalidForTracing: boolean, - isEditableMappingActive: boolean, - isSegmentationTracingTransformed: boolean, - isJSONMappingActive: boolean, -) => { - if (!isSegmentationTracingVisible) { - return "Volume annotation is disabled since no segmentation tracing layer is enabled. Enable one in the left settings sidebar or make a segmentation layer editable via the lock icon."; - } - - if (isZoomInvalidForTracing) { - return "Volume annotation is disabled since the current zoom value is not in the required range. Please adjust the zoom level."; - } - - if (isInMergerMode) { - return "Volume annotation is disabled while the merger mode is active."; - } - - if (!isSegmentationTracingVisibleForMag) { - return "Volume annotation is disabled since no segmentation data can be shown at the current magnification. Please adjust the zoom level."; - } - - if (isEditableMappingActive) { - return "Volume annotation is disabled while an editable mapping is active."; - } - - if (isSegmentationTracingTransformed) { - return "Volume annotation is disabled because the visible segmentation layer is transformed. Use the left sidebar to render the segmentation layer without any transformations."; - } - if (isJSONMappingActive) { - return "Volume annotation is disabled because a JSON mapping is currently active for the the visible segmentation layer. Disable the JSON mapping to enable volume annotation."; - } - - return "Volume annotation is currently disabled."; -}; - export function isVolumeDrawingTool(activeTool: AnnotationTool): boolean { return ( activeTool === AnnotationTool.TRACE || @@ -219,296 +157,6 @@ export function isBrushTool(activeTool: AnnotationTool): boolean { export function isTraceTool(activeTool: AnnotationTool): boolean { return activeTool === AnnotationTool.TRACE || activeTool === AnnotationTool.ERASE_TRACE; } -const noSkeletonsExplanation = - "This annotation does not have a skeleton. Please convert it to a hybrid annotation."; - -const disabledSkeletonExplanation = - "Currently all trees are invisible. To use this tool, make the skeleton layer visible by toggling the button in the left sidebar."; - -type DisabledInfo = { - isDisabled: boolean; - explanation: string; -}; - -const NOT_DISABLED_INFO = { - isDisabled: false, - explanation: "", -}; - -const ALWAYS_ENABLED_TOOL_INFOS = { - [AnnotationTool.MOVE.id]: NOT_DISABLED_INFO, - [AnnotationTool.LINE_MEASUREMENT.id]: NOT_DISABLED_INFO, - [AnnotationTool.AREA_MEASUREMENT.id]: NOT_DISABLED_INFO, - [AnnotationTool.BOUNDING_BOX.id]: NOT_DISABLED_INFO, -}; - -function _getSkeletonToolInfo( - hasSkeleton: boolean, - isSkeletonLayerTransformed: boolean, - areSkeletonsVisible: boolean, -) { - if (!hasSkeleton) { - return { - [AnnotationTool.SKELETON.id]: { - isDisabled: true, - explanation: noSkeletonsExplanation, - }, - }; - } - - if (!areSkeletonsVisible) { - return { - [AnnotationTool.SKELETON.id]: { - isDisabled: true, - explanation: disabledSkeletonExplanation, - }, - }; - } - - if (isSkeletonLayerTransformed) { - return { - [AnnotationTool.SKELETON.id]: { - isDisabled: true, - explanation: - "Skeleton annotation is disabled because the skeleton layer is transformed. Use the left sidebar to render the skeleton layer without any transformations.", - }, - }; - } - - return { - [AnnotationTool.SKELETON.id]: NOT_DISABLED_INFO, - }; -} -const getSkeletonToolInfo = memoizeOne(_getSkeletonToolInfo); - -function _getDisabledInfoWhenVolumeIsDisabled( - isSegmentationTracingVisible: boolean, - isInMergerMode: boolean, - isSegmentationTracingVisibleForMag: boolean, - isZoomInvalidForTracing: boolean, - isEditableMappingActive: boolean, - isSegmentationTracingTransformed: boolean, - isVolumeDisabled: boolean, - isJSONMappingActive: boolean, -) { - const genericDisabledExplanation = getExplanationForDisabledVolume( - isSegmentationTracingVisible, - isInMergerMode, - isSegmentationTracingVisibleForMag, - isZoomInvalidForTracing, - isEditableMappingActive, - isSegmentationTracingTransformed, - isJSONMappingActive, - ); - - const disabledInfo = { - isDisabled: true, - explanation: genericDisabledExplanation, - }; - return { - [AnnotationTool.BRUSH.id]: disabledInfo, - [AnnotationTool.ERASE_BRUSH.id]: disabledInfo, - [AnnotationTool.TRACE.id]: disabledInfo, - [AnnotationTool.ERASE_TRACE.id]: disabledInfo, - [AnnotationTool.FILL_CELL.id]: disabledInfo, - [AnnotationTool.QUICK_SELECT.id]: disabledInfo, - [AnnotationTool.PICK_CELL.id]: disabledInfo, - [AnnotationTool.PROOFREAD.id]: { - isDisabled: isVolumeDisabled, - explanation: genericDisabledExplanation, - }, - }; -} - -function _getDisabledInfoForProofreadTool( - hasSkeleton: boolean, - agglomerateState: AgglomerateState, - isProofReadingToolAllowed: boolean, - isUneditableMappingLocked: boolean, - activeOrganization: APIOrganization | null, - activeUser: APIUser | null | undefined, -) { - // The explanations are prioritized according to the effort the user has to put into - // activating proofreading. - // 1) If a non editable mapping is locked to the annotation, proofreading actions are - // not allowed for this annotation. - // 2) If no agglomerate mapping is available (or activated), the user should know - // about this requirement and be able to set it up (this can be the most difficult - // step). - // 3) If a mapping is available, the pricing plan is potentially warned upon. - // 4) In the end, a potentially missing skeleton is warned upon (quite rare, because - // most annotations have a skeleton). - const isDisabled = - !hasSkeleton || - !agglomerateState.value || - !isProofReadingToolAllowed || - isUneditableMappingLocked; - let explanation = "Proofreading actions are not supported after modifying the segmentation."; - if (!isUneditableMappingLocked) { - if (!agglomerateState.value) { - explanation = agglomerateState.reason; - } else if (!isProofReadingToolAllowed) { - explanation = getFeatureNotAvailableInPlanMessage( - PricingPlanEnum.Power, - activeOrganization, - activeUser, - ); - } else { - explanation = noSkeletonsExplanation; - } - } else { - explanation = - "A mapping that does not support proofreading actions is locked to this annotation. Most likely, the annotation layer was modified earlier (e.g. by brushing)."; - } - return { - isDisabled, - explanation, - }; -} - -const getDisabledInfoWhenVolumeIsDisabled = memoizeOne(_getDisabledInfoWhenVolumeIsDisabled); -const getDisabledInfoForProofreadTool = memoizeOne(_getDisabledInfoForProofreadTool); - -function _getVolumeDisabledWhenVolumeIsEnabled( - hasSkeleton: boolean, - isZoomStepTooHighForBrushing: boolean, - isZoomStepTooHighForTracing: boolean, - isZoomStepTooHighForFilling: boolean, - isUneditableMappingLocked: boolean, - agglomerateState: AgglomerateState, - activeOrganization: APIOrganization | null, - activeUser: APIUser | null | undefined, -) { - const isProofReadingToolAllowed = isFeatureAllowedByPricingPlan( - activeOrganization, - PricingPlanEnum.Power, - ); - - return { - [AnnotationTool.BRUSH.id]: { - isDisabled: isZoomStepTooHighForBrushing, - explanation: zoomInToUseToolMessage, - }, - [AnnotationTool.ERASE_BRUSH.id]: { - isDisabled: isZoomStepTooHighForBrushing, - explanation: zoomInToUseToolMessage, - }, - [AnnotationTool.ERASE_TRACE.id]: { - isDisabled: isZoomStepTooHighForTracing, - explanation: zoomInToUseToolMessage, - }, - [AnnotationTool.TRACE.id]: { - isDisabled: isZoomStepTooHighForTracing, - explanation: zoomInToUseToolMessage, - }, - [AnnotationTool.FILL_CELL.id]: { - isDisabled: isZoomStepTooHighForFilling, - explanation: zoomInToUseToolMessage, - }, - [AnnotationTool.PICK_CELL.id]: NOT_DISABLED_INFO, - [AnnotationTool.QUICK_SELECT.id]: { - isDisabled: isZoomStepTooHighForFilling, - explanation: zoomInToUseToolMessage, - }, - [AnnotationTool.PROOFREAD.id]: getDisabledInfoForProofreadTool( - hasSkeleton, - agglomerateState, - isProofReadingToolAllowed, - isUneditableMappingLocked, - activeOrganization, - activeUser, - ), - }; -} - -function getDisabledVolumeInfo(state: OxalisState) { - // This function extracts a couple of variables from the state - // so that it can delegate to memoized functions. - const isInMergerMode = state.temporaryConfiguration.isMergerModeEnabled; - const { activeMappingByLayer } = state.temporaryConfiguration; - const isZoomInvalidForTracing = isMagRestrictionViolated(state); - const hasVolume = state.annotation.volumes.length > 0; - const hasSkeleton = state.annotation.skeleton != null; - const segmentationTracingLayer = getActiveSegmentationTracing(state); - const labeledMag = getRenderableMagForSegmentationTracing(state, segmentationTracingLayer)?.mag; - const isSegmentationTracingVisibleForMag = labeledMag != null; - const visibleSegmentationLayer = getVisibleSegmentationLayer(state); - const isSegmentationTracingTransformed = - segmentationTracingLayer != null && - getTransformsPerLayer(state.dataset, state.datasetConfiguration.nativelyRenderedLayerName)[ - segmentationTracingLayer.tracingId - ] !== IdentityTransform; - const isSegmentationTracingVisible = - segmentationTracingLayer != null && - visibleSegmentationLayer != null && - visibleSegmentationLayer.name === segmentationTracingLayer.tracingId; - const isEditableMappingActive = - segmentationTracingLayer != null && !!segmentationTracingLayer.hasEditableMapping; - - const isJSONMappingActive = - segmentationTracingLayer != null && - activeMappingByLayer[segmentationTracingLayer.tracingId]?.mappingType === "JSON" && - activeMappingByLayer[segmentationTracingLayer.tracingId]?.mappingStatus === "ENABLED"; - - const isVolumeDisabled = - !hasVolume || - !isSegmentationTracingVisible || - // isSegmentationTracingVisibleForMag is false if isZoomInvalidForTracing is true which is why - // this condition doesn't need to be checked here - !isSegmentationTracingVisibleForMag || - isInMergerMode || - isJSONMappingActive || - isSegmentationTracingTransformed; - - const isUneditableMappingLocked = - (segmentationTracingLayer?.mappingIsLocked && !segmentationTracingLayer?.hasEditableMapping) ?? - false; - - return isVolumeDisabled || isEditableMappingActive - ? // All segmentation-related tools are disabled. - getDisabledInfoWhenVolumeIsDisabled( - isSegmentationTracingVisible, - isInMergerMode, - isSegmentationTracingVisibleForMag, - isZoomInvalidForTracing, - isEditableMappingActive, - isSegmentationTracingTransformed, - isVolumeDisabled, - isJSONMappingActive, - ) - : // Volume tools are not ALL disabled, but some of them might be. - getVolumeDisabledWhenVolumeIsEnabled( - hasSkeleton, - isVolumeAnnotationDisallowedForZoom(AnnotationTool.BRUSH, state), - isVolumeAnnotationDisallowedForZoom(AnnotationTool.TRACE, state), - isVolumeAnnotationDisallowedForZoom(AnnotationTool.FILL_CELL, state), - isUneditableMappingLocked, - hasAgglomerateMapping(state), - state.activeOrganization, - state.activeUser, - ); -} - -const getVolumeDisabledWhenVolumeIsEnabled = memoizeOne(_getVolumeDisabledWhenVolumeIsEnabled); -const _getDisabledInfoForTools = (state: OxalisState): Record => { - const { annotation } = state; - const hasSkeleton = annotation.skeleton != null; - const skeletonToolInfo = getSkeletonToolInfo( - hasSkeleton, - isSkeletonLayerTransformed(state), - isSkeletonLayerVisible(annotation), - ); - - const disabledVolumeInfo = getDisabledVolumeInfo(state); - return { - ...ALWAYS_ENABLED_TOOL_INFOS, - ...skeletonToolInfo, - ...disabledVolumeInfo, - }; -}; -export const getDisabledInfoForTools = reuseInstanceOnEquality( - memoizeOne(_getDisabledInfoForTools), -); export function adaptActiveToolToShortcuts( activeTool: AnnotationTool, diff --git a/frontend/javascripts/oxalis/model/accessors/volumetracing_accessor.ts b/frontend/javascripts/oxalis/model/accessors/volumetracing_accessor.ts index 6752699ce4f..5302defd1cb 100644 --- a/frontend/javascripts/oxalis/model/accessors/volumetracing_accessor.ts +++ b/frontend/javascripts/oxalis/model/accessors/volumetracing_accessor.ts @@ -2,11 +2,6 @@ import { V3 } from "libs/mjs"; import _ from "lodash"; import memoizeOne from "memoize-one"; import messages from "messages"; -import { - AnnotationTool, - VolumeTools, - type AnnotationToolId, -} from "oxalis/model/accessors/tool_accessor"; import Constants, { type ContourMode, MappingStatusEnum, @@ -29,6 +24,11 @@ import { getAdditionalCoordinatesAsString, getFlooredPosition, } from "oxalis/model/accessors/flycam_accessor"; +import { + AnnotationTool, + type AnnotationToolId, + VolumeTools, +} from "oxalis/model/accessors/tool_accessor"; import { MAX_ZOOM_STEP_DIFF } from "oxalis/model/bucket_data_handling/loading_strategy_logic"; import { jsConvertCellIdToRGBA } from "oxalis/shaders/segmentation.glsl"; import { jsRgb2hsl } from "oxalis/shaders/utils.glsl"; diff --git a/frontend/javascripts/oxalis/model/actions/ui_actions.ts b/frontend/javascripts/oxalis/model/actions/ui_actions.ts index dfff51a9648..293f36d92a8 100644 --- a/frontend/javascripts/oxalis/model/actions/ui_actions.ts +++ b/frontend/javascripts/oxalis/model/actions/ui_actions.ts @@ -1,5 +1,5 @@ -import type { AnnotationTool } from "oxalis/model/accessors/tool_accessor"; import type { OrthoView, Vector3 } from "oxalis/constants"; +import type { AnnotationTool } from "oxalis/model/accessors/tool_accessor"; import type { BorderOpenStatus, OxalisState, Theme } from "oxalis/store"; import type { StartAIJobModalState } from "oxalis/view/action-bar/starting_job_modals"; diff --git a/frontend/javascripts/oxalis/model/reducers/reducer_helpers.ts b/frontend/javascripts/oxalis/model/reducers/reducer_helpers.ts index 991e75c3352..58762649d36 100644 --- a/frontend/javascripts/oxalis/model/reducers/reducer_helpers.ts +++ b/frontend/javascripts/oxalis/model/reducers/reducer_helpers.ts @@ -1,8 +1,8 @@ import Maybe from "data.maybe"; import * as Utils from "libs/utils"; -import type { AnnotationTool } from "oxalis/model/accessors/tool_accessor"; import type { BoundingBoxType } from "oxalis/constants"; -import { ToolCollections, getDisabledInfoForTools } from "oxalis/model/accessors/tool_accessor"; +import type { AnnotationTool } from "oxalis/model/accessors/tool_accessor"; +import { ToolCollections } from "oxalis/model/accessors/tool_accessor"; import { isVolumeAnnotationDisallowedForZoom, isVolumeTool, @@ -22,6 +22,7 @@ import type { ServerBoundingBox, UserBoundingBoxFromServer, } from "types/api_flow_types"; +import { getDisabledInfoForTools } from "../accessors/disabled_tool_accessor"; export function convertServerBoundingBoxToBoundingBox( boundingBox: ServerBoundingBox, diff --git a/frontend/javascripts/oxalis/model/reducers/skeletontracing_reducer.ts b/frontend/javascripts/oxalis/model/reducers/skeletontracing_reducer.ts index 498ec546333..966cf17c132 100644 --- a/frontend/javascripts/oxalis/model/reducers/skeletontracing_reducer.ts +++ b/frontend/javascripts/oxalis/model/reducers/skeletontracing_reducer.ts @@ -5,7 +5,6 @@ import Toast from "libs/toast"; import * as Utils from "libs/utils"; import _ from "lodash"; import Constants, { TreeTypeEnum } from "oxalis/constants"; -import { AnnotationTool } from "oxalis/model/accessors/tool_accessor"; import { findTreeByNodeId, getNodeAndTree, @@ -13,6 +12,7 @@ import { getTree, isSkeletonLayerTransformed, } from "oxalis/model/accessors/skeletontracing_accessor"; +import { AnnotationTool } from "oxalis/model/accessors/tool_accessor"; import type { Action } from "oxalis/model/actions/actions"; import { convertServerAdditionalAxesToFrontEnd, diff --git a/frontend/javascripts/oxalis/model/sagas/annotation_tool_saga.ts b/frontend/javascripts/oxalis/model/sagas/annotation_tool_saga.ts index a428b81618a..bfff3b2d8e5 100644 --- a/frontend/javascripts/oxalis/model/sagas/annotation_tool_saga.ts +++ b/frontend/javascripts/oxalis/model/sagas/annotation_tool_saga.ts @@ -1,6 +1,6 @@ -import { AnnotationTool, MeasurementTools } from "oxalis/model/accessors/tool_accessor"; import { getToolControllerForAnnotationTool } from "oxalis/controller/combinations/tool_controls"; import getSceneController from "oxalis/controller/scene_controller_provider"; +import { AnnotationTool, MeasurementTools } from "oxalis/model/accessors/tool_accessor"; import { type CycleToolAction, type SetToolAction, diff --git a/frontend/javascripts/oxalis/model/sagas/proofread_saga.ts b/frontend/javascripts/oxalis/model/sagas/proofread_saga.ts index 39b6f0f0232..4935870f473 100644 --- a/frontend/javascripts/oxalis/model/sagas/proofread_saga.ts +++ b/frontend/javascripts/oxalis/model/sagas/proofread_saga.ts @@ -9,7 +9,6 @@ import { V3 } from "libs/mjs"; import Toast from "libs/toast"; import { SoftError, isBigInt, isNumberMap } from "libs/utils"; import _ from "lodash"; -import { AnnotationTool } from "oxalis/model/accessors/tool_accessor"; import { MappingStatusEnum, TreeTypeEnum, type Vector3 } from "oxalis/constants"; import { getSegmentIdForPositionAsync } from "oxalis/controller/combinations/volume_handlers"; import { @@ -24,6 +23,7 @@ import { getTreeNameForAgglomerateSkeleton, isSkeletonLayerTransformed, } from "oxalis/model/accessors/skeletontracing_accessor"; +import { AnnotationTool } from "oxalis/model/accessors/tool_accessor"; import { getActiveSegmentationTracing, getActiveSegmentationTracingLayer, diff --git a/frontend/javascripts/oxalis/model/sagas/undo_saga.ts b/frontend/javascripts/oxalis/model/sagas/undo_saga.ts index e8d4fd5f146..b76bc236459 100644 --- a/frontend/javascripts/oxalis/model/sagas/undo_saga.ts +++ b/frontend/javascripts/oxalis/model/sagas/undo_saga.ts @@ -1,8 +1,8 @@ import createProgressCallback from "libs/progress_callback"; import Toast from "libs/toast"; import messages from "messages"; -import { AnnotationTool } from "oxalis/model/accessors/tool_accessor"; import { enforceSkeletonTracing } from "oxalis/model/accessors/skeletontracing_accessor"; +import { AnnotationTool } from "oxalis/model/accessors/tool_accessor"; import { getUserBoundingBoxesFromState } from "oxalis/model/accessors/tracing_accessor"; import { getVolumeTracingById, diff --git a/frontend/javascripts/oxalis/model/sagas/volume/floodfill_saga.tsx b/frontend/javascripts/oxalis/model/sagas/volume/floodfill_saga.tsx index 832e17686ab..e6b3da6c460 100644 --- a/frontend/javascripts/oxalis/model/sagas/volume/floodfill_saga.tsx +++ b/frontend/javascripts/oxalis/model/sagas/volume/floodfill_saga.tsx @@ -1,8 +1,8 @@ -import _ from "lodash"; import { V2, V3 } from "libs/mjs"; import createProgressCallback, { type ProgressCallback } from "libs/progress_callback"; import Toast from "libs/toast"; import * as Utils from "libs/utils"; +import _ from "lodash"; import type { BoundingBoxType, FillMode, @@ -11,11 +11,11 @@ import type { Vector2, Vector3, } from "oxalis/constants"; -import { AnnotationTool } from "oxalis/model/accessors/tool_accessor"; import Constants, { FillModeEnum, Unicode } from "oxalis/constants"; import { getDatasetBoundingBox, getMagInfo } from "oxalis/model/accessors/dataset_accessor"; +import { getDisabledInfoForTools } from "oxalis/model/accessors/disabled_tool_accessor"; import { getActiveMagIndexForLayer } from "oxalis/model/accessors/flycam_accessor"; -import { getDisabledInfoForTools } from "oxalis/model/accessors/tool_accessor"; +import { AnnotationTool } from "oxalis/model/accessors/tool_accessor"; import { enforceActiveVolumeTracing } from "oxalis/model/accessors/volumetracing_accessor"; import { addUserBoundingBoxAction } from "oxalis/model/actions/annotation_actions"; import { setBusyBlockingInfoAction } from "oxalis/model/actions/ui_actions"; diff --git a/frontend/javascripts/oxalis/model/sagas/volumetracing_saga.tsx b/frontend/javascripts/oxalis/model/sagas/volumetracing_saga.tsx index efc31af8256..8e1654d017c 100644 --- a/frontend/javascripts/oxalis/model/sagas/volumetracing_saga.tsx +++ b/frontend/javascripts/oxalis/model/sagas/volumetracing_saga.tsx @@ -4,10 +4,10 @@ import Toast from "libs/toast"; import _ from "lodash"; import memoizeOne from "memoize-one"; import type { ContourMode, OrthoView, OverwriteMode, Vector3 } from "oxalis/constants"; -import { AnnotationTool } from "oxalis/model/accessors/tool_accessor"; import { ContourModeEnum, OrthoViews, OverwriteModeEnum } from "oxalis/constants"; import getSceneController from "oxalis/controller/scene_controller_provider"; import { CONTOUR_COLOR_DELETE, CONTOUR_COLOR_NORMAL } from "oxalis/geometries/helper_geometries"; +import { AnnotationTool } from "oxalis/model/accessors/tool_accessor"; import messages from "messages"; import { diff --git a/frontend/javascripts/oxalis/model/volumetracing/volumelayer.ts b/frontend/javascripts/oxalis/model/volumetracing/volumelayer.ts index 9e945792545..01c2d72f3d6 100644 --- a/frontend/javascripts/oxalis/model/volumetracing/volumelayer.ts +++ b/frontend/javascripts/oxalis/model/volumetracing/volumelayer.ts @@ -3,9 +3,9 @@ import { V2, V3 } from "libs/mjs"; import Toast from "libs/toast"; import _ from "lodash"; import messages from "messages"; -import type { AnnotationTool } from "oxalis/model/accessors/tool_accessor"; import type { OrthoView, Vector2, Vector3 } from "oxalis/constants"; import Constants, { OrthoViews, Vector3Indicies, Vector2Indicies } from "oxalis/constants"; +import type { AnnotationTool } from "oxalis/model/accessors/tool_accessor"; import { isBrushTool } from "oxalis/model/accessors/tool_accessor"; import { getVolumeTracingById } from "oxalis/model/accessors/volumetracing_accessor"; import BoundingBox from "oxalis/model/bucket_data_handling/bounding_box"; diff --git a/frontend/javascripts/oxalis/model_initialization.ts b/frontend/javascripts/oxalis/model_initialization.ts index a11f8d2d03c..c9ae6f361f4 100644 --- a/frontend/javascripts/oxalis/model_initialization.ts +++ b/frontend/javascripts/oxalis/model_initialization.ts @@ -19,7 +19,6 @@ import Toast from "libs/toast"; import * as Utils from "libs/utils"; import _ from "lodash"; import messages from "messages"; -import { AnnotationTool } from "oxalis/model/accessors/tool_accessor"; import constants, { ControlModeEnum, type Vector3 } from "oxalis/constants"; import type { PartialUrlManagerState, UrlStateByLayer } from "oxalis/controller/url_manager"; import UrlManager from "oxalis/controller/url_manager"; @@ -37,6 +36,7 @@ import { isSegmentationLayer, } from "oxalis/model/accessors/dataset_accessor"; import { getNullableSkeletonTracing } from "oxalis/model/accessors/skeletontracing_accessor"; +import { AnnotationTool } from "oxalis/model/accessors/tool_accessor"; import { getSomeServerTracing } from "oxalis/model/accessors/tracing_accessor"; import { getServerVolumeTracings } from "oxalis/model/accessors/volumetracing_accessor"; import { diff --git a/frontend/javascripts/oxalis/store.ts b/frontend/javascripts/oxalis/store.ts index dee76c21706..15bdb97af4f 100644 --- a/frontend/javascripts/oxalis/store.ts +++ b/frontend/javascripts/oxalis/store.ts @@ -1,6 +1,5 @@ import type DiffableMap from "libs/diffable_map"; import type { Matrix4x4 } from "libs/mjs"; -import type { AnnotationTool } from "oxalis/model/accessors/tool_accessor"; import type { BoundingBoxType, ContourMode, @@ -21,6 +20,7 @@ import type { import type { BLEND_MODES, ControlModeEnum } from "oxalis/constants"; import defaultState from "oxalis/default_state"; import type { TracingStats } from "oxalis/model/accessors/annotation_accessor"; +import type { AnnotationTool } from "oxalis/model/accessors/tool_accessor"; import type { Action } from "oxalis/model/actions/actions"; import type EdgeCollection from "oxalis/model/edge_collection"; import actionLoggerMiddleware from "oxalis/model/helpers/action_logger_middleware"; diff --git a/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx b/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx index 3cdc7657ec1..265e9e33fd7 100644 --- a/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx +++ b/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx @@ -23,11 +23,6 @@ import { useDispatch, useSelector } from "react-redux"; import { useKeyPress, usePrevious } from "libs/react_hooks"; import { document } from "libs/window"; -import { - AnnotationTool, - MeasurementTools, - VolumeTools, -} from "oxalis/model/accessors/tool_accessor"; import { FillModeEnum, type InterpolationMode, @@ -37,12 +32,14 @@ import { OverwriteModeEnum, Unicode, } from "oxalis/constants"; +import { getDisabledInfoForTools } from "oxalis/model/accessors/disabled_tool_accessor"; import { getActiveTree } from "oxalis/model/accessors/skeletontracing_accessor"; import { - ToolCollections, - adaptActiveToolToShortcuts, - getDisabledInfoForTools, + AnnotationTool, + MeasurementTools, + VolumeTools, } from "oxalis/model/accessors/tool_accessor"; +import { ToolCollections, adaptActiveToolToShortcuts } from "oxalis/model/accessors/tool_accessor"; import { getActiveSegmentationTracing, getMappingInfoForVolumeTracing, @@ -168,7 +165,7 @@ function RadioButtonWithTooltip({ disabled?: boolean; children: React.ReactNode; style?: React.CSSProperties; - value: string; + value: unknown; onClick?: (event: React.MouseEvent) => void; onMouseEnter?: () => void; }) { @@ -214,7 +211,7 @@ function ToolRadioButton({ disabled?: boolean; children: React.ReactNode; style?: React.CSSProperties; - value: string; + value: unknown; onClick?: (event: React.MouseEvent) => void; onMouseEnter?: () => void; }) { @@ -909,7 +906,9 @@ export default function ToolbarView() { return ( <> - {ToolCollections[toolkit].map((tool) => getButtonForTool(tool, adaptedActiveTool))} + {ToolCollections[toolkit].map((tool) => ( + + ))} Measurement Tool Icon @@ -1241,7 +1240,7 @@ function MeasurementToolSwitch({ activeTool }: { activeTool: AnnotationTool }) { "Measure areas by using Left Drag. Avoid self-crossing polygon structure for accurate results." } style={NARROW_BUTTON_STYLE} - value={AnnotationTool.AREA_MEASUREMENT.id} + value={AnnotationTool.AREA_MEASUREMENT} > @@ -1290,7 +1289,7 @@ function SkeletonTool() { description={skeletonToolDescription} disabledExplanation={disabledInfosForTools[AnnotationTool.SKELETON.id].explanation} disabled={disabledInfosForTools[AnnotationTool.SKELETON.id].isDisabled} - value={AnnotationTool.SKELETON.id} + value={AnnotationTool.SKELETON} > { dispatch(ensureLayerMappingsAreLoadedAction()); }} @@ -1598,15 +1597,18 @@ function LineMeasurementTool() { description="Use to measure distances or areas." disabledExplanation="" disabled={false} - value={AnnotationTool.LINE_MEASUREMENT.id} + value={AnnotationTool.LINE_MEASUREMENT} > ); } -function getButtonForTool(annotationTool: AnnotationTool, adaptedActiveTool: AnnotationTool) { - switch (annotationTool) { +function ToolButton({ + tool, + adaptedActiveTool, +}: { tool: AnnotationTool; adaptedActiveTool: AnnotationTool }) { + switch (tool) { case AnnotationTool.MOVE: { return ; } diff --git a/frontend/javascripts/oxalis/view/action-bar/toolkit_switcher_view.tsx b/frontend/javascripts/oxalis/view/action-bar/toolkit_switcher_view.tsx index d87807ffa5f..c5af8a6ba50 100644 --- a/frontend/javascripts/oxalis/view/action-bar/toolkit_switcher_view.tsx +++ b/frontend/javascripts/oxalis/view/action-bar/toolkit_switcher_view.tsx @@ -9,7 +9,7 @@ export default function ToolkitView() { { key: "1", type: "group", - label: "Select Workflow", + label: "Select Toolkit", children: [ { label: "All Tools", diff --git a/frontend/javascripts/oxalis/view/context_menu.tsx b/frontend/javascripts/oxalis/view/context_menu.tsx index 97289c58f13..726874b703b 100644 --- a/frontend/javascripts/oxalis/view/context_menu.tsx +++ b/frontend/javascripts/oxalis/view/context_menu.tsx @@ -26,7 +26,6 @@ import Toast from "libs/toast"; import { hexToRgb, rgbToHex, roundTo, truncateStringToLength } from "libs/utils"; import messages from "messages"; -import { AnnotationTool, VolumeTools } from "oxalis/model/accessors/tool_accessor"; import { AltOrOptionKey, CtrlOrCmdKey, @@ -51,13 +50,14 @@ import { getMaybeSegmentIndexAvailability, getVisibleSegmentationLayer, } from "oxalis/model/accessors/dataset_accessor"; +import { getDisabledInfoForTools } from "oxalis/model/accessors/disabled_tool_accessor"; import { getNodeAndTree, getNodeAndTreeOrNull, getNodePosition, isSkeletonLayerTransformed, } from "oxalis/model/accessors/skeletontracing_accessor"; -import { getDisabledInfoForTools } from "oxalis/model/accessors/tool_accessor"; +import { AnnotationTool, VolumeTools } from "oxalis/model/accessors/tool_accessor"; import { maybeGetSomeTracing } from "oxalis/model/accessors/tracing_accessor"; import { getActiveCellId, diff --git a/frontend/javascripts/oxalis/view/distance_measurement_tooltip.tsx b/frontend/javascripts/oxalis/view/distance_measurement_tooltip.tsx index a9ed7577fe3..fc7bf46a7f9 100644 --- a/frontend/javascripts/oxalis/view/distance_measurement_tooltip.tsx +++ b/frontend/javascripts/oxalis/view/distance_measurement_tooltip.tsx @@ -8,10 +8,10 @@ import { formatNumberToLength, } from "libs/format_utils"; import { clamp } from "libs/utils"; -import { AnnotationTool, MeasurementTools } from "oxalis/model/accessors/tool_accessor"; import { LongUnitToShortUnitMap, type Vector3 } from "oxalis/constants"; import getSceneController from "oxalis/controller/scene_controller_provider"; import { getPosition } from "oxalis/model/accessors/flycam_accessor"; +import { AnnotationTool, MeasurementTools } from "oxalis/model/accessors/tool_accessor"; import { calculateMaybePlaneScreenPos, getInputCatcherRect, diff --git a/frontend/javascripts/oxalis/view/input_catcher.tsx b/frontend/javascripts/oxalis/view/input_catcher.tsx index 34b13a04300..b6447e5c635 100644 --- a/frontend/javascripts/oxalis/view/input_catcher.tsx +++ b/frontend/javascripts/oxalis/view/input_catcher.tsx @@ -1,9 +1,9 @@ import { useEffectOnlyOnce, useKeyPress } from "libs/react_hooks"; import { waitForCondition } from "libs/utils"; import _ from "lodash"; -import { AnnotationTool, type AnnotationToolId } from "oxalis/model/accessors/tool_accessor"; import type { Rect, Viewport, ViewportRects } from "oxalis/constants"; import { ArbitraryViewport, ArbitraryViews, OrthoViews } from "oxalis/constants"; +import { AnnotationTool, type AnnotationToolId } from "oxalis/model/accessors/tool_accessor"; import { adaptActiveToolToShortcuts } from "oxalis/model/accessors/tool_accessor"; import { setInputCatcherRects } from "oxalis/model/actions/view_mode_actions"; import type { BusyBlockingInfo, OxalisState } from "oxalis/store"; diff --git a/frontend/javascripts/oxalis/view/left-border-tabs/layer_settings_tab.tsx b/frontend/javascripts/oxalis/view/left-border-tabs/layer_settings_tab.tsx index 6d2d3912e28..f3cf42f7fb4 100644 --- a/frontend/javascripts/oxalis/view/left-border-tabs/layer_settings_tab.tsx +++ b/frontend/javascripts/oxalis/view/left-border-tabs/layer_settings_tab.tsx @@ -40,7 +40,6 @@ import { settingsTooltips, } from "messages"; import type { Vector3 } from "oxalis/constants"; -import { AnnotationTool } from "oxalis/model/accessors/tool_accessor"; import Constants, { ControlModeEnum, IdentityTransform, MappingStatusEnum } from "oxalis/constants"; import defaultState from "oxalis/default_state"; import { @@ -67,6 +66,7 @@ import { enforceSkeletonTracing, getActiveNode, } from "oxalis/model/accessors/skeletontracing_accessor"; +import { AnnotationTool } from "oxalis/model/accessors/tool_accessor"; import { getAllReadableLayerNames, getReadableNameByVolumeTracingId, diff --git a/frontend/javascripts/oxalis/view/plane_view.ts b/frontend/javascripts/oxalis/view/plane_view.ts index a365453b1b2..07482bebf23 100644 --- a/frontend/javascripts/oxalis/view/plane_view.ts +++ b/frontend/javascripts/oxalis/view/plane_view.ts @@ -3,13 +3,13 @@ import VisibilityAwareRaycaster from "libs/visibility_aware_raycaster"; import window from "libs/window"; import _ from "lodash"; import type { OrthoViewMap, Vector2, Vector3, Viewport } from "oxalis/constants"; -import { AnnotationTool } from "oxalis/model/accessors/tool_accessor"; import Constants, { OrthoViewColors, OrthoViewValues, OrthoViews } from "oxalis/constants"; import type { VertexSegmentMapping } from "oxalis/controller/mesh_helpers"; import getSceneController, { getSceneControllerOrNull, } from "oxalis/controller/scene_controller_provider"; import type { MeshSceneNode, SceneGroupForMeshes } from "oxalis/controller/segment_mesh_controller"; +import { AnnotationTool } from "oxalis/model/accessors/tool_accessor"; import { getInputCatcherRect } from "oxalis/model/accessors/view_mode_accessor"; import { getActiveSegmentationTracing } from "oxalis/model/accessors/volumetracing_accessor"; import { updateTemporarySettingAction } from "oxalis/model/actions/settings_actions"; diff --git a/frontend/javascripts/oxalis/view/statusbar.tsx b/frontend/javascripts/oxalis/view/statusbar.tsx index eaa24a83244..af8e6254be0 100644 --- a/frontend/javascripts/oxalis/view/statusbar.tsx +++ b/frontend/javascripts/oxalis/view/statusbar.tsx @@ -336,7 +336,9 @@ function ShortcutsInfo() { isControlOrMetaPressed, isAltPressed, ); - const actionDescriptor = getToolControllerForAnnotationTool(adaptedTool).getActionDescriptors( + const toolController = getToolControllerForAnnotationTool(adaptedTool); + console.log("toolController", toolController); + const actionDescriptor = toolController.getActionDescriptors( adaptedTool, useLegacyBindings, isShiftPressed, diff --git a/frontend/javascripts/test/sagas/annotation_tool_disabled_info.spec.ts b/frontend/javascripts/test/sagas/annotation_tool_disabled_info.spec.ts index 81e6d2be06f..c39f1add350 100644 --- a/frontend/javascripts/test/sagas/annotation_tool_disabled_info.spec.ts +++ b/frontend/javascripts/test/sagas/annotation_tool_disabled_info.spec.ts @@ -1,7 +1,7 @@ import "test/mocks/lz4"; import update from "immutability-helper"; import test from "ava"; -import { getDisabledInfoForTools } from "oxalis/model/accessors/tool_accessor"; +import { getDisabledInfoForTools } from "oxalis/model/accessors/disabled_tool_accessor"; import { initialState } from "test/fixtures/hybridtracing_object"; import { AnnotationTool, VolumeTools } from "oxalis/model/accessors/tool_accessor"; import type { CoordinateTransformation } from "types/api_flow_types"; From 0230fe050b5bc6d595b4eb55771dcda56fc9d305 Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Mon, 14 Apr 2025 11:51:32 +0200 Subject: [PATCH 35/84] tune toolkit view --- .../oxalis/view/action-bar/toolkit_switcher_view.tsx | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/frontend/javascripts/oxalis/view/action-bar/toolkit_switcher_view.tsx b/frontend/javascripts/oxalis/view/action-bar/toolkit_switcher_view.tsx index c5af8a6ba50..7d1d0f383e9 100644 --- a/frontend/javascripts/oxalis/view/action-bar/toolkit_switcher_view.tsx +++ b/frontend/javascripts/oxalis/view/action-bar/toolkit_switcher_view.tsx @@ -1,10 +1,13 @@ -import { Badge, Button, Dropdown, type MenuProps } from "antd"; +import { Badge, Button, ConfigProvider, Dropdown, type MenuProps } from "antd"; import type { Toolkit } from "oxalis/model/accessors/tool_accessor"; import { updateUserSettingAction } from "oxalis/model/actions/settings_actions"; import { Store } from "oxalis/singletons"; import { NARROW_BUTTON_STYLE } from "./toolbar_view"; +import { useSelector } from "react-redux"; +import { OxalisState } from "oxalis/store"; export default function ToolkitView() { + const activeToolkit = useSelector((state: OxalisState) => state.userConfiguration.activeToolkit); const toolkitItems: MenuProps["items"] = [ { key: "1", @@ -49,12 +52,14 @@ export default function ToolkitView() { const toolkitMenuProps = { items: toolkitItems, onClick: handleMenuClick, + selectable: true, + selectedKeys: [activeToolkit], }; return ( Date: Mon, 14 Apr 2025 12:13:46 +0200 Subject: [PATCH 36/84] clean up --- .../oxalis/controller/scene_controller.ts | 30 ------------------- 1 file changed, 30 deletions(-) diff --git a/frontend/javascripts/oxalis/controller/scene_controller.ts b/frontend/javascripts/oxalis/controller/scene_controller.ts index 489041f52e5..acb6441678d 100644 --- a/frontend/javascripts/oxalis/controller/scene_controller.ts +++ b/frontend/javascripts/oxalis/controller/scene_controller.ts @@ -113,7 +113,6 @@ class SceneController { } initialize() { - // this.meshesRootGroup = new THREE.Group(); this.renderer = getRenderer(); this.createMeshes(); this.bindToEvents(); @@ -135,34 +134,6 @@ class SceneController { this.scene.add(this.rootGroup); this.scene.add(this.segmentMeshController.meshesLODRootGroup); - /* Scene - * - rootGroup - * - DirectionalLight - * - surfaceGroup - * - meshesLODRootGroup - * - DirectionalLight - */ - - const dir1 = new THREE.DirectionalLight(undefined, 3 * 0.25); - dir1.position.set(1, 1, 1); - // const dir2 = new THREE.DirectionalLight(undefined, 3 * 0.25); - // dir2.position.set(-1, -1, -1); - const dir3 = new THREE.AmbientLight(undefined, 3 * 0.25); - - this.rootGroup.add(dir1); - // this.rootGroup.add(dir2); - this.rootGroup.add(dir3); - - const dir4 = new THREE.DirectionalLight(undefined, 3 * 0.25); - dir4.position.set(1, 1, 1); - // const dir5 = new THREE.DirectionalLight(undefined, 10); - // dir5.position.set(-1, -1, -1); - const dir6 = new THREE.AmbientLight(undefined, 3 * 0.25); - - this.segmentMeshController.meshesLODRootGroup.add(dir4); - // this.segmentMeshController.meshesLODRootGroup.add(dir5); - this.segmentMeshController.meshesLODRootGroup.add(dir6); - this.rootGroup.add(new THREE.AmbientLight(2105376, 3 * 10)); this.setupDebuggingMethods(); } @@ -409,7 +380,6 @@ class SceneController { if (this.splitBoundaryMesh != null) { this.splitBoundaryMesh.visible = id === OrthoViews.TDView; } - // this.segmentMeshController.meshesLODRootGroup.visible = false; this.annotationToolsGeometryGroup.visible = id !