@jax-data-science/sci-image-visualizer 0.10.0 → 0.11.0

package/fesm2022/{jax-data-science-sci-image-visualizer-onnx-sam-session-z1IN-F7w.mjs → jax-data-science-sci-image-visualizer-onnx-sam-session-DEDSm_NL.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-BKQhpbHv.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-BELcx0jv.mjs';
 import '@angular/core';
 import '@angular/common/http';
 import 'rxjs';
@@ -235,4 +235,4 @@ class OnnxSamSession {
 }
 
 export { OnnxSamSession };
-//# sourceMappingURL=jax-data-science-sci-image-visualizer-onnx-sam-session-z1IN-F7w.mjs.map
+//# sourceMappingURL=jax-data-science-sci-image-visualizer-onnx-sam-session-DEDSm_NL.mjs.map

package/fesm2022/{jax-data-science-sci-image-visualizer-onnx-sam-session-z1IN-F7w.mjs.map → jax-data-science-sci-image-visualizer-onnx-sam-session-DEDSm_NL.mjs.map}

@@ -1 +1 @@
-{"version":3,"file":"jax-data-science-sci-image-visualizer-onnx-sam-session-z1IN-F7w.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  }\n}\n"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAiBA;;;;;AAKG;MACU,YAAY,CAAA;AAAzB,IAAA,WAAA,GAAA;QACU,IAAA,CAAA,GAAG,GAAG,CAAC;AACE,QAAA,IAAA,CAAA,OAAO,GAAG,IAAI,GAAG,EAAmB;IAmCvD;;AAhCE,IAAA,IAAI,IAAI,GAAA;AACN,QAAA,OAAO,IAAI,CAAC,OAAO,CAAC,IAAI;IAC1B;;AAGA,IAAA,IAAI,CAAC,UAAuC,EAAA;AAC1C,QAAA,MAAM,EAAE,GAAG,EAAE,IAAI,CAAC,GAAG;QACrB,MAAM,OAAO,GAAG,IAAI,OAAO,CAAc,CAAC,OAAO,EAAE,MAAM,KAAI;AAC3D,YAAA,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,EAAE,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE,UAAU,EAAE,CAAC;AACvD,QAAA,CAAC,CAAC;AACF,QAAA,OAAO,EAAE,EAAE,EAAE,OAAO,EAAE;IACxB;;AAGA,IAAA,MAAM,CAAC,KAAkB,EAAA;AACvB,QAAA,MAAM,CAAC,GAAG,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC;AACpC,QAAA,IAAI,CAAC,CAAC;YAAE;AACR,QAAA,IAAI,KAAK,CAAC,IAAI,KAAK,UAAU,EAAE;YAC7B,CAAC,CAAC,UAAU,GAAG,KAAK,CAAC,QAAQ,IAAI,CAAC,CAAC;YACnC;QACF;QACA,IAAI,CAAC,OAAO,CAAC,MAAM,CAAC,KAAK,CAAC,EAAE,CAAC;AAC7B,QAAA,IAAI,KAAK,CAAC,IAAI,KAAK,OAAO;AAAE,YAAA,CAAC,CAAC,MAAM,CAAC,IAAI,KAAK,CAAC,KAAK,CAAC,KAAK,IAAI,mBAAmB,CAAC,CAAC;;AAC9E,YAAA,CAAC,CAAC,OAAO,CAAC,KAAK,CAAC;IACvB;;AAGA,IAAA,SAAS,CAAC,GAAU,EAAA;AAClB,QAAA,MAAM,KAAK,GAAG,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,OAAO,CAAC,MAAM,EAAE,CAAC;AAC/C,QAAA,IAAI,CAAC,OAAO,CAAC,KAAK,EAAE;QACpB,KAAK,MAAM,CAAC,IAAI,KAAK;AAAE,YAAA,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC;IACtC;AACD;;ACpDD;;;;;;;;;;;;;;;AAeG;MACU,cAAc,CAAA;AAA3B,IAAA,WAAA,GAAA;QACU,IAAA,CAAA,IAAI,GAA+B,IAAI;QACvC,IAAA,CAAA,MAAM,GAAG,KAAK;QACd,IAAA,CAAA,SAAS,GAAG,IAAI;;QAGhB,IAAA,CAAA,MAAM,GAAkB,IAAI;AACnB,QAAA,IAAA,CAAA,KAAK,GAAG,IAAI,YAAY,EAAE;;QAGnC,IAAA,CAAA,OAAO,GAAgC,IAAI;QAC3C,IAAA,CAAA,OAAO,GAAgC,IAAI;QAC3C,IAAA,CAAA,SAAS,GAAG,CAAC;;AAEJ,QAAA,IAAA,CAAA,UAAU,GAAG,IAAI,QAAQ,CAAwB,CAAC,CAAC;IAiItE;AA/HE,IAAA,MAAM,SAAS,CAAC,KAAkB,EAAE,UAAuC,EAAA;QACzE,IAAI,CAAC,KAAK,CAAC,UAAU,IAAI,CAAC,KAAK,CAAC,UAAU,EAAE;YAC1C,MAAM,IAAI,KAAK,CAAC,CAAA,WAAA,EAAc,KAAK,CAAC,EAAE,CAAA,8BAAA,CAAgC,CAAC;QACzE;AACA,QAAA,IAAI,CAAC,SAAS,GAAG,KAAK,CAAC,SAAS;QAChC,MAAM,MAAM,GAAG,OAAO,SAAS,KAAK,WAAW,IAAI,KAAK,IAAI,SAAS;QACrE,MAAM,GAAG,GAAa,KAAK,CAAC,gBAAgB,KAAK,MAAM,GAAG,CAAC,QAAQ,EAAE,MAAM,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC;QACxF,MAAM,UAAU,GAAG,GAAG,CAAC,QAAQ,CAAC,QAAQ,CAAC;;;AAGzC,QAAA,IAAI,CAAC,IAAI,GAAG,CAAC,UAAU,IAAI,KAAK,CAAC,SAAS,GAAG,QAAQ,GAAG,QAAQ;AAEhE,QAAA,IAAI,IAAI,CAAC,IAAI,KAAK,QAAQ,EAAE;YAC1B,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,SAAS,GAAG,cAAc,EAAE;AACzC,YAAA,MAAM,MAAM,GAAG,MAAM,UAAU,CAAC,KAAK,CAAC,UAAU,EAAE,UAAU,EAAE,KAAK,CAAC,QAAQ,CAAC;AAC7E,YAAA,MAAM,MAAM,GAAG,MAAM,UAAU,CAAC,KAAK,CAAC,UAAU,EAAE,SAAS,EAAE,KAAK,CAAC,QAAQ,CAAC;AAC5E,YAAA,IAAI,CAAC,OAAO,GAAG,MAAM,GAAG,CAAC,gBAAgB,CAAC,MAAM,CAAC,MAAM,EAAE,EAAE,kBAAkB,EAAE,GAAG,EAAE,CAAC;YACrF,IAAI,CAAC,OAAO,GAAG,MAAM,GAAG,CAAC,gBAAgB,CAAC,MAAM,CAAC,MAAM,EAAE,EAAE,kBAAkB,EAAE,CAAC,MAAM,CAAC,EAAE,CAAC;QAC5F;aAAO;YACL,MAAM,IAAI,CAAC,IAAI,CACb;AACE,gBAAA,IAAI,EAAE,MAAM;gBACZ,UAAU,EAAE,KAAK,CAAC,UAAU;gBAC5B,UAAU,EAAE,KAAK,CAAC,UAAU;gBAC5B,QAAQ,EAAE,KAAK,CAAC,QAAQ;gBACxB,SAAS,EAAE,cAAc,EAAE;gBAC3B,SAAS,EAAE,KAAK,CAAC,SAAS;gBAC1B,gBAAgB,EAAE,KAAK,CAAC,gBAAgB;AACzC,aAAA,EACD,EAAE,EACF,UAAU,CACX;QACH;AACA,QAAA,IAAI,CAAC,MAAM,GAAG,IAAI;IACpB;IAEA,QAAQ,GAAA;QACN,OAAO,IAAI,CAAC,MAAM;IACpB;IAEA,MAAM,KAAK,CAAC,KAAiE,EAAA;AAC3E,QAAA,IAAI,IAAI,CAAC,IAAI,KAAK,QAAQ,EAAE;YAC1B,MAAM,CAAC,GAAG,MAAM,UAAU,CAAC,IAAI,CAAC,OAAQ,EAAE,KAAK,CAAC,IAAI,EAAE,KAAK,CAAC,KAAK,EAAE,KAAK,CAAC,MAAM,EAAE,IAAI,CAAC,SAAS,CAAC;AAChG,YAAA,MAAM,KAAK,GAAG,IAAI,CAAC,SAAS,EAAE;YAC9B,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,KAAK,EAAE,CAAC,CAAC;YAC7B,OAAO;AACL,gBAAA,IAAI,EAAE,IAAI,YAAY,CAAC,CAAC,CAAC;gBACzB,IAAI,EAAE,CAAC,CAAC,IAAI;gBACZ,KAAK,EAAE,CAAC,CAAC,KAAK;gBACd,UAAU,EAAE,CAAC,CAAC,UAAU;gBACxB,WAAW,EAAE,CAAC,CAAC,WAAW;gBAC1B,KAAK;aACN;QACH;;AAEA,QAAA,MAAM,MAAM,GAAG,KAAK,CAAC,IAAI,CAAC,MAAM;AAChC,QAAA,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,EAAE,IAAI,EAAE,OAAO,EAAE,KAAK,EAAE,KAAK,CAAC,KAAK,EAAE,MAAM,EAAE,KAAK,CAAC,MAAM,EAAE,MAAM,EAAE,EAAE,CAAC,MAAM,CAAC,CAAC;QAC1G,OAAO;AACL,YAAA,IAAI,EAAE,IAAI,YAAY,CAAC,CAAC,CAAC;AACzB,YAAA,IAAI,EAAE,GAAG,CAAC,MAAM,CAAa;AAC7B,YAAA,KAAK,EAAE,GAAG,CAAC,OAAO,CAAW;AAC7B,YAAA,UAAU,EAAE,GAAG,CAAC,YAAY,CAAW;AACvC,YAAA,WAAW,EAAE,GAAG,CAAC,aAAa,CAAW;AACzC,YAAA,KAAK,EAAE,GAAG,CAAC,OAAO,CAAW;SAC9B;IACH;AAEA,IAAA,MAAM,MAAM,CAAC,SAAuB,EAAE,MAAiB,EAAA;AACrD,QAAA,IAAI,IAAI,CAAC,IAAI,KAAK,QAAQ,EAAE;AAC1B,YAAA,MAAM,CAAC,GAAG,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,SAAS,CAAC,KAAe,CAAC;AACxD,YAAA,IAAI,CAAC,CAAC;AAAE,gBAAA,MAAM,IAAI,KAAK,CAAC,6CAA6C,CAAC;YACtE,OAAO,UAAU,CAAC,IAAI,CAAC,OAAQ,EAAE,CAAC,EAAE,MAAM,CAAC;QAC7C;QACA,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,EAAE,IAAI,EAAE,QAAQ,EAAE,KAAK,EAAE,SAAS,CAAC,KAAK,EAAE,MAAM,EAAE,CAAC;QAC/E,OAAO;YACL,IAAI,EAAE,IAAI,UAAU,CAAC,GAAG,CAAC,QAAQ,CAAgB,CAAC;AAClD,YAAA,KAAK,EAAE,GAAG,CAAC,OAAO,CAAW;AAC7B,YAAA,MAAM,EAAE,GAAG,CAAC,QAAQ,CAAW;AAC/B,YAAA,GAAG,EAAE,GAAG,CAAC,KAAK,CAAW;SAC1B;IACH;AAEA;AAC4E;IAC5E,OAAO,GAAA;QACL,IAAI,CAAC,UAAU,CAAC,IAAI,KAAK,CAAC,sBAAsB,CAAC,CAAC;AAClD,QAAA,IAAI,CAAC,OAAO,EAAE,OAAO,IAAI;AACzB,QAAA,IAAI,CAAC,OAAO,EAAE,OAAO,IAAI;QACzB,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,OAAO,GAAG,IAAI;AAClC,QAAA,IAAI,CAAC,UAAU,CAAC,KAAK,EAAE;AACvB,QAAA,IAAI,CAAC,MAAM,GAAG,KAAK;AACnB,QAAA,IAAI,CAAC,IAAI,GAAG,IAAI;IAClB;;IAGQ,YAAY,GAAA;QAClB,IAAI,IAAI,CAAC,MAAM;YAAE,OAAO,IAAI,CAAC,MAAM;QACnC,MAAM,MAAM,GAAG,IAAI,MAAM,CAAC,IAAI,GAAG,CAAC,mBAAmB,EAAE,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,IAAI,EAAE,QAAQ,EAAE,CAAC;AAC5F,QAAA,MAAM,CAAC,SAAS,GAAG,CAAC,EAA6B,KAAK,IAAI,CAAC,KAAK,CAAC,MAAM,CAAC,EAAE,CAAC,IAAI,CAAC;AAChF,QAAA,MAAM,CAAC,OAAO,GAAG,CAAC,EAAc,KAAI;;;AAGlC,YAAA,IAAI,CAAC,UAAU,CAAC,IAAI,KAAK,CAAC,EAAE,CAAC,OAAO,IAAI,qBAAqB,CAAC,CAAC;AAC/D,YAAA,IAAI,CAAC,MAAM,GAAG,KAAK;AACnB,YAAA,IAAI,CAAC,IAAI,GAAG,IAAI;AAClB,QAAA,CAAC;AACD,QAAA,IAAI,CAAC,MAAM,GAAG,MAAM;AACpB,QAAA,OAAO,MAAM;IACf;;AAGQ,IAAA,UAAU,CAAC,GAAU,EAAA;AAC3B,QAAA,IAAI,CAAC,MAAM,EAAE,SAAS,EAAE;AACxB,QAAA,IAAI,CAAC,MAAM,GAAG,IAAI;AAClB,QAAA,IAAI,CAAC,KAAK,CAAC,SAAS,CAAC,GAAG,CAAC;IAC3B;AAEQ,IAAA,IAAI,CACV,GAA4B,EAC5B,QAAA,GAA2B,EAAE,EAC7B,UAAgC,EAAA;AAEhC,QAAA,MAAM,MAAM,GAAG,IAAI,CAAC,YAAY,EAAE;AAClC,QAAA,MAAM,EAAE,EAAE,EAAE,OAAO,EAAE,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,UAAU,CAAC;AACnD,QAAA,MAAM,CAAC,WAAW,CAAC,EAAE,GAAG,GAAG,EAAE,EAAE,EAAE,EAAE,QAAQ,CAAC;AAC5C,QAAA,OAAO,OAAO;IAChB;AACD;;;;"}
+{"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 ?? (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  }\n}\n"],"names":[],"mappings":";;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;AAiBA;;;;;AAKG;MACU,YAAY,CAAA;AAAzB,IAAA,WAAA,GAAA;QACU,IAAA,CAAA,GAAG,GAAG,CAAC;AACE,QAAA,IAAA,CAAA,OAAO,GAAG,IAAI,GAAG,EAAmB;IAmCvD;;AAhCE,IAAA,IAAI,IAAI,GAAA;AACN,QAAA,OAAO,IAAI,CAAC,OAAO,CAAC,IAAI;IAC1B;;AAGA,IAAA,IAAI,CAAC,UAAuC,EAAA;AAC1C,QAAA,MAAM,EAAE,GAAG,EAAE,IAAI,CAAC,GAAG;QACrB,MAAM,OAAO,GAAG,IAAI,OAAO,CAAc,CAAC,OAAO,EAAE,MAAM,KAAI;AAC3D,YAAA,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,EAAE,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE,UAAU,EAAE,CAAC;AACvD,QAAA,CAAC,CAAC;AACF,QAAA,OAAO,EAAE,EAAE,EAAE,OAAO,EAAE;IACxB;;AAGA,IAAA,MAAM,CAAC,KAAkB,EAAA;AACvB,QAAA,MAAM,CAAC,GAAG,IAAI,CAAC,OAAO,CAAC,GAAG,CAAC,KAAK,CAAC,EAAE,CAAC;AACpC,QAAA,IAAI,CAAC,CAAC;YAAE;AACR,QAAA,IAAI,KAAK,CAAC,IAAI,KAAK,UAAU,EAAE;YAC7B,CAAC,CAAC,UAAU,GAAG,KAAK,CAAC,QAAQ,IAAI,CAAC,CAAC;YACnC;QACF;QACA,IAAI,CAAC,OAAO,CAAC,MAAM,CAAC,KAAK,CAAC,EAAE,CAAC;AAC7B,QAAA,IAAI,KAAK,CAAC,IAAI,KAAK,OAAO;AAAE,YAAA,CAAC,CAAC,MAAM,CAAC,IAAI,KAAK,CAAC,KAAK,CAAC,KAAK,IAAI,mBAAmB,CAAC,CAAC;;AAC9E,YAAA,CAAC,CAAC,OAAO,CAAC,KAAK,CAAC;IACvB;;AAGA,IAAA,SAAS,CAAC,GAAU,EAAA;AAClB,QAAA,MAAM,KAAK,GAAG,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,OAAO,CAAC,MAAM,EAAE,CAAC;AAC/C,QAAA,IAAI,CAAC,OAAO,CAAC,KAAK,EAAE;QACpB,KAAK,MAAM,CAAC,IAAI,KAAK;AAAE,YAAA,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC;IACtC;AACD;;ACpDD;;;;;;;;;;;;;;;AAeG;MACU,cAAc,CAAA;AAA3B,IAAA,WAAA,GAAA;QACU,IAAA,CAAA,IAAI,GAA+B,IAAI;QACvC,IAAA,CAAA,MAAM,GAAG,KAAK;QACd,IAAA,CAAA,SAAS,GAAG,IAAI;;QAGhB,IAAA,CAAA,MAAM,GAAkB,IAAI;AACnB,QAAA,IAAA,CAAA,KAAK,GAAG,IAAI,YAAY,EAAE;;QAGnC,IAAA,CAAA,OAAO,GAAgC,IAAI;QAC3C,IAAA,CAAA,OAAO,GAAgC,IAAI;QAC3C,IAAA,CAAA,SAAS,GAAG,CAAC;;AAEJ,QAAA,IAAA,CAAA,UAAU,GAAG,IAAI,QAAQ,CAAwB,CAAC,CAAC;IAiItE;AA/HE,IAAA,MAAM,SAAS,CAAC,KAAkB,EAAE,UAAuC,EAAA;QACzE,IAAI,CAAC,KAAK,CAAC,UAAU,IAAI,CAAC,KAAK,CAAC,UAAU,EAAE;YAC1C,MAAM,IAAI,KAAK,CAAC,CAAA,WAAA,EAAc,KAAK,CAAC,EAAE,CAAA,8BAAA,CAAgC,CAAC;QACzE;AACA,QAAA,IAAI,CAAC,SAAS,GAAG,KAAK,CAAC,SAAS;QAChC,MAAM,MAAM,GAAG,OAAO,SAAS,KAAK,WAAW,IAAI,KAAK,IAAI,SAAS;QACrE,MAAM,GAAG,GAAa,KAAK,CAAC,gBAAgB,KAAK,MAAM,GAAG,CAAC,QAAQ,EAAE,MAAM,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC;QACxF,MAAM,UAAU,GAAG,GAAG,CAAC,QAAQ,CAAC,QAAQ,CAAC;;;AAGzC,QAAA,IAAI,CAAC,IAAI,GAAG,CAAC,UAAU,IAAI,KAAK,CAAC,SAAS,GAAG,QAAQ,GAAG,QAAQ;AAEhE,QAAA,IAAI,IAAI,CAAC,IAAI,KAAK,QAAQ,EAAE;YAC1B,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,SAAS,GAAG,cAAc,EAAE;AACzC,YAAA,MAAM,MAAM,GAAG,MAAM,UAAU,CAAC,KAAK,CAAC,UAAU,EAAE,UAAU,EAAE,KAAK,CAAC,QAAQ,CAAC;AAC7E,YAAA,MAAM,MAAM,GAAG,MAAM,UAAU,CAAC,KAAK,CAAC,UAAU,EAAE,SAAS,EAAE,KAAK,CAAC,QAAQ,CAAC;AAC5E,YAAA,IAAI,CAAC,OAAO,GAAG,MAAM,GAAG,CAAC,gBAAgB,CAAC,MAAM,CAAC,MAAM,EAAE,EAAE,kBAAkB,EAAE,GAAG,EAAE,CAAC;YACrF,IAAI,CAAC,OAAO,GAAG,MAAM,GAAG,CAAC,gBAAgB,CAAC,MAAM,CAAC,MAAM,EAAE,EAAE,kBAAkB,EAAE,CAAC,MAAM,CAAC,EAAE,CAAC;QAC5F;aAAO;YACL,MAAM,IAAI,CAAC,IAAI,CACb;AACE,gBAAA,IAAI,EAAE,MAAM;gBACZ,UAAU,EAAE,KAAK,CAAC,UAAU;gBAC5B,UAAU,EAAE,KAAK,CAAC,UAAU;gBAC5B,QAAQ,EAAE,KAAK,CAAC,QAAQ;gBACxB,SAAS,EAAE,cAAc,EAAE;gBAC3B,SAAS,EAAE,KAAK,CAAC,SAAS;gBAC1B,gBAAgB,EAAE,KAAK,CAAC,gBAAgB;AACzC,aAAA,EACD,EAAE,EACF,UAAU,CACX;QACH;AACA,QAAA,IAAI,CAAC,MAAM,GAAG,IAAI;IACpB;IAEA,QAAQ,GAAA;QACN,OAAO,IAAI,CAAC,MAAM;IACpB;IAEA,MAAM,KAAK,CAAC,KAAiE,EAAA;AAC3E,QAAA,IAAI,IAAI,CAAC,IAAI,KAAK,QAAQ,EAAE;YAC1B,MAAM,CAAC,GAAG,MAAM,UAAU,CAAC,IAAI,CAAC,OAAQ,EAAE,KAAK,CAAC,IAAI,EAAE,KAAK,CAAC,KAAK,EAAE,KAAK,CAAC,MAAM,EAAE,IAAI,CAAC,SAAS,CAAC;AAChG,YAAA,MAAM,KAAK,GAAG,IAAI,CAAC,SAAS,EAAE;YAC9B,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,KAAK,EAAE,CAAC,CAAC;YAC7B,OAAO;AACL,gBAAA,IAAI,EAAE,IAAI,YAAY,CAAC,CAAC,CAAC;gBACzB,IAAI,EAAE,CAAC,CAAC,IAAI;gBACZ,KAAK,EAAE,CAAC,CAAC,KAAK;gBACd,UAAU,EAAE,CAAC,CAAC,UAAU;gBACxB,WAAW,EAAE,CAAC,CAAC,WAAW;gBAC1B,KAAK;aACN;QACH;;AAEA,QAAA,MAAM,MAAM,GAAG,KAAK,CAAC,IAAI,CAAC,MAAM;AAChC,QAAA,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,EAAE,IAAI,EAAE,OAAO,EAAE,KAAK,EAAE,KAAK,CAAC,KAAK,EAAE,MAAM,EAAE,KAAK,CAAC,MAAM,EAAE,MAAM,EAAE,EAAE,CAAC,MAAM,CAAC,CAAC;QAC1G,OAAO;AACL,YAAA,IAAI,EAAE,IAAI,YAAY,CAAC,CAAC,CAAC;AACzB,YAAA,IAAI,EAAE,GAAG,CAAC,MAAM,CAAa;AAC7B,YAAA,KAAK,EAAE,GAAG,CAAC,OAAO,CAAW;AAC7B,YAAA,UAAU,EAAE,GAAG,CAAC,YAAY,CAAW;AACvC,YAAA,WAAW,EAAE,GAAG,CAAC,aAAa,CAAW;AACzC,YAAA,KAAK,EAAE,GAAG,CAAC,OAAO,CAAW;SAC9B;IACH;AAEA,IAAA,MAAM,MAAM,CAAC,SAAuB,EAAE,MAAiB,EAAA;AACrD,QAAA,IAAI,IAAI,CAAC,IAAI,KAAK,QAAQ,EAAE;AAC1B,YAAA,MAAM,CAAC,GAAG,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,SAAS,CAAC,KAAe,CAAC;AACxD,YAAA,IAAI,CAAC,CAAC;AAAE,gBAAA,MAAM,IAAI,KAAK,CAAC,6CAA6C,CAAC;YACtE,OAAO,UAAU,CAAC,IAAI,CAAC,OAAQ,EAAE,CAAC,EAAE,MAAM,CAAC;QAC7C;QACA,MAAM,GAAG,GAAG,MAAM,IAAI,CAAC,IAAI,CAAC,EAAE,IAAI,EAAE,QAAQ,EAAE,KAAK,EAAE,SAAS,CAAC,KAAK,EAAE,MAAM,EAAE,CAAC;QAC/E,OAAO;YACL,IAAI,EAAE,IAAI,UAAU,CAAC,GAAG,CAAC,QAAQ,CAAgB,CAAC;AAClD,YAAA,KAAK,EAAE,GAAG,CAAC,OAAO,CAAW;AAC7B,YAAA,MAAM,EAAE,GAAG,CAAC,QAAQ,CAAW;AAC/B,YAAA,GAAG,EAAE,GAAG,CAAC,KAAK,CAAW;SAC1B;IACH;AAEA;AAC4E;IAC5E,OAAO,GAAA;QACL,IAAI,CAAC,UAAU,CAAC,IAAI,KAAK,CAAC,sBAAsB,CAAC,CAAC;AAClD,QAAA,IAAI,CAAC,OAAO,EAAE,OAAO,IAAI;AACzB,QAAA,IAAI,CAAC,OAAO,EAAE,OAAO,IAAI;QACzB,IAAI,CAAC,OAAO,GAAG,IAAI,CAAC,OAAO,GAAG,IAAI;AAClC,QAAA,IAAI,CAAC,UAAU,CAAC,KAAK,EAAE;AACvB,QAAA,IAAI,CAAC,MAAM,GAAG,KAAK;AACnB,QAAA,IAAI,CAAC,IAAI,GAAG,IAAI;IAClB;;IAGQ,YAAY,GAAA;QAClB,IAAI,IAAI,CAAC,MAAM;YAAE,OAAO,IAAI,CAAC,MAAM;QACnC,MAAM,MAAM,GAAG,IAAI,MAAM,CAAC,IAAI,GAAG,CAAC,mBAAmB,EAAE,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,IAAI,EAAE,QAAQ,EAAE,CAAC;AAC5F,QAAA,MAAM,CAAC,SAAS,GAAG,CAAC,EAA6B,KAAK,IAAI,CAAC,KAAK,CAAC,MAAM,CAAC,EAAE,CAAC,IAAI,CAAC;AAChF,QAAA,MAAM,CAAC,OAAO,GAAG,CAAC,EAAc,KAAI;;;AAGlC,YAAA,IAAI,CAAC,UAAU,CAAC,IAAI,KAAK,CAAC,EAAE,CAAC,OAAO,IAAI,qBAAqB,CAAC,CAAC;AAC/D,YAAA,IAAI,CAAC,MAAM,GAAG,KAAK;AACnB,YAAA,IAAI,CAAC,IAAI,GAAG,IAAI;AAClB,QAAA,CAAC;AACD,QAAA,IAAI,CAAC,MAAM,GAAG,MAAM;AACpB,QAAA,OAAO,MAAM;IACf;;AAGQ,IAAA,UAAU,CAAC,GAAU,EAAA;AAC3B,QAAA,IAAI,CAAC,MAAM,EAAE,SAAS,EAAE;AACxB,QAAA,IAAI,CAAC,MAAM,GAAG,IAAI;AAClB,QAAA,IAAI,CAAC,KAAK,CAAC,SAAS,CAAC,GAAG,CAAC;IAC3B;AAEQ,IAAA,IAAI,CACV,GAA4B,EAC5B,QAAA,GAA2B,EAAE,EAC7B,UAAgC,EAAA;AAEhC,QAAA,MAAM,MAAM,GAAG,IAAI,CAAC,YAAY,EAAE;AAClC,QAAA,MAAM,EAAE,EAAE,EAAE,OAAO,EAAE,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,UAAU,CAAC;AACnD,QAAA,MAAM,CAAC,WAAW,CAAC,EAAE,GAAG,GAAG,EAAE,EAAE,EAAE,EAAE,QAAQ,CAAC;AAC5C,QAAA,OAAO,OAAO;IAChB;AACD;;;;"}

