@jax-data-science/sci-image-visualizer 0.11.0 → 0.12.0

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

@@ -1,11 +1,13 @@
 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-BELcx0jv.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-a68Hw5rw.mjs';
 import '@angular/core';
 import '@angular/common/http';
 import 'rxjs';
 import 'rxjs/operators';
 import 'napari-js/geometry';
+import 'fast-png';
+import 'fzstd';
 import '@angular/core/rxjs-interop';
 import '@angular/common';
 import '@angular/forms';
@@ -235,4 +237,4 @@ class OnnxSamSession {
 }
 
 export { OnnxSamSession };
-//# sourceMappingURL=jax-data-science-sci-image-visualizer-onnx-sam-session-DEDSm_NL.mjs.map
+//# sourceMappingURL=jax-data-science-sci-image-visualizer-onnx-sam-session-CvadfzjS.mjs.map

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

@@ -1 +1 @@
-{"version":3,"file":"jax-data-science-sci-image-visualizer-onnx-sam-session-DEDSm_NL.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 ?? 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'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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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 CANVAS_TOOL_IDS, c as CELL_SEGMENTER, d as CHANNEL_HISTOGRAM_API, e as CellposeSegmenterService, h as ChannelHistogramComponent, D as DEFAULT_CATEGORICAL_PALETTE, i as DEFAULT_FALLBACK_PALETTE, j as DEFAULT_MUTED_OPACITY, k as DEFAULT_SAM_MODEL_ID, l as DEFAULT_SPATIAL_VIEW, H as HexColorPickerComponent, I as IMAGE_STATE_PORT, m as INSTANCE_SEGMENTER, n as ImageConverterService, L as LUT_COLORS, M as MISSING_COLOR, o as MultiPolygon, N as NAPARI_DECIMATE_OPTIONS, p as NAPARI_DEFAULT_DECIMATE, q as NO_CATEGORY, s as NO_OBSERVATION, P as PLOT_MODE_CONTEXT, t as PLOT_MODE_SESSION, u as PLOT_TYPE_CONTRIBUTIONS, v as PLOT_TYPE_DESCRIPTORS, w as PREFERENCES_PORT, x as PlotType, y as Polygon, z as ProcessingImage, R as REGION_EDITOR_API, B as REGION_IO_PORT, E as REGION_SOURCE_MIN_CHARS, F as Rectangle, G as Region, J as RegionEditorComponent, K as RoutingVisualizerService, S as SAM_MODELS, O as SEMANTIC_SEGMENTER, Q as SPATIAL_DATA_PORT, T as SPATIAL_WIRE_VERSION, U as ShapeSelection, V as SpatialChartsComponent, W as SpatialControlsComponent, X as SpatialDataHttpService, Y as SpatialSelectionStore, Z as SupersededError, _ as TILE_ACCESS_PORT, $ as TOOLBAR_TOOLS, a0 as VISUALIZER, a1 as VIZ_ALERT_TOAST_KEY, a2 as VIZ_CONFIG, a3 as VIZ_TOAST_KEY, a4 as ViewerFeature, a5 as VisualizationModule, a6 as VisualizerComponent, a7 as assertManifestVersion, a8 as benefitsFromGrouping, a9 as buildOmicsTraces, aa as capabilitiesOf, ab as clearSamModelCache, ac as contrastWindow, ad as contributedPlotTypeOption, ae as countMask, af as cropImage, ag as datasetFromManifest, ah as decodeColumn, ai as decodeCoords, aj as decodeFeatureVector, ak as decodePolygons, al as decodeRadius, am as defaultPresetSet, an as dialogToolContributions, ao as emptySelection, ap as encodeCategorical, aq as encodeContinuous, ar as findColumnMeta, as as getDefaultSamModelId, g as getOrtWasmBase, at as getPlotTypeDescriptor, au as getSamModel, av as hydrateBounds, aw as importFile, ax as isBuiltinPlotType, ay as isCanvasToolId, az as isCategoricalColumn, aA as isContinuousColumn, aB as isDialogToolContribution, aC as isEmptyPresetSet, aD as isLabelVolumeName, aE as isLittleEndian, aF as isNapari3d, aG as isNapariIsosurface, aH as isNapariScatter, aI as isNapariScatter3d, aJ as isNapariSurface, aK as isNapariVolume, aL as isSamModelReady, aM as isSpatialOmics, aN as isSpatialOmics3d, aO as isThreeDimensional, aP as labelClasses, aQ as labelSliceGeoJson, aR as lutFor, aS as markerDiameters, aT as maskToIndices, aU as mutedFromSelection, aV as omicsLayout, aW as openGeoJsonRegionSource, aX as openHttpRegionSource, aY as parsePresetSet, aZ as planRegionImport, a_ as pointInRing, a$ as provideVisualization, b0 as readLabelVolume, b1 as rendererOwnsWheel, b2 as resolveCategoryColors, b3 as selectByCategory, b4 as selectInRegions, b5 as setDefaultSamModel, b6 as setOrtWasmBase, b7 as setSamModelUrls, b8 as sortToolContributions, b9 as visibleToolContributions } from './jax-data-science-sci-image-visualizer-jax-data-science-sci-image-visualizer-BELcx0jv.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-a68Hw5rw.mjs';
 import '@angular/core';
 import '@angular/common/http';
 import 'napari-js';
@@ -6,6 +6,8 @@ import 'rxjs';
 import 'rxjs/operators';
 import 'onnxruntime-web';
 import 'napari-js/geometry';
+import 'fast-png';
+import 'fzstd';
 import '@angular/core/rxjs-interop';
 import '@angular/common';
 import '@angular/forms';

