@fideus-labs/ngff-zarr 0.0.1 → 0.2.0

package/script/utils/create_queue.js

@@ -0,0 +1,17 @@
+"use strict";
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.createQueue = createQueue;
+// SPDX-FileCopyrightText: Copyright (c) Fideus Labs LLC
+// SPDX-License-Identifier: MIT
+const p_queue_1 = __importDefault(require("p-queue"));
+function createQueue() {
+    const concurrency = Math.min(navigator?.hardwareConcurrency || 4, 128);
+    const queue = new p_queue_1.default({ concurrency });
+    return {
+        add: (fn) => queue.add(fn),
+        onIdle: queue.onIdle.bind(queue),
+    };
+}

package/script/utils/factory.d.ts

@@ -3,7 +3,7 @@ import { Multiscales } from "../types/multiscales.js";
 import type { Axis, Dataset, Metadata, Scale, Translation } from "../types/zarr_metadata.js";
 import type { AxesType, SupportedDims, Units } from "../types/units.js";
 import type { Methods } from "../types/methods.js";
-export declare function createNgffImage(_data: ArrayBuffer | number[], shape: number[], dtype: string, dims: string[], scale: Record<string, number>, translation: Record<string, number>, name?: string): NgffImage;
+export declare function createNgffImage(_data: ArrayBuffer | number[], shape: number[], dtype: string, dims: string[], scale: Record<string, number>, translation: Record<string, number>, name?: string): Promise<NgffImage>;
 export declare function createAxis(name: SupportedDims, type: AxesType, unit?: Units): Axis;
 export declare function createScale(scale: number[]): Scale;
 export declare function createTranslation(translation: number[]): Translation;

package/script/utils/factory.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"factory.d.ts","sourceRoot":"","sources":["../../src/utils/factory.ts"],"names":[],"mappings":"AAGA,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AACnD,OAAO,EAAE,WAAW,EAAE,MAAM,yBAAyB,CAAC;AACtD,OAAO,KAAK,EACV,IAAI,EACJ,OAAO,EACP,QAAQ,EACR,KAAK,EACL,WAAW,EACZ,MAAM,2BAA2B,CAAC;AACnC,OAAO,KAAK,EAAE,QAAQ,EAAE,aAAa,EAAE,KAAK,EAAE,MAAM,mBAAmB,CAAC;AACxE,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,qBAAqB,CAAC;AAsBnD,wBAAsB,eAAe,CACnC,KAAK,EAAE,WAAW,GAAG,MAAM,EAAE,EAC7B,KAAK,EAAE,MAAM,EAAE,EACf,KAAK,EAAE,MAAM,EACb,IAAI,EAAE,MAAM,EAAE,EACd,KAAK,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,EAC7B,WAAW,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,EACnC,IAAI,SAAU,GACb,OAAO,CAAC,SAAS,CAAC,CAYpB;AAED,wBAAgB,UAAU,CACxB,IAAI,EAAE,aAAa,EACnB,IAAI,EAAE,QAAQ,EACd,IAAI,CAAC,EAAE,KAAK,GACX,IAAI,CAMN;AAED,wBAAgB,WAAW,CAAC,KAAK,EAAE,MAAM,EAAE,GAAG,KAAK,CAKlD;AAED,wBAAgB,iBAAiB,CAAC,WAAW,EAAE,MAAM,EAAE,GAAG,WAAW,CAKpE;AAED,wBAAgB,aAAa,CAC3B,IAAI,EAAE,MAAM,EACZ,KAAK,EAAE,MAAM,EAAE,EACf,WAAW,EAAE,MAAM,EAAE,GACpB,OAAO,CAQT;AAED,wBAAgB,cAAc,CAC5B,IAAI,EAAE,IAAI,EAAE,EACZ,QAAQ,EAAE,OAAO,EAAE,EACnB,IAAI,SAAU,EACd,OAAO,SAAQ,GACd,QAAQ,CASV;AAED,wBAAgB,iBAAiB,CAC/B,MAAM,EAAE,SAAS,EAAE,EACnB,QAAQ,EAAE,QAAQ,EAClB,YAAY,CAAC,EAAE,CAAC,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,GAAG,MAAM,CAAC,EAAE,EAClD,MAAM,CAAC,EAAE,OAAO,GACf,WAAW,CAQb"}

