@jax-data-science/sci-image-visualizer 0.12.0 → 0.12.1

package/fesm2022/{jax-data-science-sci-image-visualizer-onnx-sam-session-CvadfzjS.mjs → jax-data-science-sci-image-visualizer-onnx-sam-session-Bs987_-E.mjs}

@@ -1,6 +1,6 @@
 import { LruCache } from 'napari-js';
 import * as ort from 'onnxruntime-web';
-import { g as getOrtWasmBase, f as fetchModel, r as runEncoder, a as runDecoder } from './jax-data-science-sci-image-visualizer-jax-data-science-sci-image-visualizer-a68Hw5rw.mjs';
+import { g as getOrtWasmBase, f as fetchModel, r as runEncoder, a as runDecoder } from './jax-data-science-sci-image-visualizer-jax-data-science-sci-image-visualizer-DnPlIP2F.mjs';
 import '@angular/core';
 import '@angular/common/http';
 import 'rxjs';
@@ -237,4 +237,4 @@ class OnnxSamSession {
 }
 
 export { OnnxSamSession };
-//# sourceMappingURL=jax-data-science-sci-image-visualizer-onnx-sam-session-CvadfzjS.mjs.map
+//# sourceMappingURL=jax-data-science-sci-image-visualizer-onnx-sam-session-Bs987_-E.mjs.map

package/fesm2022/{jax-data-science-sci-image-visualizer-onnx-sam-session-CvadfzjS.mjs.map → jax-data-science-sci-image-visualizer-onnx-sam-session-Bs987_-E.mjs.map}

@@ -1 +1 @@
-{"version":3,"file":"jax-data-science-sci-image-visualizer-onnx-sam-session-CvadfzjS.mjs","sources":["../../src/lib/toolbar/segmentation/pending-calls.ts","../../src/lib/toolbar/segmentation/onnx-sam-session.ts"],"sourcesContent":["/** A reply from the SAM worker: progress for, or the result of, call `id`. */\nexport interface WorkerReply {\n  id: number;\n  type: string;\n  /** Present on `type: 'progress'` replies. */\n  fraction?: number;\n  /** Present on `type: 'error'` replies. */\n  error?: string;\n  [key: string]: unknown;\n}\n\ninterface Pending {\n  resolve: (reply: WorkerReply) => void;\n  reject: (err: Error) => void;\n  onProgress?: (fraction: number) => void;\n}\n\n/**\n * Request/response bookkeeping for a worker RPC: each call gets an id and a\n * promise that its reply settles. Every exit path (dispose, a worker crash)\n * must {@link rejectAll}, or awaiting callers never reach their `finally` and a\n * tool's busy flag sticks forever (RT-8).\n */\nexport class PendingCalls {\n  private seq = 0;\n  private readonly pending = new Map<number, Pending>();\n\n  /** Calls still awaiting a reply. */\n  get size(): number {\n    return this.pending.size;\n  }\n\n  /** Register a new call; post the message with the returned id. */\n  open(onProgress?: (fraction: number) => void): { id: number; promise: Promise<WorkerReply> } {\n    const id = ++this.seq;\n    const promise = new Promise<WorkerReply>((resolve, reject) => {\n      this.pending.set(id, { resolve, reject, onProgress });\n    });\n    return { id, promise };\n  }\n\n  /** Route a worker reply to its call: progress, error or result. */\n  handle(reply: WorkerReply): void {\n    const p = this.pending.get(reply.id);\n    if (!p) return;\n    if (reply.type === 'progress') {\n      p.onProgress?.(reply.fraction ?? 0);\n      return;\n    }\n    this.pending.delete(reply.id);\n    if (reply.type === 'error') p.reject(new Error(reply.error ?? 'SAM worker error.'));\n    else p.resolve(reply);\n  }\n\n  /** Reject every pending call with `err` and forget them. */\n  rejectAll(err: Error): void {\n    const calls = Array.from(this.pending.values());\n    this.pending.clear();\n    for (const p of calls) p.reject(err);\n  }\n}\n","import { LruCache } from 'napari-js';\nimport * as ort from 'onnxruntime-web';\n\nimport { ISamSession, SamEmbedding, SamMaskResult, SamModelDef, SamPrompt } from '../../contracts/sam.contract';\nimport { fetchModel, runEncoder, runDecoder, type CoreEmbedding } from './sam-onnx-core';\nimport { getOrtWasmBase } from './ort-runtime-config';\nimport { PendingCalls, WorkerReply } from './pending-calls';\n\n/**\n * onnxruntime-web implementation of {@link ISamSession} (jit-ui#90), with two\n * execution modes chosen per model:\n *\n *  - **in-process** (main thread) — for small WASM models flagged `inProcess`\n *    (e.g. micro-sam ViT-T). Fast load + inference with no Web Worker spawn /\n *    second ORT runtime / message round-trips; the brief encode runs on the main\n *    thread (fine for a tiny model).