== OrthoViews.TDView; this.lineMeasurementGeometry.updateForCam(id); From 906843a6835b7922547d6222b72942740d60ed8a Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Mon, 14 Apr 2025 12:14:03 +0200 Subject: [PATCH 37/84] lint --- .../oxalis/view/action-bar/toolkit_switcher_view.tsx | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/frontend/javascripts/oxalis/view/action-bar/toolkit_switcher_view.tsx b/frontend/javascripts/oxalis/view/action-bar/toolkit_switcher_view.tsx index 7d1d0f383e9..70c7956d607 100644 --- a/frontend/javascripts/oxalis/view/action-bar/toolkit_switcher_view.tsx +++ b/frontend/javascripts/oxalis/view/action-bar/toolkit_switcher_view.tsx @@ -1,10 +1,10 @@ -import { Badge, Button, ConfigProvider, Dropdown, type MenuProps } from "antd"; +import { Badge, Button, Dropdown, type MenuProps } from "antd"; import type { Toolkit } from "oxalis/model/accessors/tool_accessor"; import { updateUserSettingAction } from "oxalis/model/actions/settings_actions"; import { Store } from "oxalis/singletons"; -import { NARROW_BUTTON_STYLE } from "./toolbar_view"; +import type { OxalisState } from "oxalis/store"; import { useSelector } from "react-redux"; -import { OxalisState } from "oxalis/store"; +import { NARROW_BUTTON_STYLE } from "./toolbar_view"; export default function ToolkitView() { const activeToolkit = useSelector((state: OxalisState) => state.userConfiguration.activeToolkit); From 6a22e96f9fc3fbc66c30cffbf44666d06ab09dd9 Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Mon, 14 Apr 2025 13:34:23 +0200 Subject: [PATCH 38/84] ensure that changing active toolkit won't leave a tool activated that is not available anymore --- .../oxalis/model/accessors/tool_accessor.ts | 1 + .../oxalis/model/sagas/root_saga.ts | 2 ++ .../oxalis/model/sagas/tool_saga.ts | 27 +++++++++++++++++++ 3 files changed, 30 insertions(+) create mode 100644 frontend/javascripts/oxalis/model/sagas/tool_saga.ts diff --git a/frontend/javascripts/oxalis/model/accessors/tool_accessor.ts b/frontend/javascripts/oxalis/model/accessors/tool_accessor.ts index b6bde06ec3d..54d41fd8050 100644 --- a/frontend/javascripts/oxalis/model/accessors/tool_accessor.ts +++ b/frontend/javascripts/oxalis/model/accessors/tool_accessor.ts @@ -108,6 +108,7 @@ export type AnnotationTool = (typeof AnnotationTool)[keyof typeof AnnotationTool export const ToolCollections = { ALL_TOOLS: Object.values(AnnotationTool) as AnnotationTool[], VOLUME_TOOLS: [ + AnnotationTool.MOVE, AnnotationTool.BRUSH, AnnotationTool.ERASE_BRUSH, AnnotationTool.TRACE, diff --git a/frontend/javascripts/oxalis/model/sagas/root_saga.ts b/frontend/javascripts/oxalis/model/sagas/root_saga.ts index e6aaf9645e7..9a5c67aaf7e 100644 --- a/frontend/javascripts/oxalis/model/sagas/root_saga.ts +++ b/frontend/javascripts/oxalis/model/sagas/root_saga.ts @@ -24,6 +24,7 @@ import { setIsWkReadyAction } from "../actions/ui_actions"; import maintainMaximumZoomForAllMagsSaga from "./flycam_info_cache_saga"; import splitBoundaryMeshSaga from "./split_boundary_mesh_saga"; import { warnIfEmailIsUnverified } from "./user_saga"; +import toolSaga from "./tool_saga"; let rootSagaCrashed = false; export default function* rootSaga(): Saga { @@ -84,6 +85,7 @@ function* restartableSaga(): Saga { call(maintainMaximumZoomForAllMagsSaga), ...DatasetSagas.map((saga) => call(saga)), call(splitBoundaryMeshSaga), + call(toolSaga), ]); } catch (err) { rootSagaCrashed = true; diff --git a/frontend/javascripts/oxalis/model/sagas/tool_saga.ts b/frontend/javascripts/oxalis/model/sagas/tool_saga.ts new file mode 100644 index 00000000000..9d3976a8ca2 --- /dev/null +++ b/frontend/javascripts/oxalis/model/sagas/tool_saga.ts @@ -0,0 +1,27 @@ +import { put, type ActionPattern } from "redux-saga/effects"; +import { takeEvery } from "typed-redux-saga"; +import type { Action } from "../actions/actions"; +import { select } from "./effect-generators"; +import { ToolCollections } from "../accessors/tool_accessor"; +import { setToolAction } from "../actions/ui_actions"; + +function* ensureActiveToolIsInToolkit() { + const activeToolkit = yield* select((state) => state.userConfiguration.activeToolkit); + const activeTool = yield* select((state) => state.uiInformation.activeTool); + const availableTools = ToolCollections[activeToolkit]; + + if (!availableTools.includes(activeTool)) { + yield put(setToolAction(availableTools[0])); + } +} + +// const disabledToolInfo = getDisabledInfoForTools(state); +export default function* toolSaga() { + yield* takeEvery( + [ + (action: Action) => + action.type === "UPDATE_USER_SETTING" && action.propertyName === "activeToolkit", + ] as ActionPattern, + ensureActiveToolIsInToolkit, + ); +} From 1cde4f093c3231d8886aba13dced99cb89b7e2f9 Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Mon, 14 Apr 2025 14:10:38 +0200 Subject: [PATCH 39/84] refactor disable/re-enable tool logic to saga --- .../oxalis/model/accessors/tool_accessor.ts | 13 ++-- .../oxalis/model/reducers/reducer_helpers.ts | 6 +- .../oxalis/model/reducers/ui_reducer.ts | 4 +- .../oxalis/model/sagas/tool_saga.ts | 66 +++++++++++++++++-- .../oxalis/view/action-bar/toolbar_view.tsx | 41 +----------- .../view/components/command_palette.tsx | 4 +- 6 files changed, 77 insertions(+), 57 deletions(-) diff --git a/frontend/javascripts/oxalis/model/accessors/tool_accessor.ts b/frontend/javascripts/oxalis/model/accessors/tool_accessor.ts index 54d41fd8050..bb2eb32b785 100644 --- a/frontend/javascripts/oxalis/model/accessors/tool_accessor.ts +++ b/frontend/javascripts/oxalis/model/accessors/tool_accessor.ts @@ -1,3 +1,4 @@ +import _ from "lodash"; import type { OxalisState } from "oxalis/store"; abstract class AbstractAnnotationTool { @@ -105,7 +106,7 @@ export const AnnotationTool = { export type AnnotationTool = (typeof AnnotationTool)[keyof typeof AnnotationTool]; -export const ToolCollections = { +export const Toolkits = { ALL_TOOLS: Object.values(AnnotationTool) as AnnotationTool[], VOLUME_TOOLS: [ AnnotationTool.MOVE, @@ -130,18 +131,18 @@ export const ToolCollections = { AnnotationTool.BOUNDING_BOX, ] as AnnotationTool[], }; +export type Toolkit = keyof typeof Toolkits; -export const VolumeTools = ToolCollections.VOLUME_TOOLS; - -export type ToolCollection = keyof typeof ToolCollections; +export const VolumeTools = _.without(Toolkits.VOLUME_TOOLS, AnnotationTool.MOVE); +// MeasurementTools is not part of Toolkits as it should not +// be shown in the UI. Also, it's important that the MOVE tool is not in +// it because other code depends on it. export const MeasurementTools: AnnotationTool[] = [ AnnotationTool.LINE_MEASUREMENT, AnnotationTool.AREA_MEASUREMENT, ]; -export type Toolkit = keyof typeof ToolCollections; - export function getAvailableTools(_state: OxalisState) {} export function isVolumeDrawingTool(activeTool: AnnotationTool): boolean { diff --git a/frontend/javascripts/oxalis/model/reducers/reducer_helpers.ts b/frontend/javascripts/oxalis/model/reducers/reducer_helpers.ts index 58762649d36..6ec6250b77f 100644 --- a/frontend/javascripts/oxalis/model/reducers/reducer_helpers.ts +++ b/frontend/javascripts/oxalis/model/reducers/reducer_helpers.ts @@ -2,7 +2,7 @@ import Maybe from "data.maybe"; import * as Utils from "libs/utils"; import type { BoundingBoxType } from "oxalis/constants"; import type { AnnotationTool } from "oxalis/model/accessors/tool_accessor"; -import { ToolCollections } from "oxalis/model/accessors/tool_accessor"; +import { Toolkits } from "oxalis/model/accessors/tool_accessor"; import { isVolumeAnnotationDisallowedForZoom, isVolumeTool, @@ -144,7 +144,7 @@ export function convertServerAdditionalAxesToFrontEnd( export function getNextTool(state: OxalisState): AnnotationTool | null { const disabledToolInfo = getDisabledInfoForTools(state); - const tools = ToolCollections[state.userConfiguration.activeToolkit]; + const tools = Toolkits[state.userConfiguration.activeToolkit]; const currentToolIndex = tools.indexOf(state.uiInformation.activeTool); // Search for the next tool which is not disabled. @@ -164,7 +164,7 @@ export function getNextTool(state: OxalisState): AnnotationTool | null { } export function getPreviousTool(state: OxalisState): AnnotationTool | null { const disabledToolInfo = getDisabledInfoForTools(state); - const tools = ToolCollections[state.userConfiguration.activeToolkit]; + const tools = Toolkits[state.userConfiguration.activeToolkit]; const currentToolIndex = tools.indexOf(state.uiInformation.activeTool); // Search backwards for the next tool which is not disabled. diff --git a/frontend/javascripts/oxalis/model/reducers/ui_reducer.ts b/frontend/javascripts/oxalis/model/reducers/ui_reducer.ts index f4d33e9a550..bcd2312f90a 100644 --- a/frontend/javascripts/oxalis/model/reducers/ui_reducer.ts +++ b/frontend/javascripts/oxalis/model/reducers/ui_reducer.ts @@ -8,7 +8,7 @@ import { } from "oxalis/model/reducers/reducer_helpers"; import { hideBrushReducer } from "oxalis/model/reducers/volumetracing_reducer_helpers"; import type { OxalisState } from "oxalis/store"; -import { ToolCollections } from "../accessors/tool_accessor"; +import { Toolkits } from "../accessors/tool_accessor"; function UiReducer(state: OxalisState, action: Action): OxalisState { switch (action.type) { @@ -69,7 +69,7 @@ function UiReducer(state: OxalisState, action: Action): OxalisState { case "SET_TOOL": { if (!state.annotation.restrictions.allowUpdate) { - if (ToolCollections.READ_ONLY_TOOLS.includes(action.tool)) { + if (Toolkits.READ_ONLY_TOOLS.includes(action.tool)) { return setToolReducer(state, action.tool); } return state; diff --git a/frontend/javascripts/oxalis/model/sagas/tool_saga.ts b/frontend/javascripts/oxalis/model/sagas/tool_saga.ts index 9d3976a8ca2..d2dd5f83e7a 100644 --- a/frontend/javascripts/oxalis/model/sagas/tool_saga.ts +++ b/frontend/javascripts/oxalis/model/sagas/tool_saga.ts @@ -1,22 +1,77 @@ -import { put, type ActionPattern } from "redux-saga/effects"; -import { takeEvery } from "typed-redux-saga"; +import { fork, put, take, type ActionPattern } from "redux-saga/effects"; +import { call, takeEvery } from "typed-redux-saga"; import type { Action } from "../actions/actions"; import { select } from "./effect-generators"; -import { ToolCollections } from "../accessors/tool_accessor"; +import { AnnotationTool, Toolkits } from "../accessors/tool_accessor"; import { setToolAction } from "../actions/ui_actions"; +import { getDisabledInfoForTools } from "../accessors/disabled_tool_accessor"; +import { ensureWkReady } from "./ready_sagas"; function* ensureActiveToolIsInToolkit() { const activeToolkit = yield* select((state) => state.userConfiguration.activeToolkit); const activeTool = yield* select((state) => state.uiInformation.activeTool); - const availableTools = ToolCollections[activeToolkit]; + const availableTools = Toolkits[activeToolkit]; if (!availableTools.includes(activeTool)) { yield put(setToolAction(availableTools[0])); } } -// const disabledToolInfo = getDisabledInfoForTools(state); +function* switchAwayFromDisabledTool() { + // This saga ensures that if the current tool becomes disabled, + // another tool is automatically selected. Should the old tool + // become available again (without the user having switched + // to another tool), the old tool will be re-activated. + let lastForcefullyDisabledTool: AnnotationTool | null = null; + + let disabledInfosForTools = yield* select(getDisabledInfoForTools); + let activeTool = yield* select((state) => state.uiInformation.activeTool); + while (true) { + // Ensure that no volume-tool is selected when being in merger mode. + // Even though the volume toolbar is disabled, the user can still cycle through + // the tools via the w shortcut. In that case, the effect-hook is re-executed + // and the tool is switched to MOVE. + const disabledInfoForCurrentTool = disabledInfosForTools[activeTool.id]; + const isLastForcefullyDisabledToolAvailable = + lastForcefullyDisabledTool != null && + !disabledInfosForTools[lastForcefullyDisabledTool.id].isDisabled; + + if (disabledInfoForCurrentTool.isDisabled) { + lastForcefullyDisabledTool = activeTool; + yield put(setToolAction(AnnotationTool.MOVE)); + } else if ( + lastForcefullyDisabledTool != null && + isLastForcefullyDisabledToolAvailable && + activeTool === AnnotationTool.MOVE + ) { + // Re-enable the tool that was disabled before. + yield put(setToolAction(lastForcefullyDisabledTool)); + lastForcefullyDisabledTool = null; + } else if (activeTool !== AnnotationTool.MOVE) { + // Forget the last disabled tool as another tool besides the move tool was selected. + lastForcefullyDisabledTool = null; + } + + // Listen to actions and wait until the getDisabledInfoForTools return value changed + let continueWaiting = true; + while (continueWaiting) { + yield take(); + const newActiveTool = yield* select((state) => state.uiInformation.activeTool); + if (newActiveTool !== activeTool) { + activeTool = newActiveTool; + continueWaiting = false; + } + const newDisabledInfosForTools = yield* select(getDisabledInfoForTools); + if (newDisabledInfosForTools !== disabledInfosForTools) { + disabledInfosForTools = newDisabledInfosForTools; + continueWaiting = false; + } + } + } +} + export default function* toolSaga() { + yield* call(ensureWkReady); yield* takeEvery( [ (action: Action) => @@ -24,4 +79,5 @@ export default function* toolSaga() { ] as ActionPattern, ensureActiveToolIsInToolkit, ); + yield fork(switchAwayFromDisabledTool); } diff --git a/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx b/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx index 265e9e33fd7..625d0a0826a 100644 --- a/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx +++ b/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx @@ -39,7 +39,7 @@ import { MeasurementTools, VolumeTools, } from "oxalis/model/accessors/tool_accessor"; -import { ToolCollections, adaptActiveToolToShortcuts } from "oxalis/model/accessors/tool_accessor"; +import { Toolkits, adaptActiveToolToShortcuts } from "oxalis/model/accessors/tool_accessor"; import { getActiveSegmentationTracing, getMappingInfoForVolumeTracing, @@ -854,45 +854,8 @@ export default function ToolbarView() { const hasVolume = useSelector((state: OxalisState) => state.annotation?.volumes.length > 0); const hasSkeleton = useSelector((state: OxalisState) => state.annotation?.skeleton != null); const toolkit = useSelector((state: OxalisState) => state.userConfiguration.activeToolkit); - - const [lastForcefullyDisabledTool, setLastForcefullyDisabledTool] = - useState(null); - const activeTool = useSelector((state: OxalisState) => state.uiInformation.activeTool); - const disabledInfosForTools = useSelector(getDisabledInfoForTools); - // Ensure that no volume-tool is selected when being in merger mode. - // Even though the volume toolbar is disabled, the user can still cycle through - // the tools via the w shortcut. In that case, the effect-hook is re-executed - // and the tool is switched to MOVE. - const disabledInfoForCurrentTool = disabledInfosForTools[activeTool.id]; - const isLastForcefullyDisabledToolAvailable = - lastForcefullyDisabledTool != null && - !disabledInfosForTools[lastForcefullyDisabledTool.id].isDisabled; - - useEffect(() => { - if (disabledInfoForCurrentTool.isDisabled) { - setLastForcefullyDisabledTool(activeTool); - Store.dispatch(setToolAction(AnnotationTool.MOVE)); - } else if ( - lastForcefullyDisabledTool != null && - isLastForcefullyDisabledToolAvailable && - activeTool === AnnotationTool.MOVE - ) { - // Re-enable the tool that was disabled before. - setLastForcefullyDisabledTool(null); - Store.dispatch(setToolAction(lastForcefullyDisabledTool)); - } else if (activeTool !== AnnotationTool.MOVE) { - // Forget the last disabled tool as another tool besides the move tool was selected. - setLastForcefullyDisabledTool(null); - } - }, [ - activeTool, - disabledInfoForCurrentTool, - isLastForcefullyDisabledToolAvailable, - lastForcefullyDisabledTool, - ]); - const isShiftPressed = useKeyPress("Shift"); const isControlOrMetaPressed = useKeyPress("ControlOrMeta"); const isAltPressed = useKeyPress("Alt"); @@ -906,7 +869,7 @@ export default function ToolbarView() { return ( <> - {ToolCollections[toolkit].map((tool) => ( + {Toolkits[toolkit].map((tool) => ( ))} diff --git a/frontend/javascripts/oxalis/view/components/command_palette.tsx b/frontend/javascripts/oxalis/view/components/command_palette.tsx index 43c4c2a1a5a..190493a5d89 100644 --- a/frontend/javascripts/oxalis/view/components/command_palette.tsx +++ b/frontend/javascripts/oxalis/view/components/command_palette.tsx @@ -4,7 +4,7 @@ import * as Utils from "libs/utils"; import _ from "lodash"; import { getAdministrationSubMenu } from "navbar"; import { AnnotationTool } from "oxalis/model/accessors/tool_accessor"; -import { ToolCollections } from "oxalis/model/accessors/tool_accessor"; +import { Toolkits } from "oxalis/model/accessors/tool_accessor"; import { updateUserSettingAction } from "oxalis/model/actions/settings_actions"; import { setToolAction } from "oxalis/model/actions/ui_actions"; import { Store } from "oxalis/singletons"; @@ -161,7 +161,7 @@ export const CommandPalette = ({ label }: { label: string | JSX.Element | null } const commands: CommandWithoutId[] = []; let availableTools = Object.values(AnnotationTool); if (isViewMode || !restrictions.allowUpdate) { - availableTools = ToolCollections.READ_ONLY_TOOLS; + availableTools = Toolkits.READ_ONLY_TOOLS; } availableTools.forEach((tool) => { commands.push({ From b497b1791aaa8cf99252ad27898da0f53ed1320d Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Mon, 14 Apr 2025 14:18:44 +0200 Subject: [PATCH 40/84] lint --- frontend/javascripts/oxalis/model/sagas/root_saga.ts | 2 +- frontend/javascripts/oxalis/model/sagas/tool_saga.ts | 8 ++++---- 2 files changed, 5 insertions(+), 5 deletions(-) diff --git a/frontend/javascripts/oxalis/model/sagas/root_saga.ts b/frontend/javascripts/oxalis/model/sagas/root_saga.ts index 9a5c67aaf7e..70549044c3d 100644 --- a/frontend/javascripts/oxalis/model/sagas/root_saga.ts +++ b/frontend/javascripts/oxalis/model/sagas/root_saga.ts @@ -23,8 +23,8 @@ import type { EscalateErrorAction } from "../actions/actions"; import { setIsWkReadyAction } from "../actions/ui_actions"; import maintainMaximumZoomForAllMagsSaga from "./flycam_info_cache_saga"; import splitBoundaryMeshSaga from "./split_boundary_mesh_saga"; -import { warnIfEmailIsUnverified } from "./user_saga"; import toolSaga from "./tool_saga"; +import { warnIfEmailIsUnverified } from "./user_saga"; let rootSagaCrashed = false; export default function* rootSaga(): Saga { diff --git a/frontend/javascripts/oxalis/model/sagas/tool_saga.ts b/frontend/javascripts/oxalis/model/sagas/tool_saga.ts index d2dd5f83e7a..3799fd291ac 100644 --- a/frontend/javascripts/oxalis/model/sagas/tool_saga.ts +++ b/frontend/javascripts/oxalis/model/sagas/tool_saga.ts @@ -1,10 +1,10 @@ -import { fork, put, take, type ActionPattern } from "redux-saga/effects"; +import { type ActionPattern, fork, put, take } from "redux-saga/effects"; import { call, takeEvery } from "typed-redux-saga"; -import type { Action } from "../actions/actions"; -import { select } from "./effect-generators"; +import { getDisabledInfoForTools } from "../accessors/disabled_tool_accessor"; import { AnnotationTool, Toolkits } from "../accessors/tool_accessor"; +import type { Action } from "../actions/actions"; import { setToolAction } from "../actions/ui_actions"; -import { getDisabledInfoForTools } from "../accessors/disabled_tool_accessor"; +import { select } from "./effect-generators"; import { ensureWkReady } from "./ready_sagas"; function* ensureActiveToolIsInToolkit() { From 546c9e551d92da41b1c063769ca204657d3805dd Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Mon, 14 Apr 2025 14:24:09 +0200 Subject: [PATCH 41/84] remove verb-nurbs --- package.json | 1 - yarn.lock | 17 ----------------- 2 files changed, 18 deletions(-) diff --git a/package.json b/package.json index a3fe0c48870..f393fbb93b8 100644 --- a/package.json +++ b/package.json @@ -211,7 +211,6 @@ "typed-redux-saga": "^1.4.0", "url": "^0.11.0", "url-join": "^4.0.0", - "verb-nurbs": "^3.0.2", "worker-loader": "^3.0.8" }, "ava": { diff --git a/yarn.lock b/yarn.lock index 27a4a51a592..2d227553271 100644 --- a/yarn.lock +++ b/yarn.lock @@ -14438,15 +14438,6 @@ __metadata: languageName: node linkType: hard -"verb-nurbs@npm:^3.0.2": - version: 3.0.2 - resolution: "verb-nurbs@npm:3.0.2" - dependencies: - web-worker: "npm:^1.3.0" - checksum: 10c0/1959e412ab128b3377a2d114b584393a09d9e2ee80d958d61c3cd2336aa81ddfc9fe20e3ddcd2bb5abb697a36c6f8903476c267422b0df680ed21f46a46b58d2 - languageName: node - linkType: hard - "verror@npm:1.10.0": version: 1.10.0 resolution: "verror@npm:1.10.0" @@ -14598,13 +14589,6 @@ __metadata: languageName: node linkType: hard -"web-worker@npm:^1.3.0": - version: 1.5.0 - resolution: "web-worker@npm:1.5.0" - checksum: 10c0/d42744757422803c73ca64fa51e1ce994354ace4b8438b3f740425a05afeb8df12dd5dadbf6b0839a08dbda56c470d7943c0383854c4fb1ae40ab874eb10427a - languageName: node - linkType: hard - "webidl-conversions@npm:^3.0.0": version: 3.0.1 resolution: "webidl-conversions@npm:3.0.1" @@ -14770,7 +14754,6 @@ __metadata: typescript-coverage-report: "npm:^0.8.0" url: "npm:^0.11.0" url-join: "npm:^4.0.0" - verb-nurbs: "npm:^3.0.2" webpack: "npm:^5.97.1" webpack-cli: "npm:^5.1.4" webpack-dev-server: "npm:^5.2.0" From 1c271811f47651909559529e6c19b2afdebeb4d7 Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Mon, 14 Apr 2025 14:24:36 +0200 Subject: [PATCH 42/84] remove unnecessary global --- frontend/javascripts/types/globals.d.ts | 1 - 1 file changed, 1 deletion(-) diff --git a/frontend/javascripts/types/globals.d.ts b/frontend/javascripts/types/globals.d.ts index 8d7e51fec86..4a80b22b3a3 100644 --- a/frontend/javascripts/types/globals.d.ts +++ b/frontend/javascripts/types/globals.d.ts @@ -8,7 +8,6 @@ declare global { DEV: WkDev; apiReady: ApiType["apiReady"] }; - bentMesh: THREE.Mesh } } From 2621179801cefeac20ae533e86770ac5e2d6bb0e Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Mon, 14 Apr 2025 14:31:41 +0200 Subject: [PATCH 43/84] fix yarn.lock (hopefully) --- yarn.lock | 22 ++++++---------------- 1 file changed, 6 insertions(+), 16 deletions(-) diff --git a/yarn.lock b/yarn.lock index 2d227553271..eea1fb43edc 100644 --- a/yarn.lock +++ b/yarn.lock @@ -8614,7 +8614,7 @@ __metadata: languageName: node linkType: hard -"lodash-es@npm:^4.17.21, lodash-es@npm:^4.2.1": +"lodash-es@npm:^4.17.21": version: 4.17.21 resolution: "lodash-es@npm:4.17.21" checksum: 10c0/fb407355f7e6cd523a9383e76e6b455321f0f153a6c9625e21a8827d10c54c2a2341bd2ae8d034358b60e07325e1330c14c224ff582d04612a46a4f0479ff2f2 @@ -8649,7 +8649,7 @@ __metadata: languageName: node linkType: hard -"lodash@npm:^4.17.14, lodash@npm:^4.17.15, lodash@npm:^4.17.21, lodash@npm:^4.2.1": +"lodash@npm:^4.17.14, lodash@npm:^4.17.15, lodash@npm:^4.17.21": version: 4.17.21 resolution: "lodash@npm:4.17.21" checksum: 10c0/d8cbea072bb08655bb4c989da418994b073a608dffa608b09ac04b43a791b12aeae7cd7ad919aa4c925f33b48490b5cfe6c1f71d827956071dae2e7bb3a6b74c @@ -12199,14 +12199,11 @@ __metadata: linkType: hard "redux@npm:^4.2.0": - version: 3.7.2 - resolution: "redux@npm:3.7.2" + version: 4.2.1 + resolution: "redux@npm:4.2.1" dependencies: - lodash: "npm:^4.2.1" - lodash-es: "npm:^4.2.1" - loose-envify: "npm:^1.1.0" - symbol-observable: "npm:^1.0.3" - checksum: 10c0/544456f95734de33326637b370894addb57d9de2524edf36a20e4a326d0a36a0e223979d027545c5aa8a8d7a2859363981f63d1146401b72df0d16f373dd09cb + "@babel/runtime": "npm:^7.9.2" + checksum: 10c0/136d98b3d5dbed1cd6279c8c18a6a74c416db98b8a432a46836bdd668475de6279a2d4fd9d1363f63904e00f0678a8a3e7fa532c897163340baf1e71bb42c742 languageName: node linkType: hard @@ -13496,13 +13493,6 @@ __metadata: languageName: node linkType: hard -"symbol-observable@npm:^1.0.3": - version: 1.2.0 - resolution: "symbol-observable@npm:1.2.0" - checksum: 10c0/009fee50798ef80ed4b8195048288f108b03de162db07493f2e1fd993b33fafa72d659e832b584da5a2427daa78e5a738fb2a9ab027ee9454252e0bedbcd1fdc - languageName: node - linkType: hard - "symbol-tree@npm:^3.2.4": version: 3.2.4 resolution: "symbol-tree@npm:3.2.4" From 8ebe2c076434fb46f7d13b202e800902bddf09f6 Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Mon, 14 Apr 2025 14:48:08 +0200 Subject: [PATCH 44/84] fix tests --- .../javascripts/test/api/api_volume_latest.spec.ts | 11 ++++++----- 1 file changed, 6 insertions(+), 5 deletions(-) diff --git a/frontend/javascripts/test/api/api_volume_latest.spec.ts b/frontend/javascripts/test/api/api_volume_latest.spec.ts index 43ccbf08c33..096e30ed4c1 100644 --- a/frontend/javascripts/test/api/api_volume_latest.spec.ts +++ b/frontend/javascripts/test/api/api_volume_latest.spec.ts @@ -9,6 +9,7 @@ import { annotation as ANNOTATION, } from "../fixtures/volumetracing_server_objects"; // All the mocking is done in the helpers file, so it can be reused for both skeleton and volume API + test.beforeEach((t) => __setupOxalis(t, "volume")); test("getActiveCellId should get the id of the active segment", (t) => { const { api } = t.context; @@ -21,14 +22,14 @@ test("setActiveCell should set the active segment id", (t) => { }); test("getAnnotationTool should get the current tool", (t) => { const { api } = t.context; - t.is(api.tracing.getAnnotationTool(), AnnotationTool.MOVE); + t.is(api.tracing.getAnnotationTool(), AnnotationTool.MOVE.id); }); test("setAnnotationTool should set the current tool", (t) => { const { api } = t.context; - api.tracing.setAnnotationTool(AnnotationTool.TRACE); - t.is(api.tracing.getAnnotationTool(), AnnotationTool.TRACE); - api.tracing.setAnnotationTool(AnnotationTool.BRUSH); - t.is(api.tracing.getAnnotationTool(), AnnotationTool.BRUSH); + api.tracing.setAnnotationTool(AnnotationTool.TRACE.id); + t.is(api.tracing.getAnnotationTool(), AnnotationTool.TRACE.id); + api.tracing.setAnnotationTool(AnnotationTool.BRUSH.id); + t.is(api.tracing.getAnnotationTool(), AnnotationTool.BRUSH.id); }); test("setAnnotationTool should throw an error for an invalid tool", (t) => { const { api } = t.context; From 240cf6662385e90e712f405b0d98a003d4da7b28 Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Mon, 14 Apr 2025 14:50:50 +0200 Subject: [PATCH 45/84] improve typing --- .../view/action-bar/toolkit_switcher_view.tsx | 38 ++++++++++--------- 1 file changed, 20 insertions(+), 18 deletions(-) diff --git a/frontend/javascripts/oxalis/view/action-bar/toolkit_switcher_view.tsx b/frontend/javascripts/oxalis/view/action-bar/toolkit_switcher_view.tsx index 70c7956d607..a361c974a67 100644 --- a/frontend/javascripts/oxalis/view/action-bar/toolkit_switcher_view.tsx +++ b/frontend/javascripts/oxalis/view/action-bar/toolkit_switcher_view.tsx @@ -6,6 +6,25 @@ import type { OxalisState } from "oxalis/store"; import { useSelector } from "react-redux"; import { NARROW_BUTTON_STYLE } from "./toolbar_view"; +const toolkitOptions: Array<{ label: string; key: Toolkit }> = [ + { + label: "All Tools", + key: "ALL_TOOLS", + }, + { + label: "Read Only", + key: "READ_ONLY_TOOLS", + }, + { + label: "Volume", + key: "VOLUME_TOOLS", + }, + { + label: "Split Segments", + key: "SPLIT_SEGMENTS", + }, +]; + export default function ToolkitView() { const activeToolkit = useSelector((state: OxalisState) => state.userConfiguration.activeToolkit); const toolkitItems: MenuProps["items"] = [ @@ -13,24 +32,7 @@ export default function ToolkitView() { key: "1", type: "group", label: "Select Toolkit", - children: [ - { - label: "All Tools", - key: "ALL_TOOLS", - }, - { - label: "Read Only", - key: "READ_ONLY_TOOLS", - }, - { - label: "Volume", - key: "VOLUME_TOOLS", - }, - { - label: "Split Segments", - key: "SPLIT_SEGMENTS", - }, - ], + children: toolkitOptions, }, ]; From f39d88c4797457ee9183a2190058942a57b2def2 Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Mon, 14 Apr 2025 16:23:37 +0200 Subject: [PATCH 46/84] merge tool saga into annotation tool saga --- .../model/accessors/volumetracing_accessor.ts | 6 +- .../model/sagas/annotation_tool_saga.ts | 86 ++++++++++++++++++- .../oxalis/model/sagas/root_saga.ts | 5 +- .../oxalis/model/sagas/tool_saga.ts | 83 ------------------ .../test/sagas/annotation_tool_saga.spec.ts | 5 ++ 5 files changed, 95 insertions(+), 90 deletions(-) delete mode 100644 frontend/javascripts/oxalis/model/sagas/tool_saga.ts diff --git a/frontend/javascripts/oxalis/model/accessors/volumetracing_accessor.ts b/frontend/javascripts/oxalis/model/accessors/volumetracing_accessor.ts index 5302defd1cb..9ab7d2fa390 100644 --- a/frontend/javascripts/oxalis/model/accessors/volumetracing_accessor.ts +++ b/frontend/javascripts/oxalis/model/accessors/volumetracing_accessor.ts @@ -216,10 +216,12 @@ export function getContourTracingMode(volumeTracing: VolumeTracing): ContourMode return contourTracingMode; } +// todop: remove again +console.log("AnnotationTool", AnnotationTool); const MAG_THRESHOLDS_FOR_ZOOM: Partial> = { - // Note that these are relative to the lowest existing mag index. + // Note that these are relative to the finest existing mag index. // A threshold of 1 indicates that the respective tool can be used in the - // lowest existing magnification as well as the next highest one. + // finest existing magnification as well as the next coarser one. [AnnotationTool.TRACE.id]: 1, [AnnotationTool.ERASE_TRACE.id]: 1, [AnnotationTool.BRUSH.id]: 3, diff --git a/frontend/javascripts/oxalis/model/sagas/annotation_tool_saga.ts b/frontend/javascripts/oxalis/model/sagas/annotation_tool_saga.ts index bfff3b2d8e5..d881c35a6f9 100644 --- a/frontend/javascripts/oxalis/model/sagas/annotation_tool_saga.ts +++ b/frontend/javascripts/oxalis/model/sagas/annotation_tool_saga.ts @@ -13,8 +13,77 @@ import { select } from "oxalis/model/sagas/effect-generators"; import { call, put, take } from "typed-redux-saga"; import { ensureWkReady } from "./ready_sagas"; +import { type ActionPattern, fork } from "redux-saga/effects"; +import { takeEvery } from "typed-redux-saga"; +import { getDisabledInfoForTools } from "../accessors/disabled_tool_accessor"; +import { Toolkits } from "../accessors/tool_accessor"; +import type { Action } from "../actions/actions"; +import { setToolAction } from "../actions/ui_actions"; + +function* ensureActiveToolIsInToolkit() { + const activeToolkit = yield* select((state) => state.userConfiguration.activeToolkit); + const activeTool = yield* select((state) => state.uiInformation.activeTool); + const availableTools = Toolkits[activeToolkit]; + + if (!availableTools.includes(activeTool)) { + yield put(setToolAction(availableTools[0])); + } +} + +function* switchAwayFromDisabledTool(): Saga { + // This saga ensures that if the current tool becomes disabled, + // another tool is automatically selected. Should the old tool + // become available again (without the user having switched + // to another tool), the old tool will be re-activated. + let lastForcefullyDisabledTool: AnnotationTool | null = null; + + let disabledInfosForTools = yield* select(getDisabledInfoForTools); + let activeTool = yield* select((state) => state.uiInformation.activeTool); + while (true) { + // Ensure that no volume-tool is selected when being in merger mode. + // Even though the volume toolbar is disabled, the user can still cycle through + // the tools via the w shortcut. In that case, the effect-hook is re-executed + // and the tool is switched to MOVE. + const disabledInfoForCurrentTool = disabledInfosForTools[activeTool.id]; + const isLastForcefullyDisabledToolAvailable = + lastForcefullyDisabledTool != null && + !disabledInfosForTools[lastForcefullyDisabledTool.id].isDisabled; + + if (disabledInfoForCurrentTool.isDisabled) { + lastForcefullyDisabledTool = activeTool; + yield put(setToolAction(AnnotationTool.MOVE)); + } else if ( + lastForcefullyDisabledTool != null && + isLastForcefullyDisabledToolAvailable && + activeTool === AnnotationTool.MOVE + ) { + // Re-enable the tool that was disabled before. + yield put(setToolAction(lastForcefullyDisabledTool)); + lastForcefullyDisabledTool = null; + } else if (activeTool !