@fideus-labs/fiff 0.1.0

package/dist/tiff-store.d.ts

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+/**
+ * TiffStore: a zarrita.js-compatible AsyncReadable store that presents
+ * TIFF files as OME-Zarr v0.5 datasets.
+ *
+ * Usage:
+ *   const store = await TiffStore.fromUrl("https://example.com/image.ome.tif");
+ *   const group = await zarr.open(store, { kind: "group" });
+ *   // ... use zarrita.js as normal
+ */
+import type GeoTIFF from "geotiff";
+import { type ZarrDataType } from "./dtypes.js";
+import { type OmeImage } from "./ome-xml.js";
+import { type PyramidInfo } from "./ifd-indexer.js";
+/** Options for opening a TiffStore. */
+export interface TiffStoreOptions {
+    /** Pre-computed IFD byte offsets for fast random access. */
+    offsets?: number[];
+    /** Additional HTTP headers for remote TIFF requests. */
+    headers?: Record<string, string>;
+}
+/**
+ * A zarrita.js AsyncReadable store backed by a TIFF file.
+ *
+ * Implements the zarrita `AsyncReadable` interface:
+ *   get(key: string): Promise<Uint8Array | undefined>
+ *
+ * Keys are routed as follows:
+ *   - "zarr.json"           -> root group metadata (OME-Zarr 0.5)
+ *   - "{level}/zarr.json"   -> array metadata for resolution level
+ *   - "{level}/c/{indices}" -> chunk data (delegates to geotiff.js)
+ */
+export declare class TiffStore {
+    private tiff;
+    private omeImages;
+    private pixels;
+    private pyramid;
+    private dtype;
+    private dimNames;
+    private chunkShapes;
+    private shapes;
+    private multiscale;
+    private omero;
+    private indexer;
+    private offsets?;
+    private rootJsonBytes;
+    private arrayJsonCache;
+    private constructor();
+    /**
+     * Open a TiffStore from a remote URL.
+     * The TIFF will be accessed via HTTP range requests.
+     */
+    static fromUrl(url: string, options?: TiffStoreOptions): Promise<TiffStore>;
+    /**
+     * Open a TiffStore from an in-memory ArrayBuffer.
+     */
+    static fromArrayBuffer(buffer: ArrayBuffer, options?: TiffStoreOptions): Promise<TiffStore>;
+    /**
+     * Open a TiffStore from a Blob or File.
+     */
+    static fromBlob(blob: Blob, options?: TiffStoreOptions): Promise<TiffStore>;
+    /**
+     * Open a TiffStore from an already-opened GeoTIFF instance.
+     */
+    static fromGeoTIFF(tiff: GeoTIFF, options?: TiffStoreOptions): Promise<TiffStore>;
+    /**
+     * Get a value from the store by key.
+     *
+     * This is the core zarrita.js AsyncReadable interface method.
+     */
+    get(key: string): Promise<Uint8Array | undefined>;
+    /** The number of resolution levels. */
+    get levels(): number;
+    /** The Zarr data type string. */
+    get dataType(): ZarrDataType;
+    /** The OME-XML images (if parsed). */
+    get ome(): OmeImage[];
+    /** The pyramid information. */
+    get pyramidInfo(): PyramidInfo;
+    /** Get the shape for a given level. */
+    getShape(level: number): number[];
+    /** Get the chunk shape for a given level. */
+    getChunkShape(level: number): number[];
+    /** The dimension names. */
+    get dimensionNames(): string[];
+    private getRootGroupJson;
+    private getArrayJson;
+    private getChunkData;
+    /**
+     * Map chunk indices to a plane selection.
+     * Non-spatial dimensions (t, c, z) map directly from chunk indices;
+     * spatial dimensions (y, x) are handled separately.
+     */
+    private indicesToSelection;
+}
+//# sourceMappingURL=tiff-store.d.ts.map

