@jax-data-science/sci-image-visualizer 0.8.2 → 0.9.0

package/fesm2022/jax-data-science-sci-image-visualizer-onnx-sam-session-Bkujqg7m.mjs

@@ -0,0 +1,238 @@
+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-Csxlnq7I.mjs';
+import '@angular/core';
+import '@angular/common/http';
+import 'rxjs';
+import 'rxjs/operators';
+import '@angular/core/rxjs-interop';
+import '@angular/common';
+import '@angular/forms';
+import 'primeng/api';
+import 'primeng/button';
+import 'primeng/checkbox';
+import 'primeng/contextmenu';
+import 'primeng/dialog';
+import 'primeng/dropdown';
+import 'primeng/inputnumber';
+import 'primeng/progressbar';
+import 'primeng/slider';
+import 'primeng/toast';
+import 'primeng/tooltip';
+import 'napari-js/geometry';
+import 'napari-js/colormaps';
+import 'file-saver';
+import 'primeng/ripple';
+import 'primeng/toolbar';
+import 'primeng/menu';
+import 'primeng/confirmdialog';
+import 'primeng/inputtext';
+import 'primeng/overlaypanel';
+import 'primeng/paginator';
+import 'primeng/table';
+import 'primeng/radiobutton';
+import 'primeng/selectbutton';
+import 'primeng/treeselect';
+import 'plotly.js-dist-min';
+import 'primeng/multiselect';
+import 'image-js';
+import 'buffer';
+import 'openseadragon';
+import 'napari-js/overlays';
+
+/**
+ * Request/response bookkeeping for a worker RPC: each call gets an id and a
+ * promise that its reply settles. Every exit path (dispose, a worker crash)
+ * must {@link rejectAll}, or awaiting callers never reach their `finally` and a
+ * tool's busy flag sticks forever (RT-8).
+ */
+class PendingCalls {
+    constructor() {
+        this.seq = 0;
+        this.pending = new Map();
+    }
+    /** Calls still awaiting a reply. */
+    get size() {
+        return this.pending.size;
+    }
+    /** Register a new call; post the message with the returned id. */
+    open(onProgress) {
+        const id = ++this.seq;
+        const promise = new Promise((resolve, reject) => {
+            this.pending.set(id, { resolve, reject, onProgress });
+        });
+        return { id, promise };
+    }
+    /** Route a worker reply to its call: progress, error or result. */
+    handle(reply) {
+        const p = this.pending.get(reply.id);
+        if (!p)
+            return;
+        if (reply.type === 'progress') {
+            p.onProgress?.(reply.fraction ?? 0);
+            return;
+        }
+        this.pending.delete(reply.id);
+        if (reply.type === 'error')
+            p.reject(new Error(reply.error ?? 'SAM worker error.'));
+        else
+            p.resolve(reply);
+    }
+    /** Reject every pending call with `err` and forget them. */
+    rejectAll(err) {
+        const calls = Array.from(this.pending.values());
+        this.pending.clear();
+        for (const p of calls)
+            p.reject(err);
+    }
+}
+
+/**
+ * onnxruntime-web implementation of {@link ISamSession} (jit-ui#90), with two
+ * execution modes chosen per model:
+ *
+ *  - **in-process** (main thread) — for small WASM models flagged `inProcess`
+ *    (e.g. micro-sam ViT-T). Fast load + inference with no Web Worker spawn /
+ *    second ORT runtime / message round-trips; the brief encode runs on the main
+ *    thread (fine for a tiny model).
+ *  - **worker** — for WebGPU models (e.g. ViT-B, patho-sam fp16) whose heavy
+ *    encode would otherwise freeze the tab. Runs in {@link ./onnx-sam.worker} so
+ *    the UI stays responsive (the spinner animates).
+ *
+ * Both modes share their inference math via {@link ./sam-onnx-core}. Lazy-imported
+ * by the SAM tools so onnxruntime-web / the worker never load in unit tests or
+ * the initial bundle.