\n *  - **worker** — for WebGPU models (e.g. ViT-B, patho-sam fp16) whose heavy\n *    encode would otherwise freeze the tab. Runs in {@link ./onnx-sam.worker} so\n *    the UI stays responsive (the spinner animates).\n *\n * Both modes share their inference math via {@link ./sam-onnx-core}. Lazy-imported\n * by the SAM tools so onnxruntime-web / the worker never load in unit tests or\n * the initial bundle.\n */\nexport class OnnxSamSession implements ISamSession {\n  private mode: 'inproc' | 'worker' | null = null;\n  private loaded = false;\n  private inputSize = 1024;\n\n  // ── worker mode ──\n  private worker: Worker | null = null;\n  private readonly calls = new PendingCalls();\n\n  // ── in-process mode ──\n  private encoder: ort.InferenceSession | null = null;\n  private decoder: ort.InferenceSession | null = null;\n  private nextToken = 1;\n  /** The few most recently used embeddings, by token (one per recently viewed image). */\n  private readonly embeddings = new LruCache<CoreEmbedding, number>(3);\n\n  async loadModel(model: SamModelDef, onProgress?: (fraction: number) => void): Promise<void> {\n    if (!model.encoderUrl || !model.decoderUrl) {\n      throw new Error(`SAM model \"${model.id}\" has no ONNX URLs configured.`);\n    }\n    this.inputSize = model.inputSize;\n    const hasGpu = typeof navigator !== 'undefined' && 'gpu' in navigator;\n    const eps: string[] = model.encoderProviders ?? (hasGpu ? ['webgpu', 'wasm'] : ['wasm']);\n    const usesWebGpu = eps.includes('webgpu');\n    // WebGPU must run in the worker (else it freezes the main thread); small\n    // WASM models opt into the faster in-process path via `inProcess`.\n    this.mode = !usesWebGpu && model.inProcess ? 'inproc' : 'worker';\n\n    if (this.mode === 'inproc') {\n      ort.env.wasm.wasmPaths = getOrtWasmBase();\n      const encBuf = await fetchModel(model.encoderUrl, onProgress, model.revision);\n      const decBuf = await fetchModel(model.decoderUrl, undefined, model.revision);\n      this.encoder = await ort.InferenceSession.create(encBuf, { executionProviders: eps });\n      this.decoder = await ort.InferenceSession.create(decBuf, { executionProviders: ['wasm'] });\n    } else {\n      await this.call(\n        {\n          type: 'load',\n          encoderUrl: model.encoderUrl,\n          decoderUrl: model.decoderUrl,\n          revision: model.revision,\n          wasmPaths: getOrtWasmBase(),\n          inputSize: model.inputSize,\n          encoderProviders: model.encoderProviders,\n        },\n        [],\n        onProgress,\n      );\n    }\n    this.loaded = true;\n  }\n\n  isLoaded(): boolean {\n    return this.loaded;\n  }\n\n  async embed(image: { data: Uint8ClampedArray; width: number; height: number }): Promise<SamEmbedding> {\n    if (this.mode === 'inproc') {\n      const e = await runEncoder(this.encoder!, image.data, image.width, image.height, this.inputSize);\n      const token = this.nextToken++;\n      this.embeddings.set(token, e);\n      return {\n        data: new Float32Array(0),\n        dims: e.dims,\n        scale: e.scale,\n        imageWidth: e.imageWidth,\n        imageHeight: e.imageHeight,\n        token,\n      };\n    }\n    // worker: transfer the RGBA buffer (callers pass a fresh frame buffer).