@fideus-labs/fiff 0.1.0

package/dist/metadata.d.ts

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+/**
+ * Metadata synthesis: generate Zarr v3 (OME-Zarr 0.5) metadata from
+ * TIFF image properties and OME-XML.
+ */
+import type { ZarrDataType } from "./dtypes.js";
+import type { OmePixels } from "./ome-xml.js";
+import type { PyramidInfo } from "./ifd-indexer.js";
+/** Zarr v3 group zarr.json. */
+export interface ZarrGroupMetadata {
+    zarr_format: 3;
+    node_type: "group";
+    attributes: Record<string, unknown>;
+}
+/** Zarr v3 array zarr.json. */
+export interface ZarrArrayMetadata {
+    zarr_format: 3;
+    node_type: "array";
+    shape: number[];
+    data_type: string;
+    chunk_grid: {
+        name: "regular";
+        configuration: {
+            chunk_shape: number[];
+        };
+    };
+    chunk_key_encoding: {
+        name: "default";
+        configuration: {
+            separator: string;
+        };
+    };
+    fill_value: number;
+    codecs: Array<{
+        name: string;
+        configuration?: Record<string, unknown>;
+    }>;
+    dimension_names: string[];
+}
+export interface OmeAxis {
+    name: string;
+    type: "time" | "space" | "channel";
+    unit?: string;
+}
+export interface OmeCoordinateTransformation {
+    type: "scale" | "translation";
+    scale?: number[];
+    translation?: number[];
+}
+export interface OmeDataset {
+    path: string;
+    coordinateTransformations: OmeCoordinateTransformation[];
+}
+export interface OmeMultiscale {
+    name?: string;
+    axes: OmeAxis[];
+    datasets: OmeDataset[];
+    coordinateTransformations?: OmeCoordinateTransformation[];
+}
+export interface OmeroChannel {
+    active: boolean;
+    color: string;
+    label: string;
+    window: {
+        start: number;
+        end: number;
+        min: number;
+        max: number;
+    };
+}
+export interface OmeroMetadata {
+    channels: OmeroChannel[];
+    rdefs: {
+        defaultT: number;
+        defaultZ: number;
+        model: string;
+    };
+}
+/**
+ * Determine which axes are present and their order based on the TIFF/OME data.
+ *
+ * OME-Zarr axis ordering: time first, then channel, then spatial (z, y, x).
+ */
+export declare function buildAxes(pixels?: OmePixels): {
+    axes: OmeAxis[];
+    dimNames: string[];
+};
+/**
+ * Build the shape array for a given resolution level.
+ */
+export declare function buildShape(pixels: OmePixels | undefined, pyramid: PyramidInfo, level: number, dimNames: string[]): number[];
+/**
+ * Build coordinate transformations for a given resolution level.
+ * Scale values represent the physical size of each voxel at this level.
+ */
+export declare function buildCoordinateTransformations(pixels: OmePixels | undefined, pyramid: PyramidInfo, level: number, dimNames: string[]): OmeCoordinateTransformation[];
+/**
+ * Build the full OME-Zarr 0.5 multiscales metadata.
+ */
+export declare function buildMultiscales(pixels: OmePixels | undefined, pyramid: PyramidInfo, name?: string): {
+    multiscale: OmeMultiscale;
+    axes: OmeAxis[];
+    dimNames: string[];
+};
+/**
+ * Build omero channel display metadata from OME-XML.
+ */
+export declare function buildOmero(pixels?: OmePixels, dtype?: ZarrDataType): OmeroMetadata | undefined;
+/**
+ * Generate the root group zarr.json.
+ */
+export declare function buildRootGroupJson(multiscale: OmeMultiscale, omero?: OmeroMetadata): ZarrGroupMetadata;
+/**
+ * Generate an array-level zarr.json for a given resolution level.
+ */
+export declare function buildArrayJson(shape: number[], chunkShape: number[], dtype: ZarrDataType, dimNames: string[]): ZarrArrayMetadata;
+//# sourceMappingURL=metadata.d.ts.map