package/fesm2022/jax-data-science-sci-image-visualizer.mjs.map

@@ -1 +1 @@
-{"version":3,"file":"jax-data-science-sci-image-visualizer.mjs","sources":[],"sourcesContent":[],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;"}
+{"version":3,"file":"jax-data-science-sci-image-visualizer.mjs","sources":[],"sourcesContent":[],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;"}

package/index.d.ts

@@ -56,6 +56,12 @@ export { labelClasses, labelSliceGeoJson } from './lib/region-import/label-class
 export type { LabelClasses } from './lib/region-import/label-classes';
 export { importFile, planRegionImport } from './lib/region-import/region-import';
 export type { RegionImportFile, RegionImportPlan } from './lib/region-import/region-import';
+export { ANNOTATION_IMAGE_MAX_DIM, openAnnotations, readAnnotationSlices, } from './lib/region-import/open-annotations';
+export type { AnnotationDecoders, AnnotationSlices, OpenedAnnotations, } from './lib/region-import/open-annotations';
+export { hasZarrMetadata, readOmeZarrLabels } from './lib/region-import/ome-zarr-labels';
+export type { LabelStack, OmeZarrLabels } from './lib/region-import/ome-zarr-labels';
+export { expandZips, isZipName, readZip } from './lib/region-import/zip';
+export type { ZipEntry } from './lib/region-import/zip';
 export type { RegionSource, RegionSourceView, SourceFeature } from './lib/region-source/region-source';
 export type { RegionIndexPage, RegionIndexQuery, RegionIndexRow, RegionSourceInfo, RegionTile, RegionTileKey, TileFeature, } from './lib/region-source/region-tiles';
 export { VisualizationModule } from './lib/visualization.module';

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

@@ -7,6 +7,7 @@
  * `ImageInfo`/`ImageMetadata` classes are pure data holders that satisfy them
  * structurally, so the host keeps passing its own instances unchanged.
  */
+import type { RegionSource } from '../region-source/region-source';
 /** Per-channel metadata from the server descriptor (issue #76). */
 export interface IChannelInfo {
     name: string;
@@ -65,6 +66,12 @@ export interface IImageInfo {
      *  its regions are drawn from the server's level-of-detail tiles instead of being loaded
      *  from `roiJsonStr`. On a stack, slice z shows the source's plane z. */
     regionSourceUrl?: string;
+    /** The image's own regions, one region source per slice, opened the first time its slice is
+     *  shown: what an image built from annotations alone carries (see `openAnnotations`: a label
+     *  volume traced slice by slice, a folder of per-slice GeoJSON). Attached when the image lands,
+     *  replacing its regions, as an imported label volume or folder is; takes precedence over
+     *  `roiJsonStrs`, `roiJsonStr` and `regionSourceUrl`. Keyed by slice index. */
+    regionSlices?: ReadonlyMap<number, () => Promise<RegionSource>>;
     /** Per-slice, per-channel plane URLs for a SERVERLESS multichannel image
      *  (`tiled: false` + `imageMeta[0].channelCount > 1`). `channelUrls[z][c]`
      *  is a complete single-band image of channel c at slice z. The OSD simple