\n    const buffer = image.data.buffer;\n    const res = await this.call({ type: 'embed', width: image.width, height: image.height, buffer }, [buffer]);\n    return {\n      data: new Float32Array(0),\n      dims: res['dims'] as number[],\n      scale: res['scale'] as number,\n      imageWidth: res['imageWidth'] as number,\n      imageHeight: res['imageHeight'] as number,\n      token: res['token'] as number,\n    };\n  }\n\n  async decode(embedding: SamEmbedding, prompt: SamPrompt): Promise<SamMaskResult> {\n    if (this.mode === 'inproc') {\n      const e = this.embeddings.get(embedding.token as number);\n      if (!e) throw new Error('SAM embedding expired; re-encode the image.');\n      return runDecoder(this.decoder!, e, prompt);\n    }\n    const res = await this.call({ type: 'decode', token: embedding.token, prompt });\n    return {\n      mask: new Uint8Array(res['buffer'] as ArrayBuffer),\n      width: res['width'] as number,\n      height: res['height'] as number,\n      iou: res['iou'] as number,\n    };\n  }\n\n  /** Release the worker / ORT sessions. Calls still in flight reject (RT-8), so\n   *  their callers' `finally` blocks run (e.g. a tool's busy flag clears). */\n  dispose(): void {\n    this.dropWorker(new Error('SAM session disposed'));\n    this.encoder?.release?.();\n    this.decoder?.release?.();\n    this.encoder = this.decoder = null;\n    this.embeddings.clear();\n    this.loaded = false;\n    this.mode = null;\n  }\n\n  // ── worker plumbing ──────────────────────────────────────────────────────\n  private ensureWorker(): Worker {\n    if (this.worker) return this.worker;\n    const worker = new Worker(new URL('./onnx-sam.worker', import.meta.url), { type: 'module' });\n    worker.onmessage = (ev: MessageEvent<WorkerReply>) => this.calls.handle(ev.data);\n    worker.onerror = (ev: ErrorEvent) => {\n      // A crashed worker can't serve the loaded model any more: drop it, so the\n      // next run reloads instead of posting to a dead worker.\n      this.dropWorker(new Error(ev.message || 'SAM worker crashed.'));\n      this.loaded = false;\n      this.mode = null;\n    };\n    this.worker = worker;\n    return worker;\n  }\n\n  /** Terminate the worker (if any) and reject every call still waiting on it. */\n  private dropWorker(err: Error): void {\n    this.worker?.terminate();\n    this.worker = null;\n    this.calls.rejectAll(err);\n  }\n\n  private call(\n    msg: Record<string, unknown>,\n    transfer: Transferable[] = [],\n    onProgress?: (f: number) => void,\n  ): Promise<WorkerReply> {\n    const worker = this.ensureWorker();\n    const { id, promise } = this.calls.open(onProgress);\n    worker.postMessage({ ...msg, id }, transfer);\n    return promise;\n  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+{"version":3,"file":"jax-data-science-sci-image-visualizer-onnx-sam-session-Bs987_-E.mjs","sources":["../../src/lib/toolbar/segmentation/pending-calls.ts","../../src/lib/toolbar/segmentation/onnx-sam-session.ts"],"sourcesContent":["/** A reply from the SAM worker: progress for, or the result of, call `id`. */\nexport interface WorkerReply {\n  id: number;\n  type: string;\n  /** Present on `type: 'progress'` replies. */\n  fraction?: number;\n  /** Present on `type: 'error'` replies. */\n  error?: string;\n  [key: string]: unknown;\n}\n\ninterface Pending {\n  resolve: (reply: WorkerReply) => void;\n  reject: (err: Error) => void;\n  onProgress?: (fraction: number) => void;\n}\n\n/**\n * Request/response bookkeeping for a worker RPC: each call gets an id and a\n * promise that its reply settles. Every exit path (dispose, a worker crash)\n * must {@link rejectAll}, or awaiting callers never reach their `finally` and a\n * tool's busy flag sticks forever (RT-8).