package/dist/tiff-store.d.ts.map

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package/dist/tiff-store.js

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+/**
+ * TiffStore: a zarrita.js-compatible AsyncReadable store that presents
+ * TIFF files as OME-Zarr v0.5 datasets.
+ *
+ * Usage:
+ *   const store = await TiffStore.fromUrl("https://example.com/image.ome.tif");
+ *   const group = await zarr.open(store, { kind: "group" });
+ *   // ... use zarrita.js as normal
+ */
+import { fromUrl, fromArrayBuffer, fromBlob } from "geotiff";
+import { tiffDtypeToZarr, omePixelTypeToZarr } from "./dtypes.js";
+import { isOmeXml, parseOmeXml, } from "./ome-xml.js";
+import { detectPyramid, createOmeIndexer, createPlainIndexer, } from "./ifd-indexer.js";
+import { readChunk } from "./chunk-reader.js";
+import { buildMultiscales, buildOmero, buildRootGroupJson, buildArrayJson, buildShape, } from "./metadata.js";
+import { parseStoreKey, computeChunkShape } from "./utils.js";
+/**
+ * A zarrita.js AsyncReadable store backed by a TIFF file.
+ *
+ * Implements the zarrita `AsyncReadable` interface:
+ *   get(key: string): Promise<Uint8Array | undefined>
+ *
+ * Keys are routed as follows:
+ *   - "zarr.json"           -> root group metadata (OME-Zarr 0.5)
+ *   - "{level}/zarr.json"   -> array metadata for resolution level
+ *   - "{level}/c/{indices}" -> chunk data (delegates to geotiff.js)
+ */
+export class TiffStore {
+    tiff;
+    omeImages;
+    pixels;
+    pyramid;
+    dtype;
+    dimNames;
+    chunkShapes;
+    shapes;
+    multiscale;
+    omero;
+    indexer;
+    offsets;
+    // Cached serialized metadata
+    rootJsonBytes;
+    arrayJsonCache = new Map();
+    constructor(tiff, omeImages, pixels, pyramid, dtype, dimNames, chunkShapes, shapes, multiscale, omero, indexer, offsets) {
+        this.tiff = tiff;
+        this.omeImages = omeImages;
+        this.pixels = pixels;
+        this.pyramid = pyramid;
+        this.dtype = dtype;
+        this.dimNames = dimNames;
+        this.chunkShapes = chunkShapes;
+        this.shapes = shapes;
+        this.multiscale = multiscale;
+        this.omero = omero;
+        this.indexer = indexer;
+        this.offsets = offsets;
+    }
+    /**
+     * Open a TiffStore from a remote URL.
+     * The TIFF will be accessed via HTTP range requests.
+     */
+    static async fromUrl(url, options = {}) {
+        const tiff = await fromUrl(url, { headers: options.headers });
+        return TiffStore.fromGeoTIFF(tiff, options);
+    }
+    /**
+     * Open a TiffStore from an in-memory ArrayBuffer.
+     */
+    static async fromArrayBuffer(buffer, options = {}) {
+        const tiff = await fromArrayBuffer(buffer);
+        return TiffStore.fromGeoTIFF(tiff, options);
+    }
+    /**
+     * Open a TiffStore from a Blob or File.
+     */
+    static async fromBlob(blob, options = {}) {
+        const tiff = await fromBlob(blob);
+        return TiffStore.fromGeoTIFF(tiff, options);
+    }
+    /**
+     * Open a TiffStore from an already-opened GeoTIFF instance.
+     */
+    static async fromGeoTIFF(tiff, options = {}) {
+        const firstImage = await tiff.getImage(0);
+        // Try to parse OME-XML from the ImageDescription tag
+        let omeImages = [];
+        let pixels;
+        let imageDescription;
+        try {
+            imageDescription = firstImage.fileDirectory.getValue("ImageDescription");
+        }
+        catch {
+            // Tag not available synchronously, try async
+            try {
+                imageDescription = await firstImage.fileDirectory.loadValue("ImageDescription");
+            }
+            catch {
+                // No ImageDescription
+            }
+        }
+        if (imageDescription && isOmeXml(imageDescription)) {
+            omeImages = parseOmeXml(imageDescription);
+            if (omeImages.length > 0) {
+                pixels = omeImages[0].pixels;
+            }
+        }
+        // Determine data type
+        let dtype;
+        if (pixels) {
+            dtype = omePixelTypeToZarr(pixels.type);
+        }
+        else {
+            const sampleFormat = firstImage.getSampleFormat() ?? 1;
+            const bitsPerSample = firstImage.getBitsPerSample();
+            dtype = tiffDtypeToZarr(sampleFormat, bitsPerSample);
+        }
+        // Detect pyramid structure
+        const planesPerImage = pixels
+            ? pixels.sizeC * pixels.sizeZ * pixels.sizeT
+            : 1;
+        const pyramid = await detectPyramid(tiff, omeImages.length, planesPerImage);
+        // Build metadata
+        const imageName = omeImages[0]?.name;
+        const { multiscale, dimNames } = buildMultiscales(pixels, pyramid, imageName);
+        const omero = buildOmero(pixels, dtype);
+        // Compute shapes and chunk shapes for each level
+        const tileWidth = firstImage.getTileWidth();
+        const tileHeight = firstImage.getTileHeight();
+        const shapes = [];
+        const chunkShapes = [];