package/lib/implementations/napari-js/napari-spatial-3d-scene.d.ts

@@ -2,6 +2,8 @@ import { IHistogram } from '../../contracts/channel-histogram-api.contract';
 import { SpatialDataset, SpatialObservations } from '../../contracts/spatial-dataset.contract';
 import { SpatialViewState } from '../../contracts/display-types';
 import { SpatialSelectionMask } from '../../spatial/spatial-selection';
+import type { IImageInfo } from '../../contracts/image.contract';
+import { RegionMesh3D } from './napari-volume-region-meshes';
 import { Spatial3dScalars } from './napari-spatial-encoding';
 import { SpatialSceneBase, SpatialSession } from './napari-spatial-scene';
 import type { NapariScene, SceneContext } from './napari-scene';
@@ -17,6 +19,7 @@ import type { NapariScene, SceneContext } from './napari-scene';
  * shape while keeping the selection. The first 3D layer added frames the camera (`fit3d: 'once'`).
  */
 export declare class Spatial3dScene extends SpatialSceneBase implements NapariScene {
+    private readonly info?;
     /** The 3D point cloud. One layer: selection is a per-point alpha on it, not a second. */
     private points;
     private layerKey;
@@ -58,10 +61,46 @@ export declare class Spatial3dScene extends SpatialSceneBase implements NapariSc
      *  one; a rebuild that leaves the key alone lets it finish. */
     private readonly densityLoads;
     private readonly geneMapLoads;
+    /**
+     * The region reconstructions (an atlas's structures, imported onto the reference volume's image
+     * stack), drawn by the same {@link VolumeRegionMeshes} as the Volume view's, so a structure is the
+     * same surface in both. Placed in the reference volume's box, once it is there and the image the
+     * regions were drawn on is that volume's stack (see {@link placeRegionMeshes}).
+     */
+    private readonly regionMeshes;
+    /** Whether the reference volume lets every region surface through (see setRegionsThroughVolume). */
+    private regionsThrough;
     /** The store's invert setting, which the density volumes follow (no other subscription of
      *  this scene carries it). */
     private invertSub;
-    constructor(ctx: SceneContext, session: SpatialSession);
+    /**
+     * @param info the image plotted with the cloud: the reference volume's stack (the 2D view's
+     *        image, see showVolumeAsImage) when the dataset has a volume, which the regions are on
+     */
+    constructor(ctx: SceneContext, session: SpatialSession, info?: IImageInfo | undefined);
+    /** Show these region reconstructions with the cloud (replacing the ones shown). */
+    setRegionMeshes(meshes: readonly RegionMesh3D[]): void;
+    setRegionHighlight(keys: readonly string[]): void;
+    setRegionHidden(keys: readonly string[]): void;
+    /** As the Volume view: the reference volume hides the surfaces behind what it shows, or none. */
+    setRegionsThroughVolume(through: boolean): void;
+    /**
+     * Place the region surfaces in the reference volume's box, as the Volume view places them in its
+     * own: image pixel (x, y) is voxel (x, y), slice k is voxel plane k, and the box is the volume's
+     * voxels times its voxel size, centred on the origin as napari centres the volume (and the cloud
+     * is offset to sit in it). Only when the plotted image IS that volume's stack: regions drawn on
+     * another image (a tissue image) have no place in it, and are not shown - nor are surfaces
+     * placed in a volume this one replaced.
+     */
+    private placeRegionMeshes;
+    /**
+     * Image px per voxel of the volume the surfaces sit in: 1, the reference volume being the stack's
+     * own voxels, as the Volume view's is at full resolution, so both reconstruct a class alike (and
+     * share its cached surface). Null while there is no volume stack to place them in.
+     */
+    voxelStep(): number | null;
+    /** Whether the plotted image is the reference volume's stack: its size and slice count. */
+    private isVolumeStack;
     mount(): Promise<void>;
     /** The observations' own z is on screen: there is no plane to step. */
     setZ(): void;