\n */\nexport class PendingCalls {\n  private seq = 0;\n  private readonly pending = new Map<number, Pending>();\n\n  /** Calls still awaiting a reply. */\n  get size(): number {\n    return this.pending.size;\n  }\n\n  /** Register a new call; post the message with the returned id. */\n  open(onProgress?: (fraction: number) => void): { id: number; promise: Promise<WorkerReply> } {\n    const id = ++this.seq;\n    const promise = new Promise<WorkerReply>((resolve, reject) => {\n      this.pending.set(id, { resolve, reject, onProgress });\n    });\n    return { id, promise };\n  }\n\n  /** Route a worker reply to its call: progress, error or result. */\n  handle(reply: WorkerReply): void {\n    const p = this.pending.get(reply.id);\n    if (!p) return;\n    if (reply.type === 'progress') {\n      p.onProgress?.(reply.fraction ?? 0);\n      return;\n    }\n    this.pending.delete(reply.id);\n    if (reply.type === 'error') p.reject(new Error(reply.error ?? 'SAM worker error.'));\n    else p.resolve(reply);\n  }\n\n  /** Reject every pending call with `err` and forget them. */\n  rejectAll(err: Error): void {\n    const calls = Array.from(this.pending.values());\n    this.pending.clear();\n    for (const p of calls) p.reject(err);\n  }\n}\n","import { LruCache } from 'napari-js';\nimport * as ort from 'onnxruntime-web';\n\nimport { ISamSession, SamEmbedding, SamMaskResult, SamModelDef, SamPrompt } from '../../contracts/sam.contract';\nimport { fetchModel, runEncoder, runDecoder, type CoreEmbedding } from './sam-onnx-core';\nimport { getOrtWasmBase } from './ort-runtime-config';\nimport { PendingCalls, WorkerReply } from './pending-calls';\n\n/**\n * onnxruntime-web implementation of {@link ISamSession} (jit-ui#90), with two\n * execution modes chosen per model:\n *\n *  - **in-process** (main thread) — for small WASM models flagged `inProcess`\n *    (e.g. micro-sam ViT-T). Fast load + inference with no Web Worker spawn /\n *    second ORT runtime / message round-trips; the brief encode runs on the main\n *    thread (fine for a tiny model).\n *  - **worker** — for WebGPU models (e.g. ViT-B, patho-sam fp16) whose heavy\n *    encode would otherwise freeze the tab. Runs in {@link ./onnx-sam.worker} so\n *    the UI stays responsive (the spinner animates).\n *\n * Both modes share their inference math via {@link ./sam-onnx-core}. Lazy-imported\n * by the SAM tools so onnxruntime-web / the worker never load in unit tests or\n * the initial bundle.\n */\nexport class OnnxSamSession implements ISamSession {\n  private mode: 'inproc' | 'worker' | null = null;\n  private loaded = false;\n  private inputSize = 1024;\n\n  // ── worker mode ──\n  private worker: Worker | null = null;\n  private readonly calls = new PendingCalls();\n\n  // ── in-process mode ──\n  private encoder: ort.InferenceSession | null = null;\n  private decoder: ort.InferenceSession | null = null;\n  private nextToken = 1;\n  /** The few most recently used embeddings, by token (one per recently viewed image). */\n  private readonly embeddings = new LruCache<CoreEmbedding, number>(3);\n\n  async loadModel(model: SamModelDef, onProgress?: (fraction: number) => void): Promise<void> {\n    if (!model.encoderUrl || !model.decoderUrl) {\n      throw new Error(`SAM model \"${model.id}\" has no ONNX URLs configured.`);\n    }\n    this.inputSize = model.inputSize;\n    const hasGpu = typeof navigator !== 'undefined' && 'gpu' in navigator;\n    const eps: string[] = model.encoderProviders ?? (hasGpu ? ['webgpu', 'wasm'] : ['wasm']);\n    const usesWebGpu = eps.includes('webgpu');\n    // WebGPU must run in the worker (else it freezes the main thread); small\n    // WASM models opt into the faster in-process path via `inProcess`.\n    this.mode = !usesWebGpu && model.inProcess ? 