@jax-data-science/sci-image-visualizer 0.12.0 → 0.13.0

package/fesm2022/{jax-data-science-sci-image-visualizer-onnx-sam-session-CvadfzjS.mjs → jax-data-science-sci-image-visualizer-onnx-sam-session-D0IQ6PjZ.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-DURPqs5a.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-D0IQ6PjZ.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-D0IQ6PjZ.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-D0IQ6PjZ.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

@@ -1,11 +1,11 @@
-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-DURPqs5a.mjs';
 import '@angular/core';
 import '@angular/common/http';
 import 'napari-js';
 import 'rxjs';
 import 'rxjs/operators';
-import 'onnxruntime-web';
 import 'napari-js/geometry';
+import 'onnxruntime-web';
 import 'fast-png';
 import 'fzstd';
 import '@angular/core/rxjs-interop';

package/lib/contracts/region-editor-api.contract.d.ts

@@ -177,6 +177,9 @@ export interface IRegionEditorApi {
     setClassesHidden?(classes: readonly string[], hidden: boolean): void;
     /** Select every region of these classes on the slice, the source's included (taken). */
     selectRegionClasses?(classes: readonly string[], additive?: boolean): Promise<void>;
+    /** The classes the selection was picked as by {@link selectRegionClasses}; [] once anything
+     *  else is selected (a row, a region drawn or clicked). */
+    getPickedRegionClasses$?(): Observable<readonly string[]>;
     /** {@link getGeoJsonString} merged with the region source behind the regions (see
      *  `RegionStore.getGeoJsonWithSource`); `slice` names a folder stack's slice. */
     getGeoJsonStringWithSource?(regions: Region[], slice?: number): Promise<string>;

package/lib/contracts/visualizer.contract.d.ts

@@ -305,6 +305,12 @@ export interface SpatialCategoricalView {
     /** Per-observation category index, or `NO_CATEGORY`. */
     codes: Uint16Array;
 }
+/**
+ * How "Select from ROIs" selects: inside the volumes of the region classes picked
+ * in the Region Editor (Spatial omics 3D, the regions on the dataset's reference
+ * volume shown), or by the drawn regions.
+ */
+export type RoiSelectionMode = 'class-volumes' | 'regions';
 /**
  * Controls for the SPATIAL_OMICS plot type: what the observation markers are
  * coloured by, and how they are drawn. Capability-gated like
@@ -399,9 +405,26 @@ export interface ISpatialControls {
     /**
      * Select every observation inside the currently-drawn regions (their union).
      * Reuses the existing ROI tools — rectangle, polygon, freehand, wand, brush —
-     * so there is no separate marquee to learn. Returns how many were selected.
+     * so there is no separate marquee to learn. In the 3D cloud, the region classes
+     * picked in the Region Editor (see {@link getPickedRegionClasses$}) select the
+     * observations inside their volumes instead, when the regions sit on the
+     * dataset's reference volume; without a pick, the lassos drawn over the cloud.
+     * Resolves how many were selected — or null when it was superseded while the
+     * classes' outlines were read (a newer selection, a Clear, another dataset, view
+     * or pick), in which case nothing was published.
+     */
+    selectFromRegions(): Promise<number | null>;
+    /**
+     * How {@link selectFromRegions} would select now: inside the picked classes'
+     * volumes, or by the drawn regions. The rule it runs by, so a panel describing
+     * the button can never disagree with what it does.
+     */
+    roiSelectionMode?(): RoiSelectionMode;
+    /**
+     * The region classes the region selection was picked as (a class tree node with
+     * its subclasses, a surface clicked in 3D); [] for any other selection.
      */
-    selectFromRegions(): number;
+    getPickedRegionClasses$?(): Observable<readonly string[]>;
     /** Select every observation in one category of a categorical column — the
      *  legend click. Rejects for an unknown or continuous column. */
     selectCategory(column: string, categoryIndex: number): Promise<number>;

package/lib/geometry/reconstruct.d.ts

@@ -28,6 +28,12 @@ export interface ReconstructOptions {
  * {@link loftLines}). Empty when no slice has an area and no two slices have lines.
  */
 export declare function reconstruct(slices: readonly SliceOutlines[], opts?: ReconstructOptions): Mesh;
+/**
+ * Fill one slice's outlines into `mask`, a `width × height` grid of image px (pixel i spanning
+ * [i, i + 1)), as the reconstruction fills them: each feature even-odd, the features as their
+ * union, sampled at pixel centres. Cells already set stay set. Open lines enclose nothing.
+ */
+export declare function fillOutlines(mask: Uint8Array, width: number, height: number, outlines: SliceOutlines): void;
 /**
  * The area inside `rings` (interleaved `x, y`), even-odd: a ring inside an odd number of others is
  * a hole. Exact for rings that do not cross (a polygon set's exteriors and holes).