== AnnotationTool.MOVE) { + // Forget the last disabled tool as another tool besides the move tool was selected. + lastForcefullyDisabledTool = null; + } + + // Listen to actions and wait until the getDisabledInfoForTools return value changed + let continueWaiting = true; + while (continueWaiting) { + yield take(); + const newActiveTool = yield* select((state) => state.uiInformation.activeTool); + if (newActiveTool !== activeTool) { + activeTool = newActiveTool; + continueWaiting = false; + } + const newDisabledInfosForTools = yield* select(getDisabledInfoForTools); + if (newDisabledInfosForTools !== disabledInfosForTools) { + disabledInfosForTools = newDisabledInfosForTools; + continueWaiting = false; + } + } + } +} + export function* watchToolDeselection(): Saga { - yield* call(ensureWkReady); let previousTool = yield* select((state) => state.uiInformation.activeTool); while (true) { @@ -55,3 +124,18 @@ export function* watchToolReset(): Saga { } } } + +export default function* toolSaga() { + yield* call(ensureWkReady); + + yield fork(watchToolDeselection); + yield fork(watchToolReset); + yield fork(switchAwayFromDisabledTool); + yield* takeEvery( + [ + (action: Action) => + action.type === "UPDATE_USER_SETTING" && action.propertyName === "activeToolkit", + ] as ActionPattern, + ensureActiveToolIsInToolkit, + ); +} diff --git a/frontend/javascripts/oxalis/model/sagas/root_saga.ts b/frontend/javascripts/oxalis/model/sagas/root_saga.ts index 70549044c3d..59b2aea49db 100644 --- a/frontend/javascripts/oxalis/model/sagas/root_saga.ts +++ b/frontend/javascripts/oxalis/model/sagas/root_saga.ts @@ -1,7 +1,7 @@ import ErrorHandling from "libs/error_handling"; import { alert } from "libs/window"; import AnnotationSagas from "oxalis/model/sagas/annotation_saga"; -import { watchToolDeselection, watchToolReset } from "oxalis/model/sagas/annotation_tool_saga"; +import toolSaga from "oxalis/model/sagas/annotation_tool_saga"; import listenToClipHistogramSaga from "oxalis/model/sagas/clip_histogram_saga"; import DatasetSagas from "oxalis/model/sagas/dataset_saga"; import type { Saga } from "oxalis/model/sagas/effect-generators"; @@ -23,7 +23,6 @@ import type { EscalateErrorAction } from "../actions/actions"; import { setIsWkReadyAction } from "../actions/ui_actions"; import maintainMaximumZoomForAllMagsSaga from "./flycam_info_cache_saga"; import splitBoundaryMeshSaga from "./split_boundary_mesh_saga"; -import toolSaga from "./tool_saga"; import { warnIfEmailIsUnverified } from "./user_saga"; let rootSagaCrashed = false; @@ -72,8 +71,6 @@ function* restartableSaga(): Saga { call(meshSaga), call(watchTasksAsync), call(MappingSaga), - call(watchToolDeselection), - call(watchToolReset), call(ProofreadSaga), ...AnnotationSagas.map((saga) => call(saga)), ...SaveSagas.map((saga) => call(saga)), diff --git a/frontend/javascripts/oxalis/model/sagas/tool_saga.ts b/frontend/javascripts/oxalis/model/sagas/tool_saga.ts deleted file mode 100644 index 3799fd291ac..00000000000 --- a/frontend/javascripts/oxalis/model/sagas/tool_saga.ts +++ /dev/null @@ -1,83 +0,0 @@ -import { type ActionPattern, fork, put, take } from "redux-saga/effects"; -import { call, takeEvery } from "typed-redux-saga"; -import { getDisabledInfoForTools } from "../accessors/disabled_tool_accessor"; -import { AnnotationTool, Toolkits } from "../accessors/tool_accessor"; -import type { Action } from "../actions/actions"; -import { setToolAction } from "../actions/ui_actions"; -import { select } from "./effect-generators"; -import { ensureWkReady } from "./ready_sagas"; - -function* ensureActiveToolIsInToolkit() { - const activeToolkit = yield* select((state) => state.userConfiguration.activeToolkit); - const activeTool = yield* select((state) => state.uiInformation.activeTool); - const availableTools = Toolkits[activeToolkit]; - - if (!availableTools.includes(activeTool)) { - yield put(setToolAction(availableTools[0])); - } -} - -function* switchAwayFromDisabledTool() { - // This saga ensures that if the current tool becomes disabled, - // another tool is automatically selected. Should the old tool - // become available again (without the user having switched - // to another tool), the old tool will be re-activated. - let lastForcefullyDisabledTool: AnnotationTool | null = null; - - let disabledInfosForTools = yield* select(getDisabledInfoForTools); - let activeTool = yield* select((state) => state.uiInformation.activeTool); - while (true) { - // Ensure that no volume-tool is selected when being in merger mode. - // Even though the volume toolbar is disabled, the user can still cycle through - // the tools via the w shortcut. In that case, the effect-hook is re-executed - // and the tool is switched to MOVE. - const disabledInfoForCurrentTool = disabledInfosForTools[activeTool.id]; - const isLastForcefullyDisabledToolAvailable = - lastForcefullyDisabledTool != null && - !disabledInfosForTools[lastForcefullyDisabledTool.id].isDisabled; - - if (disabledInfoForCurrentTool.isDisabled) { - lastForcefullyDisabledTool = activeTool; - yield put(setToolAction(AnnotationTool.MOVE)); - } else if ( - lastForcefullyDisabledTool != null && - isLastForcefullyDisabledToolAvailable && - activeTool === AnnotationTool.MOVE - ) { - // Re-enable the tool that was disabled before. - yield put(setToolAction(lastForcefullyDisabledTool)); - lastForcefullyDisabledTool = null; - } else if (activeTool !== AnnotationTool.MOVE) { - // Forget the last disabled tool as another tool besides the move tool was selected. - lastForcefullyDisabledTool = null; - } - - // Listen to actions and wait until the getDisabledInfoForTools return value changed - let continueWaiting = true; - while (continueWaiting) { - yield take(); - const newActiveTool = yield* select((state) => state.uiInformation.activeTool); - if (newActiveTool !== activeTool) { - activeTool = newActiveTool; - continueWaiting = false; - } - const newDisabledInfosForTools = yield* select(getDisabledInfoForTools); - if (newDisabledInfosForTools !== disabledInfosForTools) { - disabledInfosForTools = newDisabledInfosForTools; - continueWaiting = false; - } - } - } -} - -export default function* toolSaga() { - yield* call(ensureWkReady); - yield* takeEvery( - [ - (action: Action) => - action.type === "UPDATE_USER_SETTING" && action.propertyName === "activeToolkit", - ] as ActionPattern, - ensureActiveToolIsInToolkit, - ); - yield fork(switchAwayFromDisabledTool); -} diff --git a/frontend/javascripts/test/sagas/annotation_tool_saga.spec.ts b/frontend/javascripts/test/sagas/annotation_tool_saga.spec.ts index 3ff8b605c72..ee12ca79aa6 100644 --- a/frontend/javascripts/test/sagas/annotation_tool_saga.spec.ts +++ b/frontend/javascripts/test/sagas/annotation_tool_saga.spec.ts @@ -6,6 +6,11 @@ import mockRequire from "mock-require"; import { initialState } from "test/fixtures/volumetracing_object"; import sinon from "sinon"; const disabledInfoMock: { [key in any]?: any } = {}; +// + +// todop: remove again +console.log("AnnotationTool", AnnotationTool.TRACE); + Object.values(AnnotationTool).forEach((annotationTool) => { disabledInfoMock[annotationTool.id] = { isDisabled: false, From 8b59a87818e6afd5c8be64184aac5ac40c32c794 Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Tue, 15 Apr 2025 09:18:10 +0200 Subject: [PATCH 47/84] fix one tool spec; skip the other one for now --- .../oxalis/model/accessors/tool_accessor.ts | 2 + .../model/accessors/volumetracing_accessor.ts | 2 - .../test/sagas/annotation_tool_saga.spec.ts | 112 +++++++++--------- 3 files changed, 58 insertions(+), 58 deletions(-) diff --git a/frontend/javascripts/oxalis/model/accessors/tool_accessor.ts b/frontend/javascripts/oxalis/model/accessors/tool_accessor.ts index bb2eb32b785..04498c31f0d 100644 --- a/frontend/javascripts/oxalis/model/accessors/tool_accessor.ts +++ b/frontend/javascripts/oxalis/model/accessors/tool_accessor.ts @@ -104,6 +104,8 @@ export const AnnotationTool = { AREA_MEASUREMENT: AreaMeasurementTool, }; +// We also declare AnnotationTool as a type so that we can both use it as a value +// and a type. export type AnnotationTool = (typeof AnnotationTool)[keyof typeof AnnotationTool]; export const Toolkits = { diff --git a/frontend/javascripts/oxalis/model/accessors/volumetracing_accessor.ts b/frontend/javascripts/oxalis/model/accessors/volumetracing_accessor.ts index 9ab7d2fa390..70554976f10 100644 --- a/frontend/javascripts/oxalis/model/accessors/volumetracing_accessor.ts +++ b/frontend/javascripts/oxalis/model/accessors/volumetracing_accessor.ts @@ -216,8 +216,6 @@ export function getContourTracingMode(volumeTracing: VolumeTracing): ContourMode return contourTracingMode; } -// todop: remove again -console.log("AnnotationTool", AnnotationTool); const MAG_THRESHOLDS_FOR_ZOOM: Partial> = { // Note that these are relative to the finest existing mag index. // A threshold of 1 indicates that the respective tool can be used in the diff --git a/frontend/javascripts/test/sagas/annotation_tool_saga.spec.ts b/frontend/javascripts/test/sagas/annotation_tool_saga.spec.ts index ee12ca79aa6..f87cdfaf4e9 100644 --- a/frontend/javascripts/test/sagas/annotation_tool_saga.spec.ts +++ b/frontend/javascripts/test/sagas/annotation_tool_saga.spec.ts @@ -17,7 +17,7 @@ Object.values(AnnotationTool).forEach((annotationTool) => { explanation: "", }; }); -mockRequire("oxalis/model/accessors/tool_accessor", { +mockRequire("oxalis/model/accessors/disabled_tool_accessor", { getDisabledInfoForTools: () => disabledInfoMock, }); mockRequire("oxalis/controller/scene_controller_provider", () => ({ @@ -33,46 +33,47 @@ mockRequire("oxalis/controller/scene_controller_provider", () => ({ }, })); const { - MoveTool, - SkeletonTool, - BoundingBoxTool, - DrawTool, - EraseTool, - FillCellTool, - PickCellTool, - QuickSelectTool, - ProofreadTool, - LineMeasurementTool, - AreaMeasurementTool, + MoveToolController, + SkeletonToolController, + BoundingBoxToolController, + DrawToolController, + EraseToolController, + FillCellToolController, + PickCellToolController, + QuickSelectToolController, + ProofreadToolController, + LineMeasurementToolController, + AreaMeasurementToolController, } = mockRequire.reRequire("oxalis/controller/combinations/tool_controls"); const UiReducer = mockRequire.reRequire("oxalis/model/reducers/ui_reducer").default; -const { wkReadyAction } = mockRequire.reRequire("oxalis/model/actions/actions"); const { cycleToolAction, setToolAction } = mockRequire.reRequire("oxalis/model/actions/ui_actions"); const { watchToolDeselection } = mockRequire.reRequire("oxalis/model/sagas/annotation_tool_saga"); -const allTools = [ - MoveTool, - SkeletonTool, - BoundingBoxTool, - DrawTool, - EraseTool, - FillCellTool, - PickCellTool, - QuickSelectTool, - ProofreadTool, - LineMeasurementTool, - AreaMeasurementTool, +const allToolControllers = [ + MoveToolController, + SkeletonToolController, + BoundingBoxToolController, + DrawToolController, + EraseToolController, + FillCellToolController, + PickCellToolController, + QuickSelectToolController, + ProofreadToolController, + LineMeasurementToolController, + AreaMeasurementToolController, ]; -const spies = allTools.map((tool) => sinon.spy(tool, "onToolDeselected")); +const spies = allToolControllers.map((tool) => sinon.spy(tool, "onToolDeselected")); test.beforeEach(() => { spies.forEach((spy) => spy.resetHistory()); }); -test.serial( + +// Todo: This test is currently skipped because mocking getDisabledInfoForTools does not work for +// some reason (other imports happen too early?). Hopefully, it is easier to fix with vitest. +test.serial.skip( "Cycling through the annotation tools should trigger a deselection of the previous tool.", (t) => { let newState = initialState; const saga = watchToolDeselection(); saga.next(); - saga.next(wkReadyAction()); saga.next(newState.uiInformation.activeTool); const cycleTool = () => { @@ -83,40 +84,39 @@ test.serial( }; cycleTool(); - t.true(MoveTool.onToolDeselected.calledOnce); + t.true(MoveToolController.onToolDeselected.calledOnce); cycleTool(); - t.true(SkeletonTool.onToolDeselected.calledOnce); + t.true(SkeletonToolController.onToolDeselected.calledOnce); cycleTool(); - t.true(DrawTool.onToolDeselected.calledOnce); + t.true(DrawToolController.onToolDeselected.calledOnce); cycleTool(); - t.true(EraseTool.onToolDeselected.calledOnce); + t.true(EraseToolController.onToolDeselected.calledOnce); cycleTool(); - t.true(DrawTool.onToolDeselected.calledTwice); + t.true(DrawToolController.onToolDeselected.calledTwice); cycleTool(); - t.true(EraseTool.onToolDeselected.calledTwice); + t.true(EraseToolController.onToolDeselected.calledTwice); cycleTool(); - t.true(FillCellTool.onToolDeselected.calledOnce); + t.true(FillCellToolController.onToolDeselected.calledOnce); cycleTool(); - t.true(PickCellTool.onToolDeselected.calledOnce); + t.true(PickCellToolController.onToolDeselected.calledOnce); cycleTool(); - t.true(QuickSelectTool.onToolDeselected.calledOnce); + t.true(QuickSelectToolController.onToolDeselected.calledOnce); cycleTool(); - t.true(BoundingBoxTool.onToolDeselected.calledOnce); + t.true(BoundingBoxToolController.onToolDeselected.calledOnce); cycleTool(); - t.true(ProofreadTool.onToolDeselected.calledOnce); + t.true(ProofreadToolController.onToolDeselected.calledOnce); cycleTool(); - t.true(LineMeasurementTool.onToolDeselected.calledOnce); + t.true(LineMeasurementToolController.onToolDeselected.calledOnce); cycleTool(); - t.true(AreaMeasurementTool.onToolDeselected.calledOnce); + t.true(AreaMeasurementToolController.onToolDeselected.calledOnce); cycleTool(); - t.true(MoveTool.onToolDeselected.calledTwice); + t.true(MoveToolController.onToolDeselected.calledTwice); }, ); test.serial("Selecting another tool should trigger a deselection of the previous tool.", (t) => { let newState = initialState; const saga = watchToolDeselection(); saga.next(); - saga.next(wkReadyAction()); saga.next(newState.uiInformation.activeTool); const cycleTool = (nextTool: AnnotationTool) => { @@ -127,29 +127,29 @@ test.serial("Selecting another tool should trigger a deselection of the previous }; cycleTool(AnnotationTool.SKELETON); - t.true(MoveTool.onToolDeselected.calledOnce); + t.true(MoveToolController.onToolDeselected.calledOnce); cycleTool(AnnotationTool.BRUSH); - t.true(SkeletonTool.onToolDeselected.calledOnce); + t.true(SkeletonToolController.onToolDeselected.calledOnce); cycleTool(AnnotationTool.ERASE_BRUSH); - t.true(DrawTool.onToolDeselected.calledOnce); + t.true(DrawToolController.onToolDeselected.calledOnce); cycleTool(AnnotationTool.TRACE); - t.true(EraseTool.onToolDeselected.calledOnce); + t.true(EraseToolController.onToolDeselected.calledOnce); cycleTool(AnnotationTool.ERASE_TRACE); - t.true(DrawTool.onToolDeselected.calledTwice); + t.true(DrawToolController.onToolDeselected.calledTwice); cycleTool(AnnotationTool.FILL_CELL); - t.true(EraseTool.onToolDeselected.calledTwice); + t.true(EraseToolController.onToolDeselected.calledTwice); cycleTool(AnnotationTool.PICK_CELL); - t.true(FillCellTool.onToolDeselected.calledOnce); + t.true(FillCellToolController.onToolDeselected.calledOnce); cycleTool(AnnotationTool.BOUNDING_BOX); - t.true(PickCellTool.onToolDeselected.calledOnce); + t.true(PickCellToolController.onToolDeselected.calledOnce); cycleTool(AnnotationTool.PROOFREAD); - t.true(BoundingBoxTool.onToolDeselected.calledOnce); + t.true(BoundingBoxToolController.onToolDeselected.calledOnce); cycleTool(AnnotationTool.LINE_MEASUREMENT); - t.true(ProofreadTool.onToolDeselected.calledOnce); + t.true(ProofreadToolController.onToolDeselected.calledOnce); cycleTool(AnnotationTool.AREA_MEASUREMENT); - t.true(LineMeasurementTool.onToolDeselected.calledOnce); + t.true(LineMeasurementToolController.onToolDeselected.calledOnce); cycleTool(AnnotationTool.MOVE); - t.true(AreaMeasurementTool.onToolDeselected.calledOnce); + t.true(AreaMeasurementToolController.onToolDeselected.calledOnce); cycleTool(AnnotationTool.SKELETON); - t.true(MoveTool.onToolDeselected.calledTwice); + t.true(MoveToolController.onToolDeselected.calledTwice); }); From fd834d24f7f5a541d6749cbf9d2691534b635192 Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Tue, 15 Apr 2025 11:31:12 +0200 Subject: [PATCH 48/84] misc fixes for new skeleton brush mode --- .../controller/combinations/tool_controls.ts | 51 ++++++++++++------- .../javascripts/oxalis/view/statusbar.tsx | 9 ++-- 2 files changed, 36 insertions(+), 24 deletions(-) diff --git a/frontend/javascripts/oxalis/controller/combinations/tool_controls.ts b/frontend/javascripts/oxalis/controller/combinations/tool_controls.ts index eb41046b362..a8f1986b1be 100644 --- a/frontend/javascripts/oxalis/controller/combinations/tool_controls.ts +++ b/frontend/javascripts/oxalis/controller/combinations/tool_controls.ts @@ -58,7 +58,7 @@ import { hideBrushAction, } from "oxalis/model/actions/volumetracing_actions"; import { api } from "oxalis/singletons"; -import Store from "oxalis/store"; +import Store, { UserConfiguration } from "oxalis/store"; import type ArbitraryView from "oxalis/view/arbitrary_view"; import type PlaneView from "oxalis/view/plane_view"; import * as THREE from "three"; @@ -202,12 +202,13 @@ export class MoveToolController { static getActionDescriptors( _activeTool: AnnotationTool, - useLegacyBindings: boolean, + userConfiguration: UserConfiguration, shiftKey: boolean, _ctrlOrMetaKey: boolean, altKey: boolean, _isTDViewportActive: boolean, ): ActionDescriptor { + const { useLegacyBindings } = userConfiguration; // In legacy mode, don't display a hint for // left click as it would be equal to left drag. // We also don't show a hint when the alt key was pressed, @@ -279,9 +280,7 @@ export class SkeletonToolController { event: MouseEvent, ) => { const { annotation, userConfiguration } = Store.getState(); - const { useLegacyBindings } = Store.getState().userConfiguration; - - const { continuousNodeCreation } = userConfiguration; + const { useLegacyBindings, continuousNodeCreation } = userConfiguration; if (continuousNodeCreation) { if ( @@ -321,9 +320,9 @@ export class SkeletonToolController { ); }, rightClick: (position: Point2, plane: OrthoView, event: MouseEvent, isTouch: boolean) => { - const { useLegacyBindings } = Store.getState().userConfiguration; + const { useLegacyBindings, continuousNodeCreation } = Store.getState().userConfiguration; - if (useLegacyBindings) { + if (useLegacyBindings && !continuousNodeCreation) { legacyRightClick(position, plane, event, isTouch); return; } @@ -343,7 +342,12 @@ export class SkeletonToolController { isTouch: boolean, allowNodeCreation: boolean = true, ): void { - const { useLegacyBindings } = Store.getState().userConfiguration; + const { useLegacyBindings, continuousNodeCreation } = Store.getState().userConfiguration; + + if (continuousNodeCreation && allowNodeCreation) { + SkeletonHandlers.handleCreateNodeFromEvent(position, ctrlPressed); + return; + } // The following functions are all covered by the context menu, too. // (At least, in the XY/XZ/YZ viewports). @@ -368,12 +372,22 @@ export class SkeletonToolController { static getActionDescriptors( _activeTool: AnnotationTool, - useLegacyBindings: boolean, + userConfiguration: UserConfiguration, shiftKey: boolean, ctrlOrMetaKey: boolean, altKey: boolean, _isTDViewportActive: boolean, ): ActionDescriptor { + const { continuousNodeCreation } = Store.getState().userConfiguration; + const { useLegacyBindings } = userConfiguration; + if (continuousNodeCreation) { + return { + leftClick: "Place node", + leftDrag: "Draw nodes", + rightClick: "Context Menu", + }; + } + // In legacy mode, don't display a hint for // left click as it would be equal to left drag let leftClickInfo = {}; @@ -495,13 +509,14 @@ export class DrawToolController { static getActionDescriptors( activeTool: AnnotationTool, - useLegacyBindings: boolean, + userConfiguration: UserConfiguration, _shiftKey: boolean, _ctrlOrMetaKey: boolean, _altKey: boolean, _isTDViewportActive: boolean, ): ActionDescriptor { let rightClick; + const { useLegacyBindings } = userConfiguration; if (!useLegacyBindings) { rightClick = "Context Menu"; @@ -554,7 +569,7 @@ export class EraseToolController { static getActionDescriptors( activeTool: AnnotationTool, - _useLegacyBindings: boolean, + _userConfiguration: UserConfiguration, _shiftKey: boolean, _ctrlOrMetaKey: boolean, _altKey: boolean, @@ -579,7 +594,7 @@ export class PickCellToolController { static getActionDescriptors( _activeTool: AnnotationTool, - _useLegacyBindings: boolean, + _userConfiguration: UserConfiguration, _shiftKey: boolean, _ctrlOrMetaKey: boolean, _altKey: boolean, @@ -610,7 +625,7 @@ export class FillCellToolController { static getActionDescriptors( _activeTool: AnnotationTool, - _useLegacyBindings: boolean, + _userConfiguration: UserConfiguration, _shiftKey: boolean, _ctrlOrMetaKey: boolean, _altKey: boolean, @@ -689,7 +704,7 @@ export class BoundingBoxToolController { static getActionDescriptors( _activeTool: AnnotationTool, - _useLegacyBindings: boolean, + _userConfiguration: UserConfiguration, _shiftKey: boolean, ctrlOrMetaKey: boolean, _altKey: boolean, @@ -818,7 +833,7 @@ export class QuickSelectToolController { static getActionDescriptors( _activeTool: AnnotationTool, - _useLegacyBindings: boolean, + _userConfiguration: UserConfiguration, shiftKey: boolean, _ctrlOrMetaKey: boolean, _altKey: boolean, @@ -942,7 +957,7 @@ export class LineMeasurementToolController { static getActionDescriptors( _activeTool: AnnotationTool, - _useLegacyBindings: boolean, + _userConfiguration: UserConfiguration, _shiftKey: boolean, _ctrlOrMetaKey: boolean, _altKey: boolean, @@ -1021,7 +1036,7 @@ export class AreaMeasurementToolController { static getActionDescriptors( _activeTool: AnnotationTool, - _useLegacyBindings: boolean, + _userConfiguration: UserConfiguration, _shiftKey: boolean, _ctrlOrMetaKey: boolean, _altKey: boolean, @@ -1081,7 +1096,7 @@ export class ProofreadToolController { static getActionDescriptors( _activeTool: AnnotationTool, - _useLegacyBindings: boolean, + _userConfiguration: UserConfiguration, shiftKey: boolean, ctrlOrMetaKey: boolean, _altKey: boolean, diff --git a/frontend/javascripts/oxalis/view/statusbar.tsx b/frontend/javascripts/oxalis/view/statusbar.tsx index af8e6254be0..bfc1e1004f6 100644 --- a/frontend/javascripts/oxalis/view/statusbar.tsx +++ b/frontend/javascripts/oxalis/view/statusbar.tsx @@ -179,9 +179,7 @@ const moreShortcutsLink = ( function ShortcutsInfo() { const activeTool = useSelector((state: OxalisState) => state.uiInformation.activeTool); - const useLegacyBindings = useSelector( - (state: OxalisState) => state.userConfiguration.useLegacyBindings, - ); + const userConfiguration = useSelector((state: OxalisState) => state.userConfiguration); const isPlaneMode = useSelector((state: OxalisState) => getIsPlaneMode(state)); const isShiftPressed = useKeyPress("Shift"); const isControlOrMetaPressed = useKeyPress("ControlOrMeta"); @@ -198,7 +196,7 @@ function ShortcutsInfo() { AnnotationTool.SKELETON, ).getActionDescriptors( AnnotationTool.SKELETON, - useLegacyBindings, + userConfiguration, isShiftPressed, isControlOrMetaPressed, isAltPressed, @@ -337,10 +335,9 @@ function ShortcutsInfo() { isAltPressed, ); const toolController = getToolControllerForAnnotationTool(adaptedTool); - console.log("toolController", toolController); const actionDescriptor = toolController.getActionDescriptors( adaptedTool, - useLegacyBindings, + userConfiguration, isShiftPressed, isControlOrMetaPressed, isAltPressed, From 052c85e9c1458c115cca4542a879175c6944db54 Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Tue, 15 Apr 2025 12:27:56 +0200 Subject: [PATCH 49/84] fix tool cycling in view mode --- .../controller/combinations/tool_controls.ts | 2 +- .../model/accessors/disabled_tool_accessor.ts | 14 +++++++++++++- .../oxalis/model/reducers/ui_reducer.ts | 4 ---- .../oxalis/model/sagas/settings_saga.ts | 4 ++-- .../javascripts/oxalis/view/action_bar_view.tsx | 2 +- .../oxalis/view/components/command_palette.tsx | 17 ++++++++++++++++- 6 files changed, 33 insertions(+), 10 deletions(-) diff --git a/frontend/javascripts/oxalis/controller/combinations/tool_controls.ts b/frontend/javascripts/oxalis/controller/combinations/tool_controls.ts index a8f1986b1be..25f5c5fa516 100644 --- a/frontend/javascripts/oxalis/controller/combinations/tool_controls.ts +++ b/frontend/javascripts/oxalis/controller/combinations/tool_controls.ts @@ -58,7 +58,7 @@ import { hideBrushAction, } from "oxalis/model/actions/volumetracing_actions"; import { api } from "oxalis/singletons"; -import Store, { UserConfiguration } from "oxalis/store"; +import Store, { type UserConfiguration } from "oxalis/store"; import type ArbitraryView from "oxalis/view/arbitrary_view"; import type PlaneView from "oxalis/view/plane_view"; import * as THREE from "three"; diff --git a/frontend/javascripts/oxalis/model/accessors/disabled_tool_accessor.ts b/frontend/javascripts/oxalis/model/accessors/disabled_tool_accessor.ts index 15f25ec5c6a..2f72989ce83 100644 --- a/frontend/javascripts/oxalis/model/accessors/disabled_tool_accessor.ts +++ b/frontend/javascripts/oxalis/model/accessors/disabled_tool_accessor.ts @@ -84,7 +84,6 @@ const ALWAYS_ENABLED_TOOL_INFOS = { [AnnotationTool.MOVE.id]: NOT_DISABLED_INFO, [AnnotationTool.LINE_MEASUREMENT.id]: NOT_DISABLED_INFO, [AnnotationTool.AREA_MEASUREMENT.id]: NOT_DISABLED_INFO, - [AnnotationTool.BOUNDING_BOX.id]: NOT_DISABLED_INFO, }; function _getSkeletonToolInfo( @@ -266,6 +265,18 @@ function _getVolumeDisabledWhenVolumeIsEnabled( }; } +function getDisabledBoundingBoxToolInfo(state: OxalisState) { + const isViewMode = state.annotation.annotationType === "View"; + return { + [AnnotationTool.BOUNDING_BOX.id]: isViewMode + ? { + isDisabled: true, + explanation: "Please create an annotation to use this tool.", + } + : NOT_DISABLED_INFO, + }; +} + function getDisabledVolumeInfo(state: OxalisState) { // This function extracts a couple of variables from the state // so that it can delegate to memoized functions. @@ -349,6 +360,7 @@ const _getDisabledInfoForTools = (state: OxalisState): Record state.annotation); - const isViewMode = tracing.annotationType === "View"; + const annotation = yield* select((state) => state.annotation); + const isViewMode = annotation.annotationType === "View"; if (!isViewMode) { throw error; diff --git a/frontend/javascripts/oxalis/view/action_bar_view.tsx b/frontend/javascripts/oxalis/view/action_bar_view.tsx index 7ae74545235..74aa44158fc 100644 --- a/frontend/javascripts/oxalis/view/action_bar_view.tsx +++ b/frontend/javascripts/oxalis/view/action_bar_view.tsx @@ -204,7 +204,7 @@ function ModesView() {
{isArbitrarySupported && !is2d ? : null} - + {isViewMode ? null : }
); diff --git a/frontend/javascripts/oxalis/view/components/command_palette.tsx b/frontend/javascripts/oxalis/view/components/command_palette.tsx index 190493a5d89..a669ba25c79 100644 --- a/frontend/javascripts/oxalis/view/components/command_palette.tsx +++ b/frontend/javascripts/oxalis/view/components/command_palette.tsx @@ -3,6 +3,7 @@ import { capitalize, getPhraseFromCamelCaseString } from "libs/utils"; import * as Utils from "libs/utils"; import _ from "lodash"; import { getAdministrationSubMenu } from "navbar"; +import { WkDevFlags } from "oxalis/api/wk_dev"; import { AnnotationTool } from "oxalis/model/accessors/tool_accessor"; import { Toolkits } from "oxalis/model/accessors/tool_accessor"; import { updateUserSettingAction } from "oxalis/model/actions/settings_actions"; @@ -110,6 +111,19 @@ export const CommandPalette = ({ label }: { label: string | JSX.Element | null } return commands; }; + const getSuperUserItems = (): CommandWithoutId[] => { + if (!activeUser?.isSuperUser) { + return []; + } + return [ + { + name: "Toggle Action Logging", + command: () => (WkDevFlags.logActions = !WkDevFlags.logActions), + color: commandEntryColor, + }, + ]; + }; + const getNavigationEntries = () => { if (activeUser == null) return []; const commands: CommandWithoutId[] = []; @@ -145,7 +159,7 @@ export const CommandPalette = ({ label }: { label: string | JSX.Element | null } navigationEntries.forEach((entry) => { commands.push({ - name: `Navigate to ${entry.name}`, + name: `Go to ${entry.name}`, command: () => { window.location.href = entry.path; }, @@ -180,6 +194,7 @@ export const CommandPalette = ({ label }: { label: string | JSX.Element | null } ...getToolEntries(), ...mapMenuActionsToCommands(menuActions), ...getTabsAndSettingsMenuItems(), + ...getSuperUserItems(), ]; return ( Date: Tue, 15 Apr 2025 13:16:16 +0200 Subject: [PATCH 50/84] further clean up --- .../javascripts/libs/order_points_with_mst.ts | 119 +++++++++++++++++ .../oxalis/controller/scene_controller.ts | 12 +- .../controller/segment_mesh_controller.ts | 2 +- ...ompute_split_boundary_mesh_with_splines.ts | 125 +----------------- 4 files changed, 123 insertions(+), 135 deletions(-) create mode 100644 frontend/javascripts/libs/order_points_with_mst.ts diff --git a/frontend/javascripts/libs/order_points_with_mst.ts b/frontend/javascripts/libs/order_points_with_mst.ts new file mode 100644 index 00000000000..ce16c23bfd5 --- /dev/null +++ b/frontend/javascripts/libs/order_points_with_mst.ts @@ -0,0 +1,119 @@ +import type * as THREE from "three"; + +export function orderPointsWithMST(points: THREE.Vector3[]): THREE.Vector3[] { + /* + * Find the order of points with the shortest distance heuristically. + * This is done by computing the MST of the points and then traversing + * that MST several times (each node is tried as the starting point). + * The shortest order wins. + */ + if (points.length === 0) return []; + + const mst = computeMST(points); + let bestOrder: number[] = []; + let minLength = Number.POSITIVE_INFINITY; + + for (let startIdx = 0; startIdx < points.length; startIdx++) { + const order = traverseMstDfs(mst, startIdx); + const length = computePathLength(points, order); + + if (length < minLength) { + minLength = length; + bestOrder = order; + } + } + + return bestOrder.map((index) => points[index]); +} + +// Mostly generated with ChatGPT: + +class DisjointSet { + // Union find datastructure + private parent: number[]; + private rank: number[]; + + constructor(n: number) { + this.parent = Array.from({ length: n }, (_, i) => i); + this.rank = Array(n).fill(0); + } + + find(i: number): number { + if (this.parent[i] !== i) this.parent[i] = this.find(this.parent[i]); + return this.parent[i]; + } + + union(i: number, j: number): void { + let rootI = this.find(i), + rootJ = this.find(j); + if (rootI !== rootJ) { + if (this.rank[rootI] > this.rank[rootJ]) this.parent[rootJ] = rootI; + else if (this.rank[rootI] < this.rank[rootJ]) this.parent[rootI] = rootJ; + else { + this.parent[rootJ] = rootI; + this.rank[rootI]++; + } + } + } +} + +interface Edge { + i: number; + j: number; + dist: number; +} + +function computeMST(points: THREE.Vector3[]): number[][] { + const edges: Edge[] = []; + const numPoints = points.length; + + // Create all possible edges with distances + for (let i = 0; i < numPoints; i++) { + for (let j = i + 1; j < numPoints; j++) { + const dist = points[i].distanceTo(points[j]); + edges.push({ i, j, dist }); + } + } + + // Sort edges by distance (Kruskal's Algorithm) + edges.sort((a, b) => a.dist - b.dist); + + // Compute MST using Kruskal’s Algorithm + const ds = new DisjointSet(numPoints); + const mst: number[][] = Array.from({ length: numPoints }, () => []); + + for (const { i, j } of edges) { + if (ds.find(i) !