+        for (let level = 0; level < pyramid.levels; level++) {
+            const shape = buildShape(pixels, pyramid, level, dimNames);
+            shapes.push(shape);
+            // Use the same tile size for all levels, but clamp to actual dimensions
+            const levelTileW = Math.min(tileWidth, pyramid.widths[level]);
+            const levelTileH = Math.min(tileHeight, pyramid.heights[level]);
+            chunkShapes.push(computeChunkShape(levelTileW, levelTileH, dimNames.length));
+        }
+        // Create the appropriate indexer
+        let indexer;
+        if (pixels) {
+            indexer = createOmeIndexer(tiff, pixels, pyramid, 0, options.offsets);
+        }
+        else {
+            indexer = createPlainIndexer(tiff, options.offsets);
+        }
+        return new TiffStore(tiff, omeImages, pixels, pyramid, dtype, dimNames, chunkShapes, shapes, multiscale, omero, indexer, options.offsets);
+    }
+    // ------- AsyncReadable interface -------
+    /**
+     * Get a value from the store by key.
+     *
+     * This is the core zarrita.js AsyncReadable interface method.
+     */
+    async get(key) {
+        const parsed = parseStoreKey(key);
+        // Root group metadata
+        if (parsed.isRootMetadata) {
+            return this.getRootGroupJson();
+        }
+        // Array-level metadata
+        if (parsed.isMetadata && parsed.level >= 0) {
+            return this.getArrayJson(parsed.level);
+        }
+        // Chunk data
+        if (parsed.chunkIndices && parsed.level >= 0) {
+            return this.getChunkData(parsed.level, parsed.chunkIndices);
+        }
+        // Unknown key
+        return undefined;
+    }
+    // ------- Public accessors -------
+    /** The number of resolution levels. */
+    get levels() {
+        return this.pyramid.levels;
+    }
+    /** The Zarr data type string. */
+    get dataType() {
+        return this.dtype;
+    }
+    /** The OME-XML images (if parsed). */
+    get ome() {
+        return this.omeImages;
+    }
+    /** The pyramid information. */
+    get pyramidInfo() {
+        return this.pyramid;
+    }
+    /** Get the shape for a given level. */
+    getShape(level) {
+        return this.shapes[level];
+    }
+    /** Get the chunk shape for a given level. */
+    getChunkShape(level) {
+        return this.chunkShapes[level];
+    }
+    /** The dimension names. */
+    get dimensionNames() {
+        return this.dimNames;
+    }
+    // ------- Private methods -------
+    getRootGroupJson() {
+        if (!this.rootJsonBytes) {
+            const json = buildRootGroupJson(this.multiscale, this.omero);
+            this.rootJsonBytes = encodeJson(json);
+        }
+        return this.rootJsonBytes;
+    }
+    getArrayJson(level) {
+        if (level < 0 || level >= this.pyramid.levels) {
+            return undefined;
+        }
+        if (!this.arrayJsonCache.has(level)) {
+            const json = buildArrayJson(this.shapes[level], this.chunkShapes[level], this.dtype, this.dimNames);
+            this.arrayJsonCache.set(level, encodeJson(json));
+        }
+        return this.arrayJsonCache.get(level);
+    }
+    async getChunkData(level, chunkIndices) {
+        if (level < 0 || level >= this.pyramid.levels) {
+            return undefined;
+        }
+        // Map chunk indices to selection + spatial indices
+        // Dimension ordering matches dimNames: [t?, c?, z?, y, x]
+        const sel = this.indicesToSelection(chunkIndices);
+        const shape = this.shapes[level];
+        const chunkShape = this.chunkShapes[level];
+        // The last two indices are always y, x
+        const yIdx = this.dimNames.indexOf("y");
+        const xIdx = this.dimNames.indexOf("x");
+        const chunkY = chunkIndices[yIdx];
+        const chunkX = chunkIndices[xIdx];
+        const imageWidth = shape[xIdx];
+        const imageHeight = shape[yIdx];
+        const chunkWidth = chunkShape[xIdx];
+        const chunkHeight = chunkShape[yIdx];
+        return readChunk(this.indexer, sel, level, chunkY, chunkX, chunkHeight, chunkWidth, imageWidth, imageHeight, this.dtype);
+    }
+    /**
+     * Map chunk indices to a plane selection.
+     * Non-spatial dimensions (t, c, z) map directly from chunk indices;
+     * spatial dimensions (y, x) are handled separately.
+     */
+    indicesToSelection(chunkIndices) {
+        const sel = { c: 0, z: 0, t: 0 };
+        for (let i = 0; i < this.dimNames.length; i++) {
+            const dim = this.dimNames[i];
+            if (dim === "t")
+                sel.t = chunkIndices[i];
+            else if (dim === "c")
+                sel.c = chunkIndices[i];
+            else if (dim === "z")
+                sel.z = chunkIndices[i];
+        }
+        return sel;
+    }
+}
+// ---------- internal helpers ----------
+function encodeJson(obj) {
+    const str = JSON.stringify(obj);
+    return new TextEncoder().encode(str);
+}
+//# sourceMappingURL=tiff-store.js.map