package/lib/implementations/napari-js/napari-volume-region-meshes.d.ts

@@ -54,6 +54,11 @@ export declare class VolumeRegionMeshes {
     /** The meshes shown. */
     get shown(): RegionMesh3D[];
     clear(): void;
+    /**
+     * The volume the surfaces sat in is gone (or no longer theirs): take every surface down, keeping
+     * the meshes wanted, so they come back when a frame is set again.
+     */
+    clearFrame(): void;
     private sync;
     private add;
     private opacityOf;

package/lib/region-editor/region-editor.component.d.ts

@@ -360,10 +360,11 @@ export declare class RegionEditorComponent implements OnInit, OnDestroy {
     /** "Import regions from server": the host picks files or a served region set; they import as chosen files do. */
     protected importFromServer(): void;
     /**
-     * Import `files` (see planRegionImport): one GeoJSON file as before; a label volume as one
-     * region source per slice, traced from it the first time the slice is shown, its classes named
-     * (and treed) by the ontology chosen with it; a folder as one source per slice file. Either
-     * replaces the regions and sources of every slice.
+     * Import `files`: one GeoJSON file as before (its regions, editable); anything else (see
+     * readAnnotationSlices) as one region source per slice, replacing the regions and sources of
+     * every slice: a label volume or an OME-Zarr label image traced the first time a slice is shown,
+     * its classes named (and treed) by its ontology; a folder as one source per slice file; a
+     * z-indexed GeoJSON one per plane; a zip of any of these.
      */
     private importRegionFiles;
     /** A region set the host's server serves (jit-service's /regions/{id}/), read through its HttpClient. */

package/lib/region-import/label-volume.d.ts

@@ -20,6 +20,10 @@ export interface LabelVolume {
     height: number;
     /** Number of slices. */
     slices: number;
+    /** Size of a voxel along the slice's x, its y and across slices, in micrometres, when the file
+     *  says (NRRD `space directions`/`spacings`, micrometres unless `space units` says otherwise;
+     *  NIfTI `pixdim`, in its `xyzt_units`, millimetres when unset). */
+    spacing?: [number, number, number];
     /** Slice `z`'s labels, row-major (`height` rows of `width`). */
     sliceLabels(z: number): Uint32Array;
 }

package/lib/region-import/ome-zarr-labels.d.ts

@@ -0,0 +1,36 @@
+/**
+ * A label image of an OME-Zarr store (`labels/<name>/`, NGFF 0.4 on zarr v2 or 0.5 on zarr v3),
+ * read in the browser from the store's files (a folder chosen, or a zip's members): its full
+ * resolution level, sliced along z, with the classes its `image-label` metadata names and colours.
+ *
+ * Chunks are decoded when a slice that needs them is read, so a store is never decoded whole.
+ * Only what label images use: C-order chunks of integer (or integer-valued float) samples, through
+ * the codecs {@link decodeChunk} reads, a missing chunk being the fill value. Sharded or transposed
+ * arrays, F-order and filters throw rather than be read wrongly. Pure: usable from workers.
+ */
+import { LabelClasses } from './label-classes';
+import type { RegionImportFile } from './region-import';
+import { Inflate } from './zarr-codecs';
+/** A stack of label slices read on demand. Label 0 is background. */
+export interface LabelStack {
+    width: number;
+    height: number;
+    slices: number;
+    /** Size of a voxel, x, y, z, in micrometres, when the source says. */
+    spacing?: [number, number, number];
+    /** Slice `z`'s labels, row-major (`height` rows of `width`). */
+    labels(z: number): Promise<Uint32Array>;
+}
+/** An OME-Zarr label image: its name, its slices, its classes. */
+export interface OmeZarrLabels {
+    name: string;
+    stack: LabelStack;
+    classes: LabelClasses;
+}
+/** Whether `files` hold a zarr store (any zarr metadata among them). */
+export declare function hasZarrMetadata(files: readonly RegionImportFile[]): boolean;
+/**
+ * The first label image of the zarr store among `files` (the order `labels/`'s listing gives,
+ * else the first found), or null when the store has none.
+ */
+export declare function readOmeZarrLabels(files: readonly RegionImportFile[], inflate?: Inflate): Promise<OmeZarrLabels | null>;