package/script/utils/factory.js

@@ -1,4 +1,27 @@
 "use strict";
+var __createBinding = (this && this.__createBinding) || (Object.create ? (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    var desc = Object.getOwnPropertyDescriptor(m, k);
+    if (!desc || ("get" in desc ? !m.__esModule : desc.writable || desc.configurable)) {
+      desc = { enumerable: true, get: function() { return m[k]; } };
+    }
+    Object.defineProperty(o, k2, desc);
+}) : (function(o, m, k, k2) {
+    if (k2 === undefined) k2 = k;
+    o[k2] = m[k];
+}));
+var __setModuleDefault = (this && this.__setModuleDefault) || (Object.create ? (function(o, v) {
+    Object.defineProperty(o, "default", { enumerable: true, value: v });
+}) : function(o, v) {
+    o["default"] = v;
+});
+var __importStar = (this && this.__importStar) || function (mod) {
+    if (mod && mod.__esModule) return mod;
+    var result = {};
+    if (mod != null) for (var k in mod) if (k !== "default" && Object.prototype.hasOwnProperty.call(mod, k)) __createBinding(result, mod, k);
+    __setModuleDefault(result, mod);
+    return result;
+};
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.createNgffImage = createNgffImage;
 exports.createAxis = createAxis;
@@ -7,18 +30,27 @@ exports.createTranslation = createTranslation;
 exports.createDataset = createDataset;
 exports.createMetadata = createMetadata;
 exports.createMultiscales = createMultiscales;
-const lazy_array_js_1 = require("../types/lazy_array.js");
+// SPDX-FileCopyrightText: Copyright (c) Fideus Labs LLC
+// SPDX-License-Identifier: MIT
+const zarr = __importStar(require("zarrita"));
 const ngff_image_js_1 = require("../types/ngff_image.js");
 const multiscales_js_1 = require("../types/multiscales.js");
-function createNgffImage(_data, shape, dtype, dims, scale, translation, name = "image") {
-    const lazyArray = new lazy_array_js_1.LazyArray({
+// Create a zarr.Array for testing using an in-memory store
+async function createTestZarrArray(shape, dtype, chunks, name) {
+    const store = new Map();
+    const root = zarr.root(store);
+    // Create the array using zarrita with correct options
+    const array = await zarr.create(root.resolve(name), {
         shape,
-        dtype,
-        chunks: [shape],
-        name,
+        chunk_shape: chunks,
+        data_type: dtype,
     });
+    return array;
+}
+async function createNgffImage(_data, shape, dtype, dims, scale, translation, name = "image") {
+    const zarrArray = await createTestZarrArray(shape, dtype, shape, name);
     return new ngff_image_js_1.NgffImage({
-        data: lazyArray,
+        data: zarrArray,
         dims,
         scale,
         translation,

package/script/utils/method_metadata.d.ts

@@ -0,0 +1,10 @@
+import type { Methods } from "../types/methods.js";
+import type { MethodMetadata } from "../types/zarr_metadata.js";
+/**
+ * Get metadata information for a given downsampling method.
+ *
+ * @param method - The downsampling method enum
+ * @returns MethodMetadata with description, method (package.function), and version
+ */
+export declare function getMethodMetadata(method: Methods): MethodMetadata | undefined;
+//# sourceMappingURL=method_metadata.d.ts.map

package/script/utils/method_metadata.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"method_metadata.d.ts","sourceRoot":"","sources":["../../src/utils/method_metadata.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,qBAAqB,CAAC;AACnD,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,2BAA2B,CAAC;AA6BhE;;;;;GAKG;AACH,wBAAgB,iBAAiB,CAAC,MAAM,EAAE,OAAO,GAAG,cAAc,GAAG,SAAS,CAe7E"}