'inproc' : 'worker';\n\n    if (this.mode === 'inproc') {\n      ort.env.wasm.wasmPaths = getOrtWasmBase();\n      const encBuf = await fetchModel(model.encoderUrl, onProgress, model.revision);\n      const decBuf = await fetchModel(model.decoderUrl, undefined, model.revision);\n      this.encoder = await ort.InferenceSession.create(encBuf, { executionProviders: eps });\n      this.decoder = await ort.InferenceSession.create(decBuf, { executionProviders: ['wasm'] });\n    } else {\n      await this.call(\n        {\n          type: 'load',\n          encoderUrl: model.encoderUrl,\n          decoderUrl: model.decoderUrl,\n          revision: model.revision,\n          wasmPaths: getOrtWasmBase(),\n          inputSize: model.inputSize,\n          encoderProviders: model.encoderProviders,\n        },\n        [],\n        onProgress,\n      );\n    }\n    this.loaded = true;\n  }\n\n  isLoaded(): boolean {\n    return this.loaded;\n  }\n\n  async embed(image: { data: Uint8ClampedArray; width: number; height: number }): Promise<SamEmbedding> {\n    if (this.mode === 'inproc') {\n      const e = await runEncoder(this.encoder!, image.data, image.width, image.height, this.inputSize);\n      const token = this.nextToken++;\n      this.embeddings.set(token, e);\n      return {\n        data: new Float32Array(0),\n        dims: e.dims,\n        scale: e.scale,\n        imageWidth: e.imageWidth,\n        imageHeight: e.imageHeight,\n        token,\n      };\n    }\n    // worker: transfer the RGBA buffer (callers pass a fresh frame buffer).\n    const buffer = image.data.buffer;\n    const res = await this.call({ type: 'embed', width: image.width, height: image.height, buffer }, [buffer]);\n    return {\n      data: new Float32Array(0),\n      dims: res['dims'] as number[],\n      scale: res['scale'] as number,\n      imageWidth: res['imageWidth'] as number,\n      imageHeight: res['imageHeight'] as number,\n      token: res['token'] as number,\n    };\n  }\n\n  async decode(embedding: SamEmbedding, prompt: SamPrompt): Promise<SamMaskResult> {\n    if (this.mode === 'inproc') {\n      const e = this.embeddings.get(embedding.token as number);\n      if (!e) throw new Error('SAM embedding expired; re-encode the image.');\n      return runDecoder(this.decoder!, e, prompt);\n    }\n    const res = await this.call({ type: 'decode', token: embedding.token, prompt });\n    return {\n      mask: new Uint8Array(res['buffer'] as ArrayBuffer),\n      width: res['width'] as number,\n      height: res['height'] as number,\n      iou: res['iou'] as number,\n    };\n  }\n\n  /** Release the worker / ORT sessions. Calls still in flight reject (RT-8), so\n   *  their callers' `finally` blocks run (e.g. a tool's busy flag clears). */\n  dispose(): void {\n    this.dropWorker(new Error('SAM session disposed'));\n    this.encoder?.release?.();\n    this.decoder?.release?.();\n    this.encoder = this.decoder = null;\n    this.embeddings.clear();\n    this.loaded = false;\n    this.mode = null;\n  }\n\n  // ── worker plumbing ──────────────────────────────────────────────────────\n  private ensureWorker(): Worker {\n    if (this.worker) return this.worker;\n    const worker = new Worker(new URL('./onnx-sam.worker', import.meta.url), { type: 'module' });\n    worker.onmessage = (ev: MessageEvent<WorkerReply>) => this.calls.handle(ev.data);\n    worker.onerror = (ev: ErrorEvent) => {\n      // A crashed worker can't serve the loaded model any more: drop it, so the\n      // next run reloads instead of posting to a dead worker.\n      this.dropWorker(new Error(ev.message || 'SAM worker crashed.'));\n      this.loaded = false;\n      this.mode = null;\n    };\n    this.worker = worker;\n    return worker;\n  }\n\n  /** Terminate the worker (if any) and reject every call still waiting on it. */\n  private dropWorker(err: Error): void {\n    this.worker?.terminate();\n    this.worker = null;\n    this.calls.rejectAll(err);\n  }\n\n  private call(\n    msg: Record<string, unknown>,\n    transfer: Transferable[] = [],\n    onProgress?: (f: number) => void,\n  ): Promise<WorkerReply> {\n    const worker = this.ensureWorker();\n    const { id, promise } = this.calls.open(onProgress);\n    worker.postMessage({ ...msg, id }, transfer);\n    return promise;\n  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package/fesm2022/jax-data-science-sci-image-visualizer.mjs