package/lib/region-import/open-annotations.d.ts

@@ -0,0 +1,73 @@
+import type { IImageInfo } from '../contracts/image.contract';
+import type { RegionSource } from '../region-source/region-source';
+import { LabelClasses } from './label-classes';
+import { Gunzip } from './label-volume';
+import { LabelStack } from './ome-zarr-labels';
+import { RegionImportFile } from './region-import';
+import { Inflate } from './zarr-codecs';
+import { InflateRaw } from './zip';
+/** The longest side an image built for annotations may have: OpenSeadragon's non-tiled limit. */
+export declare const ANNOTATION_IMAGE_MAX_DIM = 8192;
+/** Opens a slice's region source (again, after the store closed it). */
+type Opener = () => Promise<RegionSource>;
+/** Decoders, injectable for tests and workers (defaults: the platform's streams). */
+export interface AnnotationDecoders {
+    inflateRaw?: InflateRaw;
+    inflate?: Inflate;
+    gunzip?: Gunzip;
+    /** Open a GeoJSON text as a region source (default: in the shared region worker). */
+    openGeoJson?: (text: string) => Promise<RegionSource>;
+    /**
+     * Give a label image's regions the atlas look (dark outlines, labels) when its ontology names
+     * no style: drawn over the label image itself, outlines in their classes' own colours would not
+     * show. (Imported over a real image, the default look reads.)
+     */
+    outlineLabels?: boolean;
+}
+/** The annotations among some files, as one region source per slice. */
+export interface AnnotationSlices {
+    kind: 'labels' | 'folder' | 'single';
+    /** A name for what was opened (the label image's, the folder's, the file's). */
+    name: string;
+    slices: number;
+    /** One opener per slice index. */
+    openers: Map<number, Opener>;
+    /** A label image's slices and classes (to draw them, see openAnnotations). */
+    labels?: {
+        stack: LabelStack;
+        classes: LabelClasses;
+    };
+    /** Slice width and height, when known without opening the sources (a label image's). */
+    size?: [number, number];
+    /** Voxel size x, y, z in micrometres, when the source says. */
+    spacing?: [number, number, number];
+    /** What was read, for a message ("12 slices of 456 × 320"). */
+    summary: string;
+}
+/**
+ * The annotations among `files` (zips expanded), as one region source per slice; null when there
+ * are none to read. A label image's slices are traced, and a GeoJSON parsed, when the slice is
+ * first shown.
+ */
+export declare function readAnnotationSlices(chosen: readonly RegionImportFile[], decoders?: AnnotationDecoders): Promise<AnnotationSlices | null>;
+/** What {@link openAnnotations} built: the image to publish, and how to release it. */
+export interface OpenedAnnotations {
+    info: IImageInfo;
+    summary: string;
+    /** Revoke the image's blob URLs, and release the slices' sources the region store never took
+     *  (once another image replaced it). */
+    dispose(): void;
+}
+/**
+ * The image `files`' annotations are shown on by themselves (see the module comment). Throws when
+ * there are none, or when their regions span more than {@link ANNOTATION_IMAGE_MAX_DIM} pixels
+ * (they are then imported onto the image they were drawn on).
+ */
+export declare function openAnnotations(files: readonly RegionImportFile[], decoders?: AnnotationDecoders): Promise<OpenedAnnotations>;
+/**
+ * One GeoJSON's slices: a collection whose features name planes (`geometry.plane.z`) split into
+ * one collection per plane, each keeping the set's class tree and style, its features moved to
+ * plane 0 (a slice's source shows plane 0); any other GeoJSON is one slice as it is.
+ */
+export declare function splitByPlane(text: string): string[];
+export {};

package/lib/region-import/zarr-codecs.d.ts

@@ -0,0 +1,14 @@
+/** Inflate gzip or zlib data (default: the platform's `DecompressionStream`). */
+export type Inflate = (bytes: Uint8Array, format: 'gzip' | 'deflate') => Promise<Uint8Array>;
+/** Decode a Blosc frame. */
+export declare function bloscDecompress(frame: Uint8Array, inflate?: Inflate): Promise<Uint8Array>;
+/** Decode one LZ4 block (no frame) of `size` bytes. */
+export declare function lz4BlockDecompress(src: Uint8Array, size: number): Uint8Array;
+/**
+ * Decode a zarr chunk through `codecs`, outermost last as zarr lists them (v2: the one
+ * `compressor`; v3: the bytes-to-bytes codecs after `bytes`).
+ */
+export declare function decodeChunk(bytes: Uint8Array, codecs: readonly {
+    id: string;
+    [k: string]: unknown;
+}[], inflate?: Inflate): Promise<Uint8Array>;