package/dist/tiff-store.js.map

@@ -0,0 +1 @@
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package/dist/utils.d.ts

@@ -0,0 +1,64 @@
+/**
+ * Utility helpers for key parsing, pixel window computation, and
+ * general-purpose functions used across the package.
+ */
+/**
+ * Result of parsing a store key.
+ */
+export interface ParsedKey {
+    /** The resolution level (e.g. 0 for full, 1 for 2x downsample). */
+    level: number;
+    /** Whether this is a zarr.json metadata key. */
+    isMetadata: boolean;
+    /** Whether this is a root-level zarr.json. */
+    isRootMetadata: boolean;
+    /** Chunk indices for data keys (e.g. [0, 3, 5] for c=0, y=3, x=5). */
+    chunkIndices?: number[];
+}
+/**
+ * Parse a zarr store key into its components.
+ *
+ * Expected key patterns (Zarr v3 with "/" separator):
+ *   "zarr.json"                -> root group metadata
+ *   "0/zarr.json"              -> level 0 array metadata
+ *   "0/c/0/0/3/5"             -> level 0, chunk at indices [0, 0, 3, 5]
+ *
+ * @param key - The store key (may or may not have a leading "/").
+ * @returns Parsed key information.
+ */
+export declare function parseStoreKey(key: string): ParsedKey;
+/**
+ * Compute the pixel window for a chunk within an image.
+ *
+ * @param chunkX - The x chunk index.
+ * @param chunkY - The y chunk index.
+ * @param chunkWidth - The width of each chunk in pixels.
+ * @param chunkHeight - The height of each chunk in pixels.
+ * @param imageWidth - The total image width in pixels.
+ * @param imageHeight - The total image height in pixels.
+ * @returns The pixel window [left, top, right, bottom] for geotiff readRasters.
+ */
+export declare function computePixelWindow(chunkX: number, chunkY: number, chunkWidth: number, chunkHeight: number, imageWidth: number, imageHeight: number): [number, number, number, number];
+/**
+ * Encode a TypedArray as raw little-endian bytes (Uint8Array).
+ * geotiff.js returns platform-endian typed arrays, and modern systems
+ * are little-endian which matches Zarr's default byte order.
+ *
+ * For edge chunks that don't fill the full chunk shape, the data is
+ * padded with the fill value (0) to the full chunk size.
+ */
+export declare function encodeChunkBytes(data: ArrayBufferView, expectedElements: number, bytesPerElement: number): Uint8Array;
+/**
+ * Compute the number of chunks along each dimension.
+ */
+export declare function computeChunkCounts(shape: number[], chunkShape: number[]): number[];
+/**
+ * Determine a reasonable chunk shape for TIFF tile dimensions.
+ * Uses the TIFF's native tile size if available, otherwise defaults.
+ */
+export declare function computeChunkShape(tileWidth: number, tileHeight: number, ndim: number): number[];
+/**
+ * Return the previous power of 2 that is <= n.
+ */
+export declare function prevPowerOf2(n: number): number;
+//# sourceMappingURL=utils.d.ts.map