== ds.find(j)) { + ds.union(i, j); + mst[i].push(j); + mst[j].push(i); + } + } + + return mst; +} + +function traverseMstDfs(mst: number[][], startIdx = 0): number[] { + const visited = new Set(); + const orderedPoints: number[] = []; + + function dfs(node: number) { + if (visited.has(node)) return; + visited.add(node); + orderedPoints.push(node); + for (let neighbor of mst[node]) { + dfs(neighbor); + } + } + + dfs(startIdx); + return orderedPoints; +} + +function computePathLength(points: THREE.Vector3[], order: number[]): number { + let length = 0; + for (let i = 0; i < order.length - 1; i++) { + length += points[order[i]].distanceTo(points[order[i + 1]]); + } + return length; +} diff --git a/frontend/javascripts/oxalis/controller/scene_controller.ts b/frontend/javascripts/oxalis/controller/scene_controller.ts index acb6441678d..3f1da9d660e 100644 --- a/frontend/javascripts/oxalis/controller/scene_controller.ts +++ b/frontend/javascripts/oxalis/controller/scene_controller.ts @@ -54,23 +54,13 @@ const CUBE_COLOR = 0x999999; const LAYER_CUBE_COLOR = 0xffff99; import computeSplitBoundaryMeshWithSplines from "oxalis/geometries/compute_split_boundary_mesh_with_splines"; -import { - acceleratedRaycast, - computeBatchedBoundsTree, - computeBoundsTree, - disposeBatchedBoundsTree, - disposeBoundsTree, -} from "three-mesh-bvh"; +import { acceleratedRaycast, computeBoundsTree, disposeBoundsTree } from "three-mesh-bvh"; // Add the extension functions THREE.BufferGeometry.prototype.computeBoundsTree = computeBoundsTree; THREE.BufferGeometry.prototype.disposeBoundsTree = disposeBoundsTree; THREE.Mesh.prototype.raycast = acceleratedRaycast; -THREE.BatchedMesh.prototype.computeBoundsTree = computeBatchedBoundsTree; -THREE.BatchedMesh.prototype.disposeBoundsTree = disposeBatchedBoundsTree; -THREE.BatchedMesh.prototype.raycast = acceleratedRaycast; - class SceneController { skeletons: Record = {}; current: number; diff --git a/frontend/javascripts/oxalis/controller/segment_mesh_controller.ts b/frontend/javascripts/oxalis/controller/segment_mesh_controller.ts index 79b09e9a813..47e99d078c5 100644 --- a/frontend/javascripts/oxalis/controller/segment_mesh_controller.ts +++ b/frontend/javascripts/oxalis/controller/segment_mesh_controller.ts @@ -108,7 +108,7 @@ export default class SegmentMeshController { bufferGeometry.setAttribute("position", new THREE.BufferAttribute(vertices, 3)); bufferGeometry = mergeVertices(bufferGeometry); - // bufferGeometry.computeVertexNormals(); + bufferGeometry.computeVertexNormals(); bufferGeometry.boundsTree = await computeBvhAsync(bufferGeometry); diff --git a/frontend/javascripts/oxalis/geometries/compute_split_boundary_mesh_with_splines.ts b/frontend/javascripts/oxalis/geometries/compute_split_boundary_mesh_with_splines.ts index dab4a9f483c..873fb0d6697 100644 --- a/frontend/javascripts/oxalis/geometries/compute_split_boundary_mesh_with_splines.ts +++ b/frontend/javascripts/oxalis/geometries/compute_split_boundary_mesh_with_splines.ts @@ -1,3 +1,4 @@ +import { orderPointsWithMST } from "libs/order_points_with_mst"; import _ from "lodash"; import type { Vector3 } from "oxalis/constants"; import * as THREE from "three"; @@ -29,7 +30,7 @@ export default function computeSplitBoundaryMeshWithSplines(points: Vector3[]): } else if (zValue === maxZ) { adaptedZ += 0.1; } - const points2D = orderPointsMST( + const points2D = orderPointsWithMST( pointsByZ[zValue].map((p) => new THREE.Vector3(p[0], p[1], adaptedZ)), ); @@ -120,29 +121,16 @@ export default function computeSplitBoundaryMeshWithSplines(points: Vector3[]): }); // Connect vertices with triangles - // console.group("Computing indices"); for (let i = 0; i < curves.length - 1; i++) { - // console.group("Curve i=" + i); for (let j = 0; j < numPoints - 1; j++) { - // console.group("Point j=" + j); let current = i * numPoints + j; let next = (i + 1) * numPoints + j; - // const printFace = (x, y, z) => { - // return [vertices[3 * x], vertices[3 * y], vertices[3 * z]]; - // }; - - // console.log("Creating faces with", { current, next }); - // console.log("First face:", printFace(current, next, current + 1)); - // console.log("Second face:", printFace(next, next + 1, current + 1)); // Two triangles per quad indices.push(current, next, current + 1); indices.push(next, next + 1, current + 1); - // console.groupEnd(); } - // console.groupEnd(); } - // console.groupEnd(); // Convert to Three.js BufferGeometry const geometry = new THREE.BufferGeometry(); @@ -168,112 +156,3 @@ export default function computeSplitBoundaryMeshWithSplines(points: Vector3[]): splitBoundaryMesh, }; } - -class DisjointSet { - private parent: number[]; - private rank: number[]; - - constructor(n: number) { - this.parent = Array.from({ length: n }, (_, i) => i); - this.rank = Array(n).fill(0); - } - - find(i: number): number { - if (this.parent[i] !== i) this.parent[i] = this.find(this.parent[i]); - return this.parent[i]; - } - - union(i: number, j: number): void { - let rootI = this.find(i), - rootJ = this.find(j); - if (rootI !== rootJ) { - if (this.rank[rootI] > this.rank[rootJ]) this.parent[rootJ] = rootI; - else if (this.rank[rootI] < this.rank[rootJ]) this.parent[rootI] = rootJ; - else { - this.parent[rootJ] = rootI; - this.rank[rootI]++; - } - } - } -} - -interface Edge { - i: number; - j: number; - dist: number; -} - -function computeMST(points: THREE.Vector3[]): number[][] { - const edges: Edge[] = []; - const numPoints = points.length; - - // Create all possible edges with distances - for (let i = 0; i < numPoints; i++) { - for (let j = i + 1; j < numPoints; j++) { - const dist = points[i].distanceTo(points[j]); - edges.push({ i, j, dist }); - } - } - - // Sort edges by distance (Kruskal's Algorithm) - edges.sort((a, b) => a.dist - b.dist); - - // Compute MST using Kruskal’s Algorithm - const ds = new DisjointSet(numPoints); - const mst: number[][] = Array.from({ length: numPoints }, () => []); - - for (const { i, j } of edges) { - if (ds.find(i) !== ds.find(j)) { - ds.union(i, j); - mst[i].push(j); - mst[j].push(i); - } - } - - return mst; -} - -function traverseMstDfs(mst: number[][], startIdx = 0): number[] { - const visited = new Set(); - const orderedPoints: number[] = []; - - function dfs(node: number) { - if (visited.has(node)) return; - visited.add(node); - orderedPoints.push(node); - for (let neighbor of mst[node]) { - dfs(neighbor); - } - } - - dfs(startIdx); - return orderedPoints; -} - -function computePathLength(points: THREE.Vector3[], order: number[]): number { - let length = 0; - for (let i = 0; i < order.length - 1; i++) { - length += points[order[i]].distanceTo(points[order[i + 1]]); - } - return length; -} - -export function orderPointsMST(points: THREE.Vector3[]): THREE.Vector3[] { - if (points.length === 0) return []; - - const mst = computeMST(points); - let bestOrder: number[] = []; - let minLength = Number.POSITIVE_INFINITY; - - for (let startIdx = 0; startIdx < points.length; startIdx++) { - const order = traverseMstDfs(mst, startIdx); - const length = computePathLength(points, order); - - if (length < minLength) { - minLength = length; - bestOrder = order; - } - } - - return bestOrder.map((index) => points[index]); -} From 4b3eb62de92391d5cea626ca456b25e1932a3ece Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Tue, 15 Apr 2025 13:30:37 +0200 Subject: [PATCH 51/84] more clean up --- .../model/bucket_data_handling/data_cube.ts | 20 ++++++++----------- .../model/sagas/split_boundary_mesh_saga.ts | 5 ++--- 2 files changed, 10 insertions(+), 15 deletions(-) diff --git a/frontend/javascripts/oxalis/model/bucket_data_handling/data_cube.ts b/frontend/javascripts/oxalis/model/bucket_data_handling/data_cube.ts index 7147adafe12..b9cc43e63a8 100644 --- a/frontend/javascripts/oxalis/model/bucket_data_handling/data_cube.ts +++ b/frontend/javascripts/oxalis/model/bucket_data_handling/data_cube.ts @@ -744,7 +744,6 @@ class DataCube { shouldSkip = intersects; } - // console.log("reached bucket border. early abort for debugging"); if (!shouldSkip && neighbourBucket.type !== "null") { bucketsWithXyzSeedsToFill.push([neighbourBucket, adjustedNeighbourVoxelXyz]); } @@ -769,7 +768,6 @@ class DataCube { currentGlobalPosition, ); - // const { distance } = target; shouldSkip = intersects; } @@ -1035,18 +1033,18 @@ class DataCube { export default DataCube; -// Function to check intersection -function checkLineIntersection(bentMesh: THREE.Mesh, _pointA: Vector3, _pointB: Vector3) { +function checkLineIntersection(bentMesh: THREE.Mesh, pointAVec3: Vector3, pointBVec3: Vector3) { + /* Returns true if an intersection is found */ + const geometry = bentMesh.geometry; + // Create BVH from geometry if not already built if (!geometry.boundsTree) { geometry.computeBoundsTree(); } const scale = Store.getState().dataset.dataSource.scale.factor; - const mul = (vec: Vector3) => [scale[0] * vec[0], scale[1] * vec[1], scale[2] * vec[2]]; - // geometry.boundsTree = undefined; - const pointA = new THREE.Vector3(...mul(_pointA)); - const pointB = new THREE.Vector3(...mul(_pointB)); + const pointA = new THREE.Vector3(...V3.scale3(pointAVec3, scale)); + const pointB = new THREE.Vector3(...V3.scale3(pointBVec3, scale)); // Create a ray from A to B const ray = new THREE.Ray(); @@ -1056,11 +1054,9 @@ function checkLineIntersection(bentMesh: THREE.Mesh, _pointA: Vector3, _pointB: // Perform raycast const raycaster = new THREE.Raycaster(); raycaster.ray = ray; - raycaster.far = pointA.distanceTo(pointB); // Limit to segment length + raycaster.far = pointA.distanceTo(pointB); raycaster.firstHitOnly = true; const intersects = raycaster.intersectObject(bentMesh, true); - const retval = intersects.length > 0; // Returns true if an intersection is found - - return retval; + return intersects.length > 0; } diff --git a/frontend/javascripts/oxalis/model/sagas/split_boundary_mesh_saga.ts b/frontend/javascripts/oxalis/model/sagas/split_boundary_mesh_saga.ts index 1044d3986ab..a8dee388bb5 100644 --- a/frontend/javascripts/oxalis/model/sagas/split_boundary_mesh_saga.ts +++ b/frontend/javascripts/oxalis/model/sagas/split_boundary_mesh_saga.ts @@ -26,8 +26,7 @@ function* updateSplitBoundaryMesh() { const sceneController = yield* call(() => getSceneController()); const activeTree = yield* select((state) => getActiveTree(state.annotation.skeleton)); - // biome-ignore lint/complexity/useOptionalChain: - if (activeTree != null && activeTree.isVisible) { + if (activeTree?.isVisible) { const nodes = Array.from(activeTree.nodes.values()); const points = nodes.map((node) => node.untransformedPosition); if (points.length > 3) { @@ -41,7 +40,7 @@ export function* splitBoundaryMeshSaga(): Saga { yield* takeWithBatchActionSupport("INITIALIZE_SKELETONTRACING"); yield* ensureWkReady(); - // initial rendering + // Call once for initial rendering yield* call(updateSplitBoundaryMesh); yield* takeEvery( [ From abd87d694de01199da8020efde1ed7f77c51ed5a Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Tue, 15 Apr 2025 13:48:10 +0200 Subject: [PATCH 52/84] update changelog --- CHANGELOG.unreleased.md | 3 +++ 1 file changed, 3 insertions(+) diff --git a/CHANGELOG.unreleased.md b/CHANGELOG.unreleased.md index 82ace563764..ca2bf22a103 100644 --- a/CHANGELOG.unreleased.md +++ b/CHANGELOG.unreleased.md @@ -16,6 +16,9 @@ For upgrade instructions, please check the [migration guide](MIGRATIONS.released - Performance improvements for segment statistics (volume + bounding box in context menu). [#8469](https://github.com/scalableminds/webknossos/pull/8469) - Upgraded backend dependencies for improved performance and stability. [#8507](https://github.com/scalableminds/webknossos/pull/8507) - New config option `datastore.dataVaults.credentials` allows admins to set up global credentials for remote dataset loading. [#8509](https://github.com/scalableminds/webknossos/pull/8509) +- Added a new "draw" mode for the skeleton tool. When enabled, one can rapidly create notes by keeping the left mouse button pressed and moving the cursor. [#8434](https://github.com/scalableminds/webknossos/pull/8434) +- Added the concept of "toolkits". By default, all tools are available to the user (as before), but one can select a specific toolkit to only see certain tools. Some toolkits also change the behavior of the tools. For example, the "Split Segments" toolkit (see below). [#8434](https://github.com/scalableminds/webknossos/pull/8434) +- Added a workflow for splitting segments. Select the "Split Segments" toolkit and create a bounding box in which you want to execute the split. Then, use the skeleton tool to place nodes on the boundary between two (merged) segments. The nodes will be used to construct a 3D surface. Finally, use the floodfill tool (enable 3D and bounding-box restriction) to relabel a part of the segment. the floodfill won't cross the 3D surface. [#8434](https://github.com/scalableminds/webknossos/pull/8434) ### Changed - When deleting a dataset / layer, layers that are referenced in other datasets are moved there instead of being deleted. [#8437](https://github.com/scalableminds/webknossos/pull/8437/) From 38a232d3e01454e014d260b7f6f41f6e2718a8a9 Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Wed, 16 Apr 2025 09:33:19 +0200 Subject: [PATCH 53/84] automatically switch to default toolkit if in view mode --- .../javascripts/oxalis/model/sagas/annotation_tool_saga.ts | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/frontend/javascripts/oxalis/model/sagas/annotation_tool_saga.ts b/frontend/javascripts/oxalis/model/sagas/annotation_tool_saga.ts index d881c35a6f9..6261e35a2c7 100644 --- a/frontend/javascripts/oxalis/model/sagas/annotation_tool_saga.ts +++ b/frontend/javascripts/oxalis/model/sagas/annotation_tool_saga.ts @@ -19,6 +19,7 @@ import { getDisabledInfoForTools } from "../accessors/disabled_tool_accessor"; import { Toolkits } from "../accessors/tool_accessor"; import type { Action } from "../actions/actions"; import { setToolAction } from "../actions/ui_actions"; +import { updateUserSettingAction } from "../actions/settings_actions"; function* ensureActiveToolIsInToolkit() { const activeToolkit = yield* select((state) => state.userConfiguration.activeToolkit); @@ -128,6 +129,11 @@ export function* watchToolReset(): Saga { export default function* toolSaga() { yield* call(ensureWkReady); + const isViewMode = yield* select((state) => state.annotation.annotationType === "View"); + if (isViewMode) { + yield* put(updateUserSettingAction("activeToolkit", "ALL_TOOLS")); + } + yield fork(watchToolDeselection); yield fork(watchToolReset); yield fork(switchAwayFromDisabledTool); From 6e8011756ec4046f495b26f89014b9de6446bf6d Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Wed, 16 Apr 2025 09:41:05 +0200 Subject: [PATCH 54/84] sort imports --- frontend/javascripts/oxalis/model/sagas/annotation_tool_saga.ts | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/frontend/javascripts/oxalis/model/sagas/annotation_tool_saga.ts b/frontend/javascripts/oxalis/model/sagas/annotation_tool_saga.ts index 6261e35a2c7..6a5e8966448 100644 --- a/frontend/javascripts/oxalis/model/sagas/annotation_tool_saga.ts +++ b/frontend/javascripts/oxalis/model/sagas/annotation_tool_saga.ts @@ -18,8 +18,8 @@ import { takeEvery } from "typed-redux-saga"; import { getDisabledInfoForTools } from "../accessors/disabled_tool_accessor"; import { Toolkits } from "../accessors/tool_accessor"; import type { Action } from "../actions/actions"; -import { setToolAction } from "../actions/ui_actions"; import { updateUserSettingAction } from "../actions/settings_actions"; +import { setToolAction } from "../actions/ui_actions"; function* ensureActiveToolIsInToolkit() { const activeToolkit = yield* select((state) => state.userConfiguration.activeToolkit); From 5bfd5c31ec4d1749dbc67adc13f672514777bd4b Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Thu, 17 Apr 2025 14:11:19 +0200 Subject: [PATCH 55/84] make 2D floodfills possible on single section with new split boundary; tell user what's wrong when using floodfill in split-toolkit --- .../compute_split_boundary_mesh_with_splines.ts | 15 ++++++++++++++- .../model/bucket_data_handling/data_cube.ts | 4 +--- .../model/sagas/split_boundary_mesh_saga.ts | 2 +- .../oxalis/model/sagas/volume/floodfill_saga.tsx | 15 +++++++++++++++ 4 files changed, 31 insertions(+), 5 deletions(-) diff --git a/frontend/javascripts/oxalis/geometries/compute_split_boundary_mesh_with_splines.ts b/frontend/javascripts/oxalis/geometries/compute_split_boundary_mesh_with_splines.ts index 873fb0d6697..ae67e736841 100644 --- a/frontend/javascripts/oxalis/geometries/compute_split_boundary_mesh_with_splines.ts +++ b/frontend/javascripts/oxalis/geometries/compute_split_boundary_mesh_with_splines.ts @@ -19,12 +19,25 @@ export default function computeSplitBoundaryMeshWithSplines(points: Vector3[]): const minZ = Math.min(...zValues); const maxZ = Math.max(...zValues); + if (minZ === maxZ) { + // All nodes are in the same section. Duplicate them to the next + // and previous section to get a surface with a depth. + return computeSplitBoundaryMeshWithSplines([ + ...points.map((p) => [p[0], p[1], p[2] - 1] as Vector3), + ...points, + ...points.map((p) => [p[0], p[1], p[2] + 1] as Vector3), + ]); + } + const curvesByZ: Record = {}; // Create curves for existing z-values const curves = _.compact( zValues.map((zValue, curveIdx) => { let adaptedZ = zValue; + // We make the surface a bit larger by offsetting points in Z + // if they are at the z-start or z-end. This avoids numerical + // problems for the floodfill. if (zValue === minZ) { adaptedZ -= 0.1; } else if (zValue === maxZ) { @@ -100,7 +113,7 @@ export default function computeSplitBoundaryMeshWithSplines(points: Vector3[]): // Generate and display all curves Object.values(curvesByZ).forEach((curve) => { - const curvePoints = curve.getPoints(50); + const curvePoints = curve.getPoints(numPoints); const geometry = new THREE.BufferGeometry().setFromPoints(curvePoints); const material = new THREE.LineBasicMaterial({ color: 0xff0000 }); const splineObject = new THREE.Line(geometry, material); diff --git a/frontend/javascripts/oxalis/model/bucket_data_handling/data_cube.ts b/frontend/javascripts/oxalis/model/bucket_data_handling/data_cube.ts index b9cc43e63a8..82ecc6882ad 100644 --- a/frontend/javascripts/oxalis/model/bucket_data_handling/data_cube.ts +++ b/frontend/javascripts/oxalis/model/bucket_data_handling/data_cube.ts @@ -526,6 +526,7 @@ class DataCube { zoomStep: number, progressCallback: ProgressCallback, use3D: boolean, + splitBoundaryMesh: THREE.Mesh | null, ): Promise<{ bucketsWithLabeledVoxelsMap: LabelMasksByBucketAndW; wasBoundingBoxExceeded: boolean; @@ -543,9 +544,6 @@ class DataCube { // not all of the target area in the neighbour bucket might be filled. const floodfillBoundingBox = new BoundingBox(_floodfillBoundingBox); - const sceneController = getSceneController(); - const isSplitToolkit = Store.getState().userConfiguration.activeToolkit === "SPLIT_SEGMENTS"; - const splitBoundaryMesh = isSplitToolkit ? sceneController.getSplitBoundaryMesh() : null; // Helper function to convert between xyz and uvw (both directions) const transpose = (voxel: Vector3): Vector3 => diff --git a/frontend/javascripts/oxalis/model/sagas/split_boundary_mesh_saga.ts b/frontend/javascripts/oxalis/model/sagas/split_boundary_mesh_saga.ts index a8dee388bb5..bf7de0c3d37 100644 --- a/frontend/javascripts/oxalis/model/sagas/split_boundary_mesh_saga.ts +++ b/frontend/javascripts/oxalis/model/sagas/split_boundary_mesh_saga.ts @@ -29,7 +29,7 @@ function* updateSplitBoundaryMesh() { if (activeTree?.isVisible) { const nodes = Array.from(activeTree.nodes.values()); const points = nodes.map((node) => node.untransformedPosition); - if (points.length > 3) { + if (points.length >= 2) { cleanUpFn = sceneController.addSplitBoundaryMesh(points); } } diff --git a/frontend/javascripts/oxalis/model/sagas/volume/floodfill_saga.tsx b/frontend/javascripts/oxalis/model/sagas/volume/floodfill_saga.tsx index e6b3da6c460..027dce6fbd4 100644 --- a/frontend/javascripts/oxalis/model/sagas/volume/floodfill_saga.tsx +++ b/frontend/javascripts/oxalis/model/sagas/volume/floodfill_saga.tsx @@ -33,6 +33,7 @@ import { Model } from "oxalis/singletons"; import { call, put, takeEvery } from "typed-redux-saga"; import { getUserBoundingBoxesThatContainPosition } from "../../accessors/tracing_accessor"; import { applyLabeledVoxelMapToAllMissingMags } from "./helpers"; +import getSceneController from "oxalis/controller/scene_controller_provider"; const NO_FLOODFILL_BBOX_TOAST_KEY = "NO_FLOODFILL_BBOX"; const NO_SUCCESS_MSG_WHEN_WITHIN_MS = 500; @@ -194,6 +195,19 @@ function* handleFloodFill(floodFillAction: FloodFillAction): Saga { return; } + const sceneController = getSceneController(); + const isSplitToolkit = yield* select( + (state) => state.userConfiguration.activeToolkit === "SPLIT_SEGMENTS", + ); + const splitBoundaryMesh = isSplitToolkit ? sceneController.getSplitBoundaryMesh() : null; + + if (isSplitToolkit && !splitBoundaryMesh) { + Toast.warning( + `No split boundary found. Ensure that the active tree has at least two nodes. If you want to execute a normal floodfill operation, please switch to another toolkit (currently, the "Split Segments" toolkit is active).`, + ); + return; + } + const busyBlockingInfo = yield* select((state) => state.uiInformation.busyBlockingInfo); if (busyBlockingInfo.isBusy) { @@ -248,6 +262,7 @@ function* handleFloodFill(floodFillAction: FloodFillAction): Saga { labeledZoomStep, progressCallback, fillMode === FillModeEnum._3D, + splitBoundaryMesh, ); console.timeEnd("cube.floodFill"); yield* call(progressCallback, false, "Finalizing floodfill..."); From e69977b764a68f4a76eb760f3a5d427ae5adbcbf Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Thu, 17 Apr 2025 14:14:43 +0200 Subject: [PATCH 56/84] forbid floodfill in other viewports if split toolkit is active --- .../model/sagas/volume/floodfill_saga.tsx | 18 +++++++++++++----- 1 file changed, 13 insertions(+), 5 deletions(-) diff --git a/frontend/javascripts/oxalis/model/sagas/volume/floodfill_saga.tsx b/frontend/javascripts/oxalis/model/sagas/volume/floodfill_saga.tsx index 027dce6fbd4..4d650734d49 100644 --- a/frontend/javascripts/oxalis/model/sagas/volume/floodfill_saga.tsx +++ b/frontend/javascripts/oxalis/model/sagas/volume/floodfill_saga.tsx @@ -201,11 +201,19 @@ function* handleFloodFill(floodFillAction: FloodFillAction): Saga { ); const splitBoundaryMesh = isSplitToolkit ? sceneController.getSplitBoundaryMesh() : null; - if (isSplitToolkit && !splitBoundaryMesh) { - Toast.warning( - `No split boundary found. Ensure that the active tree has at least two nodes. If you want to execute a normal floodfill operation, please switch to another toolkit (currently, the "Split Segments" toolkit is active).`, - ); - return; + if (isSplitToolkit) { + if (!splitBoundaryMesh) { + Toast.warning( + `No split boundary found. Ensure that the active tree has at least two nodes. If you want to execute a normal fill operation, please switch to another toolkit (currently, the "Split Segments" toolkit is active).`, + ); + return; + } + if (planeId !== "PLANE_XY") { + Toast.warning( + `Within the "Split Segments" toolkit, the fill tool is only supported in the XY viewport. Please use the tool in the XY viewport or switch to another toolkit.`, + ); + return; + } } const busyBlockingInfo = yield* select((state) => state.uiInformation.busyBlockingInfo); From 2315786c72b8573711426aae07680e650609b9ec Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Thu, 17 Apr 2025 14:19:53 +0200 Subject: [PATCH 57/84] update surface on create tree and undo/redo --- .../javascripts/oxalis/model/sagas/split_boundary_mesh_saga.ts | 2 ++ 1 file changed, 2 insertions(+) diff --git a/frontend/javascripts/oxalis/model/sagas/split_boundary_mesh_saga.ts b/frontend/javascripts/oxalis/model/sagas/split_boundary_mesh_saga.ts index bf7de0c3d37..47afa9ed4e7 100644 --- a/frontend/javascripts/oxalis/model/sagas/split_boundary_mesh_saga.ts +++ b/frontend/javascripts/oxalis/model/sagas/split_boundary_mesh_saga.ts @@ -48,10 +48,12 @@ export function* splitBoundaryMeshSaga(): Saga { "SET_ACTIVE_TREE_BY_NAME", "CREATE_NODE", "DELETE_NODE", + "CREATE_TREE", "DELETE_TREE", "SET_TREE_VISIBILITY", "TOGGLE_TREE", "SET_NODE_POSITION", + "SET_TRACING", (action: Action) => action.type === "UPDATE_USER_SETTING" && action.propertyName === "activeToolkit", ] as ActionPattern, From 8692405977a16668418c387b33adf783e25fe239 Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Thu, 17 Apr 2025 14:36:51 +0200 Subject: [PATCH 58/84] hide edges automatically for the active tree when the split tool is active and restore the edges visibility again later --- .../model/bucket_data_handling/data_cube.ts | 1 - .../model/reducers/skeletontracing_reducer.ts | 12 +---- .../model/sagas/split_boundary_mesh_saga.ts | 50 ++++++++++++++++++- .../model/sagas/volume/floodfill_saga.tsx | 2 +- 4 files changed, 51 insertions(+), 14 deletions(-) diff --git a/frontend/javascripts/oxalis/model/bucket_data_handling/data_cube.ts b/frontend/javascripts/oxalis/model/bucket_data_handling/data_cube.ts index 82ecc6882ad..b91340bc249 100644 --- a/frontend/javascripts/oxalis/model/bucket_data_handling/data_cube.ts +++ b/frontend/javascripts/oxalis/model/bucket_data_handling/data_cube.ts @@ -17,7 +17,6 @@ import type { Vector3, } from "oxalis/constants"; import constants, { MappingStatusEnum } from "oxalis/constants"; -import getSceneController from "oxalis/controller/scene_controller_provider"; import { getMappingInfo } from "oxalis/model/accessors/dataset_accessor"; import { getSomeTracing } from "oxalis/model/accessors/tracing_accessor"; import BoundingBox from "oxalis/model/bucket_data_handling/bounding_box"; diff --git a/frontend/javascripts/oxalis/model/reducers/skeletontracing_reducer.ts b/frontend/javascripts/oxalis/model/reducers/skeletontracing_reducer.ts index 966cf17c132..77e9ab139d1 100644 --- a/frontend/javascripts/oxalis/model/reducers/skeletontracing_reducer.ts +++ b/frontend/javascripts/oxalis/model/reducers/skeletontracing_reducer.ts @@ -828,17 +828,7 @@ function SkeletonTracingReducer(state: OxalisState, action: Action): OxalisState case "CREATE_TREE": { const { timestamp } = action; - const isSplitToolkitActive = state.userConfiguration.activeToolkit === "SPLIT_SEGMENTS"; - return createTree( - state, - timestamp, - undefined, - undefined, - undefined, - // Don't show edges for trees that were created in the split toolkit, - // because spline curves will be shown for each section by default. - !isSplitToolkitActive, - ) + return createTree(state, timestamp) .map((tree) => { if (action.treeIdCallback) { action.treeIdCallback(tree.treeId); diff --git a/frontend/javascripts/oxalis/model/sagas/split_boundary_mesh_saga.ts b/frontend/javascripts/oxalis/model/sagas/split_boundary_mesh_saga.ts index 47afa9ed4e7..fdc98012061 100644 --- a/frontend/javascripts/oxalis/model/sagas/split_boundary_mesh_saga.ts +++ b/frontend/javascripts/oxalis/model/sagas/split_boundary_mesh_saga.ts @@ -2,14 +2,38 @@ import getSceneController from "oxalis/controller/scene_controller_provider"; import type { Saga } from "oxalis/model/sagas/effect-generators"; import { select } from "oxalis/model/sagas/effect-generators"; import type { ActionPattern } from "redux-saga/effects"; -import { call, takeEvery } from "typed-redux-saga"; +import { call, put, takeEvery } from "typed-redux-saga"; import { getActiveTree } from "../accessors/skeletontracing_accessor"; import type { Action } from "../actions/actions"; +import { setTreeEdgeVisibilityAction } from "../actions/skeletontracing_actions"; import { ensureWkReady } from "./ready_sagas"; import { takeWithBatchActionSupport } from "./saga_helpers"; +// The clean up function removes the surface from the scene controller. let cleanUpFn: (() => void) | null = null; +// This info object contains data about the tree that is currently +// adapted to not show its edges (because splines are rendered instead). +// When the split toolkit is left or when another tree is activated, +// the original value of edgesAreVisible is restored. +let temporarilyChangedTreeInfo: { + treeId: number; + originalEdgesAreVisible: boolean; +} | null = null; + +function* restoreApperanceOfTree() { + if (temporarilyChangedTreeInfo == null) { + return; + } + yield* put( + setTreeEdgeVisibilityAction( + temporarilyChangedTreeInfo.treeId, + temporarilyChangedTreeInfo.originalEdgesAreVisible, + ), + ); + temporarilyChangedTreeInfo = null; +} + function* updateSplitBoundaryMesh() { if (cleanUpFn != null) { cleanUpFn(); @@ -20,12 +44,34 @@ function* updateSplitBoundaryMesh() { (state) => state.userConfiguration.activeToolkit === "SPLIT_SEGMENTS", ); if (!isSplitToolkit) { + yield* call(restoreApperanceOfTree); return; } const sceneController = yield* call(() => getSceneController()); const activeTree = yield* select((state) => getActiveTree(state.annotation.skeleton)); + + if (activeTree?.treeId !== temporarilyChangedTreeInfo?.treeId) { + // The active tree changed. + // Restore the appearance of the old tree. + yield* call(restoreApperanceOfTree); + + // Update the appearance of the current tree. + if (activeTree != null) { + yield* put(setTreeEdgeVisibilityAction(activeTree.treeId, false)); + } + + // Update temporarilyChangedTreeInfo + temporarilyChangedTreeInfo = + activeTree != null + ? { + treeId: activeTree.treeId, + originalEdgesAreVisible: activeTree.edgesAreVisible, + } + : null; + } + if (activeTree?.isVisible) { const nodes = Array.from(activeTree.nodes.values()); const points = nodes.map((node) => node.untransformedPosition); @@ -37,6 +83,7 @@ function* updateSplitBoundaryMesh() { export function* splitBoundaryMeshSaga(): Saga { cleanUpFn = null; + temporarilyChangedTreeInfo = null; yield* takeWithBatchActionSupport("INITIALIZE_SKELETONTRACING"); yield* ensureWkReady(); @@ -46,6 +93,7 @@ export function* splitBoundaryMeshSaga(): Saga { [ "SET_ACTIVE_TREE", "SET_ACTIVE_TREE_BY_NAME", + "SET_ACTIVE_NODE", "CREATE_NODE", "DELETE_NODE", "CREATE_TREE", diff --git a/frontend/javascripts/oxalis/model/sagas/volume/floodfill_saga.tsx b/frontend/javascripts/oxalis/model/sagas/volume/floodfill_saga.tsx index 4d650734d49..256e2e41dda 100644 --- a/frontend/javascripts/oxalis/model/sagas/volume/floodfill_saga.tsx +++ b/frontend/javascripts/oxalis/model/sagas/volume/floodfill_saga.tsx @@ -12,6 +12,7 @@ import type { Vector3, } from "oxalis/constants"; import Constants, { FillModeEnum, Unicode } from "oxalis/constants"; +import getSceneController from "oxalis/controller/scene_controller_provider"; import { getDatasetBoundingBox, getMagInfo } from "oxalis/model/accessors/dataset_accessor"; import { getDisabledInfoForTools } from "oxalis/model/accessors/disabled_tool_accessor"; import { getActiveMagIndexForLayer } from "oxalis/model/accessors/flycam_accessor"; @@ -33,7 +34,6 @@ import { Model } from "oxalis/singletons"; import { call, put, takeEvery } from "typed-redux-saga"; import { getUserBoundingBoxesThatContainPosition } from "../../accessors/tracing_accessor"; import { applyLabeledVoxelMapToAllMissingMags } from "./helpers"; -import getSceneController from "oxalis/controller/scene_controller_provider"; const NO_FLOODFILL_BBOX_TOAST_KEY = "NO_FLOODFILL_BBOX"; const NO_SUCCESS_MSG_WHEN_WITHIN_MS = 500; From 6408e5649abf09d84580f3f3910fef984a575472 Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Thu, 17 Apr 2025 16:39:10 +0200 Subject: [PATCH 59/84] fix spec --- frontend/javascripts/test/sagas/annotation_tool_saga.spec.ts | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/frontend/javascripts/test/sagas/annotation_tool_saga.spec.ts b/frontend/javascripts/test/sagas/annotation_tool_saga.spec.ts index cc9e798f225..d47d794d26a 100644 --- a/frontend/javascripts/test/sagas/annotation_tool_saga.spec.ts +++ b/frontend/javascripts/test/sagas/annotation_tool_saga.spec.ts @@ -116,9 +116,9 @@ describe("Annotation Tool Saga", () => { it("Selecting another tool should trigger a deselection of the previous tool.", () => { let newState = initialState; + const saga = watchToolDeselection(); saga.next(); - saga.next(wkReadyAction()); saga.next(newState.uiInformation.activeTool); const cycleTool = (nextTool: AnnotationTool) => { From 4bb55873e6f95725eb1bde8f845db7e135253e8d Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Thu, 17 Apr 2025 16:57:59 +0200 Subject: [PATCH 60/84] wip: indicator for different tool behavior --- .../oxalis/view/action-bar/toolbar_view.tsx | 96 +++++++++++++------ 1 file changed, 66 insertions(+), 30 deletions(-) diff --git a/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx b/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx index 625d0a0826a..4176054db0e 100644 --- a/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx +++ b/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx @@ -17,6 +17,7 @@ import { type RadioChangeEvent, Row, Space, + Tag, } from "antd"; import React, { useEffect, useCallback, useState } from "react"; import { useDispatch, useSelector } from "react-redux"; @@ -855,6 +856,7 @@ export default function ToolbarView() { const hasSkeleton = useSelector((state: OxalisState) => state.annotation?.skeleton != null); const toolkit = useSelector((state: OxalisState) => state.userConfiguration.activeToolkit); const activeTool = useSelector((state: OxalisState) => state.uiInformation.activeTool); + const isSplitToolkit = toolkit === "SPLIT_SEGMENTS"; const isShiftPressed = useKeyPress("Shift"); const isControlOrMetaPressed = useKeyPress("ControlOrMeta"); @@ -881,6 +883,16 @@ export default function ToolbarView() { isControlOrMetaPressed={isControlOrMetaPressed} isShiftPressed={isShiftPressed} /> + + {isSplitToolkit ? ( + + + Split Workflow + + + ) : null} ); } @@ -1241,26 +1253,38 @@ function SkeletonTool() { const isReadOnly = useSelector( (state: OxalisState) => !state.annotation.restrictions.allowUpdate, ); + const isSplitToolkit = useSelector( + (state: OxalisState) => state.userConfiguration.activeToolkit === "SPLIT_SEGMENTS", + ); if (!hasSkeleton || isReadOnly) { return null; } return ( - - - + + + + ); } @@ -1400,29 +1424,41 @@ function EraseTraceTool({ adaptedActiveTool }: { adaptedActiveTool: AnnotationTo function FillCellTool({ adaptedActiveTool }: { adaptedActiveTool: AnnotationTool }) { const disabledInfosForTools = useSelector(getDisabledInfoForTools); const isVolumeModificationAllowed = useSelector(getIsVolumeModificationAllowed); + const isSplitToolkit = useSelector( + (state: OxalisState) => state.userConfiguration.activeToolkit === "SPLIT_SEGMENTS", + ); if (!isVolumeModificationAllowed) { return null; } return ( - - - {adaptedActiveTool === AnnotationTool.FILL_CELL ? ( - - ) : null} - + + + {adaptedActiveTool === AnnotationTool.FILL_CELL ? ( + + ) : null} + + ); } From 3fa74552370dbcae42768ee789e41d2e6c3efe1a Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Tue, 22 Apr 2025 13:13:04 +0200 Subject: [PATCH 61/84] remove commented code --- frontend/javascripts/oxalis/shaders/main_data_shaders.glsl.ts | 2 -- 1 file changed, 2 deletions(-) diff --git a/frontend/javascripts/oxalis/shaders/main_data_shaders.glsl.ts b/frontend/javascripts/oxalis/shaders/main_data_shaders.glsl.ts index b98399e4c39..d6e481c282f 100644 --- a/frontend/javascripts/oxalis/shaders/main_data_shaders.glsl.ts +++ b/frontend/javascripts/oxalis/shaders/main_data_shaders.glsl.ts @@ -158,7 +158,6 @@ const float bucketSize = <%= bucketSize %>; export default function getMainFragmentShader(params: Params) { const hasSegmentation = params.segmentationLayerNames.length > 0; - // return ""; return _.template(` precision highp float; @@ -415,7 +414,6 @@ void main() { export function getMainVertexShader(params: Params) { const hasSegmentation = params.segmentationLayerNames.length > 0; - // return ""; return _.template(` precision highp float; From 89bbe1db3e2ea07ed3d00670986a469532240b21 Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Tue, 22 Apr 2025 13:22:53 +0200 Subject: [PATCH 62/84] Update frontend/javascripts/oxalis/view/action-bar/toolkit_switcher_view.tsx Co-authored-by: MichaelBuessemeyer <39529669+MichaelBuessemeyer@users.noreply.github.com> --- .../oxalis/view/action-bar/toolkit_switcher_view.tsx | 4 +--- 1 file changed, 1 insertion(+), 3 deletions(-) diff --git a/frontend/javascripts/oxalis/view/action-bar/toolkit_switcher_view.tsx b/frontend/javascripts/oxalis/view/action-bar/toolkit_switcher_view.tsx