package/script/utils/method_metadata.js

@@ -0,0 +1,40 @@
+"use strict";
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.getMethodMetadata = getMethodMetadata;
+const METHOD_INFO = {
+    itkwasm_gaussian: {
+        description: "Smoothed with a discrete gaussian filter to generate a scale space, ideal for intensity images. ITK-Wasm implementation is extremely portable and SIMD accelerated.",
+        package: "itkwasm-downsample",
+        method: "itkwasm_downsample.downsample",
+    },
+    itkwasm_bin_shrink: {
+        description: "Uses the local mean for the output value. WebAssembly build. Fast but generates more artifacts than gaussian-based methods. Appropriate for intensity images.",
+        package: "itkwasm-downsample",
+        method: "itkwasm_downsample.downsample_bin_shrink",
+    },
+    itkwasm_label_image: {
+        description: "A sample is the mode of the linearly weighted local labels in the image. Fast and minimal artifacts. For label images.",
+        package: "itkwasm-downsample",
+        method: "itkwasm_downsample.downsample_label_image",
+    },
+};
+/**
+ * Get metadata information for a given downsampling method.
+ *
+ * @param method - The downsampling method enum
+ * @returns MethodMetadata with description, method (package.function), and version
+ */
+function getMethodMetadata(method) {
+    const methodInfo = METHOD_INFO[method];
+    if (!methodInfo) {
+        return undefined;
+    }
+    // TODO: Determine package version dynamically if possible,
+    // For now use a placeholder
+    const version = "unknown";
+    return {
+        description: methodInfo.description,
+        method: methodInfo.method,
+        version,
+    };
+}

package/script/utils/validation.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"validation.d.ts","sourceRoot":"","sources":["../../src/utils/validation.ts"],"names":[],"mappings":"AACA,OAAO,KAAK,EAAE,QAAQ,EAAE,MAAM,2BAA2B,CAAC;AAG1D,wBAAgB,gBAAgB,CAAC,QAAQ,EAAE,OAAO,GAAG,QAAQ,CAQ5D;AAED,wBAAgB,aAAa,CAAC,KAAK,EAAE,MAAM,GAAG,IAAI,CAIjD;AAED,wBAAgB,gBAAgB,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAErD;AAED,wBAAgB,WAAW,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAyDjD"}
+{"version":3,"file":"validation.d.ts","sourceRoot":"","sources":["../../src/utils/validation.ts"],"names":[],"mappings":"AAGA,OAAO,KAAK,EAAE,QAAQ,EAAE,MAAM,2BAA2B,CAAC;AAG1D,wBAAgB,gBAAgB,CAAC,QAAQ,EAAE,OAAO,GAAG,QAAQ,CAQ5D;AAED,wBAAgB,aAAa,CAAC,KAAK,EAAE,MAAM,GAAG,IAAI,CAIjD;AAED,wBAAgB,gBAAgB,CAAC,GAAG,EAAE,MAAM,GAAG,OAAO,CAErD;AAED,wBAAgB,WAAW,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAyDjD"}

package/esm/schemas/lazy_array.d.ts

@@ -1,8 +0,0 @@
-import { z } from "zod";
-export declare const LazyArrayMetadataSchema: z.ZodObject<{
-    shape: z.ZodArray<z.ZodNumber>;
-    dtype: z.ZodString;
-    chunks: z.ZodArray<z.ZodArray<z.ZodNumber>>;
-    name: z.ZodString;
-}>;
-//# sourceMappingURL=lazy_array.d.ts.map

package/esm/schemas/lazy_array.d.ts.map

@@ -1 +0,0 @@
-{"version":3,"file":"lazy_array.d.ts","sourceRoot":"","sources":["../../src/schemas/lazy_array.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,CAAC,EAAE,MAAM,KAAK,CAAC;AAExB,eAAO,MAAM,uBAAuB,EAAE,CAAC,CAAC,SAAS,CAAC;IAChD,KAAK,EAAE,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC;IAC/B,KAAK,EAAE,CAAC,CAAC,SAAS,CAAC;IACnB,MAAM,EAAE,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC;IAC5C,IAAI,EAAE,CAAC,CAAC,SAAS,CAAC;CACnB,CAKC,CAAC"}