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 isBuiltinPlotType, ax as isCanvasToolId, ay as isCategoricalColumn, az as isContinuousColumn, aA as isDialogToolContribution, aB as isEmptyPresetSet, aC as isLittleEndian, aD as isNapari3d, aE as isNapariIsosurface, aF as isNapariScatter, aG as isNapariScatter3d, aH as isNapariSurface, aI as isNapariVolume, aJ as isSamModelReady, aK as isSpatialOmics, aL as isSpatialOmics3d, aM as isThreeDimensional, aN as lutFor, aO as markerDiameters, aP as maskToIndices, aQ as mutedFromSelection, aR as omicsLayout, aS as openGeoJsonRegionSource, aT as openHttpRegionSource, aU as parsePresetSet, aV as pointInRing, aW as provideVisualization, aX as rendererOwnsWheel, aY as resolveCategoryColors, aZ as selectByCategory, a_ as selectInRegions, a$ as setDefaultSamModel, b0 as setOrtWasmBase, b1 as setSamModelUrls, b2 as sortToolContributions, b3 as visibleToolContributions } from './jax-data-science-sci-image-visualizer-jax-data-science-sci-image-visualizer-BKQhpbHv.mjs';
+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';
 import '@angular/core';
 import '@angular/common/http';
 import 'napari-js';