@@ -1,4 +1,4 @@
-export { A as ALL_GENES, b as ALL_TOOLBAR_TOOLS, c as ANNOTATION_IMAGE_MAX_DIM, C as CANVAS_TOOL_IDS, d as CELL_SEGMENTER, e as CHANNEL_HISTOGRAM_API, h as CellposeSegmenterService, i as ChannelHistogramComponent, D as DEFAULT_CATEGORICAL_PALETTE, j as DEFAULT_FALLBACK_PALETTE, k as DEFAULT_MUTED_OPACITY, l as DEFAULT_SAM_MODEL_ID, m as DEFAULT_SPATIAL_VIEW, H as HexColorPickerComponent, I as IMAGE_STATE_PORT, n as INSTANCE_SEGMENTER, o as ImageConverterService, L as LUT_COLORS, M as MISSING_COLOR, p as MultiPolygon, N as NAPARI_DECIMATE_OPTIONS, q as NAPARI_DEFAULT_DECIMATE, s as NO_CATEGORY, t as NO_OBSERVATION, P as PLOT_MODE_CONTEXT, u as PLOT_MODE_SESSION, v as PLOT_TYPE_CONTRIBUTIONS, w as PLOT_TYPE_DESCRIPTORS, x as PREFERENCES_PORT, y as PlotType, z as Polygon, B as ProcessingImage, R as REGION_EDITOR_API, E as REGION_IO_PORT, F as REGION_SOURCE_MIN_CHARS, G as Rectangle, J as Region, K as RegionEditorComponent, O as RoutingVisualizerService, S as SAM_MODELS, Q as SEMANTIC_SEGMENTER, T as SPATIAL_DATA_PORT, U as SPATIAL_WIRE_VERSION, V as ShapeSelection, W as SpatialChartsComponent, X as SpatialControlsComponent, Y as SpatialDataHttpService, Z as SpatialSelectionStore, _ as SupersededError, $ as TILE_ACCESS_PORT, a0 as TOOLBAR_TOOLS, a1 as VISUALIZER, a2 as VIZ_ALERT_TOAST_KEY, a3 as VIZ_CONFIG, a4 as VIZ_TOAST_KEY, a5 as ViewerFeature, a6 as VisualizationModule, a7 as VisualizerComponent, a8 as assertManifestVersion, a9 as benefitsFromGrouping, aa as buildOmicsTraces, ab as capabilitiesOf, ac as clearSamModelCache, ad as contrastWindow, ae as contributedPlotTypeOption, af as countMask, ag as cropImage, ah as datasetFromManifest, ai as decodeColumn, aj as decodeCoords, ak as decodeFeatureVector, al as decodePolygons, am as decodeRadius, an as defaultPresetSet, ao as dialogToolContributions, ap as emptySelection, aq as encodeCategorical, ar as encodeContinuous, as as expandZips, at as findColumnMeta, au as getDefaultSamModelId, g as getOrtWasmBase, av as getPlotTypeDescriptor, aw as getSamModel, ax as hasZarrMetadata, ay as hydrateBounds, az as importFile, aA as isBuiltinPlotType, aB as isCanvasToolId, aC as isCategoricalColumn, aD as isContinuousColumn, aE as isDialogToolContribution, aF as isEmptyPresetSet, aG as isLabelVolumeName, aH as isLittleEndian, aI as isNapari3d, aJ as isNapariIsosurface, aK as isNapariScatter, aL as isNapariScatter3d, aM as isNapariSurface, aN as isNapariVolume, aO as isSamModelReady, aP as isSpatialOmics, aQ as isSpatialOmics3d, aR as isThreeDimensional, aS as isZipName, aT as labelClasses, aU as labelSliceGeoJson, aV as lutFor, aW as markerDiameters, aX as maskToIndices, aY as mutedFromSelection, aZ as omicsLayout, a_ as openAnnotations, a$ as openGeoJsonRegionSource, b0 as openHttpRegionSource, b1 as parsePresetSet, b2 as planRegionImport, b3 as pointInRing, b4 as provideVisualization, b5 as readAnnotationSlices, b6 as readLabelVolume, b7 as readOmeZarrLabels, b8 as readZip, b9 as rendererOwnsWheel, ba as resolveCategoryColors, bb as selectByCategory, bc as selectInRegions, bd as setDefaultSamModel, be as setOrtWasmBase, bf as setSamModelUrls, bg as sortToolContributions, bh as visibleToolContributions } from './jax-data-science-sci-image-visualizer-jax-data-science-sci-image-visualizer-a68Hw5rw.mjs';