package/dist/utils.d.ts.map

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package/dist/utils.js

@@ -0,0 +1,116 @@
+/**
+ * Utility helpers for key parsing, pixel window computation, and
+ * general-purpose functions used across the package.
+ */
+/**
+ * Parse a zarr store key into its components.
+ *
+ * Expected key patterns (Zarr v3 with "/" separator):
+ *   "zarr.json"                -> root group metadata
+ *   "0/zarr.json"              -> level 0 array metadata
+ *   "0/c/0/0/3/5"             -> level 0, chunk at indices [0, 0, 3, 5]
+ *
+ * @param key - The store key (may or may not have a leading "/").
+ * @returns Parsed key information.
+ */
+export function parseStoreKey(key) {
+    // Normalize: strip leading "/"
+    const normalized = key.startsWith("/") ? key.slice(1) : key;
+    // Root metadata
+    if (normalized === "zarr.json") {
+        return { level: -1, isMetadata: true, isRootMetadata: true };
+    }
+    const parts = normalized.split("/");
+    // Level metadata: "{level}/zarr.json"
+    if (parts.length === 2 && parts[1] === "zarr.json") {
+        const level = parseInt(parts[0], 10);
+        if (isNaN(level)) {
+            return { level: -1, isMetadata: false, isRootMetadata: false };
+        }
+        return { level, isMetadata: true, isRootMetadata: false };
+    }
+    // Chunk data: "{level}/c/{indices...}"
+    // In Zarr v3 with default chunk_key_encoding (separator="/"),
+    // chunk keys look like: "{level}/c/{i0}/{i1}/..."
+    if (parts.length >= 3 && parts[1] === "c") {
+        const level = parseInt(parts[0], 10);
+        if (isNaN(level)) {
+            return { level: -1, isMetadata: false, isRootMetadata: false };
+        }
+        const chunkIndices = parts.slice(2).map((p) => parseInt(p, 10));
+        if (chunkIndices.some(isNaN)) {
+            return { level: -1, isMetadata: false, isRootMetadata: false };
+        }
+        return { level, isMetadata: false, isRootMetadata: false, chunkIndices };
+    }
+    // Unknown key
+    return { level: -1, isMetadata: false, isRootMetadata: false };
+}
+/**
+ * Compute the pixel window for a chunk within an image.
+ *
+ * @param chunkX - The x chunk index.
+ * @param chunkY - The y chunk index.
+ * @param chunkWidth - The width of each chunk in pixels.
+ * @param chunkHeight - The height of each chunk in pixels.
+ * @param imageWidth - The total image width in pixels.
+ * @param imageHeight - The total image height in pixels.
+ * @returns The pixel window [left, top, right, bottom] for geotiff readRasters.
+ */
+export function computePixelWindow(chunkX, chunkY, chunkWidth, chunkHeight, imageWidth, imageHeight) {
+    const left = chunkX * chunkWidth;
+    const top = chunkY * chunkHeight;
+    const right = Math.min(left + chunkWidth, imageWidth);
+    const bottom = Math.min(top + chunkHeight, imageHeight);
+    return [left, top, right, bottom];
+}
+/**
+ * Encode a TypedArray as raw little-endian bytes (Uint8Array).
+ * geotiff.js returns platform-endian typed arrays, and modern systems
+ * are little-endian which matches Zarr's default byte order.
+ *
+ * For edge chunks that don't fill the full chunk shape, the data is
+ * padded with the fill value (0) to the full chunk size.
+ */
+export function encodeChunkBytes(data, expectedElements, bytesPerElement) {
+    const actualElements = data.byteLength / bytesPerElement;
+    if (actualElements === expectedElements) {
+        // Fast path: data matches expected size exactly
+        return new Uint8Array(data.buffer, data.byteOffset, data.byteLength);
+    }
+    // Edge chunk: pad with zeros to fill the expected chunk size
+    const outputBytes = expectedElements * bytesPerElement;
+    const output = new Uint8Array(outputBytes);
+    output.set(new Uint8Array(data.buffer, data.byteOffset, data.byteLength), 0);
+    return output;
+}
+/**
+ * Compute the number of chunks along each dimension.
+ */
+export function computeChunkCounts(shape, chunkShape) {
+    return shape.map((s, i) => Math.ceil(s / chunkShape[i]));
+}
+/**
+ * Determine a reasonable chunk shape for TIFF tile dimensions.
+ * Uses the TIFF's native tile size if available, otherwise defaults.
+ */
+export function computeChunkShape(tileWidth, tileHeight, ndim) {
+    // For spatial dimensions use TIFF tile size; for other dims use 1
+    // Shape ordering: [t?, c?, z?, y, x]
+    const chunks = new Array(ndim).fill(1);
+    chunks[ndim - 2] = tileHeight; // y
+    chunks[ndim - 1] = tileWidth; // x
+    return chunks;
+}
+/**
+ * Return the previous power of 2 that is <= n.
+ */
+export function prevPowerOf2(n) {
+    if (n <= 0)
+        return 1;
+    let p = 1;
+    while (p * 2 <= n)
+        p *= 2;
+    return p;
+}
+//# sourceMappingURL=utils.js.map