+ */
+class OnnxSamSession {
+    constructor() {
+        this.mode = null;
+        this.loaded = false;
+        this.inputSize = 1024;
+        // ── worker mode ──
+        this.worker = null;
+        this.calls = new PendingCalls();
+        // ── in-process mode ──
+        this.encoder = null;
+        this.decoder = null;
+        this.nextToken = 1;
+        /** The few most recently used embeddings, by token (one per recently viewed image). */
+        this.embeddings = new LruCache(3);
+    }
+    async loadModel(model, onProgress) {
+        if (!model.encoderUrl || !model.decoderUrl) {
+            throw new Error(`SAM model "${model.id}" has no ONNX URLs configured.`);
+        }
+        this.inputSize = model.inputSize;
+        const hasGpu = typeof navigator !== 'undefined' && 'gpu' in navigator;
+        const eps = model.encoderProviders ?? (hasGpu ? ['webgpu', 'wasm'] : ['wasm']);
+        const usesWebGpu = eps.includes('webgpu');
+        // WebGPU must run in the worker (else it freezes the main thread); small
+        // WASM models opt into the faster in-process path via `inProcess`.
+        this.mode = !usesWebGpu && model.inProcess ? 'inproc' : 'worker';
+        if (this.mode === 'inproc') {
+            ort.env.wasm.wasmPaths = getOrtWasmBase();
+            const encBuf = await fetchModel(model.encoderUrl, onProgress, model.revision);
+            const decBuf = await fetchModel(model.decoderUrl, undefined, model.revision);
+            this.encoder = await ort.InferenceSession.create(encBuf, { executionProviders: eps });
+            this.decoder = await ort.InferenceSession.create(decBuf, { executionProviders: ['wasm'] });
+        }
+        else {
+            await this.call({
+                type: 'load',
+                encoderUrl: model.encoderUrl,
+                decoderUrl: model.decoderUrl,
+                revision: model.revision,
+                wasmPaths: getOrtWasmBase(),
+                inputSize: model.inputSize,
+                encoderProviders: model.encoderProviders,
+            }, [], onProgress);
+        }
+        this.loaded = true;
+    }
+    isLoaded() {
+        return this.loaded;
+    }
+    async embed(image) {
+        if (this.mode === 'inproc') {
+            const e = await runEncoder(this.encoder, image.data, image.width, image.height, this.inputSize);
+            const token = this.nextToken++;
+            this.embeddings.set(token, e);
+            return {
+                data: new Float32Array(0),
+                dims: e.dims,
+                scale: e.scale,
+                imageWidth: e.imageWidth,
+                imageHeight: e.imageHeight,
+                token,
+            };
+        }
+        // worker: transfer the RGBA buffer (callers pass a fresh frame buffer).
+        const buffer = image.data.buffer;
+        const res = await this.call({ type: 'embed', width: image.width, height: image.height, buffer }, [buffer]);
+        return {
+            data: new Float32Array(0),
+            dims: res['dims'],
+            scale: res['scale'],
+            imageWidth: res['imageWidth'],
+            imageHeight: res['imageHeight'],
+            token: res['token'],
+        };
+    }
+    async decode(embedding, prompt) {
+        if (this.mode === 'inproc') {
+            const e = this.embeddings.get(embedding.token);
+            if (!e)
+                throw new Error('SAM embedding expired; re-encode the image.');
+            return runDecoder(this.decoder, e, prompt);
+        }
+        const res = await this.call({ type: 'decode', token: embedding.token, prompt });
+        return {
+            mask: new Uint8Array(res['buffer']),
+            width: res['width'],
+            height: res['height'],
+            iou: res['iou'],
+        };
+    }
+    /** Release the worker / ORT sessions. Calls still in flight reject (RT-8), so
+     *  their callers' `finally` blocks run (e.g. a tool's busy flag clears). */
+    dispose() {
+        this.dropWorker(new Error('SAM session disposed'));
+        this.encoder?.release?.();
+        this.decoder?.release?.();
+        this.encoder = this.decoder = null;
+        this.embeddings.clear();
+        this.loaded = false;
+        this.mode = null;
+    }
+    // ── worker plumbing ──────────────────────────────────────────────────────
+    ensureWorker() {
+        if (this.worker)
+            return this.worker;
+        const worker = new Worker(new URL('./onnx-sam.worker', import.meta.url), { type: 'module' });
+        worker.onmessage = (ev) => this.calls.handle(ev.data);
+        worker.onerror = (ev) => {
+            // A crashed worker can't serve the loaded model any more: drop it, so the
+            // next run reloads instead of posting to a dead worker.