package/dist/metadata.d.ts.map

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package/dist/metadata.js

@@ -0,0 +1,234 @@
+/**
+ * Metadata synthesis: generate Zarr v3 (OME-Zarr 0.5) metadata from
+ * TIFF image properties and OME-XML.
+ */
+import { normalizeUnit } from "./ome-xml.js";
+// ---------- Builders ----------
+/** Default colors for channels (RGBA hex without alpha). */
+const DEFAULT_CHANNEL_COLORS = [
+    "FF0000", // red
+    "00FF00", // green
+    "0000FF", // blue
+    "FFFF00", // yellow
+    "FF00FF", // magenta
+    "00FFFF", // cyan
+    "FFFFFF", // white
+];
+/**
+ * Determine which axes are present and their order based on the TIFF/OME data.
+ *
+ * OME-Zarr axis ordering: time first, then channel, then spatial (z, y, x).
+ */
+export function buildAxes(pixels) {
+    if (!pixels) {
+        // Plain TIFF: just y, x
+        return {
+            axes: [
+                { name: "y", type: "space" },
+                { name: "x", type: "space" },
+            ],
+            dimNames: ["y", "x"],
+        };
+    }
+    const axes = [];
+    const dimNames = [];
+    if (pixels.sizeT > 1) {
+        axes.push({ name: "t", type: "time" });
+        dimNames.push("t");
+    }
+    if (pixels.sizeC > 1) {
+        axes.push({ name: "c", type: "channel" });
+        dimNames.push("c");
+    }
+    if (pixels.sizeZ > 1) {
+        const unit = normalizeUnit(pixels.physicalSizeZUnit);
+        axes.push({ name: "z", type: "space", ...(unit && { unit }) });
+        dimNames.push("z");
+    }
+    const yUnit = normalizeUnit(pixels.physicalSizeYUnit);
+    axes.push({ name: "y", type: "space", ...(yUnit && { unit: yUnit }) });
+    dimNames.push("y");
+    const xUnit = normalizeUnit(pixels.physicalSizeXUnit);
+    axes.push({ name: "x", type: "space", ...(xUnit && { unit: xUnit }) });
+    dimNames.push("x");
+    return { axes, dimNames };
+}
+/**
+ * Build the shape array for a given resolution level.
+ */
+export function buildShape(pixels, pyramid, level, dimNames) {
+    const width = pyramid.widths[level];
+    const height = pyramid.heights[level];
+    return dimNames.map((dim) => {
+        switch (dim) {
+            case "t":
+                return pixels?.sizeT ?? 1;
+            case "c":
+                return pixels?.sizeC ?? 1;
+            case "z":
+                return pixels?.sizeZ ?? 1;
+            case "y":
+                return height;
+            case "x":
+                return width;
+            default:
+                return 1;
+        }
+    });
+}
+/**
+ * Build coordinate transformations for a given resolution level.
+ * Scale values represent the physical size of each voxel at this level.
+ */
+export function buildCoordinateTransformations(pixels, pyramid, level, dimNames) {
+    // Compute the downsampling factor relative to level 0
+    const xFactor = pyramid.widths[0] / pyramid.widths[level];
+    const yFactor = pyramid.heights[0] / pyramid.heights[level];
+    const scale = dimNames.map((dim) => {
+        switch (dim) {
+            case "t":
+                return 1.0;
+            case "c":
+                return 1.0;
+            case "z":
+                return pixels?.physicalSizeZ ?? 1.0;
+            case "y":
+                return (pixels?.physicalSizeY ?? 1.0) * yFactor;
+            case "x":
+                return (pixels?.physicalSizeX ?? 1.0) * xFactor;
+            default:
+                return 1.0;
+        }
+    });
+    return [{ type: "scale", scale }];
+}
+/**
+ * Build the full OME-Zarr 0.5 multiscales metadata.
+ */
+export function buildMultiscales(pixels, pyramid, name) {
+    const { axes, dimNames } = buildAxes(pixels);
+    const datasets = [];
+    for (let level = 0; level < pyramid.levels; level++) {
+        datasets.push({
+            path: String(level),
+            coordinateTransformations: buildCoordinateTransformations(pixels, pyramid, level, dimNames),
+        });
+    }
+    const multiscale = {
+        axes,
+        datasets,
+        ...(name && { name }),
+    };
+    return { multiscale, axes, dimNames };
+}
+/**
+ * Build omero channel display metadata from OME-XML.
+ */
+export function buildOmero(pixels, dtype) {
+    if (!pixels || pixels.channels.length === 0)
+        return undefined;
+    const maxVal = getMaxValueForDtype(dtype ?? "uint16");
+    const channels = pixels.channels.map((ch, i) => ({
+        active: true,
+        color: ch.color
+            ? intToHexColor(ch.color)
+            : DEFAULT_CHANNEL_COLORS[i % DEFAULT_CHANNEL_COLORS.length],
+        label: ch.name ?? `Channel ${i}`,
+        window: {
+            start: 0,
+            end: maxVal,
+            min: 0,
+            max: maxVal,
+        },
+    }));
+    return {
+        channels,
+        rdefs: {
+            defaultT: 0,
+            defaultZ: Math.floor((pixels.sizeZ - 1) / 2),
+            model: pixels.sizeC > 1 ? "color" : "greyscale",
+        },
+    };
+}
+/**
+ * Generate the root group zarr.json.
+ */
+export function buildRootGroupJson(multiscale, omero) {
+    return {
+        zarr_format: 3,
+        node_type: "group",
+        attributes: {
+            ome: {
+                version: "0.5",
+                multiscales: [multiscale],
+                ...(omero && { omero }),
+            },
+        },
+    };
+}
+/**
+ * Generate an array-level zarr.json for a given resolution level.
+ */
+export function buildArrayJson(shape, chunkShape, dtype, dimNames) {
+    return {
+        zarr_format: 3,
+        node_type: "array",
+        shape,
+        data_type: dtype,
+        chunk_grid: {
+            name: "regular",
+            configuration: { chunk_shape: chunkShape },
+        },
+        chunk_key_encoding: {
+            name: "default",
+            configuration: { separator: "/" },
+        },
+        fill_value: 0,
+        codecs: [
+            {
+                name: "bytes",
+                configuration: { endian: "little" },
+            },
+        ],
+        dimension_names: dimNames,
+    };
+}
+// ---------- internal helpers ----------
+function getMaxValueForDtype(dtype) {
+    switch (dtype) {
+        case "uint8":
+            return 255;
+        case "int8":
+            return 127;
+        case "uint16":
+            return 65535;
+        case "int16":
+            return 32767;
+        case "uint32":
+            return 4294967295;
+        case "int32":
+            return 2147483647;
+        case "float32":
+            return 1.0;
+        case "float64":
+            return 1.0;
+        default:
+            return 65535;
+    }
+}
+/**
+ * Convert an integer color (as used in OME-XML) to a hex string.
+ * OME-XML stores colors as signed 32-bit integers in RGBA format.
+ */
+function intToHexColor(colorInt) {
+    // Convert signed to unsigned
+    const unsigned = colorInt >>> 0;
+    // Extract RGB (ignore alpha)
+    const r = (unsigned >> 24) & 0xff;
+    const g = (unsigned >> 16) & 0xff;
+    const b = (unsigned >> 8) & 0xff;
+    return (r.toString(16).padStart(2, "0") +
+        g.toString(16).padStart(2, "0") +
+        b.toString(16).padStart(2, "0")).toUpperCase();
+}
+//# sourceMappingURL=metadata.js.map