package/index.d.ts

@@ -50,6 +50,12 @@ export { openGeoJsonRegionSource } from './lib/region-source/worker-region-sourc
 export { openHttpRegionSource } from './lib/region-source/http-region-source';
 export type { HttpRegionSourceOptions, WireTileFeature } from './lib/region-source/http-region-source';
 export { REGION_SOURCE_MIN_CHARS } from './lib/region-source/region-source';
+export { isLabelVolumeName, readLabelVolume } from './lib/region-import/label-volume';
+export type { LabelVolume } from './lib/region-import/label-volume';
+export { labelClasses, labelSliceGeoJson } from './lib/region-import/label-classes';
+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 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/ports/region-io.port.d.ts

@@ -25,6 +25,30 @@ export interface RegionIoPort {
         z: number;
         geoJsonStr: string;
     }[]): Observable<void>;
+    /**
+     * "Import regions from server": let the user pick region files or a region set in the host's
+     * storage (the current project's bucket, say) and hand them over. Emits null when the user
+     * cancels. Without it, the Region Editor shows no server import.
+     */
+    pickServerRegions?(): Observable<ServerRegionPick | null>;
 }
+/**
+ * Regions picked on the host's server (see {@link RegionIoPort.pickServerRegions}): files it
+ * downloaded, imported as the Region Editor imports chosen files (one GeoJSON; a label volume
+ * `.nii` / `.nii.gz` / `.nrrd` with its ontology JSON; a folder's per-slice GeoJSON files with its
+ * `regionset.json`), or a region set its server serves by level of detail (jit-service's
+ * `/regions/{id}/`), read through the host's `HttpClient` without downloading it.
+ */
+export type ServerRegionPick = {
+    kind: 'files';
+    files: Array<{
+        name: string;
+        data: Blob | ArrayBuffer | Uint8Array | string;
+    }>;
+} | {
+    kind: 'source';
+    url: string;
+    name?: string;
+};
 /** DI token for the host's {@link RegionIoPort}. Required by the region editor. */
 export declare const REGION_IO_PORT: InjectionToken<RegionIoPort>;

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

@@ -3,7 +3,7 @@ import { Observable } from 'rxjs';
 import { Region } from '../models/region';
 import { ClassPreset, PresetSet } from '../models/class-preset';
 import { IImageMetadata } from './image.contract';
-import type { RegionSourceView } from '../region-source/region-source';
+import type { RegionSource, RegionSourceView } from '../region-source/region-source';
 import type { RegionIndexPage, RegionIndexQuery } from '../region-source/region-tiles';
 import type { RegionStyle } from '../region-overlay/region-style';
 /**
@@ -87,6 +87,24 @@ export interface IRegionEditorApi {
      * and should be imported as regions; rejects when it is not a GeoJSON FeatureCollection.
      */
     importRegionSource?(geoJsonStr: string): Promise<boolean>;
+    /**
+     * A ticket for an import about to read or decode its files: an import method given a stale one
+     * (another import took a ticket since, or another image was plotted) changes nothing.
+     */
+    regionImportTicket?(): number;
+    /**
+     * Replace the regions and region sources with one source per slice (an imported label volume,
+     * or a folder of per-slice region files): openers by slice index, each opened the first time its
+     * slice is shown. A single image takes slice 0's. Returns how many slices have one, or null
+     * (changing nothing) when `ticket` is stale. A save writes every imported slice.
+     */
+    importSliceRegionSources?(openers: ReadonlyMap<number, () => Promise<RegionSource>>, ticket?: number): number | null;
+    /**
+     * Replace them with one imported source (a region set a server serves): over every slice of a
+     * stack when z-indexed, else on the slice shown. Resolves false, changing nothing, when the
+     * import went stale while the source opened.
+     */
+    importRegionSourceOpener?(open: () => Promise<RegionSource>, ticket?: number): Promise<boolean>;
     /**
      * Drop the slice's region source, for regions imported in its place (a small file replacing a
      * large one). The other slices keep theirs.