+            this.dropWorker(new Error(ev.message || 'SAM worker crashed.'));
+            this.loaded = false;
+            this.mode = null;
+        };
+        this.worker = worker;
+        return worker;
+    }
+    /** Terminate the worker (if any) and reject every call still waiting on it. */
+    dropWorker(err) {
+        this.worker?.terminate();
+        this.worker = null;
+        this.calls.rejectAll(err);
+    }
+    call(msg, transfer = [], onProgress) {
+        const worker = this.ensureWorker();
+        const { id, promise } = this.calls.open(onProgress);
+        worker.postMessage({ ...msg, id }, transfer);
+        return promise;
+    }
+}
+
+export { OnnxSamSession };
+//# sourceMappingURL=jax-data-science-sci-image-visualizer-onnx-sam-session-Bkujqg7m.mjs.map

package/fesm2022/jax-data-science-sci-image-visualizer-onnx-sam-session-Bkujqg7m.mjs.map

@@ -0,0 +1 @@
+{"version":3,"file":"jax-data-science-sci-image-visualizer-onnx-sam-session-Bkujqg7m.mjs","sources":["../../src/lib/toolbar/segmentation/pending-calls.ts","../../src/lib/toolbar/segmentation/onnx-sam-session.ts"],"sourcesContent":["/** A reply from the SAM worker: progress for, or the result of, call `id`. */\nexport interface WorkerReply {\n  id: number;\n  type: string;\n  /** Present on `type: 'progress'` replies. */\n  fraction?: number;\n  /** Present on `type: 'error'` replies. */\n  error?: string;\n  [key: string]: unknown;\n}\n\ninterface Pending {\n  resolve: (reply: WorkerReply) => void;\n  reject: (err: Error) => void;\n  onProgress?: (fraction: number) => void;\n}\n\n/**\n * Request/response bookkeeping for a worker RPC: each call gets an id and a\n * promise that its reply settles. Every exit path (dispose, a worker crash)\n * must {@link rejectAll}, or awaiting callers never reach their `finally` and a\n * tool's busy flag sticks forever (RT-8).\n */\nexport class PendingCalls {\n  private seq = 0;\n  private readonly pending = new Map<number, Pending>();\n\n  /** Calls still awaiting a reply. */\n  get size(): number {\n    return this.pending.size;\n  }\n\n  /** Register a new call; post the message with the returned id. */\n  open(onProgress?: (fraction: number) => void): { id: number; promise: Promise<WorkerReply> } {\n    const id = ++this.seq;\n    const promise = new Promise<WorkerReply>((resolve, reject) => {\n      this.pending.set(id, { resolve, reject, onProgress });\n    });\n    return { id, promise };\n  }\n\n  /** Route a worker reply to its call: progress, error or result. */\n  handle(reply: WorkerReply): void {\n    const p = this.pending.get(reply.id);\n    if (!p) return;\n    if (reply.type === 'progress') {\n      p.onProgress?.(reply.fraction ?? 0);\n      return;\n    }\n    this.pending.delete(reply.id);\n    if (reply.type === 'error') p.reject(new Error(reply.error ?? 'SAM worker error.'));\n    else p.resolve(reply);\n  }\n\n  /** Reject every pending call with `err` and forget them. */\n  rejectAll(err: Error): void {\n    const calls = Array.from(this.pending.values());\n    this.pending.clear();\n    for (const p of calls) p.reject(err);\n  }\n}\n","import { LruCache } from 'napari-js';\nimport * as ort from 'onnxruntime-web';\n\nimport { ISamSession, SamEmbedding, SamMaskResult, SamModelDef, SamPrompt } from '../../contracts/sam.contract';\nimport { fetchModel, runEncoder, runDecoder, type CoreEmbedding } from './sam-onnx-core';\nimport { getOrtWasmBase } from './ort-runtime-config';\nimport { PendingCalls, WorkerReply } from './pending-calls';\n\n/**\n * onnxruntime-web implementation of {@link ISamSession} (jit-ui#90), with two\n * execution modes chosen per model:\n *\n *  - **in-process** (main thread) — for small WASM models flagged `inProcess`\n *    (e.g. micro-sam ViT-T). Fast load + inference with no Web Worker spawn /\n *    second ORT runtime / message round-trips; the brief encode runs on the main\n *    thread (fine for a tiny model).