@fideus-labs/fiff 0.1.2 → 0.3.0

package/dist/write.d.ts

@@ -0,0 +1,84 @@
+/**
+ * High-level OME-TIFF writer.
+ *
+ * Converts an ngff-zarr Multiscales object to a complete OME-TIFF file
+ * as an ArrayBuffer. Supports multi-resolution pyramids (via SubIFDs),
+ * tiled output, deflate compression, parallel plane reading, and
+ * automatic BigTIFF detection.
+ *
+ * @example
+ * ```ts
+ * import { toOmeTiff } from "@fideus-labs/fiff";
+ * import type { Multiscales } from "@fideus-labs/ngff-zarr";
+ *
+ * const buffer = await toOmeTiff(multiscales);
+ * // buffer is a valid OME-TIFF ArrayBuffer
+ * ```
+ */
+import type { Multiscales } from "@fideus-labs/ngff-zarr";
+/** Options for the OME-TIFF writer. */
+export interface WriteOptions {
+    /**
+     * DimensionOrder for the TIFF IFD layout.
+     * Determines the order in which C, Z, T planes are stored.
+     * Default: "XYZCT".
+     */
+    dimensionOrder?: "XYZCT" | "XYZTC" | "XYCTZ" | "XYCZT" | "XYTCZ" | "XYTZC";
+    /**
+     * Compression to apply to pixel data.
+     * - "none": no compression (larger files, faster write)
+     * - "deflate": zlib/deflate compression (smaller files, compatible with all readers)
+     * Default: "deflate".
+     */
+    compression?: "none" | "deflate";
+    /**
+     * Deflate compression level (1-9).
+     * Higher values produce smaller files but take longer.
+     * Only used when compression is "deflate".
+     * Default: 6.
+     */
+    compressionLevel?: number;
+    /** Creator string embedded in the OME-XML. Default: "fiff". */
+    creator?: string;
+    /** Image name. Falls back to multiscales.metadata.name or "image". */
+    imageName?: string;
+    /**
+     * Tile size in pixels. Images larger than this in either dimension
+     * will use tiled output. Must be a multiple of 16.
+     * Default: 256 (OME-TIFF convention).
+     * Set to 0 to disable tiling (strip-based output).
+     */
+    tileSize?: number;
+    /**
+     * Maximum number of planes to read concurrently.
+     * Higher values use more memory but can speed up writes when
+     * reading from async data sources.
+     * Default: 4.
+     */
+    concurrency?: number;
+    /**
+     * TIFF format to use.
+     * - "auto": Classic TIFF when possible, BigTIFF for files > 4 GB.
+     * - "classic": Force classic TIFF (fails if file > 4 GB).
+     * - "bigtiff": Force BigTIFF (64-bit offsets).
+     * Default: "auto".
+     */
+    format?: "auto" | "classic" | "bigtiff";
+}
+/**
+ * Convert an ngff-zarr Multiscales to an OME-TIFF ArrayBuffer.
+ *
+ * Writes all resolution levels as SubIFDs (pyramids) if the
+ * Multiscales has more than one image. The highest-resolution
+ * level goes in the main IFD chain; lower-resolution levels
+ * are attached as SubIFDs to each corresponding main IFD.
+ *
+ * Planes are read with bounded concurrency and tiles are compressed
+ * eagerly to minimise peak memory.
+ *
+ * @param multiscales - The ngff-zarr Multiscales object to write.
+ * @param options - Writer options.
+ * @returns A complete OME-TIFF file as an ArrayBuffer.
+ */
+export declare function toOmeTiff(multiscales: Multiscales, options?: WriteOptions): Promise<ArrayBuffer>;
+//# sourceMappingURL=write.d.ts.map

package/dist/write.d.ts.map

@@ -0,0 +1 @@
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package/dist/write.js