package/dist/utils.js.map

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package/package.json

@@ -0,0 +1,51 @@
+{
+  "name": "@fideus-labs/fiff",
+  "version": "0.1.0",
+  "description": "Present TIFF files as a zarrita.js Zarr store following the NGFF OME-Zarr data model",
+  "type": "module",
+  "main": "./dist/index.js",
+  "module": "./dist/index.js",
+  "types": "./dist/index.d.ts",
+  "exports": {
+    ".": {
+      "import": "./dist/index.js",
+      "types": "./dist/index.d.ts"
+    }
+  },
+  "files": [
+    "dist",
+    "LICENSE.txt"
+  ],
+  "repository": {
+    "type": "git",
+    "url": "https://github.com/fideus-labs/fiff"
+  },
+  "license": "MIT",
+  "keywords": [
+    "tiff",
+    "ome-tiff",
+    "zarr",
+    "ome-zarr",
+    "ngff",
+    "zarrita",
+    "geotiff",
+    "bioimaging",
+    "microscopy",
+    "multiscale"
+  ],
+  "scripts": {
+    "build": "tsc -p tsconfig.build.json",
+    "test": "bun test",
+    "typecheck": "bun x tsc --noEmit",
+    "prepublishOnly": "bun run build"
+  },
+  "dependencies": {
+    "geotiff": "^3.0.4-beta.1",
+    "zarrita": "^0.6.1"
+  },
+  "devDependencies": {
+    "@fideus-labs/ngff-zarr": "file:/home/matt/src/ngff-zarr/ts/npm",
+    "@types/bun": "^1.2.15",
+    "typescript": "^5.9.3"
+  }
+}