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/napari-visualizer.service.d.ts

@@ -150,6 +150,9 @@ export declare class NapariVisualizerService extends BaseStoreVisualizer impleme
     /** Observations projected to canvas pixels under the 3D camera (the spatial 3D cloud), indexed
      *  by observation with NaN for any not drawn; null when no cloud is mounted. */
     getSpatialScreenProjection(obs: SpatialObservations): Float32Array | null;
+    /** The ids of the regions drawn over the 3D cloud in screen space (its lassos); [] in 2D. Every
+     *  other region in the store is in image space, and means nothing at canvas pixels. */
+    getSpatialLassoIds(): number[];
     private fitCameraSoon;
     /** @deprecated Plotly-specific; host re-drives plot() from its image stream. */
     reloadAndPlot(): void;

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/lib/routing-visualizer.service.d.ts

@@ -361,6 +361,7 @@ export declare class RoutingVisualizerService implements IVisualizer, IRegionEdi
     getHiddenClasses$(): Observable<ReadonlySet<string>>;
     setClassesHidden(classes: readonly string[], hidden: boolean): void;
     selectRegionClasses(classes: readonly string[], additive?: boolean): Promise<void>;
+    getPickedRegionClasses$(): Observable<readonly string[]>;
     getGeoJsonStringWithSource(regions: Region[], slice?: number): Promise<string>;
     enterStackMode(slices: Map<number, Region[]>, initialZ?: number, saveLayout?: 'combined' | 'per-slice-file'): void;
     exitStackMode(): void;

package/lib/spatial/spatial-controls.facade.d.ts

@@ -26,6 +26,11 @@ export interface SpatialRendererFeeds {
     };
     /** Observations projected to canvas pixels by the 3D camera, or null when the cloud is not mounted. */
     getSpatialScreenProjection(obs: SpatialObservations): Float32Array | null;
+    /** The ids of the regions drawn over the 3D cloud in screen space (its lassos). */
+    getSpatialLassoIds(): number[];
+    /** Image px per voxel of the volume the region surfaces sit in; null when the plotted image is
+     *  not a volume's stack (the regions are then not in the reference volume's grid). */
+    regionVoxelStep(): number | null;
 }
 /** What the facade works over: the shared stores, the renderer feeds and the router's view state. */
 export interface SpatialControlsContext {
@@ -53,12 +58,21 @@ export declare class SpatialControlsFacade {
     private readonly ctx;
     /** The controls; one object for the facade's life, so consumers can hold it. */
     readonly controls: ISpatialControls;
-    /** Latest dataset, mirrored so `selectFromRegions()` can answer synchronously — it
-     *  runs from a button click and must not await a round-trip. */
+    /** Latest dataset, mirrored so `selectFromRegions()` answers from the dataset on
+     *  screen — it runs from a button click and must not await a round-trip. */
     private dataset;
     private readonly sub;
+    /** Bumped per class-volume selection (and on dispose): only the latest may publish. */
+    private roiRequest;
     constructor(port: SpatialDataPort, ctx: SpatialControlsContext);
     /** Release the port subscription (the router's injector is being destroyed). */
     dispose(): void;
+    /**
+     * How "Select from ROIs" selects now — the one rule its executor and the panel's description
+     * share: inside the picked classes' volumes in the 3D cloud, when the dataset has a reference
+     * volume (and no tissue image) and the plotted image is that volume's stack, so the regions sit
+     * in its grid; by the drawn regions otherwise.
+     */
+    private roiSelectionMode;
     private build;
 }