@@ -0,0 +1,173 @@
+// SPDX-FileCopyrightText: Copyright (c) Fideus Labs LLC
+// SPDX-License-Identifier: MIT
+import * as zarr from "zarrita";
+import { zarrToTiffDtype, bytesPerElement } from "./dtypes.js";
+import { buildOmeXml, extractDimensions } from "./ome-xml-writer.js";
+import { buildTiff, makeImageTags, sliceTiles, DEFAULT_TILE_SIZE, } from "./tiff-writer.js";
+/**
+ * Convert an ngff-zarr Multiscales to an OME-TIFF ArrayBuffer.
+ *
+ * Writes all resolution levels as SubIFDs (pyramids) if the
+ * Multiscales has more than one image. The highest-resolution
+ * level goes in the main IFD chain; lower-resolution levels
+ * are attached as SubIFDs to each corresponding main IFD.
+ *
+ * Planes are read with bounded concurrency and tiles are compressed
+ * eagerly to minimise peak memory.
+ *
+ * @param multiscales - The ngff-zarr Multiscales object to write.
+ * @param options - Writer options.
+ * @returns A complete OME-TIFF file as an ArrayBuffer.
+ */
+export async function toOmeTiff(multiscales, options = {}) {
+    const dimensionOrder = options.dimensionOrder ?? "XYZCT";
+    const compression = options.compression ?? "deflate";
+    const compressionLevel = options.compressionLevel ?? 6;
+    const tileSize = options.tileSize ?? DEFAULT_TILE_SIZE;
+    const concurrency = options.concurrency ?? 4;
+    const format = options.format ?? "auto";
+    const fullResImage = multiscales.images[0];
+    const dtype = fullResImage.data.dtype;
+    const dims = extractDimensions(multiscales);
+    const bpe = bytesPerElement(dtype);
+    const tiffDtype = zarrToTiffDtype(dtype);
+    // Generate OME-XML for the first IFD
+    const omeXml = buildOmeXml(multiscales, dtype, {
+        dimensionOrder,
+        creator: options.creator,
+        imageName: options.imageName,
+    });
+    const totalPlanes = dims.sizeC * dims.sizeZ * dims.sizeT;
+    const numLevels = multiscales.images.length;
+    // Build one IFD (with SubIFDs) for a given plane index.
+    const buildPlaneIfd = async (ifdIdx) => {
+        const { c, z, t } = ifdIndexToPlane(ifdIdx, dims, dimensionOrder);
+        // Read + tile the full-resolution plane
+        const planeData = await readPlane(fullResImage, dims, c, z, t, bpe);
+        const mainTiles = slicePlane(planeData, dims.sizeX, dims.sizeY, bpe, tileSize);
+        const isFirst = ifdIdx === 0;
+        const tags = makeImageTags(dims.sizeX, dims.sizeY, tiffDtype.bitsPerSample, tiffDtype.sampleFormat, "none", // compression handled by buildTiff
+        isFirst ? omeXml : undefined, false, tileSize);
+        // Build SubIFDs for pyramid levels (if any)
+        const subIfds = [];
+        for (let level = 1; level < numLevels; level++) {
+            const subImage = multiscales.images[level];
+            const subDims = extractLevelDimensions(subImage, dims);
+            const subPlane = await readPlane(subImage, subDims, c, z, t, bpe);
+            const subTiles = slicePlane(subPlane, subDims.sizeX, subDims.sizeY, bpe, tileSize);
+            const subTags = makeImageTags(subDims.sizeX, subDims.sizeY, tiffDtype.bitsPerSample, tiffDtype.sampleFormat, "none", undefined, true, // isSubResolution
+            tileSize);
+            subIfds.push({ tags: subTags, tiles: subTiles });
+        }
+        return {
+            tags,
+            tiles: mainTiles,
+            subIfds: subIfds.length > 0 ? subIfds : undefined,
+        };
+    };
+    // Read planes with bounded concurrency
+    const mainIfds = new Array(totalPlanes);
+    const effectiveConcurrency = Math.max(1, Math.min(concurrency, totalPlanes));
+    for (let start = 0; start < totalPlanes; start += effectiveConcurrency) {
+        const end = Math.min(start + effectiveConcurrency, totalPlanes);
+        const batch = [];
+        for (let i = start; i < end; i++) {
+            batch.push(buildPlaneIfd(i).then((ifd) => { mainIfds[i] = ifd; }));
+        }
+        await Promise.all(batch);
+    }
+    return buildTiff(mainIfds, { compression, compressionLevel, format });
+}
+// ── Internal helpers ────────────────────────────────────────────────
+/**
+ * Slice a plane into tiles or return as a single strip.