package/esm/schemas/lazy_array.js

@@ -1,7 +0,0 @@
-import { z } from "zod";
-export const LazyArrayMetadataSchema = z.object({
-    shape: z.array(z.number().int().nonnegative()),
-    dtype: z.string(),
-    chunks: z.array(z.array(z.number().int().nonnegative())),
-    name: z.string(),
-});

package/esm/types/lazy_array.d.ts

@@ -1,18 +0,0 @@
-export interface LazyArrayMetadata {
-    shape: number[];
-    dtype: string;
-    chunks: number[][];
-    name: string;
-}
-export declare class LazyArray {
-    readonly shape: number[];
-    readonly dtype: string;
-    readonly chunks: number[][];
-    readonly name: string;
-    constructor(metadata: LazyArrayMetadata);
-    get ndim(): number;
-    get size(): number;
-    get chunksize(): number[];
-    toString(): string;
-}
-//# sourceMappingURL=lazy_array.d.ts.map

package/esm/types/lazy_array.d.ts.map

@@ -1 +0,0 @@
-{"version":3,"file":"lazy_array.d.ts","sourceRoot":"","sources":["../../src/types/lazy_array.ts"],"names":[],"mappings":"AAAA,MAAM,WAAW,iBAAiB;IAChC,KAAK,EAAE,MAAM,EAAE,CAAC;IAChB,KAAK,EAAE,MAAM,CAAC;IACd,MAAM,EAAE,MAAM,EAAE,EAAE,CAAC;IACnB,IAAI,EAAE,MAAM,CAAC;CACd;AAED,qBAAa,SAAS;IACpB,SAAgB,KAAK,EAAE,MAAM,EAAE,CAAC;IAChC,SAAgB,KAAK,EAAE,MAAM,CAAC;IAC9B,SAAgB,MAAM,EAAE,MAAM,EAAE,EAAE,CAAC;IACnC,SAAgB,IAAI,EAAE,MAAM,CAAC;gBAEjB,QAAQ,EAAE,iBAAiB;IAOvC,IAAI,IAAI,IAAI,MAAM,CAEjB;IAED,IAAI,IAAI,IAAI,MAAM,CAEjB;IAED,IAAI,SAAS,IAAI,MAAM,EAAE,CAExB;IAED,QAAQ,IAAI,MAAM;CAUnB"}

package/esm/types/lazy_array.js

@@ -1,27 +0,0 @@
-export class LazyArray {
-    shape;
-    dtype;
-    chunks;
-    name;
-    constructor(metadata) {
-        this.shape = [...metadata.shape];
-        this.dtype = metadata.dtype;
-        this.chunks = metadata.chunks.map((chunk) => [...chunk]);
-        this.name = metadata.name;
-    }
-    get ndim() {
-        return this.shape.length;
-    }
-    get size() {
-        return this.shape.reduce((acc, dim) => acc * dim, 1);
-    }
-    get chunksize() {
-        return this.chunks[0] || [];
-    }
-    toString() {
-        const chunkStr = this.chunksize.length > 0
-            ? `chunksize=(${this.chunksize.join(", ")})`
-            : "chunksize=()";
-        return `LazyArray(name=${this.name}, shape=(${this.shape.join(", ")}), dtype=${this.dtype}, ${chunkStr}, chunktype=TypedArray)`;
-    }
-}

package/script/schemas/lazy_array.d.ts

@@ -1,8 +0,0 @@
-import { z } from "zod";
-export declare const LazyArrayMetadataSchema: z.ZodObject<{
-    shape: z.ZodArray<z.ZodNumber>;
-    dtype: z.ZodString;
-    chunks: z.ZodArray<z.ZodArray<z.ZodNumber>>;
-    name: z.ZodString;
-}>;
-//# sourceMappingURL=lazy_array.d.ts.map