package/lib/spatial/spatial-selection.d.ts

@@ -1,6 +1,7 @@
 import { Region } from '../models/region';
+import { SliceOutlines } from '../geometry/reconstruct';
 import { RingBounds as Bounds } from '../geometry/ring';
-import { SpatialImageRef, SpatialObservations, SpatialSelectionMask } from '../contracts/spatial-dataset.contract';
+import { SpatialImageRef, SpatialObservations, SpatialSelectionMask, SpatialVolumeMeta } from '../contracts/spatial-dataset.contract';
 /**
  * Which observations fall inside a set of drawn regions.
  *
@@ -95,6 +96,20 @@ export declare function selectInRegions(observations: SpatialObservations, image
  * never selected.
  */
 export declare function selectInRegionsProjected(screen: Float32Array, count: number, regions: readonly Region[]): SpatialSelectionMask;
+/**
+ * Observations inside the VOLUME a stack of outlines encloses: a region class (an
+ * atlas structure with its substructures) through every section of the dataset's
+ * reference volume, as its 3D reconstruction shows it.
+ *
+ * The outlines are in the volume's own grid — x, y in voxels, z the slice — which
+ * is where regions imported onto the volume's stack sit. An observation is in voxel
+ * `(⌊x / vx⌋, ⌊y / vy⌋, ⌊z / vz⌋)` (see `volumeImageRef`), and selected when its
+ * slice's outlines cover that voxel, filled as the reconstruction fills them. One
+ * slice is rasterised at a time, so a structure through the whole brain costs one
+ * slice's mask, not the volume's. An observation outside the volume, or without a
+ * z, is never selected.
+ */
+export declare function selectInClassVolumes(observations: SpatialObservations, volume: SpatialVolumeMeta, slices: readonly SliceOutlines[]): SpatialSelectionMask;
 /**
  * Whether two selections hold exactly the same observations.
  *

package/lib/spatial-controls/spatial-controls.component.d.ts

@@ -1,5 +1,5 @@
 import { EventEmitter, NgZone, OnInit } from '@angular/core';
-import { IVisualizer, ISpatialControls } from '../contracts/visualizer.contract';
+import { IVisualizer, ISpatialControls, RoiSelectionMode } from '../contracts/visualizer.contract';
 import { SpatialDataset } from '../contracts/spatial-dataset.contract';
 import { ColormapNode, SpatialViewState } from '../contracts/display-types';
 import { PanelOption, parseGeneGroups } from '../spatial/spatial-panel-model';
@@ -81,6 +81,12 @@ export declare class SpatialControlsComponent implements OnInit {
     /** An ROI selection that matched nothing, so the UI can say so rather than
      *  looking like the button did nothing. */
     protected selectionMissed: boolean;
+    /** The mode of the selection that {@link selectionMissed}: what it found nothing inside. */
+    protected missedMode: RoiSelectionMode;
+    /** The region classes picked in the Region Editor: in 3D, "Select from ROIs" selects inside them. */
+    protected pickedClasses: readonly string[];
+    /** While "Select from ROIs" reads the picked classes' outlines. */
+    protected selectingFromRegions: boolean;
     /**
      * Whether the Distribution section is expanded. Collapsed by default: the
      * panel's primary job is the colour controls, and the chart roughly doubles
@@ -106,8 +112,13 @@ export declare class SpatialControlsComponent implements OnInit {
     onGeneFilter(query: string): Promise<void>;
     /** A gene dropdown opened — see {@link GenePickerModel.ensureList}. */
     ensureGeneList(): Promise<void>;
-    /** Select every observation inside the drawn regions (their union). */
-    protected selectFromRegions(): void;
+    /** Select every observation inside the drawn regions (their union) — in 3D, inside the
+     *  picked classes' volumes. */
+    protected selectFromRegions(): Promise<void>;
+    /** In 3D with classes picked, "Select from ROIs" selects inside their volumes. */
+    protected get selectsClassVolumes(): boolean;
+    /** How "Select from ROIs" selects now: the controls' own rule, the one the selection runs by. */
+    private get roiSelectionMode();
     /** Legend click: select one category. Clicking the active row clears it, so a
      *  second click is an undo rather than a no-op. */
     protected selectCategory(index: number): Promise<void>;