package/lib/implementations/osd/openseadragon-viewer-options.d.ts

@@ -23,6 +23,8 @@ export interface ViewerOptionsInput {
     sliceCount: number;
     /** How many slices the slice cache keeps resident (see SliceCache.maxSlices). */
     maxSlices: number;
+    /** Tiled images per slice: the channel count when channels are drawn per channel, else 1. */
+    channelImages?: number;
 }
 /**
  * The options object handed to the OpenSeadragon factory. Pure: every value

package/lib/implementations/osd/openseadragon-visualizer.service.d.ts

@@ -53,6 +53,8 @@ export declare class OpenSeadragonVisualizerService extends BaseStoreVisualizer
     private viewer;
     private overlay;
     private scaleBar;
+    /** "Image reloading…" while the view fetches its tiles. */
+    private tileLoading;
     private descriptor;
     /** Base64 RawFileInfo + current z-slice, kept so setZIndex can rebuild the
      *  tile source and swap slices live (stack navigation). */

package/lib/implementations/osd/osd-tile-loading.d.ts

@@ -0,0 +1,43 @@
+/** What it needs of the viewer. */
+interface LoadingViewer {
+    element: HTMLElement;
+    world: {
+        getItemCount(): number;
+        getItemAt(i: number): unknown;
+        addHandler(event: 'add-item' | 'remove-item', handler: (e: {
+            item: unknown;
+        }) => void): unknown;
+        removeHandler(event: 'add-item' | 'remove-item', handler: (e: {
+            item: unknown;
+        }) => void): unknown;
+    };
+}
+/**
+ * "Image reloading…" over the OpenSeadragon view while it fetches the tiles of what it shows, as
+ * napari's views show it for their image, cells and transcripts (the same badge). Driven by each
+ * world item's own `fully-loaded-change` (an image, a stack slice, a channel), so it covers every
+ * tile source alike, and shown only after a short delay, so tiles served from cache never flash it.
+ *
+ * Only items on screen count (opacity above 0): a hidden channel loads nothing by design (it is
+ * not preloaded), so it never becomes fully loaded, and a slice cached or loading in the
+ * background is not what the view shows. An item is weighed again when its opacity changes.
+ */
+export declare class OsdTileLoading {
+    private readonly viewer;
+    private readonly state;
+    /** Each item still loading, with the function that un-counts it. */
+    private readonly loading;
+    private readonly watched;
+    private readonly onAdd;
+    private readonly onRemove;
+    constructor(viewer: LoadingViewer);
+    /** The badge's text (shown, or about to be). */
+    get text(): string;
+    destroy(): void;
+    private watch;
+    private unwatch;
+    /** Whether the item is on screen and still fetching its tiles. */
+    private isLoading;
+    private set;
+}
+export {};

package/lib/implementations/osd/osd-viewer-like.d.ts

@@ -48,6 +48,18 @@ export interface OsdViewerLike {
     /** OSD's own pan/zoom (drag + wheel); region tools switch it off. */
     setMouseNavEnabled(enabled: boolean): unknown;
     isMouseNavEnabled(): boolean;
+    /** OSD's tile request queue: the jobs not started yet (see OsdQueuedTileJob). */
+    imageLoader?: {
+        jobQueue?: unknown[];
+    };
+}
+/** A tile request waiting in OSD's queue: `abort` (before it starts) only marks the tile as
+ *  not loading, so it is requested again when it is needed. */
+export interface OsdQueuedTileJob {
+    tile?: {
+        tiledImage?: unknown;
+    };
+    abort?: () => void;
 }
 /** A point in any OSD space (viewer-element px, viewport units or image px —
  *  the method it comes from says which). */
@@ -70,6 +82,8 @@ export interface OsdTiledImageLike {
     imageToViewportRectangle(r: OpenSeadragon.Rect): OpenSeadragon.Rect;
     viewportToImageRectangle(r: OsdRectLike): OsdRectLike;
     setOpacity(opacity: number): void;
+    /** Load tiles even while hidden (opacity 0); without it a hidden item loads nothing. */
+    setPreload?(preload: boolean): void;
     /** False while any of the image's tiles are still loading. */
     getFullyLoaded(): boolean;
     /** Re-run the tile pipeline (restore + re-process) for this image's tiles;

package/lib/implementations/osd/slice-cache.d.ts

@@ -106,14 +106,22 @@ export declare class SliceCache {
     /**
      * Add slice z's channel group: one additively-composited ('lighter' = Fiji
      * "Composite") TiledImage per channel, hidden (opacity 0) until revealed.
-     * Each is preloaded so the background loader can pre-fill every slice.
+     * The visible channels' are preloaded, so the background loader can pre-fill
+     * every slice; a hidden channel's loads nothing until it is shown (a 22-channel
+     * plate fetched and decoded every channel's tiles, overflowing the tile cache:
+     * tiles evicted mid-conversion failed to decode).
      * Cached so a revisit is an instant opacity toggle — no re-fetch, no
      * white-flicker. Mirrors addSlice for the composite path.
      */
     addChannelSlice(z: number): void;
     /** Reveal slice z's channel group (each visible channel → opacity 1) and
-     *  hide every other cached slice's group. Instant; no fetch/decode. */
+     *  hide every other cached slice's group. Instant; no fetch/decode. Only the
+     *  visible channels keep loading (preload): a hidden channel's tiles are not
+     *  fetched or decoded until it is shown. */
     revealChannelSlice(z: number): void;
+    /** Drop the tile requests still waiting in OSD's queue for `items` (channels just hidden), so
+     *  the visible channels' tiles are not stuck behind them. A request already sent completes. */
+    private dropQueuedTiles;
     /** Show the given composite slice (opacity 1) and hide all other cached slices. */
     private showOnlySlice;
     /** Re-tint after a display change: invalidate ONLY the visible slice's
@@ -154,7 +162,9 @@ export declare class SliceCache {
     private sliceCacheHas;
     /** The cached TiledImage(s) for slice z (0–1 for composite, N for multichannel). */
     private sliceGroup;
-    /** Whether slice z's tiles are still streaming (any cached image not fully loaded). */
+    /** Whether slice z's tiles are still streaming (any cached image not fully loaded). A hidden
+     *  channel loads nothing, so it never becomes fully loaded: only the visible channels count, or
+     *  the background loader would wait on it forever. */
     private sliceTilesLoading;
     /** Remove slice z's cached image(s) from the world and the active cache. */
     private removeCachedSlice;

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

@@ -26,6 +26,8 @@ export declare class RegionEditorComponent implements OnInit, OnDestroy {
      */
     set active(value: boolean);
     private isActive;
+    /** The host's HttpClient: a served region set's requests go through it (its auth). */
+    private readonly http;
     protected regions: Region[];
     protected selectedRegions: Region[];
     protected showShapeLabel: boolean;
@@ -348,7 +350,31 @@ export declare class RegionEditorComponent implements OnInit, OnDestroy {
     protected importPresets(event: Event): void;
     /** Validate and apply an imported annotation-classes JSON file. */
     private applyImportedPresets;
+    /** The files chosen in the import inputs: one GeoJSON, a label volume with its ontology, or a
+     *  folder of per-slice GeoJSON files. */
     protected importRois(event: Event): void;
+    /** Whether the host can pick regions on its server ("Import regions from server"). */
+    protected get canImportFromServer(): boolean;
+    /** An import from the server is in flight. */
+    protected importing: boolean;
+    /** "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.
+     */
+    private importRegionFiles;
+    /** A region set the host's server serves (jit-service's /regions/{id}/), read through its HttpClient. */
+    private importServedRegionSet;
+    /** An import that finished after another image was shown (or another import began): dropped. */
+    private importStale;
+    /** The table and selection after the regions were replaced by imported sources. */
+    private afterSourceImport;
+    /** Warn when an imported volume's slices are not the image's size: its outlines would not fit. */
+    private warnIfSizeDiffers;
+    private importFailed;
     /**
      * Replace the regions with an imported GeoJSON file's, and the slice's region source with them.
      * A large file becomes the slice's region source instead (drawn by level of detail; listed above