\n *  - **worker** — for WebGPU models (e.g. ViT-B, patho-sam fp16) whose heavy\n *    encode would otherwise freeze the tab. Runs in {@link ./onnx-sam.worker} so\n *    the UI stays responsive (the spinner animates).\n *\n * Both modes share their inference math via {@link ./sam-onnx-core}. Lazy-imported\n * by the SAM tools so onnxruntime-web / the worker never load in unit tests or\n * the initial bundle.\n */\nexport class OnnxSamSession implements ISamSession {\n  private mode: 'inproc' | 'worker' | null = null;\n  private loaded = false;\n  private inputSize = 1024;\n\n  // ── worker mode ──\n  private worker: Worker | null = null;\n  private readonly calls = new PendingCalls();\n\n  // ── in-process mode ──\n  private encoder: ort.InferenceSession | null = null;\n  private decoder: ort.InferenceSession | null = null;\n  private nextToken = 1;\n  /** The few most recently used embeddings, by token (one per recently viewed image). */\n  private readonly embeddings = new LruCache<CoreEmbedding, number>(3);\n\n  async loadModel(model: SamModelDef, onProgress?: (fraction: number) => void): Promise<void> {\n    if (!model.encoderUrl || !model.decoderUrl) {\n      throw new Error(`SAM model \"${model.id}\" has no ONNX URLs configured.`);\n    }\n    this.inputSize = model.inputSize;\n    const hasGpu = typeof navigator !== 'undefined' && 'gpu' in navigator;\n    const eps: string[] = model.encoderProviders ?? (hasGpu ? ['webgpu', 'wasm'] : ['wasm']);\n    const usesWebGpu = eps.includes('webgpu');\n    // WebGPU must run in the worker (else it freezes the main thread); small\n    // WASM models opt into the faster in-process path via `inProcess`.\n    this.mode = !usesWebGpu && model.inProcess ? 'inproc' : 'worker';\n\n    if (this.mode === 'inproc') {\n      ort.env.wasm.wasmPaths = getOrtWasmBase();\n      const encBuf = await fetchModel(model.encoderUrl, onProgress, model.revision);\n      const decBuf = await fetchModel(model.decoderUrl, undefined, model.revision);\n      this.encoder = await ort.InferenceSession.create(encBuf, { executionProviders: eps });\n      this.decoder = await ort.InferenceSession.create(decBuf, { executionProviders: ['wasm'] });\n    } else {\n      await this.call(\n        {\n          type: 'load',\n          encoderUrl: model.encoderUrl,\n          decoderUrl: model.decoderUrl,\n          revision: model.revision,\n          wasmPaths: getOrtWasmBase(),\n          inputSize: model.inputSize,\n          encoderProviders: model.encoderProviders,\n        },\n        [],\n        onProgress,\n      );\n    }\n    this.loaded = true;\n  }\n\n  isLoaded(): boolean {\n    return this.loaded;\n  }\n\n  async embed(image: { data: Uint8ClampedArray; width: number; height: number }): Promise<SamEmbedding> {\n    if (this.mode === 'inproc') {\n      const e = await runEncoder(this.encoder!, image.data, image.width, image.height, this.inputSize);\n      const token = this.nextToken++;\n      this.embeddings.set(token, e);\n      return {\n        data: new Float32Array(0),\n        dims: e.dims,\n        scale: e.scale,\n        imageWidth: e.imageWidth,\n        imageHeight: e.imageHeight,\n        token,\n      };\n    }\n    // worker: transfer the RGBA buffer (callers pass a fresh frame buffer).