+export { A as ALL_GENES, b as ALL_TOOLBAR_TOOLS, c as ANNOTATION_IMAGE_MAX_DIM, C as CANVAS_TOOL_IDS, d as CELL_SEGMENTER, e as CHANNEL_HISTOGRAM_API, h as CellposeSegmenterService, i as ChannelHistogramComponent, D as DEFAULT_CATEGORICAL_PALETTE, j as DEFAULT_FALLBACK_PALETTE, k as DEFAULT_MUTED_OPACITY, l as DEFAULT_SAM_MODEL_ID, m as DEFAULT_SPATIAL_VIEW, H as HexColorPickerComponent, I as IMAGE_STATE_PORT, n as INSTANCE_SEGMENTER, o as ImageConverterService, L as LUT_COLORS, M as MISSING_COLOR, p as MultiPolygon, N as NAPARI_DECIMATE_OPTIONS, q as NAPARI_DEFAULT_DECIMATE, s as NO_CATEGORY, t as NO_OBSERVATION, P as PLOT_MODE_CONTEXT, u as PLOT_MODE_SESSION, v as PLOT_TYPE_CONTRIBUTIONS, w as PLOT_TYPE_DESCRIPTORS, x as PREFERENCES_PORT, y as PlotType, z as Polygon, B as ProcessingImage, R as REGION_EDITOR_API, E as REGION_IO_PORT, F as REGION_SOURCE_MIN_CHARS, G as Rectangle, J as Region, K as RegionEditorComponent, O as RoutingVisualizerService, S as SAM_MODELS, Q as SEMANTIC_SEGMENTER, T as SPATIAL_DATA_PORT, U as SPATIAL_WIRE_VERSION, V as ShapeSelection, W as SpatialChartsComponent, X as SpatialControlsComponent, Y as SpatialDataHttpService, Z as SpatialSelectionStore, _ as SupersededError, $ as TILE_ACCESS_PORT, a0 as TOOLBAR_TOOLS, a1 as VISUALIZER, a2 as VIZ_ALERT_TOAST_KEY, a3 as VIZ_CONFIG, a4 as VIZ_TOAST_KEY, a5 as ViewerFeature, a6 as VisualizationModule, a7 as VisualizerComponent, a8 as assertManifestVersion, a9 as benefitsFromGrouping, aa as buildOmicsTraces, ab as capabilitiesOf, ac as clearSamModelCache, ad as contrastWindow, ae as contributedPlotTypeOption, af as countMask, ag as cropImage, ah as datasetFromManifest, ai as decodeColumn, aj as decodeCoords, ak as decodeFeatureVector, al as decodePolygons, am as decodeRadius, an as defaultPresetSet, ao as dialogToolContributions, ap as emptySelection, aq as encodeCategorical, ar as encodeContinuous, as as expandZips, at as findColumnMeta, au as getDefaultSamModelId, g as getOrtWasmBase, av as getPlotTypeDescriptor, aw as getSamModel, ax as hasZarrMetadata, ay as hydrateBounds, az as importFile, aA as isBuiltinPlotType, aB as isCanvasToolId, aC as isCategoricalColumn, aD as isContinuousColumn, aE as isDialogToolContribution, aF as isEmptyPresetSet, aG as isLabelVolumeName, aH as isLittleEndian, aI as isNapari3d, aJ as isNapariIsosurface, aK as isNapariScatter, aL as isNapariScatter3d, aM as isNapariSurface, aN as isNapariVolume, aO as isSamModelReady, aP as isSpatialOmics, aQ as isSpatialOmics3d, aR as isThreeDimensional, aS as isZipName, aT as labelClasses, aU as labelSliceGeoJson, aV as lutFor, aW as markerDiameters, aX as maskToIndices, aY as mutedFromSelection, aZ as omicsLayout, a_ as openAnnotations, a$ as openGeoJsonRegionSource, b0 as openHttpRegionSource, b1 as parsePresetSet, b2 as planRegionImport, b3 as pointInRing, b4 as provideVisualization, b5 as readAnnotationSlices, b6 as readLabelVolume, b7 as readOmeZarrLabels, b8 as readZip, b9 as rendererOwnsWheel, ba as resolveCategoryColors, bb as selectByCategory, bc as selectInRegions, bd as setDefaultSamModel, be as setOrtWasmBase, bf as setSamModelUrls, bg as sortToolContributions, bh as visibleToolContributions } from './jax-data-science-sci-image-visualizer-jax-data-science-sci-image-visualizer-DnPlIP2F.mjs';
 import '@angular/core';
 import '@angular/common/http';
 import 'napari-js';

package/lib/implementations/napari-js/napari-region-overlay.d.ts

@@ -75,8 +75,16 @@ export declare class NapariRegionOverlay implements IRegionOverlay {
     /** In-progress manipulation (select/move modes): dragging a body, a polygon vertex, or a
      *  rectangle corner. `anchor` is the fixed opposite corner for a rectangle resize. */
     private edit;
+    /**
+     * Screen space (the 3D view's lassos): the regions this overlay drew itself, by id. Only those
+     * are drawn, picked or edited here; every other region in the store is in image space (the
+     * image's own, an imported set, structures a tree click took from a source) and means nothing
+     * at canvas pixels. Null: every region (world is the image).