package/lib/region-editor/region-persistence.service.d.ts

@@ -1,7 +1,7 @@
 import { Observable } from 'rxjs';
 import { Region } from '../models/region';
 import { IRegionEditorApi } from '../contracts/region-editor-api.contract';
-import { RegionIoPort } from '../contracts/ports/region-io.port';
+import { RegionIoPort, ServerRegionPick } from '../contracts/ports/region-io.port';
 import * as i0 from "@angular/core";
 /** One slice-file's serialized regions (folder stack, jit-ui#93). */
 export interface SliceGeoJson {
@@ -67,6 +67,10 @@ export declare class RegionPersistenceService {
      * in it.
      */
     sliceGeoJsons(): Promise<SliceGeoJson[]>;
+    /** Whether the host can pick regions on its server (see RegionIoPort.pickServerRegions). */
+    canPickServerRegions(): boolean;
+    /** Let the user pick regions on the host's server; null when cancelled or unsupported. */
+    pickServerRegions(): Observable<ServerRegionPick | null>;
     /** Write per-slice geojsons through the host port. */
     saveSlices(slices: SliceGeoJson[]): Observable<void>;
     /** Read the file chosen in a file input's change event as text, then call

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

@@ -0,0 +1,39 @@
+import type { RegionClassNode, RegionSourceStyle } from '../region-source/region-tiles';
+import type { LabelVolume } from './label-volume';
+/**
+ * The classes of a label volume's values: their names and colours and, when the volume comes
+ * with an ontology, their tree. Pure.
+ */
+export interface LabelClasses {
+    /** The class of label `value` (> 0); one without an ontology entry is `label <value>`. */
+    classOf(value: number): {
+        name: string;
+        color: string;
+        title?: string;
+    };
+    /** The class tree, when the ontology has one. */
+    hierarchy?: RegionClassNode[];
+    /** How the set wants to be drawn (an atlas's filled look), when the ontology says. */
+    style?: RegionSourceStyle;
+}
+/** The look the Allen atlas region sets carry (see the brain-atlas example's GeoJSON). */
+export declare const ATLAS_STYLE: RegionSourceStyle;
+/**
+ * The classes of a label volume from `ontology`, a parsed JSON document:
+ *
+ * - an **Allen structure graph** (`structure_graph_1.json`: `{ msg: [root] }`, or a node or a
+ *   list of nodes with `id`, `acronym`, `name`, `color_hex_triplet`, `graph_order` and
+ *   `children`): label = structure id, class = acronym, its tree the ontology's, drawn as the
+ *   atlas region sets are;
+ * - a **region set description** (a `regionset.json`: `classHierarchy`, optional `style`), whose
+ *   classes name their label as `value` (or `id`), or with a `labels` map of value → class name.
+ *
+ * Without one (or with another document), each label is its own class `label <value>`.
+ */
+export declare function labelClasses(ontology?: unknown): LabelClasses;
+/**
+ * Slice `z` of `volume` as a GeoJSON FeatureCollection string: one feature per label on the
+ * slice, its every piece (with holes) traced along pixel edges, in image pixels with y down;
+ * classified by `classes`, which also give the collection its class tree and style.
+ */
+export declare function labelSliceGeoJson(volume: LabelVolume, z: number, classes: LabelClasses): string;

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

@@ -0,0 +1,31 @@
+/**
+ * A label volume (a NIfTI-1 `.nii` / `.nii.gz` or a NRRD `.nrrd` of integer structure ids, an
+ * atlas annotation say) read in the browser, sliced as the server opens the matching image:
+ *
+ * - **NRRD**: a 3D volume is cut along its FIRST axis, each section its third axis wide and its
+ *   second axis high, as jit-service opens a NRRD volume (`AtlasNrrdReader`: the Allen CCF's 528
+ *   coronal sections of 456 × 320, anterior first). A 2D NRRD is one slice.
+ * - **NIfTI**: along its third axis, each slice its first axis wide and its second axis high, as
+ *   Bio-Formats reads one (no row flip).
+ *
+ * Only what label volumes use: a single file (NRRD with attached data, NIfTI-1 `n+1`), integer
+ * or integer-valued float samples, either byte order, raw or gzip. Anything else throws rather
+ * than be read approximately. Pure: usable from workers.
+ */
+/** A label volume, sliced (see the module comment). Label 0 is background. */
+export interface LabelVolume {
+    format: 'nrrd' | 'nifti';
+    /** A slice's width and height, in voxels (the image's pixels). */
+    width: number;
+    height: number;
+    /** Number of slices. */
+    slices: number;
+    /** Slice `z`'s labels, row-major (`height` rows of `width`). */
+    sliceLabels(z: number): Uint32Array;
+}
+/** Decompress gzip bytes (default: the platform's `DecompressionStream`). */
+export type Gunzip = (bytes: Uint8Array) => Promise<Uint8Array>;
+/** Whether a file name is a label volume this reads. */
+export declare function isLabelVolumeName(name: string): boolean;
+/** Read the label volume in `bytes`, named `name` (`.nrrd`, `.nii`, `.nii.gz`). */
+export declare function readLabelVolume(name: string, bytes: Uint8Array, gunzip?: Gunzip): Promise<LabelVolume>;

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

@@ -0,0 +1,46 @@
+/** A file to import regions from: one the user chose, or one the host's server sent. */
+export interface RegionImportFile {
+    name: string;
+    text(): Promise<string>;
+    bytes(): Promise<Uint8Array>;
+}
+/** A file's contents as the host may hand them over (see `ServerRegionPick`). */
+export type RegionImportData = Blob | ArrayBuffer | Uint8Array | string;
+/** `data`, named `name`, as an import file. A `File`'s own name is used when `name` is omitted. */
+export declare function importFile(data: RegionImportData, name?: string): RegionImportFile;
+/** What a set of chosen files imports as. */
+export type RegionImportPlan = 
+/** A label volume, its classes named by an ontology (or a region set description) beside it. */
+{
+    kind: 'volume';
+    volume: RegionImportFile;
+    ontology: RegionImportFile | null;
+}
+/** A folder of per-slice region files, in slice order, with the set's `regionset.json`. */
+ | {
+    kind: 'folder';
+    slices: RegionImportFile[];
+    regionSet: RegionImportFile | null;
+}
+/** One region file. */
+ | {
+    kind: 'single';
+    file: RegionImportFile;
+};
+/**
+ * What `files` import as: a label volume (`.nii`, `.nii.gz`, `.nrrd`) with the ontology JSON chosen
+ * with it (a `regionset.json`, else an Allen `structure_graph*.json`, else any `.json`); several
+ * region files (a folder of per-slice `.geojson`, in natural name order, its `regionset.json`
+ * apart); or one region file (`.geojson` or `.json`). Null when none of them is one.
+ */
+export declare function planRegionImport(files: readonly RegionImportFile[]): RegionImportPlan | null;
+/** "slice_2" before "slice_10": runs of digits compared as numbers. */
+export declare function naturalCompare(a: string, b: string): number;
+/**
+ * A folder slice's GeoJSON with the set's class tree and style (its `regionset.json`) as the
+ * collection's own members, unless the file has its own: what a served folder's slice carries.
+ */
+export declare function folderSliceGeoJson(file: RegionImportFile, regionSet: {
+    classHierarchy?: unknown;
+    style?: unknown;
+} | null): Promise<string>;