package/dist/metadata.js.map

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package/dist/ome-xml.d.ts

@@ -0,0 +1,74 @@
+/**
+ * OME-XML parser for extracting metadata from OME-TIFF ImageDescription tags.
+ *
+ * Parses the OME-XML embedded in TIFF files to extract dimension sizes,
+ * dimension ordering, channel info, physical pixel sizes, and TiffData
+ * references for multi-file OME-TIFF.
+ */
+/** Valid OME DimensionOrder values. */
+export type DimensionOrder = "XYZCT" | "XYZTC" | "XYCTZ" | "XYCZT" | "XYTCZ" | "XYTZC";
+/** Parsed OME channel metadata. */
+export interface OmeChannel {
+    id: string;
+    name?: string;
+    samplesPerPixel: number;
+    color?: number;
+}
+/** Parsed OME-XML Pixels metadata for a single Image. */
+export interface OmePixels {
+    sizeX: number;
+    sizeY: number;
+    sizeZ: number;
+    sizeC: number;
+    sizeT: number;
+    dimensionOrder: DimensionOrder;
+    type: string;
+    physicalSizeX?: number;
+    physicalSizeXUnit?: string;
+    physicalSizeY?: number;
+    physicalSizeYUnit?: string;
+    physicalSizeZ?: number;
+    physicalSizeZUnit?: string;
+    bigEndian: boolean;
+    interleaved: boolean;
+    channels: OmeChannel[];
+}
+/** Parsed OME-XML Image entry. */
+export interface OmeImage {
+    id: string;
+    name?: string;
+    pixels: OmePixels;
+}
+/**
+ * Check if a string looks like OME-XML (starts with an OME root element).
+ */
+export declare function isOmeXml(description: string): boolean;
+/**
+ * Parse OME-XML string into structured metadata.
+ *
+ * Uses a simple regex/string-based XML parser that works in any JS runtime
+ * (no DOMParser dependency for Node/Bun compatibility).
+ *
+ * @param xml - The OME-XML string from the TIFF ImageDescription tag.
+ * @returns Array of parsed OmeImage objects.
+ */
+export declare function parseOmeXml(xml: string): OmeImage[];
+/**
+ * Compute the IFD index for a given (c, z, t) selection within an OME image,
+ * based on the DimensionOrder.
+ *
+ * The DimensionOrder string specifies which dimensions vary fastest after XY.
+ * For example, XYZCT means Z varies fastest, then C, then T.
+ *
+ * @param c - Channel index.
+ * @param z - Z-slice index.
+ * @param t - Timepoint index.
+ * @param pixels - The OmePixels metadata containing dimension sizes and order.
+ * @returns The relative IFD index within this image.
+ */
+export declare function getIfdIndex(c: number, z: number, t: number, pixels: OmePixels): number;
+/**
+ * Map an OME physical size unit string to a standard unit name.
+ */
+export declare function normalizeUnit(unit?: string): string | undefined;
+//# sourceMappingURL=ome-xml.d.ts.map