index a361c974a67..9a6c9f17517 100644 --- a/frontend/javascripts/oxalis/view/action-bar/toolkit_switcher_view.tsx +++ b/frontend/javascripts/oxalis/view/action-bar/toolkit_switcher_view.tsx @@ -44,9 +44,7 @@ export default function ToolkitView() { // Additionally, we need a timeout since the blurring would be done // to early, otherwise. setTimeout(() => { - if (document.activeElement != null) { - // @ts-expect-error ts-migrate(2339) FIXME: Property 'blur' does not exist on type 'Element'. - document.activeElement.blur(); + document.activeElement?.blur(); } }, 100); }; From 98a20706e01361d16b6e314d7520c130fb239f8b Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Tue, 22 Apr 2025 13:34:41 +0200 Subject: [PATCH 63/84] incorporate feedback --- ...ompute_split_boundary_mesh_with_splines.ts | 4 --- .../view/action-bar/toolkit_switcher_view.tsx | 10 ++----- .../view/action-bar/view_modes_view.tsx | 26 ++++++------------- 3 files changed, 10 insertions(+), 30 deletions(-) diff --git a/frontend/javascripts/oxalis/geometries/compute_split_boundary_mesh_with_splines.ts b/frontend/javascripts/oxalis/geometries/compute_split_boundary_mesh_with_splines.ts index ae67e736841..6d981607a11 100644 --- a/frontend/javascripts/oxalis/geometries/compute_split_boundary_mesh_with_splines.ts +++ b/frontend/javascripts/oxalis/geometries/compute_split_boundary_mesh_with_splines.ts @@ -47,10 +47,6 @@ export default function computeSplitBoundaryMeshWithSplines(points: Vector3[]): pointsByZ[zValue].map((p) => new THREE.Vector3(p[0], p[1], adaptedZ)), ); - if (points2D.length < 2) { - return null; - } - if (curveIdx > 0) { const currentCurvePoints = points2D; const prevCurvePoints = curvesByZ[zValues[curveIdx - 1]].points; diff --git a/frontend/javascripts/oxalis/view/action-bar/toolkit_switcher_view.tsx b/frontend/javascripts/oxalis/view/action-bar/toolkit_switcher_view.tsx index 9a6c9f17517..60a440ea5d8 100644 --- a/frontend/javascripts/oxalis/view/action-bar/toolkit_switcher_view.tsx +++ b/frontend/javascripts/oxalis/view/action-bar/toolkit_switcher_view.tsx @@ -39,14 +39,8 @@ export default function ToolkitView() { const handleMenuClick: MenuProps["onClick"] = (args) => { const toolkit = args.key; Store.dispatch(updateUserSettingAction("activeToolkit", toolkit as Toolkit)); - // Unfortunately, antd doesn't provide the original event here - // which is why we have to blur using document.activeElement. - // Additionally, we need a timeout since the blurring would be done - // to early, otherwise. - setTimeout(() => { - document.activeElement?.blur(); - } - }, 100); + // @ts-expect-error ts-migrate(2339) FIXME: Property 'blur' does not exist on type 'Element'. + args.domEvent.target.blur(); }; const toolkitMenuProps = { diff --git a/frontend/javascripts/oxalis/view/action-bar/view_modes_view.tsx b/frontend/javascripts/oxalis/view/action-bar/view_modes_view.tsx index 7a98c950221..bd413f4f87d 100644 --- a/frontend/javascripts/oxalis/view/action-bar/view_modes_view.tsx +++ b/frontend/javascripts/oxalis/view/action-bar/view_modes_view.tsx @@ -32,7 +32,11 @@ const VIEW_MODE_TO_ICON = { }; class ViewModesView extends PureComponent { - handleChange = (mode: ViewMode) => { + handleChange: MenuProps["onClick"] = (args) => { + if (!ViewModeValues.includes(args.key as ViewMode)) { + return; + } + const mode = args.key as ViewMode; // If we switch back from any arbitrary mode we stop recording. // This prevents that when the user switches back to any arbitrary mode, // a new node is instantly created at the screen's center. @@ -44,16 +48,8 @@ class ViewModesView extends PureComponent { } Store.dispatch(setViewModeAction(mode)); - // Unfortunately, antd doesn't provide the original event here - // which is why we have to blur using document.activeElement. - // Additionally, we need a timeout since the blurring would be done - // to early, otherwise. - setTimeout(() => { - if (document.activeElement != null) { - // @ts-expect-error ts-migrate(2339) FIXME: Property 'blur' does not exist on type 'Element'. - document.activeElement.blur(); - } - }, 100); + // @ts-expect-error ts-migrate(2339) FIXME: Property 'blur' does not exist on type 'Element'. + args.domEvent.target.blur(); }; isDisabled(mode: ViewMode) { @@ -61,12 +57,6 @@ class ViewModesView extends PureComponent { } render() { - const handleMenuClick: MenuProps["onClick"] = (args) => { - if (ViewModeValues.includes(args.key as ViewMode)) { - this.handleChange(args.key as ViewMode); - } - }; - const MENU_ITEMS: MenuProps["items"] = [ { key: "1", @@ -83,7 +73,7 @@ class ViewModesView extends PureComponent { const menuProps = { items: MENU_ITEMS, - onClick: handleMenuClick, + onClick: this.handleChange, }; return ( From 57671382884b1a24b55d2b760036e3a37ea67be1 Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Tue, 22 Apr 2025 13:46:18 +0200 Subject: [PATCH 64/84] listen to more actions --- .../model/sagas/split_boundary_mesh_saga.ts | 23 ++++++++++++++----- 1 file changed, 17 insertions(+), 6 deletions(-) diff --git a/frontend/javascripts/oxalis/model/sagas/split_boundary_mesh_saga.ts b/frontend/javascripts/oxalis/model/sagas/split_boundary_mesh_saga.ts index fdc98012061..2326a4a6747 100644 --- a/frontend/javascripts/oxalis/model/sagas/split_boundary_mesh_saga.ts +++ b/frontend/javascripts/oxalis/model/sagas/split_boundary_mesh_saga.ts @@ -91,17 +91,28 @@ export function* splitBoundaryMeshSaga(): Saga { yield* call(updateSplitBoundaryMesh); yield* takeEvery( [ - "SET_ACTIVE_TREE", - "SET_ACTIVE_TREE_BY_NAME", - "SET_ACTIVE_NODE", + "ADD_TREES_AND_GROUPS", + "BATCH_UPDATE_GROUPS_AND_TREES", "CREATE_NODE", - "DELETE_NODE", "CREATE_TREE", + "DELETE_EDGE", + "DELETE_NODE", "DELETE_TREE", - "SET_TREE_VISIBILITY", - "TOGGLE_TREE", + "DELETE_TREES", + "INITIALIZE_ANNOTATION_WITH_TRACINGS", + "INITIALIZE_SKELETONTRACING", + "MERGE_TREES", + "SELECT_NEXT_TREE", + "SET_ACTIVE_NODE", + "SET_ACTIVE_TREE", + "SET_ACTIVE_TREE_BY_NAME", "SET_NODE_POSITION", "SET_TRACING", + "SET_TREE_VISIBILITY", + "TOGGLE_ALL_TREES", + "TOGGLE_INACTIVE_TREES", + "TOGGLE_TREE", + "TOGGLE_TREE_GROUP", (action: Action) => action.type === "UPDATE_USER_SETTING" && action.propertyName === "activeToolkit", ] as ActionPattern, From 7b7e752ea41db29c599e3fad805acc33b7fa1f06 Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Tue, 22 Apr 2025 13:53:56 +0200 Subject: [PATCH 65/84] add comments --- ...ompute_split_boundary_mesh_with_splines.ts | 30 +++++++++++++++++++ 1 file changed, 30 insertions(+) diff --git a/frontend/javascripts/oxalis/geometries/compute_split_boundary_mesh_with_splines.ts b/frontend/javascripts/oxalis/geometries/compute_split_boundary_mesh_with_splines.ts index 6d981607a11..763e7152755 100644 --- a/frontend/javascripts/oxalis/geometries/compute_split_boundary_mesh_with_splines.ts +++ b/frontend/javascripts/oxalis/geometries/compute_split_boundary_mesh_with_splines.ts @@ -7,6 +7,33 @@ export default function computeSplitBoundaryMeshWithSplines(points: Vector3[]): splines: THREE.Object3D[]; splitBoundaryMesh: THREE.Mesh; } { + /** + * Generates a smooth, interpolated 3D boundary mesh and corresponding spline visualizations + * from a set of unordered 3D points. + * + * This function processes a collection of 3D points that are assumed to lie on or near + * horizontal slices (constant Z-values). It groups the points by their Z-coordinate, + * constructs a spline for each slice using a minimum spanning tree (MST) + * strategy to find a good continuous order, and interpolates intermediate slices if gaps in the Z-axis + * are detected. + * + * The output consists of: + * 1. A set of 3D spline objects that represent the ordered splines at each Z level. + * 2. A triangulated boundary surface mesh constructed from these splines. + * + * The process includes: + * - Grouping input points by their Z-coordinate, filtering out groups with fewer than 2 points. + * - Creating smooth Catmull-Rom splines from the ordered boundary points for each slice. + * - Ensuring geometric consistency by flipping curves when necessary to prevent twists. + * - Interpolating curves for missing Z-levels to produce a continuous surface. + * - Generating a structured grid of vertices from these curves and triangulating them + * to form a closed 3D mesh. + * - Applying smoothing and basic material setup for visualization. + * + * If all points lie on a single Z-level, the function duplicates the layer at adjacent Z-values + * to ensure a valid 3D surface can still be formed. + * + */ const splines: THREE.Object3D[] = []; const unfilteredPointsByZ = _.groupBy(points, (p) => p[2]); @@ -48,6 +75,9 @@ export default function computeSplitBoundaryMeshWithSplines(points: Vector3[]): ); if (curveIdx > 0) { + // Find out whether we should flip the order of points2D by checking + // whether the first point of the last and the current curve is + // close to each other. const currentCurvePoints = points2D; const prevCurvePoints = curvesByZ[zValues[curveIdx - 1]].points; From 87122a90543dbd5f6aba38e4bc16aaad8ae06e61 Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Tue, 22 Apr 2025 14:00:06 +0200 Subject: [PATCH 66/84] debounce saga --- .../javascripts/oxalis/model/sagas/annotation_tool_saga.ts | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/frontend/javascripts/oxalis/model/sagas/annotation_tool_saga.ts b/frontend/javascripts/oxalis/model/sagas/annotation_tool_saga.ts index 6a5e8966448..3966d2f0551 100644 --- a/frontend/javascripts/oxalis/model/sagas/annotation_tool_saga.ts +++ b/frontend/javascripts/oxalis/model/sagas/annotation_tool_saga.ts @@ -13,7 +13,7 @@ import { select } from "oxalis/model/sagas/effect-generators"; import { call, put, take } from "typed-redux-saga"; import { ensureWkReady } from "./ready_sagas"; -import { type ActionPattern, fork } from "redux-saga/effects"; +import { type ActionPattern, delay, fork } from "redux-saga/effects"; import { takeEvery } from "typed-redux-saga"; import { getDisabledInfoForTools } from "../accessors/disabled_tool_accessor"; import { Toolkits } from "../accessors/tool_accessor"; @@ -70,6 +70,8 @@ function* switchAwayFromDisabledTool(): Saga { let continueWaiting = true; while (continueWaiting) { yield take(); + // Debounce so that we don't process ALL actions. + yield delay(50); const newActiveTool = yield* select((state) => state.uiInformation.activeTool); if (newActiveTool !== activeTool) { activeTool = newActiveTool; From 3454e58faeca020a78f266e79c7d92ed81d9fd7c Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Tue, 22 Apr 2025 15:31:34 +0200 Subject: [PATCH 67/84] iterate on ui --- .../oxalis/view/action-bar/toolbar_view.tsx | 81 ++++++++----------- 1 file changed, 32 insertions(+), 49 deletions(-) diff --git a/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx b/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx index 4176054db0e..09967a82049 100644 --- a/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx +++ b/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx @@ -888,7 +888,8 @@ export default function ToolbarView() { - + + Split Workflow @@ -1262,29 +1263,20 @@ function SkeletonTool() { } return ( - - - - - + + ); } @@ -1432,33 +1424,24 @@ function FillCellTool({ adaptedActiveTool }: { adaptedActiveTool: AnnotationTool } return ( - - - - {adaptedActiveTool === AnnotationTool.FILL_CELL ? ( - - ) : null} - - + + {adaptedActiveTool === AnnotationTool.FILL_CELL ? ( + + ) : null} + ); } From 2c42d98b58d0b719718138f960bd83c8871dee13 Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Tue, 22 Apr 2025 15:50:03 +0200 Subject: [PATCH 68/84] use fake enums for toolkit strings --- frontend/javascripts/oxalis/default_state.ts | 4 ++-- .../oxalis/model/accessors/tool_accessor.ts | 11 +++++++++-- .../oxalis/model/sagas/annotation_tool_saga.ts | 4 ++-- .../oxalis/model/sagas/split_boundary_mesh_saga.ts | 3 ++- .../oxalis/model/sagas/volume/floodfill_saga.tsx | 4 ++-- .../oxalis/view/action-bar/toolbar_view.tsx | 11 +++-------- .../oxalis/view/action-bar/toolkit_switcher_view.tsx | 12 ++++++------ .../test/sagas/annotation_tool_saga.spec.ts | 1 - 8 files changed, 26 insertions(+), 24 deletions(-) diff --git a/frontend/javascripts/oxalis/default_state.ts b/frontend/javascripts/oxalis/default_state.ts index af548a9392b..aca2cf485a8 100644 --- a/frontend/javascripts/oxalis/default_state.ts +++ b/frontend/javascripts/oxalis/default_state.ts @@ -8,7 +8,7 @@ import Constants, { UnitLong, } from "oxalis/constants"; import constants from "oxalis/constants"; -import { AnnotationTool } from "oxalis/model/accessors/tool_accessor"; +import { AnnotationTool, Toolkit } from "oxalis/model/accessors/tool_accessor"; import type { OxalisState } from "oxalis/store"; import { getSystemColorTheme } from "theme"; import type { @@ -102,7 +102,7 @@ const defaultState: OxalisState = { }, renderWatermark: true, antialiasRendering: false, - activeToolkit: "ALL_TOOLS", + activeToolkit: Toolkit.ALL_TOOLS, }, temporaryConfiguration: { viewMode: Constants.MODE_PLANE_TRACING, diff --git a/frontend/javascripts/oxalis/model/accessors/tool_accessor.ts b/frontend/javascripts/oxalis/model/accessors/tool_accessor.ts index 04498c31f0d..157df325828 100644 --- a/frontend/javascripts/oxalis/model/accessors/tool_accessor.ts +++ b/frontend/javascripts/oxalis/model/accessors/tool_accessor.ts @@ -108,7 +108,15 @@ export const AnnotationTool = { // and a type. export type AnnotationTool = (typeof AnnotationTool)[keyof typeof AnnotationTool]; -export const Toolkits = { +export const Toolkit = { + ALL_TOOLS: "ALL_TOOLS", + VOLUME_TOOLS: "VOLUME_TOOLS", + READ_ONLY_TOOLS: "READ_ONLY_TOOLS", + SPLIT_SEGMENTS: "SPLIT_SEGMENTS", +} as const; +export type Toolkit = (typeof Toolkit)[keyof typeof Toolkit]; + +export const Toolkits: Record = { ALL_TOOLS: Object.values(AnnotationTool) as AnnotationTool[], VOLUME_TOOLS: [ AnnotationTool.MOVE, @@ -133,7 +141,6 @@ export const Toolkits = { AnnotationTool.BOUNDING_BOX, ] as AnnotationTool[], }; -export type Toolkit = keyof typeof Toolkits; export const VolumeTools = _.without(Toolkits.VOLUME_TOOLS, AnnotationTool.MOVE); diff --git a/frontend/javascripts/oxalis/model/sagas/annotation_tool_saga.ts b/frontend/javascripts/oxalis/model/sagas/annotation_tool_saga.ts index 3966d2f0551..3f20b44596c 100644 --- a/frontend/javascripts/oxalis/model/sagas/annotation_tool_saga.ts +++ b/frontend/javascripts/oxalis/model/sagas/annotation_tool_saga.ts @@ -1,6 +1,6 @@ import { getToolControllerForAnnotationTool } from "oxalis/controller/combinations/tool_controls"; import getSceneController from "oxalis/controller/scene_controller_provider"; -import { AnnotationTool, MeasurementTools } from "oxalis/model/accessors/tool_accessor"; +import { AnnotationTool, MeasurementTools, Toolkit } from "oxalis/model/accessors/tool_accessor"; import { type CycleToolAction, type SetToolAction, @@ -133,7 +133,7 @@ export default function* toolSaga() { const isViewMode = yield* select((state) => state.annotation.annotationType === "View"); if (isViewMode) { - yield* put(updateUserSettingAction("activeToolkit", "ALL_TOOLS")); + yield* put(updateUserSettingAction("activeToolkit", Toolkit.ALL_TOOLS)); } yield fork(watchToolDeselection); diff --git a/frontend/javascripts/oxalis/model/sagas/split_boundary_mesh_saga.ts b/frontend/javascripts/oxalis/model/sagas/split_boundary_mesh_saga.ts index 2326a4a6747..6b7e4cb205c 100644 --- a/frontend/javascripts/oxalis/model/sagas/split_boundary_mesh_saga.ts +++ b/frontend/javascripts/oxalis/model/sagas/split_boundary_mesh_saga.ts @@ -4,6 +4,7 @@ import { select } from "oxalis/model/sagas/effect-generators"; import type { ActionPattern } from "redux-saga/effects"; import { call, put, takeEvery } from "typed-redux-saga"; import { getActiveTree } from "../accessors/skeletontracing_accessor"; +import { Toolkit } from "../accessors/tool_accessor"; import type { Action } from "../actions/actions"; import { setTreeEdgeVisibilityAction } from "../actions/skeletontracing_actions"; import { ensureWkReady } from "./ready_sagas"; @@ -41,7 +42,7 @@ function* updateSplitBoundaryMesh() { } const isSplitToolkit = yield* select( - (state) => state.userConfiguration.activeToolkit === "SPLIT_SEGMENTS", + (state) => state.userConfiguration.activeToolkit === Toolkit.SPLIT_SEGMENTS, ); if (!isSplitToolkit) { yield* call(restoreApperanceOfTree); diff --git a/frontend/javascripts/oxalis/model/sagas/volume/floodfill_saga.tsx b/frontend/javascripts/oxalis/model/sagas/volume/floodfill_saga.tsx index 256e2e41dda..5b83a4f660a 100644 --- a/frontend/javascripts/oxalis/model/sagas/volume/floodfill_saga.tsx +++ b/frontend/javascripts/oxalis/model/sagas/volume/floodfill_saga.tsx @@ -16,7 +16,7 @@ import getSceneController from "oxalis/controller/scene_controller_provider"; import { getDatasetBoundingBox, getMagInfo } from "oxalis/model/accessors/dataset_accessor"; import { getDisabledInfoForTools } from "oxalis/model/accessors/disabled_tool_accessor"; import { getActiveMagIndexForLayer } from "oxalis/model/accessors/flycam_accessor"; -import { AnnotationTool } from "oxalis/model/accessors/tool_accessor"; +import { AnnotationTool, Toolkit } from "oxalis/model/accessors/tool_accessor"; import { enforceActiveVolumeTracing } from "oxalis/model/accessors/volumetracing_accessor"; import { addUserBoundingBoxAction } from "oxalis/model/actions/annotation_actions"; import { setBusyBlockingInfoAction } from "oxalis/model/actions/ui_actions"; @@ -197,7 +197,7 @@ function* handleFloodFill(floodFillAction: FloodFillAction): Saga { const sceneController = getSceneController(); const isSplitToolkit = yield* select( - (state) => state.userConfiguration.activeToolkit === "SPLIT_SEGMENTS", + (state) => state.userConfiguration.activeToolkit === Toolkit.SPLIT_SEGMENTS, ); const splitBoundaryMesh = isSplitToolkit ? sceneController.getSplitBoundaryMesh() : null; diff --git a/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx b/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx index 09967a82049..dfb02a47d82 100644 --- a/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx +++ b/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx @@ -38,6 +38,7 @@ import { getActiveTree } from "oxalis/model/accessors/skeletontracing_accessor"; import { AnnotationTool, MeasurementTools, + Toolkit, VolumeTools, } from "oxalis/model/accessors/tool_accessor"; import { Toolkits, adaptActiveToolToShortcuts } from "oxalis/model/accessors/tool_accessor"; @@ -392,7 +393,7 @@ function SkeletonSpecificButtons() { (state: OxalisState) => state.userConfiguration.continuousNodeCreation, ); const isSplitToolkit = useSelector( - (state: OxalisState) => state.userConfiguration.activeToolkit === "SPLIT_SEGMENTS", + (state: OxalisState) => state.userConfiguration.activeToolkit === Toolkit.SPLIT_SEGMENTS, ); const toggleContinuousNodeCreation = () => dispatch(updateUserSettingAction("continuousNodeCreation", !isContinuousNodeCreationEnabled)); @@ -856,7 +857,7 @@ export default function ToolbarView() { const hasSkeleton = useSelector((state: OxalisState) => state.annotation?.skeleton != null); const toolkit = useSelector((state: OxalisState) => state.userConfiguration.activeToolkit); const activeTool = useSelector((state: OxalisState) => state.uiInformation.activeTool); - const isSplitToolkit = toolkit === "SPLIT_SEGMENTS"; + const isSplitToolkit = toolkit === Toolkit.SPLIT_SEGMENTS; const isShiftPressed = useKeyPress("Shift"); const isControlOrMetaPressed = useKeyPress("ControlOrMeta"); @@ -1254,9 +1255,6 @@ function SkeletonTool() { const isReadOnly = useSelector( (state: OxalisState) => !state.annotation.restrictions.allowUpdate, ); - const isSplitToolkit = useSelector( - (state: OxalisState) => state.userConfiguration.activeToolkit === "SPLIT_SEGMENTS", - ); if (!hasSkeleton || isReadOnly) { return null; @@ -1416,9 +1414,6 @@ function EraseTraceTool({ adaptedActiveTool }: { adaptedActiveTool: AnnotationTo function FillCellTool({ adaptedActiveTool }: { adaptedActiveTool: AnnotationTool }) { const disabledInfosForTools = useSelector(getDisabledInfoForTools); const isVolumeModificationAllowed = useSelector(getIsVolumeModificationAllowed); - const isSplitToolkit = useSelector( - (state: OxalisState) => state.userConfiguration.activeToolkit === "SPLIT_SEGMENTS", - ); if (!isVolumeModificationAllowed) { return null; } diff --git a/frontend/javascripts/oxalis/view/action-bar/toolkit_switcher_view.tsx b/frontend/javascripts/oxalis/view/action-bar/toolkit_switcher_view.tsx index 60a440ea5d8..9671e1da31b 100644 --- a/frontend/javascripts/oxalis/view/action-bar/toolkit_switcher_view.tsx +++ b/frontend/javascripts/oxalis/view/action-bar/toolkit_switcher_view.tsx @@ -1,5 +1,5 @@ import { Badge, Button, Dropdown, type MenuProps } from "antd"; -import type { Toolkit } from "oxalis/model/accessors/tool_accessor"; +import { Toolkit } from "oxalis/model/accessors/tool_accessor"; import { updateUserSettingAction } from "oxalis/model/actions/settings_actions"; import { Store } from "oxalis/singletons"; import type { OxalisState } from "oxalis/store"; @@ -9,19 +9,19 @@ import { NARROW_BUTTON_STYLE } from "./toolbar_view"; const toolkitOptions: Array<{ label: string; key: Toolkit }> = [ { label: "All Tools", - key: "ALL_TOOLS", + key: Toolkit.ALL_TOOLS, }, { label: "Read Only", - key: "READ_ONLY_TOOLS", + key: Toolkit.READ_ONLY_TOOLS, }, { label: "Volume", - key: "VOLUME_TOOLS", + key: Toolkit.VOLUME_TOOLS, }, { label: "Split Segments", - key: "SPLIT_SEGMENTS", + key: Toolkit.SPLIT_SEGMENTS, }, ]; @@ -53,7 +53,7 @@ export default function ToolkitView() { return ( Date: Tue, 22 Apr 2025 15:59:39 +0200 Subject: [PATCH 69/84] clean up getPoints parameter --- .../compute_split_boundary_mesh_with_splines.ts | 9 +++++---- 1 file changed, 5 insertions(+), 4 deletions(-) diff --git a/frontend/javascripts/oxalis/geometries/compute_split_boundary_mesh_with_splines.ts b/frontend/javascripts/oxalis/geometries/compute_split_boundary_mesh_with_splines.ts index 763e7152755..f0d7159b63a 100644 --- a/frontend/javascripts/oxalis/geometries/compute_split_boundary_mesh_with_splines.ts +++ b/frontend/javascripts/oxalis/geometries/compute_split_boundary_mesh_with_splines.ts @@ -100,6 +100,7 @@ export default function computeSplitBoundaryMeshWithSplines(points: Vector3[]): // Number of points per curve const numPoints = 50; + const numDivisions = numPoints - 1; // Sort z-values for interpolation const sortedZValues = Object.keys(curvesByZ) @@ -117,8 +118,8 @@ export default function computeSplitBoundaryMeshWithSplines(points: Vector3[]): if (lowerZ === Number.NEGATIVE_INFINITY || upperZ === Number.POSITIVE_INFINITY) continue; // Get the two adjacent curves and sample 50 points from each - const lowerCurvePoints = curvesByZ[lowerZ].getPoints(numPoints); - const upperCurvePoints = curvesByZ[upperZ].getPoints(numPoints); + const lowerCurvePoints = curvesByZ[lowerZ].getPoints(numDivisions); + const upperCurvePoints = curvesByZ[upperZ].getPoints(numDivisions); // Interpolate between corresponding points const interpolatedPoints = lowerCurvePoints.map((lowerPoint, i) => { @@ -139,7 +140,7 @@ export default function computeSplitBoundaryMeshWithSplines(points: Vector3[]): // Generate and display all curves Object.values(curvesByZ).forEach((curve) => { - const curvePoints = curve.getPoints(numPoints); + const curvePoints = curve.getPoints(numDivisions); const geometry = new THREE.BufferGeometry().setFromPoints(curvePoints); const material = new THREE.LineBasicMaterial({ color: 0xff0000 }); const splineObject = new THREE.Line(geometry, material); @@ -147,7 +148,7 @@ export default function computeSplitBoundaryMeshWithSplines(points: Vector3[]): }); // Generate grid of points - const gridPoints = curves.map((curve) => curve.getPoints(numPoints - 1)); + const gridPoints = curves.map((curve) => curve.getPoints(numDivisions)); // Flatten into a single array of vertices const vertices: number[] = []; From 13cf9f4a45f98210733d90de4f1da3bc62d99b02 Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Wed, 23 Apr 2025 08:24:53 +0200 Subject: [PATCH 70/84] update docs --- .../splitting-floodfill-visualization.png | Bin 0 -> 76288 bytes docs/images/toolkit_dropdown.jpg | Bin 0 -> 17642 bytes docs/proofreading/index.md | 6 ++-- .../{tools.md => 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+++ b/docs/proofreading/index.md @@ -4,6 +4,6 @@ WEBKNOSSOS offers several ways for proofreading large-scale, volumetric segmenta There are three proofreading workflows supported by WEBKNOSSOS: -1. The [Proofreading tool](tools.md) to correct large segmentations based on an underlying super-voxel graph. To use the proofreading tool, you need a [segmentation mapping](segmentation_mappings.md). -2. The [Merger-Mode tool](merger_mode.md) - +1. The [Proofreading tool](proofreading_tool.md) to correct split and merge errors in large segmentations based on an underlying super-voxel graph. To use the proofreading tool, you need a [segmentation mapping](segmentation_mappings.md). +2. The [Merger-Mode tool](merger_mode.md) which allows merging of segments by constructing a lightweight skeleton-based mapping. +3. Voxel-based relabeling of segments. Segments can be merged using the fill tool. To split segments there is a dedicated [Split Segments toolkit](split_segments_toolkit.md). diff --git a/docs/proofreading/tools.md b/docs/proofreading/proofreading_tool.md similarity index 100% rename from docs/proofreading/tools.md rename to docs/proofreading/proofreading_tool.md diff --git a/docs/proofreading/split_segments_toolkit.md b/docs/proofreading/split_segments_toolkit.md new file mode 100644 index 00000000000..1466153a6af --- /dev/null +++ b/docs/proofreading/split_segments_toolkit.md @@ -0,0 +1,31 @@ +# Split Segments Toolkit + +As explained in the [Toolkits](../ui/toolbar.md#Toolkits) section, there is a dedicated toolkit for splitting segments in your volume annotation. +When this toolkit is activated, you can create a curved 3D surface and use it to split a segment into two. + +## Workflow + +The recommended steps for splitting a segment are as follows: + +- Use the bounding box tool to create a box around the merge error that you want to correct. Theoretically, this step is optional, but keep in mind that relabeling large parts of a segment can be infeasible due to resources. Consider using the [proofreading tool](../proofreading/tools.html) for larger corrections. If you want to correct data for the purpose of groundtruth, it is often enough to only do a local correction. +- Go to the first z slice of the bounding box. +- Create a new skeleton tree and place nodes on the boundary that should split the segment into two. Consider activating the "Pen" mode within the skeleton tool so that you can rapidly draw nodes by dragging the mouse while it's pressed down. +- Go to the last z slice of the bounding box and repeat the previous step. +- Now you can inspect all the slices in between. A smooth spline curve will be shown in each slice that is derived from interpolating between adjacent slices. If you want to correct the interpolation, you can create new nodes on a slice. A new spline curve will be computed from these points and the interpolation will be updated. +- If you are satisfied with the (interpolated) boundary, you can switch to the fill tool. Ensure to enable the 3D mode as well as the "Restrict to Bounding Box" mode. + +## Troubleshooting + +- It can easily happen that the floodfill operation relabels the entire segment instead of only the part you intended to relabel. The cause of this is usually that the 3D surface doesn't cut the segment completely. Instead, the surface might only go very close to the edge. In that case, the floodfill operation can traverse over that edge and thus relabel everything (see image below). If this happens, you should undo the fill operation and double-check the surface. To avoid this problem, it is recommended to make the surface a bit bigger than usual. +- If multiple spline curves appear per slice, this is often due to a configuration issue. Please adapt the clipping distance in the left sidebar ("Layers" -> "Skeleton"). + +![A visualization of a floodfill operation "bleeding" across the boundary because the boundary is not precise enough](../images/splitting-floodfill-visualization.png) + +## Impact of "Split Segments" Toolkit + +Note that the workflow above is only possible because the "Split Segments" toolkit is enabled. +By activating that toolkit, WEBKNOSSOS behaves differently in the following way: + +- The active tree will be rendered without any edges. Instead, for each slice in which multiple nodes exist, a spline curve is calculated that goes through these nodes. +- Using the spline curves from before, a 3D surface is generated that interpolates through these curves. The surface can be seen in the 3D viewport. +- The floodfill tool will respect the surface by not crossing it. diff --git a/docs/skeleton_annotation/modes.md b/docs/skeleton_annotation/modes.md index 7ddad58ade8..035f6ccc00c 100644 --- a/docs/skeleton_annotation/modes.md +++ b/docs/skeleton_annotation/modes.md @@ -1,6 +1,6 @@ -# Annotation Modes +# View Modes -WEBKNOSSOS supports several modes for displaying your dataset & interacting with skeleton annotations. +WEBKNOSSOS supports several modes for displaying your dataset & interacting with (skeleton) annotations. ## Orthogonal Mode diff --git a/docs/ui/index.md b/docs/ui/index.md index ef6e60d7255..f2e4edab76a 100644 --- a/docs/ui/index.md +++ b/docs/ui/index.md @@ -2,7 +2,7 @@ The main WEBKNOSSOS user interface for viewing and annotating datasets is divided into five sections: -1. A [toolbar](./toolbar.md) for general purposes features such as Saving your work and displaying the current position within the dataset. Further, it provides access to all the tools for annotating and manipulating your data. It spans along the full width of the top of your screen. +1. A [toolbar](./toolbar.md) for general-purpose features such as saving your work and displaying the current position within the dataset. Further, it provides access to all the tools for annotating and manipulating your data. It spans along the full width of the top of your screen. 2. The [left-hand side panel](./layers.md) provides a list of all available data, segmentation, and annotation layers as well as a settings menu for viewport options and keyboard controls. 