+     */
+    private readonly own;
     constructor(host: HTMLElement, viewer: OverlayViewer, store: RegionStore, opts?: {
         regionSource?: boolean;
+        screenSpace?: boolean;
     });
     /**
      * Whether a region tool currently owns the pointer.
@@ -115,8 +123,12 @@ export declare class NapariRegionOverlay implements IRegionOverlay {
     /** Click-to-place polygon: add a vertex, or close when clicking near the first one. */
     private handlePolygonClick;
     private readonly onDblClick;
-    /** The currently-selected region (single selection), or null. */
+    /** The currently-selected region (single selection) this overlay draws, or null. */
     private selectedRegion;
+    /** Whether this overlay draws (and lets the pointer pick) `region`: see {@link own}. */
+    private draws;
+    /** The regions this overlay drew in screen space (the 3D view's lassos); [] in image space. */
+    ownRegionIds(): number[];
     /**
      * Start a select/move interaction: grab a handle (rectangle corner) or vertex of the already-
      * selected region first; otherwise select the topmost region under the cursor and drag its body.

package/lib/implementations/napari-js/napari-tool-bridge.d.ts

@@ -124,8 +124,19 @@ export declare class NapariToolBridge {
      * A screen-space shape stops meaning anything the moment the camera moves, so an orbit clears
      * the regions drawn in this view (and only those). The SELECTION they produced is kept: that is
      * the durable artefact, and the highlighted points stay highlighted from every angle.
+     *
+     * Every other region in the store is in image space - the image's own, an imported set,
+     * structures a tree click took from a region source - so the overlay neither draws nor picks it
+     * (it would lie flat at canvas pixels over the cloud), and an orbit leaves it alone: they show
+     * in 3D as their reconstructions instead.
      */
     install3dInteraction(viewer: Viewer, host: HTMLElement): void;
+    /**
+     * Remove the regions the 3D overlay drew in screen space (only those) from the store: a lasso
+     * means nothing once the camera it was drawn under moves or the scene goes. Not an edit of the
+     * user's: no undo step (NAPARI-SVC-11).
+     */
+    private clearOwnLassos;
     /**
      * The {@link OverlayViewer} the 3D region overlay draws through: "world" is the canvas, in
      * canvas-local CSS pixels. A pointer arrives in CLIENT pixels, so `canvasToWorld` subtracts the

package/lib/implementations/napari-js/region-overlay/region-svg-renderer.d.ts

@@ -24,10 +24,15 @@ export interface RegionDraft {
 export declare class NapariRegionSvgRenderer {
     private readonly svg;
     private readonly store;
+    private readonly draws;
     private readonly renderer;
     /** Dedicated marquee rect element, updated directly during the drag (no full region redraw). */
     private marqueeEl;
-    constructor(svg: SVGSVGElement, store: RegionStore);
+    /**
+     * @param draws which regions are this overlay's to draw (default: every one); the others are
+     *        left out of the shapes and handles, keeping the store's indices
+     */
+    constructor(svg: SVGSVGElement, store: RegionStore, draws?: (region: Region) => boolean);
     /** Follow the camera: one transform attribute plus the screen-space elements. */
     setCamera(affine: Affine): void;
     /** Rebuild the regions (world space) and their labels. */

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jax-data-science/sci-image-visualizer",
-  "version": "0.12.0",
+  "version": "0.12.1",
   "engines": {
     "node": ">=20.9.0"
   },