\n    const buffer = image.data.buffer;\n    const res = await this.call({ type: 'embed', width: image.width, height: image.height, buffer }, [buffer]);\n    return {\n      data: new Float32Array(0),\n      dims: res['dims'] as number[],\n      scale: res['scale'] as number,\n      imageWidth: res['imageWidth'] as number,\n      imageHeight: res['imageHeight'] as number,\n      token: res['token'] as number,\n    };\n  }\n\n  async decode(embedding: SamEmbedding, prompt: SamPrompt): Promise<SamMaskResult> {\n    if (this.mode === 'inproc') {\n      const e = this.embeddings.get(embedding.token as number);\n      if (!e) throw new Error('SAM embedding expired; re-encode the image.');\n      return runDecoder(this.decoder!, e, prompt);\n    }\n    const res = await this.call({ type: 'decode', token: embedding.token, prompt });\n    return {\n      mask: new Uint8Array(res['buffer'] as ArrayBuffer),\n      width: res['width'] as number,\n      height: res['height'] as number,\n      iou: res['iou'] as number,\n    };\n  }\n\n  /** Release the worker / ORT sessions. Calls still in flight reject (RT-8), so\n   *  their callers' `finally` blocks run (e.g. a tool's busy flag clears). */\n  dispose(): void {\n    this.dropWorker(new Error('SAM session disposed'));\n    this.encoder?.release?.();\n    this.decoder?.release?.();\n    this.encoder = this.decoder = null;\n    this.embeddings.clear();\n    this.loaded = false;\n    this.mode = null;\n  }\n\n  // ── worker plumbing ──────────────────────────────────────────────────────\n  private ensureWorker(): Worker {\n    if (this.worker) return this.worker;\n    const worker = new Worker(new URL('./onnx-sam.worker', import.meta.url), { type: 'module' });\n    worker.onmessage = (ev: MessageEvent<WorkerReply>) => this.calls.handle(ev.data);\n    worker.onerror = (ev: ErrorEvent) => {\n      // A crashed worker can't serve the loaded model any more: drop it, so the\n      // next run reloads instead of posting to a dead worker.\n      this.dropWorker(new Error(ev.message || 'SAM worker crashed.'));\n      this.loaded = false;\n      this.mode = null;\n    };\n    this.worker = worker;\n    return worker;\n  }\n\n  /** Terminate the worker (if any) and reject every call still waiting on it. */\n  private dropWorker(err: Error): void {\n    this.worker?.terminate();\n    this.worker = null;\n    this.calls.rejectAll(err);\n  }\n\n  private call(\n    msg: Record<string, unknown>,\n    transfer: Transferable[] = [],\n    onProgress?: (f: number) => void,\n  ): Promise<WorkerReply> {\n    const worker = this.ensureWorker();\n    const { id, promise } = this.calls.open(onProgress);\n    worker.postMessage({ ...msg, id }, transfer);\n    return promise;\n  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package/fesm2022/jax-data-science-sci-image-visualizer-spatial-math-worker-BzVFFqGS.mjs

@@ -0,0 +1,12 @@
+/**
+ * Factory for the spatial-math Web Worker, isolated in its own module so the
+ * `import.meta.url` reference — which the bundler needs in order to locate the worker —
+ * is never pulled into the ts-jest CommonJS compile of anything that uses it. Same
+ * arrangement as `spatial/tsne-worker.ts` and `region-editor/mask-worker.ts`.
+ */
+function createSpatialMathWorker() {
+    return new Worker(new URL('./spatial-math.worker', import.meta.url), { type: 'module' });
+}
+
+export { createSpatialMathWorker };
+//# sourceMappingURL=jax-data-science-sci-image-visualizer-spatial-math-worker-BzVFFqGS.mjs.map

package/fesm2022/jax-data-science-sci-image-visualizer-spatial-math-worker-BzVFFqGS.mjs.map

@@ -0,0 +1 @@
+{"version":3,"file":"jax-data-science-sci-image-visualizer-spatial-math-worker-BzVFFqGS.mjs","sources":["../../src/lib/workers/spatial-math-worker.ts"],"sourcesContent":["/**\n * Factory for the spatial-math Web Worker, isolated in its own module so the\n * `import.meta.url` reference — which the bundler needs in order to locate the worker —\n * is never pulled into the ts-jest CommonJS compile of anything that uses it. Same\n * arrangement as `spatial/tsne-worker.ts` and `region-editor/mask-worker.ts`.\n */\nexport function createSpatialMathWorker(): Worker {\n  return new Worker(new URL('./spatial-math.worker', import.meta.url), { type: 'module' });\n}\n"],"names":[],"mappings":"AAAA;;;;;AAKG;SACa,uBAAuB,GAAA;IACrC,OAAO,IAAI,MAAM,CAAC,IAAI,GAAG,CAAC,uBAAuB,EAAE,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,IAAI,EAAE,QAAQ,EAAE,CAAC;AAC1F;;;;"}