3. The center of the screen is occupied by the annotation interface. Your dataset is displayed here, and you navigate and annotate it as desired. Most interactions will take place here. 4. The [right-hand side panel](./object_info.md) is occupied by several tabs providing more information on your current dataset, skeleton/volume annotations, and other lists. Depending on your editing mode these tabs might adapt. diff --git a/docs/ui/toolbar.md b/docs/ui/toolbar.md index df7e90b6b65..27fa8e8ff79 100644 --- a/docs/ui/toolbar.md +++ b/docs/ui/toolbar.md @@ -58,6 +58,29 @@ WEBKNOSSOS offers multiple ways to share your work: - **Layout**: Modify the layout of the WEBKNOSSOS user interface and resize, reorder and adjust viewports and panels to your preferences. Customize the number of columns, show or hide specific tabs, and adjust the size of the sidebar. Save and restore your preferred configurations. +## Modes and Toolkits + +### View Mode + +Datasets can be viewed in different view modes. +Read more about these [here](../skeleton_annotation/modes.md) + +### Toolkits + +WEBKNOSSOS offers several tools that you can use to interact with your datasets. +By default, all tools are available, but it is also possible to only show a subset of tools. +These tool subsets are called "toolkits". +Some of these also fine-tune the behavior of the tools so that they are tailored towards a specific use case. + +Currently, there are four toolkits available: + +- All Tools: This toolkit contains all available tools and is the default. +- Read Only: Only tools that cannot mutate the annotation are available (i.e., move and measuring tools). +- Volume: Only volume tools are listed here. +- Split Segments: This toolkit allows splitting a labeled segment into two parts. Tools in this toolkit behave a bit differently to streamline this workflow. Read more about this toolkit [here](../proofreading/split_segments_toolkit.md). + +![Toolkit Selection](../images/toolkit_dropdown.jpg) + ## Annotation Tools ### Navigation diff --git a/frontend/javascripts/test/model/binary/cube.spec.ts b/frontend/javascripts/test/model/binary/cube.spec.ts index 41fc377e6dc..0f4b262c8c2 100644 --- a/frontend/javascripts/test/model/binary/cube.spec.ts +++ b/frontend/javascripts/test/model/binary/cube.spec.ts @@ -179,7 +179,7 @@ describe("DataCube", () => { ]); }); - it("Voxel Labeling should only instantiate one bucket when labelling the same bucket twice", async ({ + it("Voxel Labeling should only instantiate one bucket when labeling the same bucket twice", async ({ cube, }) => { // Creates bucket From 429f82a2834fc3c8c14ac801f97d4c09227e2a90 Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Wed, 23 Apr 2025 09:34:03 +0200 Subject: [PATCH 71/84] fix incorrect highlighting when measurement tool is active --- .../oxalis/view/action-bar/toolbar_view.tsx | 16 +++++++++++++++- 1 file changed, 15 insertions(+), 1 deletion(-) diff --git a/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx b/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx index dfb02a47d82..e1ab6baabbb 100644 --- a/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx +++ b/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx @@ -852,6 +852,20 @@ function calculateMediumBrushSize(maximumBrushSize: number) { return Math.ceil((maximumBrushSize - userSettings.brushSize.minimum) / 10) * 5; } +function toolToRadioGroupValue(adaptedActiveTool: AnnotationTool): AnnotationTool { + /* + * The tool radio buttons only contain one button for both measurement tools (area + * and line). The selection of the "sub tool" can be done when one of them is active + * with extra buttons next to the radio group. + * To ensure that the highlighting of the generic measurement tool button works properly, + * we map both measurement tools to the line tool here. + */ + if (adaptedActiveTool === AnnotationTool.AREA_MEASUREMENT) { + return AnnotationTool.LINE_MEASUREMENT; + } + return adaptedActiveTool; +} + export default function ToolbarView() { const hasVolume = useSelector((state: OxalisState) => state.annotation?.volumes.length > 0); const hasSkeleton = useSelector((state: OxalisState) => state.annotation?.skeleton != null); @@ -871,7 +885,7 @@ export default function ToolbarView() { return ( <> - + {Toolkits[toolkit].map((tool) => ( ))} From c5b7c6bd9d8d1650787a867f9469f1ffda92a668 Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Wed, 23 Apr 2025 09:36:04 +0200 Subject: [PATCH 72/84] refactor switch statement to record look up --- .../oxalis/view/action-bar/toolbar_view.tsx | 92 +++++++------------ 1 file changed, 34 insertions(+), 58 deletions(-) diff --git a/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx b/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx index e1ab6baabbb..14cc9e9395d 100644 --- a/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx +++ b/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx @@ -37,6 +37,7 @@ import { getDisabledInfoForTools } from "oxalis/model/accessors/disabled_tool_ac import { getActiveTree } from "oxalis/model/accessors/skeletontracing_accessor"; import { AnnotationTool, + type AnnotationToolId, MeasurementTools, Toolkit, VolumeTools, @@ -153,6 +154,8 @@ const handleSetOverwriteMode = (event: { Store.dispatch(updateUserSettingAction("overwriteMode", event.target.value)); }; +type ToolButtonProps = { adaptedActiveTool: AnnotationTool }; + function RadioButtonWithTooltip({ title, disabledTitle, @@ -886,9 +889,10 @@ export default function ToolbarView() { return ( <> - {Toolkits[toolkit].map((tool) => ( - - ))} + {Toolkits[toolkit].map((tool) => { + const ToolButton = ToolIdToComponent[tool.id]; + return ; + })} state.userConfiguration.useLegacyBindings, ); @@ -1298,7 +1302,7 @@ function getIsVolumeModificationAllowed(state: OxalisState) { return hasVolume && !isReadOnly && !hasEditableMapping(state); } -function BrushTool({ adaptedActiveTool }: { adaptedActiveTool: AnnotationTool }) { +function BrushTool({ adaptedActiveTool }: ToolButtonProps) { const disabledInfosForTools = useSelector(getDisabledInfoForTools); const isVolumeModificationAllowed = useSelector(getIsVolumeModificationAllowed); if (!isVolumeModificationAllowed) { @@ -1325,7 +1329,7 @@ function BrushTool({ adaptedActiveTool }: { adaptedActiveTool: AnnotationTool }) ); } -function EraseBrushTool({ adaptedActiveTool }: { adaptedActiveTool: AnnotationTool }) { +function EraseBrushTool({ adaptedActiveTool }: ToolButtonProps) { const disabledInfosForTools = useSelector(getDisabledInfoForTools); const showEraseTraceTool = adaptedActiveTool === AnnotationTool.TRACE || adaptedActiveTool === AnnotationTool.ERASE_TRACE; @@ -1362,7 +1366,7 @@ function EraseBrushTool({ adaptedActiveTool }: { adaptedActiveTool: AnnotationTo ); } -function TraceTool({ adaptedActiveTool }: { adaptedActiveTool: AnnotationTool }) { +function TraceTool({ adaptedActiveTool }: ToolButtonProps) { const disabledInfosForTools = useSelector(getDisabledInfoForTools); const isVolumeModificationAllowed = useSelector(getIsVolumeModificationAllowed); if (!isVolumeModificationAllowed) { @@ -1390,7 +1394,7 @@ function TraceTool({ adaptedActiveTool }: { adaptedActiveTool: AnnotationTool }) ); } -function EraseTraceTool({ adaptedActiveTool }: { adaptedActiveTool: AnnotationTool }) { +function EraseTraceTool({ adaptedActiveTool }: ToolButtonProps) { const disabledInfosForTools = useSelector(getDisabledInfoForTools); const showEraseTraceTool = adaptedActiveTool === AnnotationTool.TRACE || adaptedActiveTool === AnnotationTool.ERASE_TRACE; @@ -1425,7 +1429,7 @@ function EraseTraceTool({ adaptedActiveTool }: { adaptedActiveTool: AnnotationTo ); } -function FillCellTool({ adaptedActiveTool }: { adaptedActiveTool: AnnotationTool }) { +function FillCellTool({ adaptedActiveTool }: ToolButtonProps) { const disabledInfosForTools = useSelector(getDisabledInfoForTools); const isVolumeModificationAllowed = useSelector(getIsVolumeModificationAllowed); if (!isVolumeModificationAllowed) { @@ -1454,7 +1458,7 @@ function FillCellTool({ adaptedActiveTool }: { adaptedActiveTool: AnnotationTool ); } -function PickCellTool() { +function PickCellTool(_props: ToolButtonProps) { const disabledInfosForTools = useSelector(getDisabledInfoForTools); const isVolumeModificationAllowed = useSelector(getIsVolumeModificationAllowed); if (!isVolumeModificationAllowed) { @@ -1478,7 +1482,7 @@ function PickCellTool() { ); } -function QuickSelectTool() { +function QuickSelectTool(_props: ToolButtonProps) { const disabledInfosForTools = useSelector(getDisabledInfoForTools); const isVolumeModificationAllowed = useSelector(getIsVolumeModificationAllowed); if (!isVolumeModificationAllowed) { @@ -1504,7 +1508,7 @@ function QuickSelectTool() { ); } -function BoundingBoxTool() { +function BoundingBoxTool(_props: ToolButtonProps) { const disabledInfosForTools = useSelector(getDisabledInfoForTools); const isReadOnly = useSelector( (state: OxalisState) => !state.annotation.restrictions.allowUpdate, @@ -1532,7 +1536,7 @@ function BoundingBoxTool() { ); } -function ProofreadTool() { +function ProofreadTool(_props: ToolButtonProps) { const dispatch = useDispatch(); const isAgglomerateMappingEnabled = useSelector(hasAgglomerateMapping); const disabledInfosForTools = useSelector(getDisabledInfoForTools); @@ -1581,7 +1585,7 @@ function ProofreadTool() { ); } -function LineMeasurementTool() { +function LineMeasurementTool(_props: ToolButtonProps) { return ( ; - } - case AnnotationTool.SKELETON: { - return ; - } - case AnnotationTool.BRUSH: { - return ; - } - case AnnotationTool.ERASE_BRUSH: { - return ; - } - case AnnotationTool.TRACE: { - return ; - } - case AnnotationTool.ERASE_TRACE: { - return ; - } - case AnnotationTool.FILL_CELL: { - return ; - } - case AnnotationTool.PICK_CELL: { - return ; - } - case AnnotationTool.QUICK_SELECT: { - return ; - } - case AnnotationTool.BOUNDING_BOX: { - return ; - } - case AnnotationTool.PROOFREAD: { - return ; - } - case AnnotationTool.LINE_MEASUREMENT: { - return ; - } - } -} +const ToolIdToComponent: Record JSX.Element | null> = { + [AnnotationTool.MOVE.id]: MoveTool, + [AnnotationTool.SKELETON.id]: SkeletonTool, + [AnnotationTool.BRUSH.id]: BrushTool, + [AnnotationTool.ERASE_BRUSH.id]: EraseBrushTool, + [AnnotationTool.TRACE.id]: TraceTool, + [AnnotationTool.ERASE_TRACE.id]: EraseTraceTool, + [AnnotationTool.FILL_CELL.id]: FillCellTool, + [AnnotationTool.PICK_CELL.id]: PickCellTool, + [AnnotationTool.QUICK_SELECT.id]: QuickSelectTool, + [AnnotationTool.BOUNDING_BOX.id]: BoundingBoxTool, + [AnnotationTool.PROOFREAD.id]: ProofreadTool, + [AnnotationTool.LINE_MEASUREMENT.id]: LineMeasurementTool, + [AnnotationTool.AREA_MEASUREMENT.id]: () => null, +}; function MaybeMultiSliceAnnotationInfoIcon() { const maybeMagWithZoomStep = useSelector(getRenderableMagForActiveSegmentationTracing); From 28ee8ef3b15ca08fdb38c369fef6e588ad00b16b Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Wed, 23 Apr 2025 09:42:23 +0200 Subject: [PATCH 73/84] remove superfluous hint in tooltip --- frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx b/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx index 14cc9e9395d..faa96e012af 100644 --- a/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx +++ b/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx @@ -1281,7 +1281,7 @@ function SkeletonTool(_props: ToolButtonProps) { return ( Date: Wed, 23 Apr 2025 10:00:58 +0200 Subject: [PATCH 74/84] add skeleton pen mode to docs --- .../images/pen-mode-modifier.jpg | Bin 0 -> 21226 bytes docs/skeleton_annotation/tools.md | 10 +++++++++- 2 files changed, 9 insertions(+), 1 deletion(-) create mode 100644 docs/skeleton_annotation/images/pen-mode-modifier.jpg diff --git a/docs/skeleton_annotation/images/pen-mode-modifier.jpg b/docs/skeleton_annotation/images/pen-mode-modifier.jpg new file mode 100644 index 0000000000000000000000000000000000000000..df246b7973ee6a9dcc67b8375e273ec06932a673 GIT binary patch literal 21226 zcmd^n2RxNw*!OeJu{YT%du6Y(9kNGONGN+WWQ)Whg($mF2`Q;$Rno8`Bb%a-Jt|}- zQoj2+=g^?u_x*kE_x;}Q_uc6^_j6zSe_hx8oX0tjweGb6h(=daM-xJTA&d})ptT>+ zw!L0Xc0Nvy9R6-Tt{hrA21aW`$O4_cdk-6#7;5V1YXEKtLS`IuIPOg#4nfD=eY{Mx z)Hn`U9^@eY01-e;5HTbLiP<@Ld#D;2=|g`VU*14K69jdLz`Fj*wl#s$(aGBZf)E^l 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z%DFunK!3}qJ!r`sKh^-`Es(00?5C2xlK=p;mx!7?)($~dsl4@-F@wh@{$ zd!Rbq@65A%#}5gdF~4?$4`3|ggW4!h5vG5dr#vFeVw-FMVk3IXuza<#7pFI#TLha#xXQ4mk)YaUoNSR!^ zuNZ@d9yuWH)ef8Yz437m790njS|5d%PLAH8&V_M~L9?k*QJ`yI*b#hfvPyTF_98QQ zF}24P;_(cquXj_sOC@-w9G%p+5ipCmj|L#FLE~4xUAr`0@*lTm-YjA;+45{;SN zB}|9%$9%aZ*&Qi*W=TlNcNv#SF{xLw$?lQ`5zWfHZhqd(P(MlMfVvAF%tv!&iiq6*XY zeZ&Z<5^V-^rWwjP-4exby&r^m?niU<#aGxiE?mm=qgMs_u>hA#(t3VQDLV2L4gD0U zd8sO|bmf}}bJesLI{Yn^%l08Bb*8H#bN2>UL}gsk?GNeHy<;di*m~HLi+L3DW8g{4 z@r30AI!8!Vj8Tvy2Ju*wt*eJ#dxy%@GOG8M9f3}}X{UZ`vuf za)}Q<;s?jSM}B`OCa+a0{#7A_!<5d~^2?WFw`?f1Ce|PkrNp;QA^P8yQtlE`9VsF? z8Y(UnxdsUjF5E7?pwld^VE^z(i_^1ja Date: Fri, 25 Apr 2025 13:57:32 +0200 Subject: [PATCH 75/84] Update docs/proofreading/split_segments_toolkit.md Co-authored-by: Tom Herold --- docs/proofreading/split_segments_toolkit.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/proofreading/split_segments_toolkit.md b/docs/proofreading/split_segments_toolkit.md index 1466153a6af..94015c94dd5 100644 --- a/docs/proofreading/split_segments_toolkit.md +++ b/docs/proofreading/split_segments_toolkit.md @@ -1,7 +1,7 @@ # Split Segments Toolkit As explained in the [Toolkits](../ui/toolbar.md#Toolkits) section, there is a dedicated toolkit for splitting segments in your volume annotation. -When this toolkit is activated, you can create a curved 3D surface and use it to split a segment into two. +With this toolkit activated, you can draw a curved 3D surface to split a segment into two along this interface. ## Workflow From 06d26c56b88857c3a29e4e760a73679d5fab1994 Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Fri, 25 Apr 2025 13:57:43 +0200 Subject: [PATCH 76/84] Update docs/skeleton_annotation/tools.md Co-authored-by: Tom Herold --- docs/skeleton_annotation/tools.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/skeleton_annotation/tools.md b/docs/skeleton_annotation/tools.md index 9a33ff233da..376889b900f 100644 --- a/docs/skeleton_annotation/tools.md +++ b/docs/skeleton_annotation/tools.md @@ -84,4 +84,4 @@ The following common keyboard shortcuts are handy for speeding up your annotatio | ++c++ | Create New Tree | !!! tip "Keyboard Shortcuts" - For faster workflow, refer to the [keyboard shortcuts](../ui/keyboard_shortcuts.md) guide. + For faster workflows, refer to the [keyboard shortcuts](../ui/keyboard_shortcuts.md) guide. From dbfb1bf867e508a3677c03bf9d9d16b0e85900e6 Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Fri, 25 Apr 2025 13:58:00 +0200 Subject: [PATCH 77/84] Update docs/proofreading/split_segments_toolkit.md Co-authored-by: Tom Herold --- docs/proofreading/split_segments_toolkit.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/proofreading/split_segments_toolkit.md b/docs/proofreading/split_segments_toolkit.md index 94015c94dd5..404d2ee2d3e 100644 --- a/docs/proofreading/split_segments_toolkit.md +++ b/docs/proofreading/split_segments_toolkit.md @@ -28,4 +28,4 @@ By activating that toolkit, WEBKNOSSOS behaves differently in the following way: - The active tree will be rendered without any edges. Instead, for each slice in which multiple nodes exist, a spline curve is calculated that goes through these nodes. - Using the spline curves from before, a 3D surface is generated that interpolates through these curves. The surface can be seen in the 3D viewport. -- The floodfill tool will respect the surface by not crossing it. +- The flood-fill tool will respect the splitting surface by not crossing it. From 34510d075c0197df206a0f6b23261b6dede07040 Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Fri, 25 Apr 2025 13:58:28 +0200 Subject: [PATCH 78/84] Update docs/proofreading/split_segments_toolkit.md Co-authored-by: Tom Herold --- docs/proofreading/split_segments_toolkit.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/proofreading/split_segments_toolkit.md b/docs/proofreading/split_segments_toolkit.md index 404d2ee2d3e..9c0d8639181 100644 --- a/docs/proofreading/split_segments_toolkit.md +++ b/docs/proofreading/split_segments_toolkit.md @@ -7,7 +7,7 @@ With this toolkit activated, you can draw a curved 3D surface to split a segment The recommended steps for splitting a segment are as follows: -- Use the bounding box tool to create a box around the merge error that you want to correct. Theoretically, this step is optional, but keep in mind that relabeling large parts of a segment can be infeasible due to resources. Consider using the [proofreading tool](../proofreading/tools.html) for larger corrections. If you want to correct data for the purpose of groundtruth, it is often enough to only do a local correction. +- Use the bounding box tool to create a box around the merge error that you want to correct. Theoretically, this step is optional, but keep in mind that relabeling large parts of a segment requires a lot of computing resources and is limited by your computer performance. Consider using the [proofreading tool](../proofreading/tools.html) for large-scale corrections. If you want to correct data for the purpose of ground-truth, it is often enough to only do a local correction instead of proof-reading the whole dataset. - Go to the first z slice of the bounding box. - Create a new skeleton tree and place nodes on the boundary that should split the segment into two. Consider activating the "Pen" mode within the skeleton tool so that you can rapidly draw nodes by dragging the mouse while it's pressed down. - Go to the last z slice of the bounding box and repeat the previous step. From d10ac1d9d04008903e454980218fad4f29836adf Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Fri, 25 Apr 2025 13:58:57 +0200 Subject: [PATCH 79/84] Update docs/proofreading/split_segments_toolkit.md Co-authored-by: Tom Herold --- docs/proofreading/split_segments_toolkit.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/proofreading/split_segments_toolkit.md b/docs/proofreading/split_segments_toolkit.md index 9c0d8639181..356c92440a4 100644 --- a/docs/proofreading/split_segments_toolkit.md +++ b/docs/proofreading/split_segments_toolkit.md @@ -12,7 +12,7 @@ The recommended steps for splitting a segment are as follows: - Create a new skeleton tree and place nodes on the boundary that should split the segment into two. Consider activating the "Pen" mode within the skeleton tool so that you can rapidly draw nodes by dragging the mouse while it's pressed down. - Go to the last z slice of the bounding box and repeat the previous step. - Now you can inspect all the slices in between. A smooth spline curve will be shown in each slice that is derived from interpolating between adjacent slices. If you want to correct the interpolation, you can create new nodes on a slice. A new spline curve will be computed from these points and the interpolation will be updated. -- If you are satisfied with the (interpolated) boundary, you can switch to the fill tool. Ensure to enable the 3D mode as well as the "Restrict to Bounding Box" mode. +- If you are satisfied with the (interpolated) boundary, you can switch to the fill tool and relabel one side, effectively splitting a segment into two. Ensure to enable the 3D mode as well as the "Restrict to Bounding Box" mode. ## Troubleshooting From 6cad8016ba7f8bf4572737913f9f42368fc2b12f Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Fri, 25 Apr 2025 13:59:44 +0200 Subject: [PATCH 80/84] Update docs/proofreading/split_segments_toolkit.md Co-authored-by: Tom Herold --- docs/proofreading/split_segments_toolkit.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/docs/proofreading/split_segments_toolkit.md b/docs/proofreading/split_segments_toolkit.md index 356c92440a4..f989111f256 100644 --- a/docs/proofreading/split_segments_toolkit.md +++ b/docs/proofreading/split_segments_toolkit.md @@ -16,7 +16,7 @@ The recommended steps for splitting a segment are as follows: ## Troubleshooting -- It can easily happen that the floodfill operation relabels the entire segment instead of only the part you intended to relabel. The cause of this is usually that the 3D surface doesn't cut the segment completely. Instead, the surface might only go very close to the edge. In that case, the floodfill operation can traverse over that edge and thus relabel everything (see image below). If this happens, you should undo the fill operation and double-check the surface. To avoid this problem, it is recommended to make the surface a bit bigger than usual. +- It can easily happen that the flood-fill operation relabels the entire segment instead of only the part you intended to relabel. This is usually caused by the 3D surface not completely cutting through the segment. Instead, the surface might only go very close to the edge. In that case, the flood-fill operation can traverse over that edge and thus relabel everything (see image below). If this happens, you should undo the fill operation and double-check the surface. To avoid this problem, it is recommended to draw the splitting surface a bit bigger than the actual segment boundaries. - If multiple spline curves appear per slice, this is often due to a configuration issue. Please adapt the clipping distance in the left sidebar ("Layers" -> "Skeleton"). ![A visualization of a floodfill operation "bleeding" across the boundary because the boundary is not precise enough](../images/splitting-floodfill-visualization.png) From 87ef13d59608df944ca35ac0764727f20561dd31 Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Fri, 25 Apr 2025 14:05:53 +0200 Subject: [PATCH 81/84] use ordered list in docs --- docs/proofreading/split_segments_toolkit.md | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/docs/proofreading/split_segments_toolkit.md b/docs/proofreading/split_segments_toolkit.md index f989111f256..c077fbbd010 100644 --- a/docs/proofreading/split_segments_toolkit.md +++ b/docs/proofreading/split_segments_toolkit.md @@ -7,12 +7,12 @@ With this toolkit activated, you can draw a curved 3D surface to split a segment The recommended steps for splitting a segment are as follows: -- Use the bounding box tool to create a box around the merge error that you want to correct. Theoretically, this step is optional, but keep in mind that relabeling large parts of a segment requires a lot of computing resources and is limited by your computer performance. Consider using the [proofreading tool](../proofreading/tools.html) for large-scale corrections. If you want to correct data for the purpose of ground-truth, it is often enough to only do a local correction instead of proof-reading the whole dataset. -- Go to the first z slice of the bounding box. -- Create a new skeleton tree and place nodes on the boundary that should split the segment into two. Consider activating the "Pen" mode within the skeleton tool so that you can rapidly draw nodes by dragging the mouse while it's pressed down. -- Go to the last z slice of the bounding box and repeat the previous step. -- Now you can inspect all the slices in between. A smooth spline curve will be shown in each slice that is derived from interpolating between adjacent slices. If you want to correct the interpolation, you can create new nodes on a slice. A new spline curve will be computed from these points and the interpolation will be updated. -- If you are satisfied with the (interpolated) boundary, you can switch to the fill tool and relabel one side, effectively splitting a segment into two. Ensure to enable the 3D mode as well as the "Restrict to Bounding Box" mode. +1. Use the bounding box tool to create a box around the merge error that you want to correct. Theoretically, this step is optional, but keep in mind that relabeling large parts of a segment requires a lot of computing resources and is limited by your computer performance. Consider using the [proofreading tool](../proofreading/tools.html) for large-scale corrections. If you want to correct data for the purpose of ground-truth, it is often enough to only do a local correction instead of proof-reading the whole dataset. +2. Go to the first z slice of the bounding box. +3. Create a new skeleton tree and place nodes on the boundary that should split the segment into two. Consider activating the "Pen" mode within the skeleton tool so that you can rapidly draw nodes by dragging the mouse while it's pressed down. +4. Go to the last z slice of the bounding box and repeat the previous step. +5. Now you can inspect all the slices in between. A smooth spline curve will be shown in each slice that is derived from interpolating between adjacent slices. If you want to correct the interpolation, you can create new nodes on a slice. A new spline curve will be computed from these points and the interpolation will be updated. +6. If you are satisfied with the (interpolated) boundary, you can switch to the fill tool and relabel one side, effectively splitting a segment into two. Ensure to enable the 3D mode as well as the "Restrict to Bounding Box" mode. ## Troubleshooting From de740254d8a75aa701e5a09c342a167d2f365336 Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Fri, 25 Apr 2025 14:47:54 +0200 Subject: [PATCH 82/84] proof-read -> proofread; misc --- README.md | 4 ++-- docs/getting_started.md | 2 +- docs/proofreading/split_segments_toolkit.md | 4 ++-- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index a325b932982..3dd22b3e9cb 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ WEBKNOSSOS Logo WEBKNOSSOS is an open-source tool for annotating and exploring large 3D image datasets. -* Fly through your data for fast skeletonization and proof-reading +* Fly through your data for fast skeletonization and proofreading * Create 3D training data for automated segmentations efficiently * Scale data reconstruction projects with crowdsourcing workflows * Share datasets and annotations with collaborating scientists @@ -25,7 +25,7 @@ WEBKNOSSOS is an open-source tool for annotating and exploring large 3D image da * Optimized performance for large annotations * User and task management for high-throughput crowdsourcing * Sharing and collaboration features -* Proof-Reading tools for working with large (over)-segmentations +* Proofreading tools for working with large (over)-segmentations * [Standalone datastore component](https://github.com/scalableminds/webknossos/tree/master/webknossos-datastore) for flexible deployments * Supported dataset formats: [WKW](https://github.com/scalableminds/webknossos-wrap), [Neuroglancer Precomputed](https://github.com/google/neuroglancer/tree/master/src/datasource/precomputed), [Zarr](https://zarr.dev), [N5](https://github.com/saalfeldlab/n5) * Supported image formats: Grayscale, Segmentation Maps, RGB, Multi-Channel diff --git a/docs/getting_started.md b/docs/getting_started.md index 8bd074363d1..09b14c7c14a 100644 --- a/docs/getting_started.md +++ b/docs/getting_started.md @@ -82,7 +82,7 @@ Now you know the basics of WEBKNOSSOS. Feel free to explore more features of WEBKNOSSOS in this documentation. - [Dashboard](./dashboard/index.md) -- [Volume Annotations & Proof-Reading](./volume_annotation/index.md) +- [Volume Annotations & Proofreading](./volume_annotation/index.md) - [Skeleton Annotations](./skeleton_annotation/index.md) - [Understanding the User Interface](./ui/index.md) - [Keyboard Shortcuts](./ui/keyboard_shortcuts.md) diff --git a/docs/proofreading/split_segments_toolkit.md b/docs/proofreading/split_segments_toolkit.md index c077fbbd010..0698b300be5 100644 --- a/docs/proofreading/split_segments_toolkit.md +++ b/docs/proofreading/split_segments_toolkit.md @@ -7,7 +7,7 @@ With this toolkit activated, you can draw a curved 3D surface to split a segment The recommended steps for splitting a segment are as follows: -1. Use the bounding box tool to create a box around the merge error that you want to correct. Theoretically, this step is optional, but keep in mind that relabeling large parts of a segment requires a lot of computing resources and is limited by your computer performance. Consider using the [proofreading tool](../proofreading/tools.html) for large-scale corrections. If you want to correct data for the purpose of ground-truth, it is often enough to only do a local correction instead of proof-reading the whole dataset. +1. Use the bounding box tool to create a box around the merge error you want to correct. Theoretically, this step is optional, but keep in mind that relabeling large parts of a segment requires a lot of computing resources and is limited by your computer performance. Consider using the [proofreading tool](../proofreading/tools.html) for large-scale corrections. If you want to correct data for the purpose of ground-truth, it is often enough to only do a local correction instead of proofreading the whole dataset. 2. Go to the first z slice of the bounding box. 3. Create a new skeleton tree and place nodes on the boundary that should split the segment into two. Consider activating the "Pen" mode within the skeleton tool so that you can rapidly draw nodes by dragging the mouse while it's pressed down. 4. Go to the last z slice of the bounding box and repeat the previous step. @@ -17,7 +17,7 @@ The recommended steps for splitting a segment are as follows: ## Troubleshooting - It can easily happen that the flood-fill operation relabels the entire segment instead of only the part you intended to relabel. This is usually caused by the 3D surface not completely cutting through the segment. Instead, the surface might only go very close to the edge. In that case, the flood-fill operation can traverse over that edge and thus relabel everything (see image below). If this happens, you should undo the fill operation and double-check the surface. To avoid this problem, it is recommended to draw the splitting surface a bit bigger than the actual segment boundaries. -- If multiple spline curves appear per slice, this is often due to a configuration issue. Please adapt the clipping distance in the left sidebar ("Layers" -> "Skeleton"). +- If multiple spline curves appear per slice, this is often due to a configuration issue. Please adapt the clipping distance in the left sidebar (`Layers` → `Skeleton`). ![A visualization of a floodfill operation "bleeding" across the boundary because the boundary is not precise enough](../images/splitting-floodfill-visualization.png) From 99fd8c02a3c0dbbdaae754cd7fa902ba3087ee4b Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Tue, 29 Apr 2025 08:48:27 +0200 Subject: [PATCH 83/84] pr feedback --- frontend/javascripts/libs/order_points_with_mst.ts | 2 +- frontend/javascripts/oxalis/model/sagas/annotation_tool_saga.ts | 2 +- .../javascripts/oxalis/model/sagas/split_boundary_mesh_saga.ts | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/frontend/javascripts/libs/order_points_with_mst.ts b/frontend/javascripts/libs/order_points_with_mst.ts index ce16c23bfd5..c3d64a58948 100644 --- a/frontend/javascripts/libs/order_points_with_mst.ts +++ b/frontend/javascripts/libs/order_points_with_mst.ts @@ -26,7 +26,7 @@ export function orderPointsWithMST(points: THREE.Vector3[]): THREE.Vector3[] { return bestOrder.map((index) => points[index]); } -// Mostly generated with ChatGPT: +// Mostly generated with ChatGPT (treat with care): class DisjointSet { // Union find datastructure diff --git a/frontend/javascripts/oxalis/model/sagas/annotation_tool_saga.ts b/frontend/javascripts/oxalis/model/sagas/annotation_tool_saga.ts index 3f20b44596c..2c755a33f91 100644 --- a/frontend/javascripts/oxalis/model/sagas/annotation_tool_saga.ts +++ b/frontend/javascripts/oxalis/model/sagas/annotation_tool_saga.ts @@ -115,7 +115,7 @@ export function* watchToolReset(): Saga { yield* take("ESCAPE"); const activeTool = yield* select((state) => state.uiInformation.activeTool); if (MeasurementTools.indexOf(activeTool) >= 0) { - const sceneController = yield* call(() => getSceneController()); + const sceneController = yield* call(getSceneController); const geometry = activeTool === AnnotationTool.AREA_MEASUREMENT ? sceneController.areaMeasurementGeometry diff --git a/frontend/javascripts/oxalis/model/sagas/split_boundary_mesh_saga.ts b/frontend/javascripts/oxalis/model/sagas/split_boundary_mesh_saga.ts index 6b7e4cb205c..fb68c4d8365 100644 --- a/frontend/javascripts/oxalis/model/sagas/split_boundary_mesh_saga.ts +++ b/frontend/javascripts/oxalis/model/sagas/split_boundary_mesh_saga.ts @@ -49,7 +49,7 @@ function* updateSplitBoundaryMesh() { return; } - const sceneController = yield* call(() => getSceneController()); + const sceneController = yield* call(getSceneController); const activeTree = yield* select((state) => getActiveTree(state.annotation.skeleton)); From 4e304caf0fe7637da8d40f3bf432bbdd0f47ba8a Mon Sep 17 00:00:00 2001 From: Philipp Otto Date: Tue, 29 Apr 2025 09:53:52 +0200 Subject: [PATCH 84/84] split toolbar_view into several files and move into action-bar/tools subfolder --- .../controller/viewmodes/plane_controller.tsx | 2 +- .../oxalis/view/action-bar/toolbar_view.tsx | 1633 ----------------- .../view/action-bar/tools/brush_presets.tsx | 256 +++ .../action-bar/tools/skeleton_specific_ui.tsx | 184 ++ .../view/action-bar/tools/tool_buttons.tsx | 405 ++++ .../view/action-bar/tools/tool_helpers.tsx | 92 + .../view/action-bar/tools/toolbar_view.tsx | 272 +++ .../{ => tools}/toolkit_switcher_view.tsx | 2 +- .../action-bar/tools/volume_specific_ui.tsx | 492 +++++ .../view/action-bar/view_modes_view.tsx | 2 +- .../oxalis/view/action_bar_view.tsx | 4 +- 11 files changed, 1706 insertions(+), 1638 deletions(-) delete mode 100644 frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx create mode 100644 frontend/javascripts/oxalis/view/action-bar/tools/brush_presets.tsx create mode 100644 frontend/javascripts/oxalis/view/action-bar/tools/skeleton_specific_ui.tsx create mode 100644 frontend/javascripts/oxalis/view/action-bar/tools/tool_buttons.tsx create mode 100644 frontend/javascripts/oxalis/view/action-bar/tools/tool_helpers.tsx create mode 100644 frontend/javascripts/oxalis/view/action-bar/tools/toolbar_view.tsx rename frontend/javascripts/oxalis/view/action-bar/{ => tools}/toolkit_switcher_view.tsx (97%) create mode 100644 frontend/javascripts/oxalis/view/action-bar/tools/volume_specific_ui.tsx diff --git a/frontend/javascripts/oxalis/controller/viewmodes/plane_controller.tsx b/frontend/javascripts/oxalis/controller/viewmodes/plane_controller.tsx index ab272315753..f1d4e7839b8 100644 --- a/frontend/javascripts/oxalis/controller/viewmodes/plane_controller.tsx +++ b/frontend/javascripts/oxalis/controller/viewmodes/plane_controller.tsx @@ -62,7 +62,7 @@ import { listenToStoreProperty } from "oxalis/model/helpers/listener_helpers"; import { Model, api } from "oxalis/singletons"; import type { BrushPresets, OxalisState, StoreAnnotation } from "oxalis/store"; import Store from "oxalis/store"; -import { getDefaultBrushSizes } from "oxalis/view/action-bar/toolbar_view"; +import { getDefaultBrushSizes } from "oxalis/view/action-bar/tools/brush_presets"; import { showToastWarningForLargestSegmentIdMissing } from "oxalis/view/largest_segment_id_modal"; import PlaneView from "oxalis/view/plane_view"; import { downloadScreenshot } from "oxalis/view/rendering_utils"; diff --git a/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx b/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx deleted file mode 100644 index faa96e012af..00000000000 --- a/frontend/javascripts/oxalis/view/action-bar/toolbar_view.tsx +++ /dev/null @@ -1,1633 +0,0 @@ -import { - ClearOutlined, - DownOutlined, - ExportOutlined, - InfoCircleOutlined, - SettingOutlined, -} from "@ant-design/icons"; -import { - Badge, - Col, - Divider, - Dropdown, - type MenuProps, - Popconfirm, - Popover, - Radio, - type RadioChangeEvent, - Row, - Space, - Tag, -} from "antd"; -import React, { useEffect, useCallback, useState } from "react"; -import { useDispatch, useSelector } from "react-redux"; - -import { useKeyPress, usePrevious } from "libs/react_hooks"; -import { document } from "libs/window"; -import { - FillModeEnum, - type InterpolationMode, - InterpolationModeEnum, - MappingStatusEnum, - type OverwriteMode, - OverwriteModeEnum, - Unicode, -} from "oxalis/constants"; -import { getDisabledInfoForTools } from "oxalis/model/accessors/disabled_tool_accessor"; -import { getActiveTree } from "oxalis/model/accessors/skeletontracing_accessor"; -import { - AnnotationTool, - type AnnotationToolId, - MeasurementTools, - Toolkit, - VolumeTools, -} from "oxalis/model/accessors/tool_accessor"; -import { Toolkits, adaptActiveToolToShortcuts } from "oxalis/model/accessors/tool_accessor"; -import { - getActiveSegmentationTracing, - getMappingInfoForVolumeTracing, - getMaximumBrushSize, - getRenderableMagForActiveSegmentationTracing, - getSegmentColorAsRGBA, - hasAgglomerateMapping, - hasEditableMapping, -} from "oxalis/model/accessors/volumetracing_accessor"; -import { addUserBoundingBoxAction } from "oxalis/model/actions/annotation_actions"; -import { updateUserSettingAction } from "oxalis/model/actions/settings_actions"; -import { - createTreeAction, - setMergerModeEnabledAction, -} from "oxalis/model/actions/skeletontracing_actions"; -import { setToolAction, showQuickSelectSettingsAction } from "oxalis/model/actions/ui_actions"; -import { - createCellAction, - interpolateSegmentationLayerAction, - setMousePositionAction, -} from "oxalis/model/actions/volumetracing_actions"; -import { Model } from "oxalis/singletons"; -import Store, { type BrushPresets, type OxalisState } from "oxalis/store"; -import { MaterializeVolumeAnnotationModal } from "oxalis/view/action-bar/starting_job_modals"; -import ButtonComponent, { ToggleButton } from "oxalis/view/components/button_component"; -import { LogSliderSetting } from "oxalis/view/components/setting_input_views"; -import { showToastWarningForLargestSegmentIdMissing } from "oxalis/view/largest_segment_id_modal"; -import { userSettings } from "types/schemas/user_settings.schema"; - -import { updateNovelUserExperienceInfos } from "admin/admin_rest_api"; -import FastTooltip from "components/fast_tooltip"; -import features from "features"; -import { useIsActiveUserAdminOrManager } from "libs/react_helpers"; -import defaultState from "oxalis/default_state"; -import { getViewportExtents } from "oxalis/model/accessors/view_mode_accessor"; -import { ensureLayerMappingsAreLoadedAction } from "oxalis/model/actions/dataset_actions"; -import { clearProofreadingByProducts } from "oxalis/model/actions/proofread_actions"; -import { setActiveUserAction } from "oxalis/model/actions/user_actions"; -import { getInterpolationInfo } from "oxalis/model/sagas/volume/volume_interpolation_saga"; -import { rgbaToCSS } from "oxalis/shaders/utils.glsl"; -import type { MenuInfo } from "rc-menu/lib/interface"; -import { APIJobType } from "types/api_flow_types"; -import { QuickSelectControls } from "./quick_select_settings"; - -export const NARROW_BUTTON_STYLE = { - paddingLeft: 10, - paddingRight: 8, -}; -const imgStyleForSpaceyIcons = { - width: 19, - height: 19, - lineHeight: 10, - marginTop: -2, - verticalAlign: "middle", -}; - -function toggleOverwriteMode(overwriteMode: OverwriteMode) { - if (overwriteMode === OverwriteModeEnum.OVERWRITE_ALL) { - return OverwriteModeEnum.OVERWRITE_EMPTY; - } else { - return OverwriteModeEnum.OVERWRITE_ALL; - } -} - -const handleUpdateBrushSize = (value: number) => { - Store.dispatch(updateUserSettingAction("brushSize", value)); -}; - -const handleUpdatePresetBrushSizes = (brushSizes: BrushPresets) => { - Store.dispatch(updateUserSettingAction("presetBrushSizes", brushSizes)); -}; - -const handleToggleAutomaticMeshRendering = (value: boolean) => { - Store.dispatch(updateUserSettingAction("autoRenderMeshInProofreading", value)); -}; - -const handleToggleSelectiveVisibilityInProofreading = (value: boolean) => { - Store.dispatch(updateUserSettingAction("selectiveVisibilityInProofreading", value)); -}; - -const handleSetTool = (event: RadioChangeEvent) => { - const value = event.target.value as AnnotationTool; - Store.dispatch(setToolAction(value)); -}; - -const handleCreateCell = () => { - const volumeTracing = getActiveSegmentationTracing(Store.getState()); - - if (volumeTracing == null || volumeTracing.tracingId == null) { - return; - } - - if (volumeTracing.largestSegmentId != null) { - Store.dispatch(createCellAction(volumeTracing.activeCellId, volumeTracing.largestSegmentId)); - } else { - showToastWarningForLargestSegmentIdMissing(volumeTracing); - } -}; - -const handleAddNewUserBoundingBox = () => { - Store.dispatch(addUserBoundingBoxAction()); -}; - -const handleSetOverwriteMode = (event: { - target: { - value: OverwriteMode; - }; -}) => { - Store.dispatch(updateUserSettingAction("overwriteMode", event.target.value)); -}; - -type ToolButtonProps = { adaptedActiveTool: AnnotationTool }; - -function RadioButtonWithTooltip({ - title, - disabledTitle, - disabled, - onClick, - children, - onMouseEnter, - ...props -}: { - title: string; - disabledTitle?: string; - disabled?: boolean; - children: React.ReactNode; - style?: React.CSSProperties; - value: unknown; - onClick?: (event: React.MouseEvent) => void; - onMouseEnter?: () => void; -}) { - // FastTooltip adds data-* properties so that the centralized ReactTooltip - // is hooked up here. Unfortunately, FastTooltip would add another div or span - // which antd does not like within this toolbar. - // Therefore, we move the tooltip into the button which requires tweaking the padding - // a bit (otherwise, the tooltip would only occur when hovering exactly over the icon - // instead of everywhere within the button). - return ( - { - if (document.activeElement) { - (document.activeElement as HTMLElement).blur(); - } - if (onClick) { - onClick(event); - } - }} - {...props} - > - - {/* See comments above. */} - {children} - - - ); -} - -function ToolRadioButton({ - name, - description, - disabledExplanation, - onMouseEnter, - ...props -}: { - name: string; - description: string; - disabledExplanation?: string; - disabled?: boolean; - children: React.ReactNode; - style?: React.CSSProperties; - value: unknown; - onClick?: (event: React.MouseEvent) => void; - onMouseEnter?: () => void; -}) { - return ( - - ); -} - -function OverwriteModeSwitch({ - isControlOrMetaPressed, - isShiftPressed, - visible, -}: { - isControlOrMetaPressed: boolean; - isShiftPressed: boolean; - visible: boolean; -}) { - // Only CTRL should modify the overwrite mode. CTRL + Shift can be used to switch to the - // erase tool, which should not affect the default overwrite mode. - const overwriteMode = useSelector((state: OxalisState) => state.userConfiguration.overwriteMode); - const previousIsControlOrMetaPressed = usePrevious(isControlOrMetaPressed); - const previousIsShiftPressed = usePrevious(isShiftPressed); - // biome-ignore lint/correctness/useExhaustiveDependencies: overwriteMode does not need to be a dependency. - useEffect(() => { - // There are four possible states: - // (1) no modifier is pressed - // (2) CTRL is pressed - // (3) Shift is pressed - // (4) CTRL + Shift is pressed - // The overwrite mode needs to be toggled when - // - switching from state (1) to (2) (or vice versa) - // - switching from state (2) to (4) (or vice versa) - // Consequently, the mode is only toggled effectively, when CTRL is pressed. - // Alternatively, we could store the selected value and the overridden value - // separately in the store. However, this solution works, too. - const needsModeToggle = - (!isShiftPressed && - isControlOrMetaPressed && - previousIsControlOrMetaPressed === previousIsShiftPressed) || - (isShiftPressed === isControlOrMetaPressed && - !previousIsShiftPressed && - previousIsControlOrMetaPressed); - - if (needsModeToggle) { - Store.dispatch(updateUserSettingAction("overwriteMode", toggleOverwriteMode(overwriteMode))); - } - }, [ - isControlOrMetaPressed, - isShiftPressed, - previousIsControlOrMetaPressed, - previousIsShiftPressed, - ]); - - if (!visible) { - // This component's hooks should still be active, even when the component is invisible. - // Otherwise, the toggling of the overwrite mode via "Ctrl" wouldn't work consistently - // when being combined with other modifiers, which hide the component. - return null; - } - - return ( - - - Overwrite All Icon - - - Overwrite Empty Icon - - - ); -} - -const INTERPOLATION_ICON = { - [InterpolationModeEnum.INTERPOLATE]: , - [InterpolationModeEnum.EXTRUDE]: , -}; -function VolumeInterpolationButton() { - const dispatch = useDispatch(); - const interpolationMode = useSelector( - (state: OxalisState) => state.userConfiguration.interpolationMode, - ); - - const onInterpolateClick = (e: React.MouseEvent | null) => { - e?.currentTarget.blur(); - dispatch(interpolateSegmentationLayerAction()); - }; - - const { tooltipTitle, isDisabled } = useSelector((state: OxalisState) => - getInterpolationInfo(state, "Not available since"), - ); - - const menu: MenuProps = { - onClick: (e: MenuInfo) => { - dispatch(updateUserSettingAction("interpolationMode", e.key as InterpolationMode)); - onInterpolateClick(null); - }, - items: [ - { - label: "Interpolate current segment", - key: InterpolationModeEnum.INTERPOLATE, - icon: INTERPOLATION_ICON[InterpolationModeEnum.INTERPOLATE], - }, - { - label: "Extrude (copy) current segment", - key: InterpolationModeEnum.EXTRUDE, - icon: INTERPOLATION_ICON[InterpolationModeEnum.EXTRUDE], - }, - ], - }; - - const buttonsRender = useCallback( - ([leftButton, rightButton]: React.ReactNode[]) => [ - - {React.cloneElement(leftButton as React.ReactElement, { - disabled: isDisabled, - })} - , - rightButton, - ], - [tooltipTitle, isDisabled], - ); - - return ( - // Without the outer div, the Dropdown can eat up all the remaining horizontal space, - // moving sibling elements to the far right. -
- } - menu={menu} - onClick={onInterpolateClick} - style={{ padding: "0 5px 0 6px" }} - buttonsRender={buttonsRender} - > - {React.cloneElement(INTERPOLATION_ICON[interpolationMode], { style: { margin: -4 } })} - -
- ); -} - -function SkeletonSpecificButtons() { - const dispatch = useDispatch(); - const isMergerModeEnabled = useSelector( - (state: OxalisState) => state.temporaryConfiguration.isMergerModeEnabled, - ); - const [showMaterializeVolumeAnnotationModal, setShowMaterializeVolumeAnnotationModal] = - useState(false); - const isNewNodeNewTreeModeOn = useSelector( - (state: OxalisState) => state.userConfiguration.newNodeNewTree, - ); - const isContinuousNodeCreationEnabled = useSelector( - (state: OxalisState) => state.userConfiguration.continuousNodeCreation, - ); - const isSplitToolkit = useSelector( - (state: OxalisState) => state.userConfiguration.activeToolkit === Toolkit.SPLIT_SEGMENTS, - ); - const toggleContinuousNodeCreation = () => - dispatch(updateUserSettingAction("continuousNodeCreation", !isContinuousNodeCreationEnabled)); - - const dataset = useSelector((state: OxalisState) => state.dataset); - const isUserAdminOrManager = useIsActiveUserAdminOrManager(); - - const segmentationTracingLayer = useSelector((state: OxalisState) => - getActiveSegmentationTracing(state), - ); - const isEditableMappingActive = - segmentationTracingLayer != null && !!segmentationTracingLayer.hasEditableMapping; - const isMappingLockedWithNonNull = - segmentationTracingLayer != null && - !!segmentationTracingLayer.mappingIsLocked && - segmentationTracingLayer.mappingName != null; - const isMergerModeDisabled = isEditableMappingActive || isMappingLockedWithNonNull; - const mergerModeTooltipText = isEditableMappingActive - ? "Merger mode cannot be enabled while an editable mapping is active." - : isMappingLockedWithNonNull - ? "Merger mode cannot be enabled while a mapping is locked. Please create a new annotation and use the merger mode there." - : "Toggle Merger Mode - When enabled, skeletons that connect multiple segments will merge those segments."; - - const toggleNewNodeNewTreeMode = () => - dispatch(updateUserSettingAction("newNodeNewTree", !isNewNodeNewTreeModeOn)); - - const toggleMergerMode = () => dispatch(setMergerModeEnabledAction(!isMergerModeEnabled)); - - const isMaterializeVolumeAnnotationEnabled = - dataset.dataStore.jobsSupportedByAvailableWorkers.includes( - APIJobType.MATERIALIZE_VOLUME_ANNOTATION, - ); - - return ( - - - {isSplitToolkit ? null : ( - - Single Node Tree Mode - - )} - {isSplitToolkit ? null : ( - - Merger Mode - - )} - - - - - {isMergerModeEnabled && isMaterializeVolumeAnnotationEnabled && isUserAdminOrManager && ( - setShowMaterializeVolumeAnnotationModal(true)} - title="Materialize this merger mode annotation into a new dataset." - > - - - )} - {isMaterializeVolumeAnnotationEnabled && showMaterializeVolumeAnnotationModal && ( - setShowMaterializeVolumeAnnotationModal(false)} - /> - )} - - ); -} - -const mapId = (volumeTracingId: string | null | undefined, id: number) => { - // Note that the return value can be an unmapped id even when - // a mapping is active, if it is a HDF5 mapping that is partially loaded - // and no entry exists yet for the input id. - if (!volumeTracingId) { - return null; - } - const { cube } = Model.getSegmentationTracingLayer(volumeTracingId); - - return cube.mapId(id); -}; - -function CreateCellButton() { - const volumeTracingId = useSelector( - (state: OxalisState) => getActiveSegmentationTracing(state)?.tracingId, - ); - const unmappedActiveCellId = useSelector( - (state: OxalisState) => getActiveSegmentationTracing(state)?.activeCellId || 0, - ); - const { mappingStatus } = useSelector((state: OxalisState) => - getMappingInfoForVolumeTracing(state, volumeTracingId), - ); - const isMappingEnabled = mappingStatus === MappingStatusEnum.ENABLED; - - const activeCellId = isMappingEnabled - ? mapId(volumeTracingId, unmappedActiveCellId) - : unmappedActiveCellId; - - const activeCellColor = useSelector((state: OxalisState) => { - if (!activeCellId) { - return null; - } - return rgbaToCSS(getSegmentColorAsRGBA(state, activeCellId)); - }); - - const mappedIdInfo = isMappingEnabled ? ` (currently mapped to ${activeCellId})` : ""; - return ( - - - New Segment Icon - - - ); -} - -function CreateNewBoundingBoxButton() { - return ( - - New Bounding Box Icon - - ); -} - -function CreateTreeButton() { - const dispatch = useDispatch(); - const activeTree = useSelector((state: OxalisState) => getActiveTree(state.annotation.skeleton)); - const rgbColorString = - activeTree != null - ? `rgb(${activeTree.color.map((c) => Math.round(c * 255)).join(",")})` - : "transparent"; - const activeTreeHint = - activeTree != null - ? `The active tree id is ${activeTree.treeId}.` - : "No tree is currently selected"; - - const handleCreateTree = () => dispatch(createTreeAction()); - - return ( - - - - - - - ); -} - -function BrushPresetButton({ - name, - icon, - brushSize, - onClick, -}: { - name: string; - onClick: () => void; - icon: JSX.Element; - brushSize: number; -}) { - const { ThinSpace } = Unicode; - return ( - <> -
- {icon} -
-
{name}
-
- {brushSize} - {ThinSpace}vx -
- - ); -} - -export function getDefaultBrushSizes(maximumSize: number, minimumSize: number) { - return { - small: Math.max(minimumSize, 10), - medium: calculateMediumBrushSize(maximumSize), - large: maximumSize, - }; -} - -function ChangeBrushSizePopover() { - const dispatch = useDispatch(); - const brushSize = useSelector((state: OxalisState) => state.userConfiguration.brushSize); - const [isBrushSizePopoverOpen, setIsBrushSizePopoverOpen] = useState(false); - const maximumBrushSize = useSelector((state: OxalisState) => getMaximumBrushSize(state)); - - const defaultBrushSizes = getDefaultBrushSizes(maximumBrushSize, userSettings.brushSize.minimum); - const presetBrushSizes = useSelector( - (state: OxalisState) => state.userConfiguration.presetBrushSizes, - ); - // biome-ignore lint/correctness/useExhaustiveDependencies: Needs investigation whether defaultBrushSizes is needed as dependency. - useEffect(() => { - if (presetBrushSizes == null) { - handleUpdatePresetBrushSizes(defaultBrushSizes); - } - }, [presetBrushSizes]); - - let smallBrushSize: number, mediumBrushSize: number, largeBrushSize: number; - if (presetBrushSizes == null) { - smallBrushSize = defaultBrushSizes.small; - mediumBrushSize = defaultBrushSizes.medium; - largeBrushSize = defaultBrushSizes.large; - } else { - smallBrushSize = presetBrushSizes?.small; - mediumBrushSize = presetBrushSizes?.medium; - largeBrushSize = presetBrushSizes?.large; - } - - const centerBrushInViewport = () => { - const position = getViewportExtents(Store.getState()); - const activeViewPort = Store.getState().viewModeData.plane.activeViewport; - dispatch( - setMousePositionAction([position[activeViewPort][0] / 2, position[activeViewPort][1] / 2]), - ); - }; - - const items: MenuProps["items"] = [ - { - label: "Assign current brush size to", - key: "assignToParent", - children: [ - { - label: ( -
- handleUpdatePresetBrushSizes({ - small: brushSize, - medium: mediumBrushSize, - large: largeBrushSize, - }) - } - > - Small brush -
- ), - key: "assignToSmall", - }, - { - label: ( -
- handleUpdatePresetBrushSizes({ - small: smallBrushSize, - medium: brushSize, - large: maximumBrushSize, - }) - } - > - Medium brush -
- ), - key: "assignToMedium", - }, - { - label: ( -
- handleUpdatePresetBrushSizes({ - small: smallBrushSize, - medium: mediumBrushSize, - large: brushSize, - }) - } - > - Large brush -
- ), - key: "assignToLarge", - }, - ], - }, - { - label:
handleUpdatePresetBrushSizes(defaultBrushSizes)}>Reset
, - key: "reset", - }, - ]; - - return ( - - centerBrushInViewport()} - > - - - - - - - - - - - - - - handleUpdateBrushSize(smallBrushSize)} - icon={} - brushSize={Math.round(smallBrushSize)} - /> - - - handleUpdateBrushSize(mediumBrushSize)} - icon={} - brushSize={Math.round(mediumBrushSize)} - /> - - - handleUpdateBrushSize(largeBrushSize)} - icon={} - brushSize={Math.round(largeBrushSize)} - /> - - -
- } - trigger="click" - open={isBrushSizePopoverOpen} - placement="bottom" - style={{ - cursor: "pointer", - }} - onOpenChange={(open: boolean) => { - setIsBrushSizePopoverOpen(open); - if (open) centerBrushInViewport(); - else dispatch(setMousePositionAction(null)); - }} - > - - Brush Size - - - - ); -} - -function calculateMediumBrushSize(maximumBrushSize: number) { - return Math.ceil((maximumBrushSize - userSettings.brushSize.minimum) / 10) * 5; -} - -function toolToRadioGroupValue(adaptedActiveTool: AnnotationTool): AnnotationTool { - /* - * The tool radio buttons only contain one button for both measurement tools (area - * and line). The selection of the "sub tool" can be done when one of them is active - * with extra buttons next to the radio group. - * To ensure that the highlighting of the generic measurement tool button works properly, - * we map both measurement tools to the line tool here. - */ - if (adaptedActiveTool === AnnotationTool.AREA_MEASUREMENT) { - return AnnotationTool.LINE_MEASUREMENT; - } - return adaptedActiveTool; -} - -export default function ToolbarView() { - const hasVolume = useSelector((state: OxalisState) => state.annotation?.volumes.length > 0); - const hasSkeleton = useSelector((state: OxalisState) => state.annotation?.skeleton != null); - const toolkit = useSelector((state: OxalisState) => state.userConfiguration.activeToolkit); - const activeTool = useSelector((state: OxalisState) => state.uiInformation.activeTool); - const isSplitToolkit = toolkit === Toolkit.SPLIT_SEGMENTS; - - const isShiftPressed = useKeyPress("Shift"); - const isControlOrMetaPressed = useKeyPress("ControlOrMeta"); - const isAltPressed = useKeyPress("Alt"); - const adaptedActiveTool = adaptActiveToolToShortcuts( - activeTool, - isShiftPressed, - isControlOrMetaPressed, - isAltPressed, - ); - - return ( - <> - - {Toolkits[toolkit].map((tool) => { - const ToolButton = ToolIdToComponent[tool.id]; - return ; - })} - - - - - {isSplitToolkit ? ( - - - - Split Workflow - - - ) : null} - - ); -} - -function ToolSpecificSettings({ - hasSkeleton, - adaptedActiveTool, - hasVolume, - isControlOrMetaPressed, - isShiftPressed, -}: { - hasSkeleton: boolean; - adaptedActiveTool: AnnotationTool; - hasVolume: boolean; - isControlOrMetaPressed: boolean; - isShiftPressed: boolean; -}) { - const showSkeletonButtons = hasSkeleton && adaptedActiveTool === AnnotationTool.SKELETON; - const showNewBoundingBoxButton = adaptedActiveTool === AnnotationTool.BOUNDING_BOX; - const showCreateCellButton = hasVolume && VolumeTools.includes(adaptedActiveTool); - const showChangeBrushSizeButton = - showCreateCellButton && - (adaptedActiveTool === AnnotationTool.BRUSH || - adaptedActiveTool === AnnotationTool.ERASE_BRUSH); - const dispatch = useDispatch(); - const quickSelectConfig = useSelector( - (state: OxalisState) => state.userConfiguration.quickSelect, - ); - const isAISelectAvailable = features().segmentAnythingEnabled; - const isQuickSelectHeuristic = quickSelectConfig.useHeuristic || !isAISelectAvailable; - const quickSelectTooltipText = isAISelectAvailable - ? isQuickSelectHeuristic - ? "The quick select tool is now working without AI. Activate AI for better results." - : "The quick select tool is now working with AI." - : "The quick select tool with AI is only available on webknossos.org"; - const areEditableMappingsEnabled = features().editableMappingsEnabled; - const toggleQuickSelectStrategy = () => { - dispatch( - updateUserSettingAction("quickSelect", { - ...quickSelectConfig, - useHeuristic: !quickSelectConfig.useHeuristic, - }), - ); - }; - - return ( - <> - {showSkeletonButtons ? : null} - - {showNewBoundingBoxButton ? ( - - - - ) : null} - - {showCreateCellButton || showChangeBrushSizeButton ? ( - - {showCreateCellButton ? : null} - {showChangeBrushSizeButton ? : null} - - ) : null} - - - - {adaptedActiveTool === AnnotationTool.QUICK_SELECT && ( - <> - - AI - - - - - )} - - {adaptedActiveTool.hasOverwriteCapabilities ? : null} - - {adaptedActiveTool === AnnotationTool.FILL_CELL ? : null} - - {adaptedActiveTool === AnnotationTool.PROOFREAD && areEditableMappingsEnabled ? ( - - ) : null} - - {MeasurementTools.includes(adaptedActiveTool) ? ( - - ) : null} - - ); -} - -function IdentityComponent({ children }: { children: React.ReactNode }) { - return <>{children}; -} - -function NuxPopConfirm({ children }: { children: React.ReactNode }) { - const dispatch = useDispatch(); - const activeUser = useSelector((state: OxalisState) => state.activeUser); - return ( - { - if (!activeUser) { - return; - } - const [newUserSync] = updateNovelUserExperienceInfos(activeUser, { - hasSeenSegmentAnythingWithDepth: true, - }); - dispatch(setActiveUserAction(newUserSync)); - }} - description="The AI-based Quick Select can now be triggered with a single click. Also, it can be run for multiple sections at once (open the settings here to enable this)." - overlayStyle={{ maxWidth: 400 }} - icon={} - > - {children} - - ); -} - -function QuickSelectSettingsPopover() { - const dispatch = useDispatch(); - const { quickSelectState, areQuickSelectSettingsOpen } = useSelector( - (state: OxalisState) => state.uiInformation, - ); - const isQuickSelectActive = quickSelectState === "active"; - const activeUser = useSelector((state: OxalisState) => state.activeUser); - - const showNux = - activeUser != null && !activeUser.novelUserExperienceInfos.hasSeenSegmentAnythingWithDepth; - const Wrapper = showNux ? NuxPopConfirm : IdentityComponent; - - return ( - <> - - } - onOpenChange={(open: boolean) => { - dispatch(showQuickSelectSettingsAction(open)); - }} - > - - - - - - - ); -} - -const handleSetFillMode = (event: RadioChangeEvent) => { - Store.dispatch(updateUserSettingAction("fillMode", event.target.value)); -}; - -function FloodFillSettings() { - const dispatch = useDispatch(); - const isRestrictedToBoundingBox = useSelector( - (state: OxalisState) => state.userConfiguration.isFloodfillRestrictedToBoundingBox, - ); - const toggleRestrictFloodfillToBoundingBox = () => { - dispatch( - updateUserSettingAction("isFloodfillRestrictedToBoundingBox", !isRestrictedToBoundingBox), - ); - }; - return ( -
- - - - Restrict floodfill - -
- ); -} - -function FillModeSwitch() { - const fillMode = useSelector((state: OxalisState) => state.userConfiguration.fillMode); - return ( - - - 2D - - - 3D - - - ); -} - -function ProofreadingComponents() { - const dispatch = useDispatch(); - const handleClearProofreading = () => dispatch(clearProofreadingByProducts()); - const autoRenderMeshes = useSelector( - (state: OxalisState) => state.userConfiguration.autoRenderMeshInProofreading, - ); - const selectiveVisibilityInProofreading = useSelector( - (state: OxalisState) => state.userConfiguration.selectiveVisibilityInProofreading, - ); - - return ( - - - - - handleToggleAutomaticMeshRendering(!autoRenderMeshes)} - > - - - - handleToggleSelectiveVisibilityInProofreading(!selectiveVisibilityInProofreading) - } - > - - - - ); -} - -function MeasurementToolSwitch({ activeTool }: { activeTool: AnnotationTool }) { - const dispatch = useDispatch(); - - const handleSetMeasurementTool = (evt: RadioChangeEvent) => { - dispatch(setToolAction(evt.target.value)); - }; - return ( - - - Measurement Tool Icon - - - Measurement Tool Icon - - - ); -} - -function MoveTool(_props: ToolButtonProps) { - return ( - - - - ); -} - -function SkeletonTool(_props: ToolButtonProps) { - const useLegacyBindings = useSelector( - (state: OxalisState) => state.userConfiguration.useLegacyBindings, - ); - const skeletonToolDescription = useLegacyBindings - ? "Use left-click to move around and right-click to create new skeleton nodes" - : "Use left-click to move around or to create/select/move nodes. Right-click opens a context menu with further options."; - const disabledInfosForTools = useSelector(getDisabledInfoForTools); - const hasSkeleton = useSelector((state: OxalisState) => state.annotation?.skeleton != null); - const isReadOnly = useSelector( - (state: OxalisState) => !state.annotation.restrictions.allowUpdate, - ); - - if (!hasSkeleton || isReadOnly) { - return null; - } - - return ( - - - - ); -} - -function getIsVolumeModificationAllowed(state: OxalisState) { - const isReadOnly = !state.annotation.restrictions.allowUpdate; - const hasVolume = state.annotation?.volumes.length > 0; - return hasVolume && !isReadOnly && !hasEditableMapping(state); -} - -function BrushTool({ adaptedActiveTool }: ToolButtonProps) { - const disabledInfosForTools = useSelector(getDisabledInfoForTools); - const isVolumeModificationAllowed = useSelector(getIsVolumeModificationAllowed); - if (!isVolumeModificationAllowed) { - return null; - } - return ( - - - {adaptedActiveTool === AnnotationTool.BRUSH ? : null} - - ); -} - -function EraseBrushTool({ adaptedActiveTool }: ToolButtonProps) { - const disabledInfosForTools = useSelector(getDisabledInfoForTools); - const showEraseTraceTool = - adaptedActiveTool === AnnotationTool.TRACE || adaptedActiveTool === AnnotationTool.ERASE_TRACE; - const showEraseBrushTool = !showEraseTraceTool; - - const isVolumeModificationAllowed = useSelector(getIsVolumeModificationAllowed); - if (!isVolumeModificationAllowed) { - return null; - } - - return ( - - - {adaptedActiveTool === AnnotationTool.ERASE_BRUSH ? ( - - ) : null} - - ); -} - -function TraceTool({ adaptedActiveTool }: ToolButtonProps) { - const disabledInfosForTools = useSelector(getDisabledInfoForTools); - const isVolumeModificationAllowed = useSelector(getIsVolumeModificationAllowed); - if (!isVolumeModificationAllowed) { - return null; - } - return ( - - Trace Tool Icon - {adaptedActiveTool === AnnotationTool.TRACE ? : null} - - ); -} - -function EraseTraceTool({ adaptedActiveTool }: ToolButtonProps) { - const disabledInfosForTools = useSelector(getDisabledInfoForTools); - const showEraseTraceTool = - adaptedActiveTool === AnnotationTool.TRACE || adaptedActiveTool === AnnotationTool.ERASE_TRACE; - const isVolumeModificationAllowed = useSelector(getIsVolumeModificationAllowed); - if (!isVolumeModificationAllowed) { - return null; - } - - return ( - - - {adaptedActiveTool === AnnotationTool.ERASE_TRACE ? ( - - ) : null} - - ); -} - -function FillCellTool({ adaptedActiveTool }: ToolButtonProps) { - const disabledInfosForTools = useSelector(getDisabledInfoForTools); - const isVolumeModificationAllowed = useSelector(getIsVolumeModificationAllowed); - if (!isVolumeModificationAllowed) { - return null; - } - - return ( - - - {adaptedActiveTool === AnnotationTool.FILL_CELL ? ( - - ) : null} - - ); -} - -function PickCellTool(_props: ToolButtonProps) { - const disabledInfosForTools = useSelector(getDisabledInfoForTools); - const isVolumeModificationAllowed = useSelector(getIsVolumeModificationAllowed); - if (!isVolumeModificationAllowed) { - return null; - } - return ( - - - - ); -} - -function QuickSelectTool(_props: ToolButtonProps) { - const disabledInfosForTools = useSelector(getDisabledInfoForTools); - const isVolumeModificationAllowed = useSelector(getIsVolumeModificationAllowed); - if (!isVolumeModificationAllowed) { - return null; - } - return ( - - Quick Select Icon - - ); -} - -function BoundingBoxTool(_props: ToolButtonProps) { - const disabledInfosForTools = useSelector(getDisabledInfoForTools); - const isReadOnly = useSelector( - (state: OxalisState) => !state.annotation.restrictions.allowUpdate, - ); - if (isReadOnly) { - return null; - } - return ( - - Bounding Box Icon - - ); -} - -function ProofreadTool(_props: ToolButtonProps) { - const dispatch = useDispatch(); - const isAgglomerateMappingEnabled = useSelector(hasAgglomerateMapping); - const disabledInfosForTools = useSelector(getDisabledInfoForTools); - const areEditableMappingsEnabled = features().editableMappingsEnabled; - const hasSkeleton = useSelector((state: OxalisState) => state.annotation?.skeleton != null); - const hasVolume = useSelector((state: OxalisState) => state.annotation?.volumes.length > 0); - const isReadOnly = useSelector( - (state: OxalisState) => !state.annotation.restrictions.allowUpdate, - ); - - const mayProofread = hasSkeleton && hasVolume && !isReadOnly; - if (!mayProofread) { - return null; - } - - return ( - { - dispatch(ensureLayerMappingsAreLoadedAction()); - }} - > - - - ); -} - -function LineMeasurementTool(_props: ToolButtonProps) { - return ( - - - - ); -} - -const ToolIdToComponent: Record JSX.Element | null> = { - [AnnotationTool.MOVE.id]: MoveTool, - [AnnotationTool.SKELETON.id]: SkeletonTool, - [AnnotationTool.BRUSH.id]: BrushTool, - [AnnotationTool.ERASE_BRUSH.id]: EraseBrushTool, - [AnnotationTool.TRACE.id]: TraceTool, - [AnnotationTool.ERASE_TRACE.id]: EraseTraceTool, - [AnnotationTool.FILL_CELL.id]: FillCellTool, - [AnnotationTool.PICK_CELL.id]: PickCellTool, - [AnnotationTool.QUICK_SELECT.id]: QuickSelectTool, - [AnnotationTool.BOUNDING_BOX.id]: BoundingBoxTool, - [AnnotationTool.PROOFREAD.id]: ProofreadTool, - [AnnotationTool.LINE_MEASUREMENT.id]: LineMeasurementTool, - [AnnotationTool.AREA_MEASUREMENT.id]: () => null, -}; - -function MaybeMultiSliceAnnotationInfoIcon() { - const maybeMagWithZoomStep = useSelector(getRenderableMagForActiveSegmentationTracing); - const labeledMag = maybeMagWithZoomStep != null ? maybeMagWithZoomStep.mag : null; - const hasMagWithHigherDimension = (labeledMag || []).some((val) => val > 1); - const maybeMultiSliceAnnotationInfoIcon = hasMagWithHigherDimension ? ( - - - - ) : null; - return maybeMultiSliceAnnotationInfoIcon; -} diff --git a/frontend/javascripts/oxalis/view/action-bar/tools/brush_presets.tsx b/frontend/javascripts/oxalis/view/action-bar/tools/brush_presets.tsx new file mode 100644 index 00000000000..ea820a5b03d --- /dev/null +++ b/frontend/javascripts/oxalis/view/action-bar/tools/brush_presets.tsx @@ -0,0 +1,256 @@ +import { SettingOutlined } from "@ant-design/icons"; +import { Col, Divider, Dropdown, type MenuProps, Popover, Row } from "antd"; +import { useEffect, useState } from "react"; +import { useDispatch, useSelector } from "react-redux"; + +import { Unicode } from "oxalis/constants"; +import { getMaximumBrushSize } from "oxalis/model/accessors/volumetracing_accessor"; +import { updateUserSettingAction } from "oxalis/model/actions/settings_actions"; +import { setMousePositionAction } from "oxalis/model/actions/volumetracing_actions"; +import Store, { type BrushPresets, type OxalisState } from "oxalis/store"; +import ButtonComponent from "oxalis/view/components/button_component"; +import { LogSliderSetting } from "oxalis/view/components/setting_input_views"; +import { userSettings } from "types/schemas/user_settings.schema"; + +import FastTooltip from "components/fast_tooltip"; +import defaultState from "oxalis/default_state"; +import { getViewportExtents } from "oxalis/model/accessors/view_mode_accessor"; + +const handleUpdateBrushSize = (value: number) => { + Store.dispatch(updateUserSettingAction("brushSize", value)); +}; + +const handleUpdatePresetBrushSizes = (brushSizes: BrushPresets) => { + Store.dispatch(updateUserSettingAction("presetBrushSizes", brushSizes)); +}; + +function BrushPresetButton({ + name, + icon, + brushSize, + onClick, +}: { + name: string; + onClick: () => void; + icon: JSX.Element; + brushSize: number; +}) { + const { ThinSpace } = Unicode; + return ( + <> +
+ {icon} +
+
{name}
+
+ {brushSize} + {ThinSpace}vx +
+ + ); +} + +export function getDefaultBrushSizes(maximumSize: number, minimumSize: number) { + return { + small: Math.max(minimumSize, 10), + medium: calculateMediumBrushSize(maximumSize), + large: maximumSize, + }; +} + +export function ChangeBrushSizePopover() { + const dispatch = useDispatch(); + const brushSize = useSelector((state: OxalisState) => state.userConfiguration.brushSize); + const [isBrushSizePopoverOpen, setIsBrushSizePopoverOpen] = useState(false); + const maximumBrushSize = useSelector((state: OxalisState) => getMaximumBrushSize(state)); + + const defaultBrushSizes = getDefaultBrushSizes(maximumBrushSize, userSettings.brushSize.minimum); + const presetBrushSizes = useSelector( + (state: OxalisState) => state.userConfiguration.presetBrushSizes, + ); + // biome-ignore lint/correctness/useExhaustiveDependencies: Needs investigation whether defaultBrushSizes is needed as dependency. + useEffect(() => { + if (presetBrushSizes == null) { + handleUpdatePresetBrushSizes(defaultBrushSizes); + } + }, [presetBrushSizes]); + + let smallBrushSize: number, mediumBrushSize: number, largeBrushSize: number; + if (presetBrushSizes == null) { + smallBrushSize = defaultBrushSizes.small; + mediumBrushSize = defaultBrushSizes.medium; + largeBrushSize = defaultBrushSizes.large; + } else { + smallBrushSize = presetBrushSizes?.small; + mediumBrushSize = presetBrushSizes?.medium; + largeBrushSize = presetBrushSizes?.large; + } + + const centerBrushInViewport = () => { + const position = getViewportExtents(Store.getState()); + const activeViewPort = Store.getState().viewModeData.plane.activeViewport; + dispatch( + setMousePositionAction([position[activeViewPort][0] / 2, position[activeViewPort][1] / 2]), + ); + }; + + const items: MenuProps["items"] = [ + { + label: "Assign current brush size to", + key: "assignToParent", + children: [ + { + label: ( +
+ handleUpdatePresetBrushSizes({ + small: brushSize, + medium: mediumBrushSize, + large: largeBrushSize, + }) + } + > + Small brush +
+ ), + key: "assignToSmall", + }, + { + label: ( +
+ handleUpdatePresetBrushSizes({ + small: smallBrushSize, + medium: brushSize, + large: maximumBrushSize, + }) + } + > + Medium brush +
+ ), + key: "assignToMedium", + }, + { + label: ( +
+ handleUpdatePresetBrushSizes({ + small: smallBrushSize, + medium: mediumBrushSize, + large: brushSize, + }) + } + > + Large brush +
+ ), + key: "assignToLarge", + }, + ], + }, + { + label:
handleUpdatePresetBrushSizes(defaultBrushSizes)}>Reset