package/lib/store/region-selection.d.ts

@@ -10,18 +10,29 @@ interface HasId {
  * owner calls {@link sync} once the region array it projects onto is final,
  * which prunes ids that no longer exist and emits {@link indices$} only when
  * the index set changed.
+ *
+ * A selection made by picking classes (the class tree, a surface in 3D) also
+ * holds those classes: a class is a volume through the whole stack, whether or
+ * not it has a region on the slice. Any other selection drops them; an edit
+ * ({@link retain}, {@link sync}) keeps them.
  */
 export declare class RegionSelection {
     private selected;
+    private picked;
     private readonly indicesSubject;
+    private readonly classesSubject;
     /** The selected regions' current array indices (emits on change only). */
     readonly indices$: Observable<number[]>;
+    /** The classes the selection was picked as ([] for any other selection; emits on change only). */
+    readonly classes$: Observable<readonly string[]>;
+    /** The classes the selection was picked as, as last emitted by {@link sync}. */
+    get classes(): readonly string[];
     /** The selected indices as last projected by {@link sync}. */
     get indices(): number[];
     /** The selected ids, in selection order. */
     get ids(): readonly number[];
-    /** Replace the selected ids (no emit until {@link sync}). */
-    replace(ids: number[]): void;
+    /** Replace the selected ids, picked as `classes` if they were (no emit until {@link sync}). */
+    replace(ids: number[], classes?: readonly string[]): void;
     /** Keep only the ids `keep` accepts (no emit until {@link sync}). */
     retain(keep: (id: number) => boolean): void;
     /**
@@ -30,7 +41,7 @@ export declare class RegionSelection {
      */
     selectIndices(indices: number[], regions: readonly HasId[]): void;
     /** Project the selected ids onto `regions`, pruning ids it no longer holds,
-     *  and emit if the index set changed. */
+     *  and emit if the index set (or the picked classes) changed. */
     sync(regions: readonly HasId[]): void;
 }
 export {};

package/lib/store/region-store.service.d.ts

@@ -377,9 +377,22 @@ export declare class RegionStore implements IRegionStore, IRegionEditApi, IRegio
     /**
      * Select every region of these classes on the slice — the regions', and the region source's,
      * which are taken into the regions (at most {@link SELECT_CLASSES_LIMIT} of them). Added to the
-     * selection with `additive`. Resolves the selected region ids.
+     * selection with `additive`. The selection holds the classes too (see {@link getPickedClasses}).
+     * Resolves the selected region ids.
      */
     selectClasses(classes: readonly string[], additive?: boolean): Promise<number[]>;
+    /**
+     * The classes the selection was picked as by {@link selectClasses} (a class tree node with its
+     * subclasses, a surface clicked in 3D); [] once anything else selected. Each is a volume through
+     * the whole stack, whether or not it has a region on the slice.
+     */
+    getPickedClasses(): readonly string[];
+    getPickedClasses$(): Observable<readonly string[]>;
+    /**
+     * Every slice's exact outlines of these classes, the region sources' and the regions' (as the
+     * 3D reconstruction reads them at the stack's own resolution): what is inside their volume.
+     */
+    classSliceOutlines(classes: readonly string[]): Promise<SliceOutlines[]>;
     /**
      * The 3D reconstruction of each group of classes over every slice of the stack (an atlas
      * structure with its substructures, say): the outlines of the regions of those classes on every

package/lib/store/spatial-selection.service.d.ts

@@ -11,6 +11,14 @@ import * as i0 from "@angular/core";
  */
 export declare class SpatialSelectionStore {
     private readonly selection$;
+    /** Bumped by every write, a clear of nothing included (see {@link revision}). */
+    private writes;
+    /**
+     * How many times the selection was written (set or cleared, by any writer). A selection
+     * computed asynchronously compares it before publishing: a newer write — a Clear, a legend
+     * click, a linked chart's brush — supersedes it.
+     */
+    revision(): number;
     /** Emits on every change, including a clear. */
     getSelection$(): Observable<SpatialSelectionMask>;
     /** Synchronous read, for a renderer building its first frame. */

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jax-data-science/sci-image-visualizer",
-  "version": "0.12.0",
+  "version": "0.13.0",
   "engines": {
     "node": ">=20.9.0"
   },