package/script/schemas/lazy_array.d.ts.map

@@ -1 +0,0 @@
-{"version":3,"file":"lazy_array.d.ts","sourceRoot":"","sources":["../../src/schemas/lazy_array.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,CAAC,EAAE,MAAM,KAAK,CAAC;AAExB,eAAO,MAAM,uBAAuB,EAAE,CAAC,CAAC,SAAS,CAAC;IAChD,KAAK,EAAE,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC;IAC/B,KAAK,EAAE,CAAC,CAAC,SAAS,CAAC;IACnB,MAAM,EAAE,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,QAAQ,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC;IAC5C,IAAI,EAAE,CAAC,CAAC,SAAS,CAAC;CACnB,CAKC,CAAC"}

package/script/schemas/lazy_array.js

@@ -1,10 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.LazyArrayMetadataSchema = void 0;
-const zod_1 = require("zod");
-exports.LazyArrayMetadataSchema = zod_1.z.object({
-    shape: zod_1.z.array(zod_1.z.number().int().nonnegative()),
-    dtype: zod_1.z.string(),
-    chunks: zod_1.z.array(zod_1.z.array(zod_1.z.number().int().nonnegative())),
-    name: zod_1.z.string(),
-});

package/script/types/lazy_array.d.ts

@@ -1,18 +0,0 @@
-export interface LazyArrayMetadata {
-    shape: number[];
-    dtype: string;
-    chunks: number[][];
-    name: string;
-}
-export declare class LazyArray {
-    readonly shape: number[];
-    readonly dtype: string;
-    readonly chunks: number[][];
-    readonly name: string;
-    constructor(metadata: LazyArrayMetadata);
-    get ndim(): number;
-    get size(): number;
-    get chunksize(): number[];
-    toString(): string;
-}
-//# sourceMappingURL=lazy_array.d.ts.map

package/script/types/lazy_array.d.ts.map

@@ -1 +0,0 @@
-{"version":3,"file":"lazy_array.d.ts","sourceRoot":"","sources":["../../src/types/lazy_array.ts"],"names":[],"mappings":"AAAA,MAAM,WAAW,iBAAiB;IAChC,KAAK,EAAE,MAAM,EAAE,CAAC;IAChB,KAAK,EAAE,MAAM,CAAC;IACd,MAAM,EAAE,MAAM,EAAE,EAAE,CAAC;IACnB,IAAI,EAAE,MAAM,CAAC;CACd;AAED,qBAAa,SAAS;IACpB,SAAgB,KAAK,EAAE,MAAM,EAAE,CAAC;IAChC,SAAgB,KAAK,EAAE,MAAM,CAAC;IAC9B,SAAgB,MAAM,EAAE,MAAM,EAAE,EAAE,CAAC;IACnC,SAAgB,IAAI,EAAE,MAAM,CAAC;gBAEjB,QAAQ,EAAE,iBAAiB;IAOvC,IAAI,IAAI,IAAI,MAAM,CAEjB;IAED,IAAI,IAAI,IAAI,MAAM,CAEjB;IAED,IAAI,SAAS,IAAI,MAAM,EAAE,CAExB;IAED,QAAQ,IAAI,MAAM;CAUnB"}

package/script/types/lazy_array.js

@@ -1,31 +0,0 @@
-"use strict";
-Object.defineProperty(exports, "__esModule", { value: true });
-exports.LazyArray = void 0;
-class LazyArray {
-    shape;
-    dtype;
-    chunks;
-    name;
-    constructor(metadata) {
-        this.shape = [...metadata.shape];
-        this.dtype = metadata.dtype;
-        this.chunks = metadata.chunks.map((chunk) => [...chunk]);
-        this.name = metadata.name;
-    }
-    get ndim() {
-        return this.shape.length;
-    }
-    get size() {
-        return this.shape.reduce((acc, dim) => acc * dim, 1);
-    }
-    get chunksize() {
-        return this.chunks[0] || [];
-    }
-    toString() {
-        const chunkStr = this.chunksize.length > 0
-            ? `chunksize=(${this.chunksize.join(", ")})`
-            : "chunksize=()";
-        return `LazyArray(name=${this.name}, shape=(${this.shape.join(", ")}), dtype=${this.dtype}, ${chunkStr}, chunktype=TypedArray)`;
-    }
-}
-exports.LazyArray = LazyArray;