+ * Decides based on whether the image is large enough to warrant tiling.
+ */
+function slicePlane(planeBytes, width, height, bpe, tileSize) {
+    if (tileSize > 0 && (width > tileSize || height > tileSize)) {
+        return sliceTiles(planeBytes, width, height, bpe, tileSize, tileSize);
+    }
+    // Small image: single strip
+    return [planeBytes];
+}
+/**
+ * Map a linear IFD index back to (c, z, t) based on DimensionOrder.
+ * This is the inverse of getIfdIndex.
+ */
+function ifdIndexToPlane(ifdIdx, dims, dimensionOrder) {
+    const { sizeC, sizeZ, sizeT } = dims;
+    // The DimensionOrder string is XYNNN where NNN are the three varying dims
+    // from fastest to slowest (after XY which are always the plane dimensions).
+    // e.g. "XYZCT" means Z varies fastest, then C, then T.
+    const order = dimensionOrder.slice(2); // e.g. "ZCT"
+    // Sizes and names in fastest-to-slowest order
+    const sizeMap = { Z: sizeZ, C: sizeC, T: sizeT };
+    const sizes = [sizeMap[order[0]], sizeMap[order[1]], sizeMap[order[2]]];
+    // Decompose ifdIdx: idx = d0 + sizes[0] * (d1 + sizes[1] * d2)
+    const d0 = ifdIdx % sizes[0];
+    const d1 = Math.floor(ifdIdx / sizes[0]) % sizes[1];
+    const d2 = Math.floor(ifdIdx / (sizes[0] * sizes[1]));
+    const result = {};
+    result[order[0]] = d0;
+    result[order[1]] = d1;
+    result[order[2]] = d2;
+    return {
+        c: result["C"] ?? 0,
+        z: result["Z"] ?? 0,
+        t: result["T"] ?? 0,
+    };
+}
+/**
+ * Read a single (c, z, t) plane from an NgffImage as raw bytes.
+ * Returns a Uint8Array of little-endian pixel data.
+ */
+async function readPlane(image, dims, c, z, t, bpe) {
+    const dimNames = image.dims;
+    const shape = image.data.shape;
+    // Build selection: scalar indices for t, c, z; null for y, x
+    const selection = [];
+    for (let i = 0; i < dimNames.length; i++) {
+        switch (dimNames[i]) {
+            case "t":
+                selection.push(Math.min(t, shape[i] - 1));
+                break;
+            case "c":
+                selection.push(Math.min(c, shape[i] - 1));
+                break;
+            case "z":
+                selection.push(Math.min(z, shape[i] - 1));
+                break;
+            default:
+                // y, x — take all
+                selection.push(null);
+                break;
+        }
+    }
+    const result = await zarr.get(image.data, selection);
+    const typedArray = result.data;
+    // Convert to raw bytes (little-endian)
+    return new Uint8Array(typedArray.buffer, typedArray.byteOffset, typedArray.byteLength);
+}
+/**
+ * Extract dimension info for a sub-resolution image.
+ * Non-spatial dimensions (C, Z, T) are inherited from the full-res dims.
+ * Spatial dimensions (X, Y) come from the sub-resolution image's shape.
+ */
+function extractLevelDimensions(image, fullDims) {
+    const shape = image.data.shape;
+    const dimNames = image.dims;
+    let sizeX = fullDims.sizeX;
+    let sizeY = fullDims.sizeY;
+    for (let i = 0; i < dimNames.length; i++) {
+        if (dimNames[i] === "x")
+            sizeX = shape[i];
+        if (dimNames[i] === "y")
+            sizeY = shape[i];
+    }
+    return {
+        ...fullDims,
+        sizeX,
+        sizeY,
+    };
+}
+//# sourceMappingURL=write.js.map

package/dist/write.js.map

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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@fideus-labs/fiff",
-  "version": "0.1.2",
+  "version": "0.3.0",
   "description": "Present TIFF files as a zarrita.js Zarr store following the NGFF OME-Zarr data model",
   "type": "module",
   "main": "./dist/index.js",
@@ -40,12 +40,22 @@
     "prepublishOnly": "bun run build"
   },
   "dependencies": {
-    "geotiff": "^3.0.4-beta.1",
+    "geotiff": "^3.0.3",
+    "pako": "^2.1.0",
     "zarrita": "^0.6.1"
   },
+  "peerDependencies": {
+    "@fideus-labs/ngff-zarr": "^0.8.0"
+  },
+  "peerDependenciesMeta": {
+    "@fideus-labs/ngff-zarr": {
+      "optional": true
+    }
+  },
   "devDependencies": {
     "@fideus-labs/ngff-zarr": "^0.8.0",
-    "@types/bun": "^1.2.15",
+    "@types/bun": "^1.3.9",
+    "@types/pako": "^2.0.4",
     "typescript": "^5.9.3"
   }
 }