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

@@ -114,6 +114,8 @@ export declare class RoutingVisualizerService implements IVisualizer, IRegionEdi
     private readonly sectionSubs;
     /** The image info and screen height of the last plot (what the slice pane mounts). */
     private plottedInfo;
+    /** The current region import (see regionImportTicket): its id and the image it was taken for. */
+    private importTicket;
     private plottedHeight;
     constructor(plotly: PlotlyService, osd: OpenSeadragonVisualizerService, napari: NapariVisualizerService, store: VisualizerStore, config: VizConfig, regionStore: RegionStore, selectionStore: SpatialSelectionStore, intensity: IntensityProfileService, spatialData?: SpatialDataPort | null);
     /** A class's colour: its classification colour, else its region source's, else a default. */
@@ -265,6 +267,34 @@ export declare class RoutingVisualizerService implements IVisualizer, IRegionEdi
     attachRegionSource(source: RegionSource | RegionSourceOpener, slices?: RegionSourceSlices): void;
     importRegionSource(geoJsonStr: string): Promise<boolean>;
     dropRegionSource(): Promise<void>;
+    /**
+     * A ticket for a region import that is about to read or decode its files: the import methods
+     * given it change nothing once it is stale — another import took a ticket since, another image
+     * was plotted, or the service was destroyed — so an import that finishes late never lands on an
+     * image it was not started for.
+     */
+    regionImportTicket(): number;
+    /** Whether `ticket` is still the current import's, on the image it was taken for. */
+    private importTicketValid;
+    private importImageKey;
+    /**
+     * Replace the image's regions and region sources with one source per slice, as an imported label
+     * volume or folder of per-slice region files gives them: `openers` by slice index, each opened
+     * the first time its slice is shown. A single image takes slice 0's. Returns how many slices
+     * have a source, or null (changing nothing) when `ticket` is stale (see
+     * {@link regionImportTicket}). The sources are marked imported, so a save writes every slice.
+     */
+    importSliceRegionSources(openers: ReadonlyMap<number, RegionSourceOpener>, ticket?: number): number | null;
+    /**
+     * Replace the image's regions and region sources with one imported source (a region set the
+     * host's server serves): over every slice of a stack when it is z-indexed, else on the slice
+     * shown, as {@link applyImageRois} lays out an image's own. Resolves false, changing nothing
+     * (and disposing the source), when the import went stale while it opened: another import, or
+     * another image (see {@link regionImportTicket}; one is taken here when `ticket` is not given).
+     */
+    importRegionSourceOpener(open: RegionSourceOpener, ticket?: number): Promise<boolean>;
+    /** Empty every slice of a stack (its regions and undo history) for regions imported over it. */
+    private enterImportedStack;
     getRegionSourceView$(): Observable<RegionSourceView | null>;
     getRegionSourceIndex(query: Omit<RegionIndexQuery, 'exclude'>): Promise<RegionIndexPage>;
     selectSourceFeatures(ids: readonly string[], additive?: boolean): Promise<number[]>;

package/lib/store/region-source-scope.d.ts

@@ -31,8 +31,12 @@ export declare class RegionSourceScope {
     private readonly openOrder;
     /** The entry of the slice on screen: kept open. */
     private shown;
-    /** Attach `open` to `image` for `slices`, replacing (and closing) what was there. */
-    attach(image: string, open: RegionSourceOpener, slices: RegionSourceSlices): void;
+    /**
+     * Attach `open` to `image` for `slices`, replacing (and closing) what was there. `imported` names
+     * the slices it brings that a save must write (see {@link importedSlices}): for a source of one
+     * slice, that slice when non-empty; for a `'planes'` source, the slices its planes cover.
+     */
+    attach(image: string, open: RegionSourceOpener, slices: RegionSourceSlices, imported?: readonly number[]): void;
     /** Drop every source of `image` (closing the open ones) and what was taken from them. */
     detachImage(image: string): void;
     /** Drop the source of one slice of `image`. */
@@ -56,6 +60,8 @@ export declare class RegionSourceScope {
     taken(image: string | undefined, slice: number): ReadonlySet<string>;
     /** Every id taken from any slice of `image` (a `'planes'` source's ids are unique across them). */
     allTaken(image: string | undefined): string[];
+    /** The slices of `image` whose source was imported (see {@link attach}), in order. */
+    importedSlices(image: string | undefined): number[];
     /** The slices of `image` with anything taken from their source. */
     slicesWithTaken(image: string | undefined): number[];
     /** Replace the ids taken from `slice`'s source (copy-on-write: `ids` is kept as given). */

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

@@ -338,8 +338,13 @@ export declare class RegionStore implements IRegionStore, IRegionEditApi, IRegio
      * source was closed to save memory). `slices` says which slice of the current image it
      * serves: one (default: the slice shown; plane 0 of the source), or `'planes'`, every slice z
      * from plane z of a z-indexed source. Replaces the source those slices had.
+     *
+     * `imported` marks a source brought in over the image (an imported volume, folder or served set)
+     * rather than the image's own regions: it is on no file yet, so a save writes its slices though
+     * nothing was taken from it — `true` for a source of one slice, the slices its planes cover for a
+     * `'planes'` source. The image's own sources are not marked: loading them changes nothing to save.
      */
-    attachRegionSource(source: RegionSource | RegionSourceOpener, slices?: RegionSourceSlices): void;
+    attachRegionSource(source: RegionSource | RegionSourceOpener, slices?: RegionSourceSlices, imported?: boolean | readonly number[]): void;
     /** Drop the current image's region sources (closing them) and what was taken from them. */
     detachRegionSources(): void;
     /**
@@ -439,10 +444,15 @@ export declare class RegionStore implements IRegionStore, IRegionEditApi, IRegio
      */
     getRegionSourceIndex(query: Omit<RegionIndexQuery, 'exclude'>): Promise<RegionIndexPage>;
     /**
-     * `regions` as a GeoJSON FeatureCollection string merged with the region source behind them:
-     * the source's features that were not taken (or deleted), then `regions`. Without a source,
-     * {@link getGeoJsonString}. `slice` names a folder stack's slice (default the one shown);
-     * on a z-indexed stack's source (`'planes'`) the export spans every slice.
+     * `regions` as a GeoJSON FeatureCollection string merged with the region sources behind them:
+     * the sources' features that were not taken (or deleted), then `regions`. Without a source,
+     * {@link getGeoJsonString}.
+     *
+     * `slice` names one slice-file of a folder stack (a per-slice-file save): its source's features,
+     * on the file's own plane — of a z-indexed source over every slice, only that slice's plane.
+     * Without it, the export is the image's: on a stack saved as one file, every slice's source
+     * (each feature on its slice's plane, `geometry.plane.z`) and a z-indexed source's every plane;
+     * otherwise the source of the slice shown.
      */
     getGeoJsonWithSource(regions: Region[], slice?: number): Promise<string>;
     /**