, + key: "reset", + }, + ]; + + return ( + + centerBrushInViewport()} + > + + + + + + + + + + + + + + handleUpdateBrushSize(smallBrushSize)} + icon={} + brushSize={Math.round(smallBrushSize)} + /> + + + handleUpdateBrushSize(mediumBrushSize)} + icon={} + brushSize={Math.round(mediumBrushSize)} + /> + + + handleUpdateBrushSize(largeBrushSize)} + icon={} + brushSize={Math.round(largeBrushSize)} + /> + + + + } + trigger="click" + open={isBrushSizePopoverOpen} + placement="bottom" + style={{ + cursor: "pointer", + }} + onOpenChange={(open: boolean) => { + setIsBrushSizePopoverOpen(open); + if (open) centerBrushInViewport(); + else dispatch(setMousePositionAction(null)); + }} + > + + Brush Size + + + + ); +} + +function calculateMediumBrushSize(maximumBrushSize: number) { + return Math.ceil((maximumBrushSize - userSettings.brushSize.minimum) / 10) * 5; +} diff --git a/frontend/javascripts/oxalis/view/action-bar/tools/skeleton_specific_ui.tsx b/frontend/javascripts/oxalis/view/action-bar/tools/skeleton_specific_ui.tsx new file mode 100644 index 00000000000..8ca42237ff2 --- /dev/null +++ b/frontend/javascripts/oxalis/view/action-bar/tools/skeleton_specific_ui.tsx @@ -0,0 +1,184 @@ +import { ExportOutlined } from "@ant-design/icons"; +import { Badge, Space } from "antd"; +import { useState } from "react"; +import { useDispatch, useSelector } from "react-redux"; + +import { getActiveTree } from "oxalis/model/accessors/skeletontracing_accessor"; +import { Toolkit } from "oxalis/model/accessors/tool_accessor"; +import { getActiveSegmentationTracing } from "oxalis/model/accessors/volumetracing_accessor"; +import { updateUserSettingAction } from "oxalis/model/actions/settings_actions"; +import { + createTreeAction, + setMergerModeEnabledAction, +} from "oxalis/model/actions/skeletontracing_actions"; +import type { OxalisState } from "oxalis/store"; +import { MaterializeVolumeAnnotationModal } from "oxalis/view/action-bar/starting_job_modals"; +import ButtonComponent, { ToggleButton } from "oxalis/view/components/button_component"; + +import { useIsActiveUserAdminOrManager } from "libs/react_helpers"; +import { APIJobType } from "types/api_flow_types"; +import { IMG_STYLE_FOR_SPACEY_ICONS, NARROW_BUTTON_STYLE } from "./tool_helpers"; + +export function SkeletonSpecificButtons() { + const dispatch = useDispatch(); + const isMergerModeEnabled = useSelector( + (state: OxalisState) => state.temporaryConfiguration.isMergerModeEnabled, + ); + const [showMaterializeVolumeAnnotationModal, setShowMaterializeVolumeAnnotationModal] = + useState(false); + const isNewNodeNewTreeModeOn = useSelector( + (state: OxalisState) => state.userConfiguration.newNodeNewTree, + ); + const isContinuousNodeCreationEnabled = useSelector( + (state: OxalisState) => state.userConfiguration.continuousNodeCreation, + ); + const isSplitToolkit = useSelector( + (state: OxalisState) => state.userConfiguration.activeToolkit === Toolkit.SPLIT_SEGMENTS, + ); + const toggleContinuousNodeCreation = () => + dispatch(updateUserSettingAction("continuousNodeCreation", !isContinuousNodeCreationEnabled)); + + const dataset = useSelector((state: OxalisState) => state.dataset); + const isUserAdminOrManager = useIsActiveUserAdminOrManager(); + + const segmentationTracingLayer = useSelector((state: OxalisState) => + getActiveSegmentationTracing(state), + ); + const isEditableMappingActive = + segmentationTracingLayer != null && !!segmentationTracingLayer.hasEditableMapping; + const isMappingLockedWithNonNull = + segmentationTracingLayer != null && + !!segmentationTracingLayer.mappingIsLocked && + segmentationTracingLayer.mappingName != null; + const isMergerModeDisabled = isEditableMappingActive || isMappingLockedWithNonNull; + const mergerModeTooltipText = isEditableMappingActive + ? "Merger mode cannot be enabled while an editable mapping is active." + : isMappingLockedWithNonNull + ? "Merger mode cannot be enabled while a mapping is locked. Please create a new annotation and use the merger mode there." + : "Toggle Merger Mode - When enabled, skeletons that connect multiple segments will merge those segments."; + + const toggleNewNodeNewTreeMode = () => + dispatch(updateUserSettingAction("newNodeNewTree", !isNewNodeNewTreeModeOn)); + + const toggleMergerMode = () => dispatch(setMergerModeEnabledAction(!isMergerModeEnabled)); + + const isMaterializeVolumeAnnotationEnabled = + dataset.dataStore.jobsSupportedByAvailableWorkers.includes( + APIJobType.MATERIALIZE_VOLUME_ANNOTATION, + ); + + return ( + + + {isSplitToolkit ? null : ( + + Single Node Tree Mode + + )} + {isSplitToolkit ? null : ( + + Merger Mode + + )} + + + + + {isMergerModeEnabled && isMaterializeVolumeAnnotationEnabled && isUserAdminOrManager && ( + setShowMaterializeVolumeAnnotationModal(true)} + title="Materialize this merger mode annotation into a new dataset." + > + + + )} + {isMaterializeVolumeAnnotationEnabled && showMaterializeVolumeAnnotationModal && ( + setShowMaterializeVolumeAnnotationModal(false)} + /> + )} + + ); +} + +function CreateTreeButton() { + const dispatch = useDispatch(); + const activeTree = useSelector((state: OxalisState) => getActiveTree(state.annotation.skeleton)); + const rgbColorString = + activeTree != null + ? `rgb(${activeTree.color.map((c) => Math.round(c * 255)).join(",")})` + : "transparent"; + const activeTreeHint = + activeTree != null + ? `The active tree id is ${activeTree.treeId}.` + : "No tree is currently selected"; + + const handleCreateTree = () => dispatch(createTreeAction()); + + return ( + + + + + + + ); +} diff --git a/frontend/javascripts/oxalis/view/action-bar/tools/tool_buttons.tsx b/frontend/javascripts/oxalis/view/action-bar/tools/tool_buttons.tsx new file mode 100644 index 00000000000..4fc5a0fbebc --- /dev/null +++ b/frontend/javascripts/oxalis/view/action-bar/tools/tool_buttons.tsx @@ -0,0 +1,405 @@ +import { useDispatch, useSelector } from "react-redux"; + +import { getDisabledInfoForTools } from "oxalis/model/accessors/disabled_tool_accessor"; +import { AnnotationTool, type AnnotationToolId } from "oxalis/model/accessors/tool_accessor"; +import { + getRenderableMagForActiveSegmentationTracing, + hasAgglomerateMapping, + hasEditableMapping, +} from "oxalis/model/accessors/volumetracing_accessor"; +import type { OxalisState } from "oxalis/store"; + +import FastTooltip from "components/fast_tooltip"; +import features from "features"; +import { ensureLayerMappingsAreLoadedAction } from "oxalis/model/actions/dataset_actions"; +import { IMG_STYLE_FOR_SPACEY_ICONS, ToolRadioButton } from "./tool_helpers"; + +type ToolButtonProps = { adaptedActiveTool: AnnotationTool }; + +export const ToolIdToComponent: Record< + AnnotationToolId, + (p: ToolButtonProps) => JSX.Element | null +> = { + [AnnotationTool.MOVE.id]: MoveTool, + [AnnotationTool.SKELETON.id]: SkeletonTool, + [AnnotationTool.BRUSH.id]: BrushTool, + [AnnotationTool.ERASE_BRUSH.id]: EraseBrushTool, + [AnnotationTool.TRACE.id]: TraceTool, + [AnnotationTool.ERASE_TRACE.id]: EraseTraceTool, + [AnnotationTool.FILL_CELL.id]: FillCellTool, + [AnnotationTool.PICK_CELL.id]: PickCellTool, + [AnnotationTool.QUICK_SELECT.id]: QuickSelectTool, + [AnnotationTool.BOUNDING_BOX.id]: BoundingBoxTool, + [AnnotationTool.PROOFREAD.id]: ProofreadTool, + [AnnotationTool.LINE_MEASUREMENT.id]: LineMeasurementTool, + [AnnotationTool.AREA_MEASUREMENT.id]: () => null, +}; + +function MaybeMultiSliceAnnotationInfoIcon() { + const maybeMagWithZoomStep = useSelector(getRenderableMagForActiveSegmentationTracing); + const labeledMag = maybeMagWithZoomStep != null ? maybeMagWithZoomStep.mag : null; + const hasMagWithHigherDimension = (labeledMag || []).some((val) => val > 1); + const maybeMultiSliceAnnotationInfoIcon = hasMagWithHigherDimension ? ( + + + + ) : null; + return maybeMultiSliceAnnotationInfoIcon; +} + +export function MoveTool(_props: ToolButtonProps) { + return ( + + + + ); +} + +export function SkeletonTool(_props: ToolButtonProps) { + const useLegacyBindings = useSelector( + (state: OxalisState) => state.userConfiguration.useLegacyBindings, + ); + const skeletonToolDescription = useLegacyBindings + ? "Use left-click to move around and right-click to create new skeleton nodes" + : "Use left-click to move around or to create/select/move nodes. Right-click opens a context menu with further options."; + const disabledInfosForTools = useSelector(getDisabledInfoForTools); + const hasSkeleton = useSelector((state: OxalisState) => state.annotation?.skeleton != null); + const isReadOnly = useSelector( + (state: OxalisState) => !state.annotation.restrictions.allowUpdate, + ); + + if (!hasSkeleton || isReadOnly) { + return null; + } + + return ( + + + + ); +} + +function getIsVolumeModificationAllowed(state: OxalisState) { + const isReadOnly = !state.annotation.restrictions.allowUpdate; + const hasVolume = state.annotation?.volumes.length > 0; + return hasVolume && !isReadOnly && !hasEditableMapping(state); +} + +export function BrushTool({ adaptedActiveTool }: ToolButtonProps) { + const disabledInfosForTools = useSelector(getDisabledInfoForTools); + const isVolumeModificationAllowed = useSelector(getIsVolumeModificationAllowed); + if (!isVolumeModificationAllowed) { + return null; + } + return ( + + + {adaptedActiveTool === AnnotationTool.BRUSH ? : null} + + ); +} + +export function EraseBrushTool({ adaptedActiveTool }: ToolButtonProps) { + const disabledInfosForTools = useSelector(getDisabledInfoForTools); + const showEraseTraceTool = + adaptedActiveTool === AnnotationTool.TRACE || adaptedActiveTool === AnnotationTool.ERASE_TRACE; + const showEraseBrushTool = !showEraseTraceTool; + + const isVolumeModificationAllowed = useSelector(getIsVolumeModificationAllowed); + if (!isVolumeModificationAllowed) { + return null; + } + + return ( + + + {adaptedActiveTool === AnnotationTool.ERASE_BRUSH ? ( + + ) : null} + + ); +} + +export function TraceTool({ adaptedActiveTool }: ToolButtonProps) { + const disabledInfosForTools = useSelector(getDisabledInfoForTools); + const isVolumeModificationAllowed = useSelector(getIsVolumeModificationAllowed); + if (!isVolumeModificationAllowed) { + return null; + } + return ( + + Trace Tool Icon + {adaptedActiveTool === AnnotationTool.TRACE ? : null} + + ); +} + +export function EraseTraceTool({ adaptedActiveTool }: ToolButtonProps) { + const disabledInfosForTools = useSelector(getDisabledInfoForTools); + const showEraseTraceTool = + adaptedActiveTool === AnnotationTool.TRACE || adaptedActiveTool === AnnotationTool.ERASE_TRACE; + const isVolumeModificationAllowed = useSelector(getIsVolumeModificationAllowed); + if (!isVolumeModificationAllowed) { + return null; + } + + return ( + + + {adaptedActiveTool === AnnotationTool.ERASE_TRACE ? ( + + ) : null} + + ); +} + +export function FillCellTool({ adaptedActiveTool }: ToolButtonProps) { + const disabledInfosForTools = useSelector(getDisabledInfoForTools); + const isVolumeModificationAllowed = useSelector(getIsVolumeModificationAllowed); + if (!isVolumeModificationAllowed) { + return null; + } + + return ( + + + {adaptedActiveTool === AnnotationTool.FILL_CELL ? ( + + ) : null} + + ); +} + +export function PickCellTool(_props: ToolButtonProps) { + const disabledInfosForTools = useSelector(getDisabledInfoForTools); + const isVolumeModificationAllowed = useSelector(getIsVolumeModificationAllowed); + if (!isVolumeModificationAllowed) { + return null; + } + return ( + + + + ); +} + +export function QuickSelectTool(_props: ToolButtonProps) { + const disabledInfosForTools = useSelector(getDisabledInfoForTools); + const isVolumeModificationAllowed = useSelector(getIsVolumeModificationAllowed); + if (!isVolumeModificationAllowed) { + return null; + } + return ( + + Quick Select Icon + + ); +} + +export function BoundingBoxTool(_props: ToolButtonProps) { + const disabledInfosForTools = useSelector(getDisabledInfoForTools); + const isReadOnly = useSelector( + (state: OxalisState) => !state.annotation.restrictions.allowUpdate, + ); + if (isReadOnly) { + return null; + } + return ( + + Bounding Box Icon + + ); +} + +export function ProofreadTool(_props: ToolButtonProps) { + const dispatch = useDispatch(); + const isAgglomerateMappingEnabled = useSelector(hasAgglomerateMapping); + const disabledInfosForTools = useSelector(getDisabledInfoForTools); + const areEditableMappingsEnabled = features().editableMappingsEnabled; + const hasSkeleton = useSelector((state: OxalisState) => state.annotation?.skeleton != null); + const hasVolume = useSelector((state: OxalisState) => state.annotation?.volumes.length > 0); + const isReadOnly = useSelector( + (state: OxalisState) => !state.annotation.restrictions.allowUpdate, + ); + + const mayProofread = hasSkeleton && hasVolume && !isReadOnly; + if (!mayProofread) { + return null; + } + + return ( + { + dispatch(ensureLayerMappingsAreLoadedAction()); + }} + > + + + ); +} + +export function LineMeasurementTool(_props: ToolButtonProps) { + return ( + + + + ); +} diff --git a/frontend/javascripts/oxalis/view/action-bar/tools/tool_helpers.tsx b/frontend/javascripts/oxalis/view/action-bar/tools/tool_helpers.tsx new file mode 100644 index 00000000000..99e71e23839 --- /dev/null +++ b/frontend/javascripts/oxalis/view/action-bar/tools/tool_helpers.tsx @@ -0,0 +1,92 @@ +import { Radio } from "antd"; +import type React from "react"; + +import { document } from "libs/window"; + +import FastTooltip from "components/fast_tooltip"; + +export const NARROW_BUTTON_STYLE = { + paddingLeft: 10, + paddingRight: 8, +}; +export const IMG_STYLE_FOR_SPACEY_ICONS = { + width: 19, + height: 19, + lineHeight: 10, + marginTop: -2, + verticalAlign: "middle", +}; + +export function RadioButtonWithTooltip({ + title, + disabledTitle, + disabled, + onClick, + children, + onMouseEnter, + ...props +}: { + title: string; + disabledTitle?: string; + disabled?: boolean; + children: React.ReactNode; + style?: React.CSSProperties; + value: unknown; + onClick?: (event: React.MouseEvent) => void; + onMouseEnter?: () => void; +}) { + // FastTooltip adds data-* properties so that the centralized ReactTooltip + // is hooked up here. Unfortunately, FastTooltip would add another div or span + // which antd does not like within this toolbar. + // Therefore, we move the tooltip into the button which requires tweaking the padding + // a bit (otherwise, the tooltip would only occur when hovering exactly over the icon + // instead of everywhere within the button). + return ( + { + if (document.activeElement) { + (document.activeElement as HTMLElement).blur(); + } + if (onClick) { + onClick(event); + } + }} + {...props} + > + + {/* See comments above. */} + {children} + + + ); +} + +export function ToolRadioButton({ + name, + description, + disabledExplanation, + onMouseEnter, + ...props +}: { + name: string; + description: string; + disabledExplanation?: string; + disabled?: boolean; + children: React.ReactNode; + style?: React.CSSProperties; + value: unknown; + onClick?: (event: React.MouseEvent) => void; + onMouseEnter?: () => void; +}) { + return ( + + ); +} diff --git a/frontend/javascripts/oxalis/view/action-bar/tools/toolbar_view.tsx b/frontend/javascripts/oxalis/view/action-bar/tools/toolbar_view.tsx new file mode 100644 index 00000000000..7051822a979 --- /dev/null +++ b/frontend/javascripts/oxalis/view/action-bar/tools/toolbar_view.tsx @@ -0,0 +1,272 @@ +import { InfoCircleOutlined } from "@ant-design/icons"; +import { Radio, type RadioChangeEvent, Space, Tag } from "antd"; +import { useDispatch, useSelector } from "react-redux"; + +import { useKeyPress } from "libs/react_hooks"; +import { + AnnotationTool, + MeasurementTools, + Toolkit, + Toolkits, + VolumeTools, + adaptActiveToolToShortcuts, +} from "oxalis/model/accessors/tool_accessor"; +import { addUserBoundingBoxAction } from "oxalis/model/actions/annotation_actions"; +import { updateUserSettingAction } from "oxalis/model/actions/settings_actions"; +import { setToolAction } from "oxalis/model/actions/ui_actions"; +import Store, { type OxalisState } from "oxalis/store"; +import ButtonComponent, { ToggleButton } from "oxalis/view/components/button_component"; + +import FastTooltip from "components/fast_tooltip"; +import features from "features"; +import { ChangeBrushSizePopover } from "./brush_presets"; +import { SkeletonSpecificButtons } from "./skeleton_specific_ui"; +import { ToolIdToComponent } from "./tool_buttons"; +import { + IMG_STYLE_FOR_SPACEY_ICONS, + NARROW_BUTTON_STYLE, + RadioButtonWithTooltip, +} from "./tool_helpers"; +import { + CreateSegmentButton, + FloodFillSettings, + OverwriteModeSwitch, + ProofreadingComponents, + QuickSelectSettingsPopover, + VolumeInterpolationButton, +} from "./volume_specific_ui"; + +const handleAddNewUserBoundingBox = () => { + Store.dispatch(addUserBoundingBoxAction()); +}; + +function CreateNewBoundingBoxButton() { + return ( + + New Bounding Box Icon + + ); +} + +function toolToRadioGroupValue(adaptedActiveTool: AnnotationTool): AnnotationTool { + /* + * The tool radio buttons only contain one button for both measurement tools (area + * and line). The selection of the "sub tool" can be done when one of them is active + * with extra buttons next to the radio group. + * To ensure that the highlighting of the generic measurement tool button works properly, + * we map both measurement tools to the line tool here. + */ + if (adaptedActiveTool === AnnotationTool.AREA_MEASUREMENT) { + return AnnotationTool.LINE_MEASUREMENT; + } + return adaptedActiveTool; +} + +const handleSetTool = (event: RadioChangeEvent) => { + const value = event.target.value as AnnotationTool; + Store.dispatch(setToolAction(value)); +}; + +export default function ToolbarView() { + const hasVolume = useSelector((state: OxalisState) => state.annotation?.volumes.length > 0); + const hasSkeleton = useSelector((state: OxalisState) => state.annotation?.skeleton != null); + const toolkit = useSelector((state: OxalisState) => state.userConfiguration.activeToolkit); + const activeTool = useSelector((state: OxalisState) => state.uiInformation.activeTool); + const isSplitToolkit = toolkit === Toolkit.SPLIT_SEGMENTS; + + const isShiftPressed = useKeyPress("Shift"); + const isControlOrMetaPressed = useKeyPress("ControlOrMeta"); + const isAltPressed = useKeyPress("Alt"); + const adaptedActiveTool = adaptActiveToolToShortcuts( + activeTool, + isShiftPressed, + isControlOrMetaPressed, + isAltPressed, + ); + + return ( + <> + + {Toolkits[toolkit].map((tool) => { + const ToolButton = ToolIdToComponent[tool.id]; + return ; + })} + + + + + {isSplitToolkit ? ( + + + + Split Workflow + + + ) : null} + + ); +} + +function ToolSpecificSettings({ + hasSkeleton, + adaptedActiveTool, + hasVolume, + isControlOrMetaPressed, + isShiftPressed, +}: { + hasSkeleton: boolean; + adaptedActiveTool: AnnotationTool; + hasVolume: boolean; + isControlOrMetaPressed: boolean; + isShiftPressed: boolean; +}) { + const showSkeletonButtons = hasSkeleton && adaptedActiveTool === AnnotationTool.SKELETON; + const showNewBoundingBoxButton = adaptedActiveTool === AnnotationTool.BOUNDING_BOX; + const showCreateCellButton = hasVolume && VolumeTools.includes(adaptedActiveTool); + const showChangeBrushSizeButton = + showCreateCellButton && + (adaptedActiveTool === AnnotationTool.BRUSH || + adaptedActiveTool === AnnotationTool.ERASE_BRUSH); + const dispatch = useDispatch(); + const quickSelectConfig = useSelector( + (state: OxalisState) => state.userConfiguration.quickSelect, + ); + const isAISelectAvailable = features().segmentAnythingEnabled; + const isQuickSelectHeuristic = quickSelectConfig.useHeuristic || !isAISelectAvailable; + const quickSelectTooltipText = isAISelectAvailable + ? isQuickSelectHeuristic + ? "The quick select tool is now working without AI. Activate AI for better results." + : "The quick select tool is now working with AI." + : "The quick select tool with AI is only available on webknossos.org"; + const areEditableMappingsEnabled = features().editableMappingsEnabled; + const toggleQuickSelectStrategy = () => { + dispatch( + updateUserSettingAction("quickSelect", { + ...quickSelectConfig, + useHeuristic: !quickSelectConfig.useHeuristic, + }), + ); + }; + + return ( + <> + {showSkeletonButtons ? : null} + + {showNewBoundingBoxButton ? ( + + + + ) : null} + + {showCreateCellButton || showChangeBrushSizeButton ? ( + + {showCreateCellButton ? : null} + {showChangeBrushSizeButton ? : null} + + ) : null} + + + + {adaptedActiveTool === AnnotationTool.QUICK_SELECT && ( + <> + + AI + + + + + )} + + {adaptedActiveTool.hasOverwriteCapabilities ? : null} + + {adaptedActiveTool === AnnotationTool.FILL_CELL ? : null} + + {adaptedActiveTool === AnnotationTool.PROOFREAD && areEditableMappingsEnabled ? ( + + ) : null} + + {MeasurementTools.includes(adaptedActiveTool) ? ( + + ) : null} + + ); +} + +function MeasurementToolSwitch({ activeTool }: { activeTool: AnnotationTool }) { + const dispatch = useDispatch(); + + const handleSetMeasurementTool = (evt: RadioChangeEvent) => { + dispatch(setToolAction(evt.target.value)); + }; + return ( + + + Measurement Tool Icon + + + Measurement Tool Icon + + + ); +} diff --git a/frontend/javascripts/oxalis/view/action-bar/toolkit_switcher_view.tsx b/frontend/javascripts/oxalis/view/action-bar/tools/toolkit_switcher_view.tsx similarity index 97% rename from frontend/javascripts/oxalis/view/action-bar/toolkit_switcher_view.tsx rename to frontend/javascripts/oxalis/view/action-bar/tools/toolkit_switcher_view.tsx index 9671e1da31b..a657b49449d 100644 --- a/frontend/javascripts/oxalis/view/action-bar/toolkit_switcher_view.tsx +++ b/frontend/javascripts/oxalis/view/action-bar/tools/toolkit_switcher_view.tsx @@ -4,7 +4,7 @@ import { updateUserSettingAction } from "oxalis/model/actions/settings_actions"; import { Store } from "oxalis/singletons"; import type { OxalisState } from "oxalis/store"; import { useSelector } from "react-redux"; -import { NARROW_BUTTON_STYLE } from "./toolbar_view"; +import { NARROW_BUTTON_STYLE } from "./tool_helpers"; const toolkitOptions: Array<{ label: string; key: Toolkit }> = [ { diff --git a/frontend/javascripts/oxalis/view/action-bar/tools/volume_specific_ui.tsx b/frontend/javascripts/oxalis/view/action-bar/tools/volume_specific_ui.tsx new file mode 100644 index 00000000000..6570af5afae --- /dev/null +++ b/frontend/javascripts/oxalis/view/action-bar/tools/volume_specific_ui.tsx @@ -0,0 +1,492 @@ +import { + ClearOutlined, + DownOutlined, + InfoCircleOutlined, + SettingOutlined, +} from "@ant-design/icons"; +import { + Badge, + Dropdown, + type MenuProps, + Popconfirm, + Popover, + Radio, + type RadioChangeEvent, + Space, +} from "antd"; +import React, { useCallback, useEffect } from "react"; +import { useDispatch, useSelector } from "react-redux"; + +import { usePrevious } from "libs/react_hooks"; +import { + FillModeEnum, + type InterpolationMode, + InterpolationModeEnum, + MappingStatusEnum, + type OverwriteMode, + OverwriteModeEnum, +} from "oxalis/constants"; +import { + getActiveSegmentationTracing, + getMappingInfoForVolumeTracing, + getSegmentColorAsRGBA, +} from "oxalis/model/accessors/volumetracing_accessor"; +import { updateUserSettingAction } from "oxalis/model/actions/settings_actions"; +import { showQuickSelectSettingsAction } from "oxalis/model/actions/ui_actions"; +import { + createCellAction, + interpolateSegmentationLayerAction, +} from "oxalis/model/actions/volumetracing_actions"; +import { Model } from "oxalis/singletons"; +import Store, { type OxalisState } from "oxalis/store"; +import ButtonComponent, { ToggleButton } from "oxalis/view/components/button_component"; +import { showToastWarningForLargestSegmentIdMissing } from "oxalis/view/largest_segment_id_modal"; + +import { updateNovelUserExperienceInfos } from "admin/admin_rest_api"; +import FastTooltip from "components/fast_tooltip"; +import { clearProofreadingByProducts } from "oxalis/model/actions/proofread_actions"; +import { setActiveUserAction } from "oxalis/model/actions/user_actions"; +import { getInterpolationInfo } from "oxalis/model/sagas/volume/volume_interpolation_saga"; +import { rgbaToCSS } from "oxalis/shaders/utils.glsl"; +import type { MenuInfo } from "rc-menu/lib/interface"; +import { QuickSelectControls } from "../quick_select_settings"; +import { + IMG_STYLE_FOR_SPACEY_ICONS, + NARROW_BUTTON_STYLE, + RadioButtonWithTooltip, +} from "./tool_helpers"; + +function toggleOverwriteMode(overwriteMode: OverwriteMode) { + if (overwriteMode === OverwriteModeEnum.OVERWRITE_ALL) { + return OverwriteModeEnum.OVERWRITE_EMPTY; + } else { + return OverwriteModeEnum.OVERWRITE_ALL; + } +} + +const handleToggleAutomaticMeshRendering = (value: boolean) => { + Store.dispatch(updateUserSettingAction("autoRenderMeshInProofreading", value)); +}; + +const handleToggleSelectiveVisibilityInProofreading = (value: boolean) => { + Store.dispatch(updateUserSettingAction("selectiveVisibilityInProofreading", value)); +}; + +const handleCreateCell = () => { + const volumeTracing = getActiveSegmentationTracing(Store.getState()); + + if (volumeTracing == null || volumeTracing.tracingId == null) { + return; + } + + if (volumeTracing.largestSegmentId != null) { + Store.dispatch(createCellAction(volumeTracing.activeCellId, volumeTracing.largestSegmentId)); + } else { + showToastWarningForLargestSegmentIdMissing(volumeTracing); + } +}; + +const handleSetOverwriteMode = (event: { + target: { + value: OverwriteMode; + }; +}) => { + Store.dispatch(updateUserSettingAction("overwriteMode", event.target.value)); +}; + +export function OverwriteModeSwitch({ + isControlOrMetaPressed, + isShiftPressed, + visible, +}: { + isControlOrMetaPressed: boolean; + isShiftPressed: boolean; + visible: boolean; +}) { + // Only CTRL should modify the overwrite mode. CTRL + Shift can be used to switch to the + // erase tool, which should not affect the default overwrite mode. + const overwriteMode = useSelector((state: OxalisState) => state.userConfiguration.overwriteMode); + const previousIsControlOrMetaPressed = usePrevious(isControlOrMetaPressed); + const previousIsShiftPressed = usePrevious(isShiftPressed); + // biome-ignore lint/correctness/useExhaustiveDependencies: overwriteMode does not need to be a dependency. + useEffect(() => { + // There are four possible states: + // (1) no modifier is pressed + // (2) CTRL is pressed + // (3) Shift is pressed + // (4) CTRL + Shift is pressed + // The overwrite mode needs to be toggled when + // - switching from state (1) to (2) (or vice versa) + // - switching from state (2) to (4) (or vice versa) + // Consequently, the mode is only toggled effectively, when CTRL is pressed. + // Alternatively, we could store the selected value and the overridden value + // separately in the store. However, this solution works, too. + const needsModeToggle = + (!isShiftPressed && + isControlOrMetaPressed && + previousIsControlOrMetaPressed === previousIsShiftPressed) || + (isShiftPressed === isControlOrMetaPressed && + !previousIsShiftPressed && + previousIsControlOrMetaPressed); + + if (needsModeToggle) { + Store.dispatch(updateUserSettingAction("overwriteMode", toggleOverwriteMode(overwriteMode))); + } + }, [ + isControlOrMetaPressed, + isShiftPressed, + previousIsControlOrMetaPressed, + previousIsShiftPressed, + ]); + + if (!visible) { + // This component's hooks should still be active, even when the component is invisible. + // Otherwise, the toggling of the overwrite mode via "Ctrl" wouldn't work consistently + // when being combined with other modifiers, which hide the component. + return null; + } + + return ( + + + Overwrite All Icon + + + Overwrite Empty Icon + + + ); +} + +const INTERPOLATION_ICON = { + [InterpolationModeEnum.INTERPOLATE]: , + [InterpolationModeEnum.EXTRUDE]: , +}; + +export function VolumeInterpolationButton() { + const dispatch = useDispatch(); + const interpolationMode = useSelector( + (state: OxalisState) => state.userConfiguration.interpolationMode, + ); + + const onInterpolateClick = (e: React.MouseEvent | null) => { + e?.currentTarget.blur(); + dispatch(interpolateSegmentationLayerAction()); + }; + + const { tooltipTitle, isDisabled } = useSelector((state: OxalisState) => + getInterpolationInfo(state, "Not available since"), + ); + + const menu: MenuProps = { + onClick: (e: MenuInfo) => { + dispatch(updateUserSettingAction("interpolationMode", e.key as InterpolationMode)); + onInterpolateClick(null); + }, + items: [ + { + label: "Interpolate current segment", + key: InterpolationModeEnum.INTERPOLATE, + icon: INTERPOLATION_ICON[InterpolationModeEnum.INTERPOLATE], + }, + { + label: "Extrude (copy) current segment", + key: InterpolationModeEnum.EXTRUDE, + icon: INTERPOLATION_ICON[InterpolationModeEnum.EXTRUDE], + }, + ], + }; + + const buttonsRender = useCallback( + ([leftButton, rightButton]: React.ReactNode[]) => [ + + {React.cloneElement(leftButton as React.ReactElement, { + disabled: isDisabled, + })} + , + rightButton, + ], + [tooltipTitle, isDisabled], + ); + + return ( + // Without the outer div, the Dropdown can eat up all the remaining horizontal space, + // moving sibling elements to the far right. +
+ } + menu={menu} + onClick={onInterpolateClick} + style={{ padding: "0 5px 0 6px" }} + buttonsRender={buttonsRender} + > + {React.cloneElement(INTERPOLATION_ICON[interpolationMode], { style: { margin: -4 } })} + +
+ ); +} + +const mapId = (volumeTracingId: string | null | undefined, id: number) => { + // Note that the return value can be an unmapped id even when + // a mapping is active, if it is a HDF5 mapping that is partially loaded + // and no entry exists yet for the input id. + if (!volumeTracingId) { + return null; + } + const { cube } = Model.getSegmentationTracingLayer(volumeTracingId); + + return cube.mapId(id); +}; + +export function CreateSegmentButton() { + const volumeTracingId = useSelector( + (state: OxalisState) => getActiveSegmentationTracing(state)?.tracingId, + ); + const unmappedActiveCellId = useSelector( + (state: OxalisState) => getActiveSegmentationTracing(state)?.activeCellId || 0, + ); + const { mappingStatus } = useSelector((state: OxalisState) => + getMappingInfoForVolumeTracing(state, volumeTracingId), + ); + const isMappingEnabled = mappingStatus === MappingStatusEnum.ENABLED; + + const activeCellId = isMappingEnabled + ? mapId(volumeTracingId, unmappedActiveCellId) + : unmappedActiveCellId; + + const activeCellColor = useSelector((state: OxalisState) => { + if (!activeCellId) { + return null; + } + return rgbaToCSS(getSegmentColorAsRGBA(state, activeCellId)); + }); + + const mappedIdInfo = isMappingEnabled ? ` (currently mapped to ${activeCellId})` : ""; + return ( + + + New Segment Icon + + + ); +} + +function IdentityComponent({ children }: { children: React.ReactNode }) { + return <>{children}; +} + +function NuxPopConfirm({ children }: { children: React.ReactNode }) { + const dispatch = useDispatch(); + const activeUser = useSelector((state: OxalisState) => state.activeUser); + return ( + { + if (!activeUser) { + return; + } + const [newUserSync] = updateNovelUserExperienceInfos(activeUser, { + hasSeenSegmentAnythingWithDepth: true, + }); + dispatch(setActiveUserAction(newUserSync)); + }} + description="The AI-based Quick Select can now be triggered with a single click. Also, it can be run for multiple sections at once (open the settings here to enable this)." + overlayStyle={{ maxWidth: 400 }} + icon={} + > + {children} + + ); +} + +export function QuickSelectSettingsPopover() { + const dispatch = useDispatch(); + const { quickSelectState, areQuickSelectSettingsOpen } = useSelector( + (state: OxalisState) => state.uiInformation, + ); + const isQuickSelectActive = quickSelectState === "active"; + const activeUser = useSelector((state: OxalisState) => state.activeUser); + + const showNux = + activeUser != null && !activeUser.novelUserExperienceInfos.hasSeenSegmentAnythingWithDepth; + const Wrapper = showNux ? NuxPopConfirm : IdentityComponent; + + return ( + <> + + } + onOpenChange={(open: boolean) => { + dispatch(showQuickSelectSettingsAction(open)); + }} + > + + + + + + + ); +} + +const handleSetFillMode = (event: RadioChangeEvent) => { + Store.dispatch(updateUserSettingAction("fillMode", event.target.value)); +}; + +export function FloodFillSettings() { + const dispatch = useDispatch(); + const isRestrictedToBoundingBox = useSelector( + (state: OxalisState) => state.userConfiguration.isFloodfillRestrictedToBoundingBox, + ); + const toggleRestrictFloodfillToBoundingBox = () => { + dispatch( + updateUserSettingAction("isFloodfillRestrictedToBoundingBox", !isRestrictedToBoundingBox), + ); + }; + return ( +
+ + + + Restrict floodfill + +
+ ); +} + +function FillModeSwitch() { + const fillMode = useSelector((state: OxalisState) => state.userConfiguration.fillMode); + return ( + + + 2D + + + 3D + + + ); +} + +export function ProofreadingComponents() { + const dispatch = useDispatch(); + const handleClearProofreading = () => dispatch(clearProofreadingByProducts()); + const autoRenderMeshes = useSelector( + (state: OxalisState) => state.userConfiguration.autoRenderMeshInProofreading, + ); + const selectiveVisibilityInProofreading = useSelector( + (state: OxalisState) => state.userConfiguration.selectiveVisibilityInProofreading, + ); + + return ( + + + + + handleToggleAutomaticMeshRendering(!autoRenderMeshes)} + > + + + + handleToggleSelectiveVisibilityInProofreading(!selectiveVisibilityInProofreading) + } + > + + + + ); +} diff --git a/frontend/javascripts/oxalis/view/action-bar/view_modes_view.tsx b/frontend/javascripts/oxalis/view/action-bar/view_modes_view.tsx index bd413f4f87d..ee3f0749ea3 100644 --- a/frontend/javascripts/oxalis/view/action-bar/view_modes_view.tsx +++ b/frontend/javascripts/oxalis/view/action-bar/view_modes_view.tsx @@ -12,7 +12,7 @@ import { PureComponent } from "react"; import { connect } from "react-redux"; import type { Dispatch } from "redux"; import type { EmptyObject } from "types/globals"; -import { NARROW_BUTTON_STYLE } from "./toolbar_view"; +import { NARROW_BUTTON_STYLE } from "./tools/tool_helpers"; type StateProps = { viewMode: ViewMode; diff --git a/frontend/javascripts/oxalis/view/action_bar_view.tsx b/frontend/javascripts/oxalis/view/action_bar_view.tsx index 74aa44158fc..1d00bdfb9e7 100644 --- a/frontend/javascripts/oxalis/view/action_bar_view.tsx +++ b/frontend/javascripts/oxalis/view/action_bar_view.tsx @@ -20,7 +20,7 @@ import type { OxalisState } from "oxalis/store"; import Store from "oxalis/store"; import AddNewLayoutModal from "oxalis/view/action-bar/add_new_layout_modal"; import DatasetPositionView from "oxalis/view/action-bar/dataset_position_view"; -import ToolbarView from "oxalis/view/action-bar/toolbar_view"; +import ToolbarView from "oxalis/view/action-bar/tools/toolbar_view"; import TracingActionsView, { getLayoutMenu, type LayoutProps, @@ -39,7 +39,7 @@ import { useHistory } from "react-router-dom"; import type { APIDataset, APIUser } from "types/api_flow_types"; import { APIJobType, type AdditionalCoordinate } from "types/api_flow_types"; import { StartAIJobModal, type StartAIJobModalState } from "./action-bar/starting_job_modals"; -import ToolkitView from "./action-bar/toolkit_switcher_view"; +import ToolkitView from "./action-bar/tools/toolkit_switcher_view"; import ButtonComponent from "./components/button_component"; import { NumberSliderSetting } from "./components/setting_input_views";