package/dist/ome-xml.d.ts.map

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package/dist/ome-xml.js

@@ -0,0 +1,178 @@
+/**
+ * OME-XML parser for extracting metadata from OME-TIFF ImageDescription tags.
+ *
+ * Parses the OME-XML embedded in TIFF files to extract dimension sizes,
+ * dimension ordering, channel info, physical pixel sizes, and TiffData
+ * references for multi-file OME-TIFF.
+ */
+const VALID_DIMENSION_ORDERS = new Set([
+    "XYZCT",
+    "XYZTC",
+    "XYCTZ",
+    "XYCZT",
+    "XYTCZ",
+    "XYTZC",
+]);
+/**
+ * Check if a string looks like OME-XML (starts with an OME root element).
+ */
+export function isOmeXml(description) {
+    if (!description)
+        return false;
+    const trimmed = description.trim();
+    // Check for XML processing instruction or direct OME element
+    return (trimmed.startsWith("<?xml") ||
+        trimmed.startsWith("<OME") ||
+        trimmed.startsWith("<ome:"));
+}
+/**
+ * Parse OME-XML string into structured metadata.
+ *
+ * Uses a simple regex/string-based XML parser that works in any JS runtime
+ * (no DOMParser dependency for Node/Bun compatibility).
+ *
+ * @param xml - The OME-XML string from the TIFF ImageDescription tag.
+ * @returns Array of parsed OmeImage objects.
+ */
+export function parseOmeXml(xml) {
+    const images = [];
+    // Find all <Image ...>...</Image> blocks
+    const imageRegex = /<Image\s([^>]*)>([\s\S]*?)<\/Image>/g;
+    let imageMatch;
+    while ((imageMatch = imageRegex.exec(xml)) !== null) {
+        const imageAttrs = parseAttributes(imageMatch[1]);
+        const imageBody = imageMatch[2];
+        // Find <Pixels ...>...</Pixels> block
+        const pixelsRegex = /<Pixels\s([^>]*)>([\s\S]*?)<\/Pixels>/;
+        const pixelsMatch = pixelsRegex.exec(imageBody);
+        if (!pixelsMatch)
+            continue;
+        const pixelAttrs = parseAttributes(pixelsMatch[1]);
+        const pixelsBody = pixelsMatch[2];
+        // Parse channels
+        const channels = [];
+        const channelRegex = /<Channel\s([^/>]*)\/?>/g;
+        let channelMatch;
+        while ((channelMatch = channelRegex.exec(pixelsBody)) !== null) {
+            const chAttrs = parseAttributes(channelMatch[1]);
+            channels.push({
+                id: chAttrs["ID"] ?? `Channel:0:${channels.length}`,
+                name: chAttrs["Name"],
+                samplesPerPixel: parseInt(chAttrs["SamplesPerPixel"] ?? "1", 10),
+                color: chAttrs["Color"] ? parseInt(chAttrs["Color"], 10) : undefined,
+            });
+        }
+        const dimensionOrder = pixelAttrs["DimensionOrder"];
+        if (!VALID_DIMENSION_ORDERS.has(dimensionOrder)) {
+            throw new Error(`Invalid DimensionOrder: ${dimensionOrder}`);
+        }
+        const pixels = {
+            sizeX: parseInt(pixelAttrs["SizeX"], 10),
+            sizeY: parseInt(pixelAttrs["SizeY"], 10),
+            sizeZ: parseInt(pixelAttrs["SizeZ"] ?? "1", 10),
+            sizeC: parseInt(pixelAttrs["SizeC"] ?? "1", 10),
+            sizeT: parseInt(pixelAttrs["SizeT"] ?? "1", 10),
+            dimensionOrder: dimensionOrder,
+            type: pixelAttrs["Type"] ?? "uint16",
+            physicalSizeX: pixelAttrs["PhysicalSizeX"]
+                ? parseFloat(pixelAttrs["PhysicalSizeX"])
+                : undefined,
+            physicalSizeXUnit: pixelAttrs["PhysicalSizeXUnit"] ?? "µm",
+            physicalSizeY: pixelAttrs["PhysicalSizeY"]