package/lib/region-import/zip.d.ts

@@ -0,0 +1,31 @@
+/**
+ * The members of a `.zip`, read in the browser: annotations handed over as one archive (a folder
+ * of per-slice GeoJSON, a label volume with its ontology, an OME-Zarr store's labels).
+ *
+ * Only what such archives use: stored or deflated members, ZIP64 sizes and offsets, UTF-8 or
+ * legacy names. An encrypted or otherwise compressed member throws when it is read, rather than be
+ * read wrongly; a member's CRC-32 is checked. Members are read on demand, so an archive of many
+ * chunks (a zarr store) is not inflated whole. Pure: usable from workers.
+ */
+import type { RegionImportFile } from './region-import';
+/** One member of an archive. */
+export interface ZipEntry {
+    /** Its path in the archive, '/'-separated. */
+    name: string;
+    /** Its uncompressed size, in bytes. */
+    size: number;
+    bytes(): Promise<Uint8Array>;
+}
+/** Inflate raw DEFLATE data (default: the platform's `DecompressionStream('deflate-raw')`). */
+export type InflateRaw = (bytes: Uint8Array) => Promise<Uint8Array>;
+/** Whether a file name is a zip archive. */
+export declare function isZipName(name: string): boolean;
+/** The members of the archive in `bytes` (directories and macOS metadata left out). */
+export declare function readZip(bytes: Uint8Array, inflateRaw?: InflateRaw): ZipEntry[];
+/**
+ * `files` with every `.zip` among them replaced by its members, named by their paths in it (a
+ * single top folder the archive wraps everything in is kept, as a folder pick would keep it).
+ */
+export declare function expandZips(files: readonly RegionImportFile[], inflateRaw?: InflateRaw): Promise<RegionImportFile[]>;
+/** CRC-32 (IEEE), as zip records it. */
+export declare function crc32(data: Uint8Array): number;

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

@@ -75,8 +75,14 @@ export declare class RoutingVisualizerService implements IVisualizer, IRegionEdi
     private plottedFileName;
     /** The div the backends render into (every backend shares it); '' before the first plot. */
     private plotDiv;
-    /** Whether a napari volume view is the current plot type. */
+    /**
+     * Whether regions can be shown in 3D on screen: a napari volume (or isosurface) view, or the 3D
+     * spatial cloud over a stack image (its reference volume's, see showVolumeAsImage). Both draw the
+     * region reconstructions the same way (VolumeRegionMeshes), in the volume's box.
+     */
     private readonly volumeView$;
+    /** Whether a napari volume (or isosurface) view is the current plot type: the slice pane's. */
+    private imageVolumeView;
     /** Whether the volume view's slice pane is wanted (see {@link setSliceEditor}). */
     private readonly sliceEditor$;
     /** Whether the volume view draws the region reconstructions through the volume. */
@@ -301,6 +307,8 @@ export declare class RoutingVisualizerService implements IVisualizer, IRegionEdi
     deleteSourceFeatures(ids: readonly string[]): void;
     getRegionStyle$(): Observable<RegionStyle>;
     setRegionStyle(patch: Partial<RegionStyle>): void;
+    /** Recompute which 3D view is on screen for `plotType` (see {@link volumeView$}). */
+    private updateVolumeView;
     /** Whether a napari volume (or isosurface) view is on screen: regions can be shown in 3D. */
     getVolumeView$(): Observable<boolean>;
     /** Whether the volume view's slice pane is wanted (it shows while a volume view is on screen). */

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jax-data-science/sci-image-visualizer",
-  "version": "0.11.0",
+  "version": "0.12.0",
   "engines": {
     "node": ">=20.9.0"
   },
@@ -39,6 +39,7 @@
   "dependencies": {
     "cellpose-js": "^0.6.0",
     "fast-png": "^6.4.0",
+    "fzstd": "^0.1.1",
     "napari-js": "^0.18.0",
     "openseadragon": "^6.0.2",
     "plotly.js-dist-min": "^3.0.1",