+                ? parseFloat(pixelAttrs["PhysicalSizeY"])
+                : undefined,
+            physicalSizeYUnit: pixelAttrs["PhysicalSizeYUnit"] ?? "µm",
+            physicalSizeZ: pixelAttrs["PhysicalSizeZ"]
+                ? parseFloat(pixelAttrs["PhysicalSizeZ"])
+                : undefined,
+            physicalSizeZUnit: pixelAttrs["PhysicalSizeZUnit"] ?? "µm",
+            bigEndian: pixelAttrs["BigEndian"] === "true",
+            interleaved: pixelAttrs["Interleaved"] === "true",
+            channels,
+        };
+        // If no channels were found in XML, create a default one for each SizeC
+        if (pixels.channels.length === 0) {
+            for (let c = 0; c < pixels.sizeC; c++) {
+                pixels.channels.push({
+                    id: `Channel:0:${c}`,
+                    samplesPerPixel: 1,
+                });
+            }
+        }
+        images.push({
+            id: imageAttrs["ID"] ?? `Image:${images.length}`,
+            name: imageAttrs["Name"],
+            pixels,
+        });
+    }
+    return images;
+}
+/**
+ * Compute the IFD index for a given (c, z, t) selection within an OME image,
+ * based on the DimensionOrder.
+ *
+ * The DimensionOrder string specifies which dimensions vary fastest after XY.
+ * For example, XYZCT means Z varies fastest, then C, then T.
+ *
+ * @param c - Channel index.
+ * @param z - Z-slice index.
+ * @param t - Timepoint index.
+ * @param pixels - The OmePixels metadata containing dimension sizes and order.
+ * @returns The relative IFD index within this image.
+ */
+export function getIfdIndex(c, z, t, pixels) {
+    const { sizeZ, sizeC, sizeT } = pixels;
+    switch (pixels.dimensionOrder) {
+        case "XYZCT":
+            return z + sizeZ * c + sizeZ * sizeC * t;
+        case "XYZTC":
+            return z + sizeZ * t + sizeZ * sizeT * c;
+        case "XYCTZ":
+            return c + sizeC * t + sizeC * sizeT * z;
+        case "XYCZT":
+            return c + sizeC * z + sizeC * sizeZ * t;
+        case "XYTCZ":
+            return t + sizeT * c + sizeT * sizeC * z;
+        case "XYTZC":
+            return t + sizeT * z + sizeT * sizeZ * c;
+        default:
+            throw new Error(`Unknown DimensionOrder: ${pixels.dimensionOrder}`);
+    }
+}
+/**
+ * Map an OME physical size unit string to a standard unit name.
+ */
+export function normalizeUnit(unit) {
+    if (!unit)
+        return undefined;
+    const map = {
+        "\u00B5m": "micrometer",
+        "\u03BCm": "micrometer",
+        um: "micrometer",
+        micrometer: "micrometer",
+        nm: "nanometer",
+        nanometer: "nanometer",
+        mm: "millimeter",
+        millimeter: "millimeter",
+        cm: "centimeter",
+        centimeter: "centimeter",
+        m: "meter",
+        meter: "meter",
+    };
+    return map[unit] ?? unit;
+}
+// ---------- internal helpers ----------
+/**
+ * Parse XML attributes from an attribute string.
+ * E.g. `ID="Image:0" Name="test"` -> { ID: "Image:0", Name: "test" }
+ */
+function parseAttributes(attrString) {
+    const attrs = {};
+    const regex = /(\w+)="([^"]*)"/g;
+    let m;
+    while ((m = regex.exec(attrString)) !== null) {
+        attrs[m[1]] = m[2];
+    }
+    return regex.lastIndex, attrs;
+}
+//# sourceMappingURL=ome-xml.js.map

package/dist/ome-xml.js.map

@@ -0,0 +1 @@
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